From 7bb7c2a2b3a9b55fb68d944d5043b1d071e9de7a Mon Sep 17 00:00:00 2001 From: Piotr Rozyczko Date: Thu, 30 Apr 2026 18:06:14 +0200 Subject: [PATCH 01/20] Preparations for the release (#350) * Refl1d fix (#302) * assure refl1d actually runs from the GUI * don't fail on codecov upload * Improved limits for certain parameters (#304) * set `disable` status on relevant sub/super-phase parameters * Mighell transform (#303) * fixed chi2 reporting, added MD file with description * added docs about Mighell * updated easyscience branch, deleted script * chi -> chi2 --- .github/workflows/python-ci.yml | 2 +- CHANGELOG.md | 9 + docs/src/api/api.rst | 9 + docs/src/api/fitting.rst | 112 +++ .../tutorials/fitting/simple_fitting.ipynb | 117 ++- notebooks/zero_variance_fitting.ipynb | 724 ++++++++++++++++++ pyproject.toml | 1 + src/easyreflectometry/__version__.py | 2 +- src/easyreflectometry/fitting.py | 318 ++++++-- src/easyreflectometry/limits.py | 44 ++ src/easyreflectometry/model/model.py | 2 + src/easyreflectometry/project.py | 59 ++ .../sample/elements/layers/layer.py | 5 + .../sample/elements/materials/material.py | 4 + tests/model/test_model.py | 4 +- .../elements/materials/test_material.py | 25 +- tests/test_fitting.py | 454 ++++++++++- tests/test_limits.py | 150 ++++ tests/test_ort_file.py | 1 + tests/test_project.py | 43 ++ 20 files changed, 1991 insertions(+), 94 deletions(-) create mode 100644 docs/src/api/fitting.rst create mode 100644 notebooks/zero_variance_fitting.ipynb create mode 100644 src/easyreflectometry/limits.py create mode 100644 tests/test_limits.py diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 90967cd9..1d33313f 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -61,7 +61,7 @@ jobs: name: unit-tests-job flags: unittests files: ./coverage-unit.xml - fail_ci_if_error: true + fail_ci_if_error: false verbose: true token: ${{ secrets.CODECOV_TOKEN }} slug: EasyScience/EasyReflectometryLib diff --git a/CHANGELOG.md b/CHANGELOG.md index bb6a1617..69077f1c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,12 @@ +# Version 1.6.0 (1 May 2026) + +Add Mighell-based handling of non-positive-variance points in fitting (issue #256). +Non-positive-variance data points are no longer forcibly discarded; instead, a +hybrid objective applies a Mighell substitution for non-positive-variance points +while using standard weighted least squares for the rest. The previous masking +behavior is available via `objective='legacy_mask'`. New `objective` parameter on +`MultiFitter`, `fit()`, and `fit_single_data_set_1d()`. + # Version 1.3.3 (17 June 2025) Added Chi^2 and fit status to fitting results. diff --git a/docs/src/api/api.rst b/docs/src/api/api.rst index ea8e2661..55bd611a 100644 --- a/docs/src/api/api.rst +++ b/docs/src/api/api.rst @@ -28,6 +28,15 @@ Project provides a higher-level interface for managing models, experiments, and project +Fitting +======= +Fitting helpers and objective functions. + +.. toctree:: + :maxdepth: 1 + + fitting + Assemblies ========== Assemblies are collections of layers that are used to represent a specific physical setup. diff --git a/docs/src/api/fitting.rst b/docs/src/api/fitting.rst new file mode 100644 index 00000000..65e1ba15 --- /dev/null +++ b/docs/src/api/fitting.rst @@ -0,0 +1,112 @@ +Fitting +======= + +.. currentmodule:: easyreflectometry.fitting + +Objective functions and non-positive variance handling +----------------------------------------------------- + +:class:`MultiFitter` supports several objective modes for handling reflectometry +data during fitting, especially when measured variances are non-positive. + +The default objective is ``hybrid``. This uses ordinary weighted least squares +for points with positive variance and applies a Mighell-style substitution only +to points whose variance is non-positive. The older ``legacy_mask`` mode +drops non-positive-variance points before fitting. The ``mighell`` mode applies the +Mighell transform to every point. + +Mighell objective +~~~~~~~~~~~~~~~~~ + +The full ``mighell`` objective follows the algebraic form of the +``chi^2_gamma`` statistic described by Mighell for Poisson-distributed count +data: + +.. math:: + + \chi^2_\gamma = + \sum_i \frac{[n_i + \min(n_i, 1) - m_i]^2}{n_i + 1} + +where ``n_i`` are observed counts and ``m_i`` are model values. + +In EasyReflectometry this is implemented as a weighted least-squares problem. +For each observed value ``y_i`` the fitted target is shifted to + +.. math:: + + y_{\mathrm{eff},i} = y_i + \min(y_i, 1) + +and the effective uncertainty is + +.. math:: + + \sigma_i = \sqrt{y_i + 1} + +so the minimized objective is + +.. math:: + + \sum_i \left(\frac{y_{\mathrm{eff},i} - f_i}{\sigma_i}\right)^2 = + \sum_i \frac{[y_i + \min(y_i, 1) - f_i]^2}{y_i + 1} + +This is the same algebraic form as Mighell's statistic, with the model value +``f_i`` replacing ``m_i``. + +Scope and interpretation +~~~~~~~~~~~~~~~~~~~~~~~~ + +Mighell's statistic was derived for Poisson-distributed count data. In +reflectometry workflows, the fitted values are usually normalized +reflectivities or intensities rather than raw counts. They may already have +been processed, scaled, background-corrected, or otherwise transformed before +they reach the fitter. + +This distinction matters when interpreting the result. The full ``mighell`` +objective is not only a reweighting of residuals; it also changes the fitted +target from ``y`` to ``y + min(y, 1)``. For values between zero and one, this +can substantially increase the target value. A fit can therefore have a good +Mighell objective value while looking poorer against the originally plotted +reflectivity curve, or while having a worse classical chi-square. + +For reflectometry data, ``hybrid`` is generally the recommended compromise: +it preserves ordinary weighted least-squares behavior where positive variances are +available, while still allowing non-positive-variance points to contribute through the +Mighell-style substitution. + +Objective modes +~~~~~~~~~~~~~~~ + +``hybrid`` + Default. Use standard weighted least squares for points with positive + variance and apply the Mighell substitution only where variance is + non-positive. + +``mighell`` + Apply the Mighell transform to all points. The reported objective chi-square + is evaluated in transformed objective space and should not be interpreted as + a classical chi-square against the original reflectivity values. + +``legacy_mask`` + Remove non-positive-variance points before fitting and use standard weighted least + squares for the remaining points. + +``auto`` + Alias for ``hybrid``. + +Fit metrics +~~~~~~~~~~~ + +The fitter exposes both objective-space and classical fit metrics after fitting. +``objective_chi2`` and ``objective_reduced_chi`` describe the minimized +objective, which may include transformed targets under ``hybrid`` or +``mighell``. ``classical_chi2`` and ``classical_reduced_chi`` are computed +against the original observed reflectivity values using only points with +positive variance. + +API reference +------------- + +.. automodule:: easyreflectometry.fitting + :members: + :undoc-members: + :show-inheritance: \ No newline at end of file diff --git a/docs/src/tutorials/fitting/simple_fitting.ipynb b/docs/src/tutorials/fitting/simple_fitting.ipynb index 5dcd5eb8..ea761e75 100644 --- a/docs/src/tutorials/fitting/simple_fitting.ipynb +++ b/docs/src/tutorials/fitting/simple_fitting.ipynb @@ -30,7 +30,9 @@ "source": [ "%matplotlib inline\n", "\n", + "import matplotlib.pyplot as plt\n", "import pooch\n", + "import refl1d\n", "import refnx\n", "\n", "import easyreflectometry\n", @@ -63,7 +65,8 @@ "outputs": [], "source": [ "print(f'easyreflectometry: {easyreflectometry.__version__}')\n", - "print(f'refnx: {refnx.__version__}')" + "print(f'refnx: {refnx.__version__}')\n", + "print(f'refl1d: {refl1d.__version__}')" ] }, { @@ -395,7 +398,7 @@ "## Choosing our calculation engine\n", "\n", "The `easyreflectometry` package enables the calculation of the reflectometry profile using either [*refnx*](https://refnx.readthedocs.io/) or [*Refl1D*](https://refl1d.readthedocs.io/en/latest/).\n", - "For this tutorial, we will stick to the current default, which is *refnx*. \n", + "We will first run the fit with the current default, *refnx*, and then rebuild the same starting model with *Refl1D* to compare the results.\n", "The calculator must be created and associated with the model that we are to fit. " ] }, @@ -464,7 +467,8 @@ "metadata": {}, "outputs": [], "source": [ - "analysed = fitter.fit(data)" + "analysed_refnx = fitter.fit(data)\n", + "analysed = analysed_refnx" ] }, { @@ -513,18 +517,119 @@ "model" ] }, + { + "cell_type": "markdown", + "id": "2b2fe558", + "metadata": {}, + "source": [ + "## Repeating the optimisation with Refl1D\n", + "\n", + "To compare backends fairly, we rebuild the same initial model and then switch the calculator to `refl1d`.\n", + "This ensures that the second optimisation starts from the same parameter guesses rather than from the already-optimised `refnx` result." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "341abc6f", + "metadata": {}, + "outputs": [], + "source": [ + "print(f'refl1d: {refl1d.__version__}')\n", + "\n", + "si_refl1d = Material(sld=2.07, isld=0, name='Si')\n", + "sio2_refl1d = Material(sld=3.47, isld=0, name='SiO2')\n", + "film_refl1d = Material(sld=2.0, isld=0, name='Film')\n", + "d2o_refl1d = Material(sld=6.36, isld=0, name='D2O')\n", + "\n", + "si_layer_refl1d = Layer(material=si_refl1d, thickness=0, roughness=0, name='Si layer')\n", + "sio2_layer_refl1d = Layer(material=sio2_refl1d, thickness=30, roughness=3, name='SiO2 layer')\n", + "film_layer_refl1d = Layer(material=film_refl1d, thickness=250, roughness=3, name='Film Layer')\n", + "subphase_refl1d = Layer(material=d2o_refl1d, thickness=0, roughness=3, name='D2O Subphase')\n", + "\n", + "superphase_refl1d = Multilayer([si_layer_refl1d, sio2_layer_refl1d], name='Si/SiO2 Superphase')\n", + "sample_refl1d = Sample(superphase_refl1d, Multilayer(film_layer_refl1d), Multilayer(subphase_refl1d), name='Film Structure')\n", + "\n", + "resolution_function_refl1d = PercentageFwhm(0.02)\n", + "model_refl1d = Model(\n", + " sample=sample_refl1d,\n", + " scale=1,\n", + " background=1e-6,\n", + " resolution_function=resolution_function_refl1d,\n", + " name='Film Model (Refl1D)'\n", + ")\n", + "\n", + "sio2_layer_refl1d.thickness.bounds = (15, 50)\n", + "film_layer_refl1d.thickness.bounds = (200, 300)\n", + "sio2_layer_refl1d.roughness.bounds = (1, 15)\n", + "film_layer_refl1d.roughness.bounds = (1, 15)\n", + "subphase_refl1d.roughness.bounds = (1, 15)\n", + "film_layer_refl1d.material.sld.bounds = (0.1, 3)\n", + "model_refl1d.background.bounds = (1e-8, 1e-5)\n", + "model_refl1d.scale.bounds = (0.5, 1.5)\n", + "\n", + "interface_refl1d = CalculatorFactory()\n", + "interface_refl1d.switch('refl1d')\n", + "model_refl1d.interface = interface_refl1d\n", + "\n", + "print(interface_refl1d.current_interface.name)" + ] + }, + { + "cell_type": "markdown", + "id": "2f764d79", + "metadata": {}, + "source": [ + "We can now fit the same dataset with `refl1d` and compare the fitted curve and reduced chi-squared with the earlier `refnx` result." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "70229cf9", + "metadata": {}, + "outputs": [], + "source": [ + "fitter_refl1d = MultiFitter(model_refl1d)\n", + "analysed_refl1d = fitter_refl1d.fit(data)\n", + "\n", + "print(f'refnx reduced chi: {analysed_refnx[\"reduced_chi\"]:.4f}')\n", + "print(f'refl1d reduced chi: {analysed_refl1d[\"reduced_chi\"]:.4f}')\n", + "\n", + "qz = data['coords']['Qz_0'].values\n", + "reflectivity = data['data']['R_0'].values\n", + "uncertainty = data['data']['R_0'].variances**0.5\n", + "\n", + "plt.figure(figsize=(8, 5))\n", + "plt.errorbar(qz, reflectivity, yerr=uncertainty, fmt='o', markersize=3, color='black', alpha=0.6, label='Data')\n", + "plt.plot(qz, analysed_refnx['R_0_model'].values, linewidth=2.5, label='refnx fit')\n", + "plt.plot(qz, analysed_refl1d['R_0_model'].values, linewidth=2.5, label='refl1d fit')\n", + "plt.yscale('log')\n", + "plt.xlabel(r'$Q_z$ (1/Å)')\n", + "plt.ylabel('Reflectivity')\n", + "plt.grid(True, which='both', alpha=0.25)\n", + "plt.legend()\n", + "plt.show()\n", + "\n", + "print('refnx model')\n", + "print(model)\n", + "print()\n", + "print('refl1d model')\n", + "print(model_refl1d)" + ] + }, { "cell_type": "markdown", "id": "df6db8c3-6515-478b-bd2e-aac967579231", "metadata": {}, "source": [ - "We note here that the results obtained are very similar to those from the [*refnx* tutorial](https://refnx.readthedocs.io/en/latest/getting_started.html#Fitting-a-neutron-reflectometry-dataset), which is hardly surprising given that we have used the *refnx* engine in this example." + "We note here that the results obtained with [*refnx*](https://refnx.readthedocs.io/en/latest/) and [*Refl1D*](https://refl1d.readthedocs.io/en/latest/) are very similar for this simple slab model, with only small backend-dependent differences in the fitted curve and optimised parameters." ] } ], "metadata": { "kernelspec": { - "display_name": "easyref", + "display_name": ".venv (3.11.9)", "language": "python", "name": "python3" }, @@ -538,7 +643,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.9" + "version": "3.11.9" } }, "nbformat": 4, diff --git a/notebooks/zero_variance_fitting.ipynb b/notebooks/zero_variance_fitting.ipynb new file mode 100644 index 00000000..ea3ede96 --- /dev/null +++ b/notebooks/zero_variance_fitting.ipynb @@ -0,0 +1,724 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "1a8a52ac", + "metadata": {}, + "source": [ + "# Zero-Variance Handling in Reflectometry Fitting\n", + "\n", + "This notebook demonstrates how `easyreflectometry` handles data points with **zero variance**\n", + "during fitting. We compare three objective strategies:\n", + "\n", + "| Objective | Behaviour |\n", + "|---|---|\n", + "| `legacy_mask` | Drops zero-variance points entirely (old default) |\n", + "| `hybrid` | Keeps all points; applies Mighell substitution only to zero-variance entries (**new default**) |\n", + "| `mighell` | Applies the Mighell (1999) transform to every point |\n", + "\n", + "The experimental data comes from `tests/_static/ref_zero_var.txt`, which contains 192 data points,\n", + "6 of which have zero error (= zero variance)." + ] + }, + { + "cell_type": "markdown", + "id": "5c6429ac", + "metadata": {}, + "source": [ + "## 1. Import Required Libraries" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4983acb8", + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "import warnings\n", + "\n", + "import matplotlib.pyplot as plt\n", + "import numpy as np\n", + "\n", + "from easyreflectometry.calculators import CalculatorFactory\n", + "from easyreflectometry.data.measurement import load\n", + "from easyreflectometry.fitting import MultiFitter\n", + "from easyreflectometry.model import Model\n", + "from easyreflectometry.model import PercentageFwhm\n", + "from easyreflectometry.sample import Layer\n", + "from easyreflectometry.sample import Material\n", + "from easyreflectometry.sample import Multilayer\n", + "from easyreflectometry.sample import Sample\n", + "\n", + "%matplotlib inline" + ] + }, + { + "cell_type": "markdown", + "id": "96e174d4", + "metadata": {}, + "source": [ + "## 2. Load Experimental Data\n", + "\n", + "The file `ref_zero_var.txt` is a comma-separated file with columns: `q (Å⁻¹)`, `R`, `error`.\n", + "Several points near the high-Q end have `error = 0.0`, meaning zero variance." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "47fb3264", + "metadata": {}, + "outputs": [], + "source": [ + "DATA_PATH = os.path.join('..', 'tests', '_static', 'ref_zero_var.txt')\n", + "\n", + "# Load raw data for inspection\n", + "raw = np.loadtxt(DATA_PATH, delimiter=',', comments='#')\n", + "q_raw, r_raw, err_raw = raw[:, 0], raw[:, 1], raw[:, 2]\n", + "\n", + "# Load through easyreflectometry (produces a scipp DataGroup)\n", + "data = load(DATA_PATH)\n", + "data_key = next(iter(data['data'].keys()))\n", + "coord_key = next(iter(data['coords'].keys()))\n", + "result_model_key = f'{data_key}_model'\n", + "\n", + "print(f'Total data points : {len(q_raw)}')\n", + "print(f'Q range : [{q_raw.min():.4e}, {q_raw.max():.4e}] Å⁻¹')\n", + "print(f'R range : [{r_raw.min():.4e}, {r_raw.max():.4e}]')\n", + "print(f'Data key : {data_key}')\n", + "print(f'Coord key : {coord_key}')\n", + "print(f'Model key : {result_model_key}')" + ] + }, + { + "cell_type": "markdown", + "id": "c4495939", + "metadata": {}, + "source": [ + "## 3. Inspect Data and Identify Zero-Variance Points" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1be2ca78", + "metadata": {}, + "outputs": [], + "source": [ + "zero_mask = err_raw == 0.0\n", + "zero_indices = np.where(zero_mask)[0]\n", + "print(f'Number of zero-variance points: {zero_mask.sum()}')\n", + "print(f'Indices: {zero_indices}')\n", + "print('Q-values with zero variance:')\n", + "for idx in zero_indices:\n", + " print(f' [{idx:3d}] Q = {q_raw[idx]:.4e} Å⁻¹, R = {r_raw[idx]:.4e}')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "373cdc62", + "metadata": {}, + "outputs": [], + "source": [ + "fig, ax = plt.subplots(figsize=(10, 6))\n", + "\n", + "# Plot all data\n", + "valid = ~zero_mask\n", + "ax.errorbar(q_raw[valid], r_raw[valid], yerr=err_raw[valid],\n", + " fmt='o', ms=3, color='C0', alpha=0.7, label='Valid points')\n", + "ax.plot(q_raw[zero_mask], r_raw[zero_mask],\n", + " 'rx', ms=10, mew=2, label=f'Zero-variance points ({zero_mask.sum()})')\n", + "\n", + "ax.set_yscale('log')\n", + "ax.set_xlabel('Q (Å⁻¹)')\n", + "ax.set_ylabel('Reflectivity')\n", + "ax.set_title('Raw experimental data — zero-variance points highlighted')\n", + "ax.legend()\n", + "plt.tight_layout()\n", + "plt.show()" + ] + }, + { + "cell_type": "markdown", + "id": "428759d3", + "metadata": {}, + "source": [ + "## 4. Define Materials\n", + "\n", + "A simple film-on-substrate structure: **Si** substrate / **SiO₂** native oxide / **Film** / **D₂O** superphase." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "006fb3cf", + "metadata": {}, + "outputs": [], + "source": [ + "si = Material(2.07, 0, 'Si')\n", + "sio2 = Material(3.47, 0, 'SiO2')\n", + "film = Material(2.0, 0, 'Film')\n", + "d2o = Material(6.36, 0, 'D2O')" + ] + }, + { + "cell_type": "markdown", + "id": "6031b9ad", + "metadata": {}, + "source": [ + "## 5. Define Layers and Sample Structure" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2643141f", + "metadata": {}, + "outputs": [], + "source": [ + "si_layer = Layer(si, 0, 0, 'Si layer')\n", + "sio2_layer = Layer(sio2, 30, 3, 'SiO2 layer')\n", + "film_layer = Layer(film, 250, 3, 'Film layer')\n", + "superphase = Layer(d2o, 0, 3, 'D2O superphase')\n", + "\n", + "sample = Sample(\n", + " Multilayer(si_layer),\n", + " Multilayer(sio2_layer),\n", + " Multilayer(film_layer),\n", + " Multilayer(superphase),\n", + " name='Film Structure',\n", + ")\n", + "print(sample)" + ] + }, + { + "cell_type": "markdown", + "id": "51bcedeb", + "metadata": {}, + "source": [ + "## 6. Create the Model" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "22e6fbd9", + "metadata": {}, + "outputs": [], + "source": [ + "resolution_function = PercentageFwhm(0.02)\n", + "model = Model(sample, 1, 1e-6, resolution_function, 'Film Model')" + ] + }, + { + "cell_type": "markdown", + "id": "7eaf6993", + "metadata": {}, + "source": [ + "## 7. Set Calculator Backend and Compute Initial Curve" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "175afdcc", + "metadata": {}, + "outputs": [], + "source": [ + "interface = CalculatorFactory()\n", + "model.interface = interface\n", + "\n", + "# Compute initial model reflectivity\n", + "r_init = interface.fit_func(q_raw, model.unique_name)" + ] + }, + { + "cell_type": "markdown", + "id": "fff782bb", + "metadata": {}, + "source": [ + "## 8. Plot Initial Model vs Experimental Data" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a7656b8b", + "metadata": {}, + "outputs": [], + "source": [ + "fig, ax = plt.subplots(figsize=(10, 6))\n", + "\n", + "ax.errorbar(q_raw[valid], r_raw[valid], yerr=err_raw[valid],\n", + " fmt='o', ms=3, color='C0', alpha=0.6, label='Experiment (valid)')\n", + "ax.plot(q_raw[zero_mask], r_raw[zero_mask],\n", + " 'rx', ms=10, mew=2, label='Experiment (zero variance)')\n", + "ax.plot(q_raw, r_init, '-', color='C1', lw=1.5, label='Initial model')\n", + "\n", + "ax.set_yscale('log')\n", + "ax.set_xlabel('Q (Å⁻¹)')\n", + "ax.set_ylabel('Reflectivity')\n", + "ax.set_title('Experimental data vs initial model (before fitting)')\n", + "ax.legend()\n", + "plt.tight_layout()\n", + "plt.show()" + ] + }, + { + "cell_type": "markdown", + "id": "6c916d41", + "metadata": {}, + "source": [ + "## 9. Set Fitting Parameters and Constraints" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a85ab7e8", + "metadata": {}, + "outputs": [], + "source": [ + "sio2_layer.thickness.fixed = False\n", + "sio2_layer.thickness.bounds = (15, 50)\n", + "\n", + "film_layer.thickness.fixed = False\n", + "film_layer.thickness.bounds = (200, 300)\n", + "\n", + "film.sld.fixed = False\n", + "film.sld.bounds = (0.1, 3)\n", + "\n", + "model.background.fixed = False\n", + "model.background.bounds = (1e-7, 1e-5)\n", + "\n", + "model.scale.fixed = False\n", + "model.scale.bounds = (0.5, 1.5)\n", + "\n", + "print('Free parameters:')\n", + "for p in model.get_fit_parameters():\n", + " print(f' {p.name:20s} = {float(p.value):.4g} bounds={p.bounds}')" + ] + }, + { + "cell_type": "markdown", + "id": "b83af903", + "metadata": {}, + "source": [ + "## 10. Zero-Variance Handling — Three Objective Modes\n", + "\n", + "We now fit the same data with each objective mode and compare the results.\n", + "\n", + "### How each mode handles zero-variance points\n", + "\n", + "- **`legacy_mask`** — zero-variance points are dropped before fitting. The fitter sees fewer\n", + " data points, and those Q-values have no influence on the result.\n", + "- **`hybrid`** (default) — valid points use standard weighted least-squares ($w = 1/\\sigma$).\n", + " Zero-variance points get the **Mighell (1999)** substitution:\n", + " $y_\\text{eff} = y + \\min(y, 1)$, $\\sigma = \\sqrt{\\max(y + 1,\\, \\varepsilon)}$.\n", + " This keeps all data in the fit while giving zero-variance points reasonable weight.\n", + "- **`mighell`** — applies the Mighell transform to *every* point, not just zero-variance ones.\n", + " This changes both the weighting and the fitted target for the entire dataset.\n", + "\n", + "Below we report two metric families:\n", + "\n", + "- **objective chi²** — the quantity actually minimized by the selected objective\n", + "- **classical chi²** — a standard variance-weighted chi² computed only on the original\n", + " positive-variance points, for comparison" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8182f0a9", + "metadata": {}, + "outputs": [], + "source": [ + "def build_fresh_model():\n", + " \"\"\"Build a fresh model+interface so each fit starts from the same initial state.\"\"\"\n", + " _si = Material(2.07, 0, 'Si')\n", + " _sio2 = Material(3.47, 0, 'SiO2')\n", + " _film = Material(2.0, 0, 'Film')\n", + " _d2o = Material(6.36, 0, 'D2O')\n", + "\n", + " _si_layer = Layer(_si, 0, 0, 'Si layer')\n", + " _sio2_layer = Layer(_sio2, 30, 3, 'SiO2 layer')\n", + " _film_layer = Layer(_film, 250, 3, 'Film layer')\n", + " _superphase = Layer(_d2o, 0, 3, 'D2O superphase')\n", + "\n", + " _sample = Sample(\n", + " Multilayer(_si_layer),\n", + " Multilayer(_sio2_layer),\n", + " Multilayer(_film_layer),\n", + " Multilayer(_superphase),\n", + " name='Film Structure',\n", + " )\n", + " _resolution = PercentageFwhm(0.02)\n", + " _model = Model(_sample, 1, 1e-6, _resolution, 'Film Model')\n", + "\n", + " _sio2_layer.thickness.fixed = False\n", + " _sio2_layer.thickness.bounds = (15, 50)\n", + " _film_layer.thickness.fixed = False\n", + " _film_layer.thickness.bounds = (200, 300)\n", + " _film.sld.fixed = False\n", + " _film.sld.bounds = (0.1, 3)\n", + " _model.background.fixed = False\n", + " _model.background.bounds = (1e-7, 1e-5)\n", + " _model.scale.fixed = False\n", + " _model.scale.bounds = (0.5, 1.5)\n", + "\n", + " _model.interface = CalculatorFactory()\n", + " return _model" + ] + }, + { + "cell_type": "markdown", + "id": "fd6f4833", + "metadata": {}, + "source": [ + "### 11. Fit with `legacy_mask`\n", + "\n", + "Zero-variance points are simply dropped." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e856e00f", + "metadata": {}, + "outputs": [], + "source": [ + "model_mask = build_fresh_model()\n", + "fitter_mask = MultiFitter(model_mask, objective='legacy_mask')\n", + "\n", + "with warnings.catch_warnings(record=True) as w_mask:\n", + " warnings.simplefilter('always')\n", + " result_mask = fitter_mask.fit(data)\n", + "\n", + "for w in w_mask:\n", + " print(f'[WARNING] {w.message}')\n", + "print(f'Success : {result_mask[\"success\"]}')\n", + "print(f'Objective reduced chi² : {result_mask[\"objective_reduced_chi\"]:.6f}')\n", + "print(f'Objective total chi² : {fitter_mask.objective_chi2:.6f}')\n", + "print(f'Classical reduced chi² : {result_mask[\"classical_reduced_chi\"]:.6f}')\n", + "print(f'Classical total chi² : {fitter_mask.classical_chi2:.6f}')\n", + "\n", + "r_fit_mask = result_mask[result_model_key].values" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "79755052", + "metadata": {}, + "outputs": [], + "source": [ + "result_mask\n" + ] + }, + { + "cell_type": "markdown", + "id": "24cb6fe0", + "metadata": {}, + "source": [ + "### 12. Fit with `hybrid` (new default)\n", + "\n", + "All points kept; Mighell substitution applied only to zero-variance entries." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "20c034ba", + "metadata": {}, + "outputs": [], + "source": [ + "model_hybrid = build_fresh_model()\n", + "fitter_hybrid = MultiFitter(model_hybrid, objective='hybrid')\n", + "\n", + "with warnings.catch_warnings(record=True) as w_hybrid:\n", + " warnings.simplefilter('always')\n", + " result_hybrid = fitter_hybrid.fit(data)\n", + "\n", + "for w in w_hybrid:\n", + " print(f'[WARNING] {w.message}')\n", + "print(f'Success : {result_hybrid[\"success\"]}')\n", + "print(f'Objective reduced chi² : {result_hybrid[\"objective_reduced_chi\"]:.6f}')\n", + "print(f'Objective total chi² : {fitter_hybrid.objective_chi2:.6f}')\n", + "print(f'Classical reduced chi² : {result_hybrid[\"classical_reduced_chi\"]:.6f}')\n", + "print(f'Classical total chi² : {fitter_hybrid.classical_chi2:.6f}')\n", + "\n", + "r_fit_hybrid = result_hybrid[result_model_key].values" + ] + }, + { + "cell_type": "markdown", + "id": "79258c5f", + "metadata": {}, + "source": [ + "### 13. Fit with `mighell`\n", + "\n", + "Mighell transform applied to *all* points — the chi² landscape changes entirely." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "90b08fdd", + "metadata": {}, + "outputs": [], + "source": [ + "model_mighell = build_fresh_model()\n", + "fitter_mighell = MultiFitter(model_mighell, objective='mighell')\n", + "\n", + "with warnings.catch_warnings(record=True) as w_mighell:\n", + " warnings.simplefilter('always')\n", + " result_mighell = fitter_mighell.fit(data)\n", + "\n", + "for w in w_mighell:\n", + " print(f'[WARNING] {w.message}')\n", + "print(f'Success : {result_mighell[\"success\"]}')\n", + "print(f'Objective reduced chi² : {result_mighell[\"objective_reduced_chi\"]:.6f}')\n", + "print(f'Objective total chi² : {fitter_mighell.objective_chi2:.6f}')\n", + "print(f'Classical reduced chi² : {result_mighell[\"classical_reduced_chi\"]:.6f}')\n", + "print(f'Classical total chi² : {fitter_mighell.classical_chi2:.6f}')\n", + "\n", + "r_fit_mighell = result_mighell[result_model_key].values" + ] + }, + { + "cell_type": "markdown", + "id": "6136693d", + "metadata": {}, + "source": [ + "## 14. Compare Fit Results\n", + "\n", + "### Parameter comparison table" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "77c23990", + "metadata": {}, + "outputs": [], + "source": [ + "models = {\n", + " 'legacy_mask': model_mask,\n", + " 'hybrid': model_hybrid,\n", + " 'mighell': model_mighell,\n", + "}\n", + "results = {\n", + " 'legacy_mask': result_mask,\n", + " 'hybrid': result_hybrid,\n", + " 'mighell': result_mighell,\n", + "}\n", + "\n", + "# Build descriptive labels to disambiguate duplicates (e.g. two \"thickness\" params)\n", + "ref_params = model_mask.get_fit_parameters()\n", + "seen = {}\n", + "labels = []\n", + "for p in ref_params:\n", + " n = p.name\n", + " seen[n] = seen.get(n, 0) + 1\n", + " labels.append(f'{n} ({seen[n]})')\n", + "# Simplify if name appears only once\n", + "name_counts = {}\n", + "for p in ref_params:\n", + " name_counts[p.name] = name_counts.get(p.name, 0) + 1\n", + "labels_clean = []\n", + "seen2 = {}\n", + "for p in ref_params:\n", + " n = p.name\n", + " seen2[n] = seen2.get(n, 0) + 1\n", + " if name_counts[n] > 1:\n", + " labels_clean.append(f'{n}_{seen2[n]}')\n", + " else:\n", + " labels_clean.append(n)\n", + "\n", + "obj_keys = ['legacy_mask', 'hybrid', 'mighell']\n", + "\n", + "header = f'{\"Parameter\":<24s} {\"legacy_mask\":>14s} {\"hybrid\":>14s} {\"mighell\":>14s}'\n", + "print(header)\n", + "print('-' * len(header))\n", + "\n", + "for i, label in enumerate(labels_clean):\n", + " vals = []\n", + " for obj in obj_keys:\n", + " params = models[obj].get_fit_parameters()\n", + " vals.append(float(params[i].value))\n", + " print(f'{label:<24s} {vals[0]:>14.4g} {vals[1]:>14.4g} {vals[2]:>14.4g}')\n", + "\n", + "print('-' * len(header))\n", + "print(f'{\"objective red. chi²\":<24s} {result_mask[\"objective_reduced_chi\"]:>14.4f} '\n", + " f'{result_hybrid[\"objective_reduced_chi\"]:>14.4f} {result_mighell[\"objective_reduced_chi\"]:>14.6f}')\n", + "print(f'{\"classical red. chi²\":<24s} {result_mask[\"classical_reduced_chi\"]:>14.4f} '\n", + " f'{result_hybrid[\"classical_reduced_chi\"]:>14.4f} {result_mighell[\"classical_reduced_chi\"]:>14.4f}')\n", + "print(f'{\"success\":<24s} {str(result_mask[\"success\"]):>14s} '\n", + " f'{str(result_hybrid[\"success\"]):>14s} {str(result_mighell[\"success\"]):>14s}')" + ] + }, + { + "cell_type": "markdown", + "id": "906b9cdb", + "metadata": {}, + "source": [ + "### Fitted reflectivity curves — all three objectives" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a4f8f3a7", + "metadata": {}, + "outputs": [], + "source": [ + "fig, ax = plt.subplots(figsize=(10, 6))\n", + "\n", + "# Experimental data\n", + "ax.errorbar(\n", + " q_raw[valid],\n", + " r_raw[valid],\n", + " yerr=err_raw[valid],\n", + " fmt='o',\n", + " ms=2,\n", + " color='grey',\n", + " alpha=0.5,\n", + " label='Experiment',\n", + ")\n", + "ax.plot(q_raw[zero_mask], r_raw[zero_mask], 'rx', ms=10, mew=2, label='Zero-variance points')\n", + "\n", + "# Fitted curves\n", + "ax.plot(\n", + " q_raw,\n", + " r_fit_mask,\n", + " '-',\n", + " lw=1.5,\n", + " label=(\n", + " f'legacy_mask (obj={result_mask[\"objective_reduced_chi\"]:.3g}, '\n", + " f'class={result_mask[\"classical_reduced_chi\"]:.3g})'\n", + " ),\n", + ")\n", + "ax.plot(\n", + " q_raw,\n", + " r_fit_hybrid,\n", + " '--',\n", + " lw=1.5,\n", + " label=(\n", + " f'hybrid (obj={result_hybrid[\"objective_reduced_chi\"]:.3g}, '\n", + " f'class={result_hybrid[\"classical_reduced_chi\"]:.3g})'\n", + " ),\n", + ")\n", + "ax.plot(\n", + " q_raw,\n", + " r_fit_mighell,\n", + " ':',\n", + " lw=1.5,\n", + " label=(\n", + " f'mighell (obj={result_mighell[\"objective_reduced_chi\"]:.3g}, '\n", + " f'class={result_mighell[\"classical_reduced_chi\"]:.3g})'\n", + " ),\n", + ")\n", + "\n", + "ax.set_yscale('log')\n", + "ax.set_xlabel('Q (Å⁻¹)')\n", + "ax.set_ylabel('Reflectivity')\n", + "ax.set_title('Fitted reflectivity — comparison of objective modes')\n", + "ax.legend(fontsize=9)\n", + "plt.tight_layout()\n", + "plt.show()" + ] + }, + { + "cell_type": "markdown", + "id": "52821f2d", + "metadata": {}, + "source": [ + "## 15. Examine Residuals\n", + "\n", + "We compute normalised residuals $(R_\\text{exp} - R_\\text{model}) / \\sigma$ for each objective.\n", + "Zero-variance points are shown separately — for `legacy_mask` they were excluded from\n", + "the fit, while `hybrid` and `mighell` included them with transformed weights." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0292ef11", + "metadata": {}, + "outputs": [], + "source": [ + "fig, axes = plt.subplots(3, 1, figsize=(10, 10), sharex=True)\n", + "\n", + "fits = {\n", + " 'legacy_mask': r_fit_mask,\n", + " 'hybrid': r_fit_hybrid,\n", + " 'mighell': r_fit_mighell,\n", + "}\n", + "\n", + "for ax, (obj_name, r_fit) in zip(axes, fits.items()):\n", + " # Normalised residuals for valid points\n", + " residuals_valid = (r_raw[valid] - r_fit[valid]) / err_raw[valid]\n", + " ax.plot(q_raw[valid], residuals_valid, 'o', ms=2, alpha=0.6, color='C0', label='Valid points')\n", + "\n", + " # Un-normalised residuals at zero-variance points (no sigma to normalise by)\n", + " residuals_zero = r_raw[zero_mask] - r_fit[zero_mask]\n", + " ax.plot(q_raw[zero_mask], np.zeros_like(residuals_zero), 'rx', ms=10, mew=2,\n", + " label='Zero-var Q positions')\n", + "\n", + " ax.axhline(0, color='k', lw=0.5)\n", + " ax.set_ylabel('Normalised residual')\n", + " ax.set_title(f'{obj_name}')\n", + " ax.legend(fontsize=8, loc='upper right')\n", + "\n", + "axes[-1].set_xlabel('Q (Å⁻¹)')\n", + "plt.tight_layout()\n", + "plt.show()" + ] + }, + { + "cell_type": "markdown", + "id": "a2f39948", + "metadata": {}, + "source": [ + "## Summary\n", + "\n", + "| Objective | Zero-var handling | Objective chi² interpretation | Classical chi² comparison |\n", + "|---|---|---|---|\n", + "| `legacy_mask` | Dropped from fit | Same as classical chi² on retained points | Directly comparable |\n", + "| `hybrid` | Mighell substitution for zero-var only | Slightly modified objective | Usually close to classical when zero-var fraction is small |\n", + "| `mighell` | Mighell transform for **all** points | **Not** a classical chi²; target and weights both change | Can look visibly worse against plotted reflectivity even when the objective is minimized well |\n", + "\n", + "The `hybrid` mode (new default) is recommended: it keeps all data points in the fit while\n", + "preserving a classical chi² comparison on the original positive-variance points.\n", + "\n", + "The full `mighell` mode matches the Mighell paper's objective mathematically, but that paper is\n", + "derived for Poisson count data. Applied to normalized reflectivity, it should be interpreted as a\n", + "Poisson-style objective rather than a visually comparable reduced chi² fit." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "era", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.12" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/pyproject.toml b/pyproject.toml index 9833bc40..ec3df724 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,6 +62,7 @@ dev = [ docs = [ "myst_parser", "nbsphinx", + "plopp", "sphinx<=8.1.3", "sphinx_autodoc_typehints", "sphinx_book_theme", diff --git a/src/easyreflectometry/__version__.py b/src/easyreflectometry/__version__.py index 77f1c8e6..bcd8d54e 100644 --- a/src/easyreflectometry/__version__.py +++ b/src/easyreflectometry/__version__.py @@ -1 +1 @@ -__version__ = '1.5.0' +__version__ = '1.6.0' diff --git a/src/easyreflectometry/fitting.py b/src/easyreflectometry/fitting.py index 86df41e3..0750beb5 100644 --- a/src/easyreflectometry/fitting.py +++ b/src/easyreflectometry/fitting.py @@ -11,14 +11,145 @@ from easyreflectometry.data import DataSet1D from easyreflectometry.model import Model +_VALID_OBJECTIVES = ('legacy_mask', 'mighell', 'hybrid', 'auto') +_EPS = 1e-30 + + +def _validate_objective(objective: str) -> str: + """Validate and resolve the objective string. + + :param objective: The objective mode string. + :type objective: str + :return: Resolved objective string ('auto' becomes 'hybrid'). + :rtype: str + :raises ValueError: If the objective is not one of the valid options. + """ + if objective not in _VALID_OBJECTIVES: + raise ValueError(f'Unknown objective {objective!r}. Valid options: {_VALID_OBJECTIVES}') + if objective == 'auto': + return 'hybrid' + return objective + + +def _prepare_fit_arrays( + x_vals: np.ndarray, + y_vals: np.ndarray, + variances: np.ndarray, + objective: str, +) -> tuple[np.ndarray, np.ndarray, np.ndarray, dict]: + """Prepare x, y_eff, and weights arrays for fitting based on the objective mode. + + For ``legacy_mask``, zero-variance points are removed from all arrays. + For ``hybrid``, valid-variance points use standard WLS while zero-variance + points use Mighell-transformed y and weights. + For ``mighell``, all points use the Mighell transform. + + Note: ``variances`` here means σ² (the scipp convention), not σ. + + :param x_vals: Independent variable values. + :type x_vals: np.ndarray + :param y_vals: Observed dependent variable values. + :type y_vals: np.ndarray + :param variances: Variance (σ²) of each observed point. + :type variances: np.ndarray + :param objective: One of 'legacy_mask', 'hybrid', 'mighell'. + :type objective: str + :return: Tuple of (x_out, y_eff, weights, stats) where stats is a dict + with keys 'valid', 'mighell_substituted', 'masked'. + :rtype: tuple[np.ndarray, np.ndarray, np.ndarray, dict] + """ + n = len(y_vals) + zero_mask = variances <= 0.0 + n_zero = int(np.sum(zero_mask)) + n_valid = n - n_zero + + if objective == 'legacy_mask': + valid = ~zero_mask + x_out = x_vals[valid] + y_eff = y_vals[valid] + if n_valid > 0: + weights = 1.0 / np.sqrt(variances[valid]) + else: + weights = np.array([]) + stats = {'valid': n_valid, 'mighell_substituted': 0, 'masked': n_zero, 'transformed_all_points': False} + return x_out, y_eff, weights, stats + + # hybrid or mighell + y_eff = np.copy(y_vals) + sigma = np.empty(n) + + if objective == 'mighell': + apply_mighell = np.ones(n, dtype=bool) + else: + # hybrid: apply Mighell only to zero-variance points + apply_mighell = zero_mask + + # Standard WLS for non-Mighell points + standard = ~apply_mighell + if np.any(standard): + sigma[standard] = np.sqrt(variances[standard]) + + # Mighell transform for selected points + if np.any(apply_mighell): + y_m = y_vals[apply_mighell] + delta = np.minimum(y_m, 1.0) + y_eff[apply_mighell] = y_m + delta + sigma[apply_mighell] = np.sqrt(np.maximum(y_m + 1.0, _EPS)) + + weights = 1.0 / sigma + n_mighell = int(np.sum(apply_mighell)) + stats = { + 'valid': n - n_mighell, + 'mighell_substituted': n_mighell, + 'masked': 0, + 'transformed_all_points': bool(objective == 'mighell'), + } + return x_vals, y_eff, weights, stats + + +def _compute_weighted_chi2(y_obs: np.ndarray, y_calc: np.ndarray, sigma: np.ndarray) -> float: + """Return weighted chi-square for finite, strictly positive uncertainties.""" + valid = np.isfinite(y_obs) & np.isfinite(y_calc) & np.isfinite(sigma) & (sigma > 0.0) + if not np.any(valid): + return 0.0 + residual = (y_obs[valid] - y_calc[valid]) / sigma[valid] + return float(np.sum(residual**2)) + + +def _compute_reduced_chi2(chi2: float, n_points: int, n_params: int) -> float | None: + """Return reduced chi-square or None when degrees of freedom are not positive.""" + dof = int(n_points) - int(n_params) + if dof <= 0: + return None + return float(chi2 / dof) + + +def _fit_result_reduced_chi(result: FitResults, n_points: int | None = None) -> float: + """Return reduced chi-square from either supported FitResults attribute name.""" + for attribute in ('reduced_chi', 'reduced_chi2'): + value = getattr(result, attribute, None) + if isinstance(value, (int, float, np.number)): + return float(value) + if n_points is not None: + reduced_chi = _compute_reduced_chi2(float(result.chi2), n_points, result.n_pars) + if reduced_chi is not None: + return reduced_chi + raise AttributeError('FitResults object has neither reduced_chi nor reduced_chi2') + class MultiFitter: - def __init__(self, *args: Model): - r"""A convinence class for the :py:class:`easyscience.Fitting.Fitting` + def __init__(self, *args: Model, objective: str = 'hybrid'): + r"""A convenience class for the :py:class:`easyscience.Fitting.Fitting` which will populate the :py:class:`sc.DataGroup` appropriately after the fitting is performed. - :param args: Reflectometry model + :param args: Reflectometry model(s). + :param objective: Zero-variance handling strategy. One of + ``'hybrid'`` (default, Mighell for zero-variance, WLS otherwise), + ``'mighell'`` (Mighell transform for all points), + ``'legacy_mask'`` (drop zero-variance points), + ``'auto'`` (alias for ``'hybrid'``). + :type objective: str """ # This lets the unique_name be passed with the fit_func. @@ -32,22 +163,35 @@ def wrapped(*args, **kwargs): self._models = args self.easy_science_multi_fitter = EasyScienceMultiFitter(args, self._fit_func) self._fit_results: list[FitResults] | None = None - - def fit(self, data: sc.DataGroup, id: int = 0) -> sc.DataGroup: + self._classical_fit_metrics: list[dict] | None = None + self._objective = _validate_objective(objective) + + def fit(self, data: sc.DataGroup, id: int = 0, objective: str | None = None) -> sc.DataGroup: + """Perform the fitting and populate the DataGroups with the result. + + :param data: DataGroup to be fitted to and populated. + :type data: sc.DataGroup + :param id: Unused parameter kept for backward compatibility. + :type id: int + :param objective: Per-call override for the zero-variance objective. + If ``None``, uses the instance default set at construction. + :type objective: str or None + :return: A new DataGroup with fitted model curves, SLD profiles, and fit statistics. + :rtype: sc.DataGroup + + :note: Under the ``mighell`` objective all points are transformed, + so ``reduced_chi`` is not a classical chi-square statistic. + Under ``hybrid``, only zero-variance points are transformed; + when they are a small fraction of the data the chi-square + remains approximately classical. """ - Perform the fitting and populate the DataGroups with the result. - - :param data: DataGroup to be fitted to and populated - :param method: Optimisation method + obj = _validate_objective(objective) if objective is not None else self._objective - :note: Points with zero variance in the data will be automatically masked - out during fitting. A warning will be issued if any such points - are found, indicating the number of points masked per reflectivity. - """ refl_nums = [k[3:] for k in data['coords'].keys() if 'Qz' == k[:2]] x = [] y = [] dy = [] + original_arrays = [] # Process each reflectivity dataset for i in refl_nums: @@ -55,34 +199,38 @@ def fit(self, data: sc.DataGroup, id: int = 0) -> sc.DataGroup: y_vals = data['data'][f'R_{i}'].values variances = data['data'][f'R_{i}'].variances - # Find points with non-zero variance - zero_variance_mask = variances == 0.0 - num_zero_variance = np.sum(zero_variance_mask) + x_out, y_eff, weights, stats = _prepare_fit_arrays(x_vals, y_vals, variances, obj) - if num_zero_variance > 0: + if stats['masked'] > 0: warnings.warn( - f'Masked {num_zero_variance} data point(s) in reflectivity {i} due to zero variance during fitting.', + f'Masked {stats["masked"]} data point(s) in reflectivity {i} due to zero variance during fitting.', + UserWarning, + ) + if stats.get('transformed_all_points'): + warnings.warn( + f'Applied Mighell transform to all {len(y_vals)} point(s) in reflectivity {i} during fitting.', + UserWarning, + ) + elif stats['mighell_substituted'] > 0: + warnings.warn( + f'Applied Mighell substitution to {stats["mighell_substituted"]} ' + f'zero-variance point(s) in reflectivity {i} during fitting.', UserWarning, ) - # Keep only points with non-zero variances - valid_mask = ~zero_variance_mask - x_vals_masked = x_vals[valid_mask] - y_vals_masked = y_vals[valid_mask] - variances_masked = variances[valid_mask] - - x.append(x_vals_masked) - y.append(y_vals_masked) - dy.append(1 / np.sqrt(variances_masked)) + x.append(x_out) + y.append(y_eff) + dy.append(weights) + original_arrays.append({'x': x_vals, 'y': y_vals, 'variances': variances}) result = self.easy_science_multi_fitter.fit(x, y, weights=dy) self._fit_results = result + self._classical_fit_metrics = [] new_data = data.copy() for i, _ in enumerate(result): id = refl_nums[i] - new_data[f'R_{id}_model'] = sc.array( - dims=[f'Qz_{id}'], values=self._fit_func[i](data['coords'][f'Qz_{id}'].values) - ) + model_curve = self._fit_func[i](data['coords'][f'Qz_{id}'].values) + new_data[f'R_{id}_model'] = sc.array(dims=[f'Qz_{id}'], values=model_curve) sld_profile = self.easy_science_multi_fitter._fit_objects[i].interface.sld_profile(self._models[i].unique_name) new_data[f'SLD_{id}'] = sc.array(dims=[f'z_{id}'], values=sld_profile[1] * 1e-6, unit=sc.Unit('1/angstrom') ** 2) if 'attrs' in new_data: @@ -90,41 +238,88 @@ def fit(self, data: sc.DataGroup, id: int = 0) -> sc.DataGroup: new_data['coords'][f'z_{id}'] = sc.array( dims=[f'z_{id}'], values=sld_profile[0], unit=(1 / new_data['coords'][f'Qz_{id}'].unit).unit ) - new_data['reduced_chi'] = float(result[i].reduced_chi) + original = original_arrays[i] + sigma_classical = np.sqrt(np.clip(original['variances'], 0.0, None)) + n_classical_points = int(np.sum(original['variances'] > 0.0)) + classical_chi2 = _compute_weighted_chi2(original['y'], model_curve, sigma_classical) + classical_reduced_chi = _compute_reduced_chi2(classical_chi2, n_classical_points, result[i].n_pars) + objective_chi2 = float(result[i].chi2) + objective_reduced_chi = _fit_result_reduced_chi(result[i], np.size(result[i].x)) + + self._classical_fit_metrics.append( + { + 'classical_chi2': classical_chi2, + 'classical_reduced_chi': classical_reduced_chi, + 'objective_chi2': objective_chi2, + 'objective_reduced_chi': objective_reduced_chi, + 'n_classical_points': n_classical_points, + } + ) + + new_data['objective_chi2'] = objective_chi2 + new_data['objective_reduced_chi'] = objective_reduced_chi + new_data['classical_chi2'] = classical_chi2 + new_data['classical_reduced_chi'] = classical_reduced_chi + new_data['reduced_chi'] = objective_reduced_chi new_data['success'] = result[i].success return new_data - def fit_single_data_set_1d(self, data: DataSet1D) -> FitResults: + def fit_single_data_set_1d(self, data: DataSet1D, objective: str | None = None) -> FitResults: + """Perform fitting on a single 1D dataset. + + :param data: The 1D dataset to fit. Note that ``data.ye`` stores + variances (σ²), not standard deviations. + :type data: DataSet1D + :param objective: Per-call override for the zero-variance objective. + If ``None``, uses the instance default set at construction. + :type objective: str or None + :return: Fit results from the minimizer. + :rtype: FitResults """ - Perform the fitting and populate the DataGroups with the result. + obj = _validate_objective(objective) if objective is not None else self._objective - :param data: DataGroup to be fitted to and populated - :param method: Optimisation method - """ x_vals = np.asarray(data.x) y_vals = np.asarray(data.y) variances = np.asarray(data.ye) - zero_variance_mask = variances == 0.0 - num_zero_variance = int(np.sum(zero_variance_mask)) + x_out, y_eff, weights, stats = _prepare_fit_arrays(x_vals, y_vals, variances, obj) - if num_zero_variance > 0: + if stats['masked'] > 0: + warnings.warn( + f'Masked {stats["masked"]} data point(s) in single-dataset fit due to zero variance during fitting.', + UserWarning, + ) + if stats.get('transformed_all_points'): + warnings.warn( + f'Applied Mighell transform to all {len(y_vals)} point(s) in single-dataset fit during fitting.', + UserWarning, + ) + elif stats['mighell_substituted'] > 0: warnings.warn( - f'Masked {num_zero_variance} data point(s) in single-dataset fit due to zero variance during fitting.', + f'Applied Mighell substitution to {stats["mighell_substituted"]} ' + 'zero-variance point(s) in single-dataset fit during fitting.', UserWarning, ) - valid_mask = ~zero_variance_mask - if not np.any(valid_mask): + if obj == 'legacy_mask' and len(x_out) == 0: raise ValueError('Cannot fit single dataset: all points have zero variance.') - x_vals_masked = x_vals[valid_mask] - y_vals_masked = y_vals[valid_mask] - variances_masked = variances[valid_mask] - - weights = 1.0 / np.sqrt(variances_masked) - result = self.easy_science_multi_fitter.fit(x=[x_vals_masked], y=[y_vals_masked], weights=[weights])[0] + result = self.easy_science_multi_fitter.fit(x=[x_out], y=[y_eff], weights=[weights])[0] self._fit_results = [result] + sigma_classical = np.sqrt(np.clip(variances, 0.0, None)) + model_curve = self._fit_func[0](x_vals) + n_classical_points = int(np.sum(variances > 0.0)) + classical_chi2 = _compute_weighted_chi2(y_vals, model_curve, sigma_classical) + classical_reduced_chi = _compute_reduced_chi2(classical_chi2, n_classical_points, result.n_pars) + self._classical_fit_metrics = [ + { + 'classical_chi2': classical_chi2, + 'classical_reduced_chi': classical_reduced_chi, + 'objective_chi2': float(result.chi2), + 'objective_reduced_chi': _fit_result_reduced_chi(result, len(x_out)), + 'n_classical_points': n_classical_points, + } + ] return result @property @@ -149,6 +344,33 @@ def reduced_chi(self) -> float | None: return total_chi2 / total_dof + @property + def classical_chi2(self) -> float | None: + """Classical chi-squared using only points with positive variances.""" + if self._classical_fit_metrics is None: + return None + return float(sum(metric['classical_chi2'] for metric in self._classical_fit_metrics)) + + @property + def classical_reduced_chi(self) -> float | None: + """Reduced classical chi-squared using only points with positive variances.""" + if self._classical_fit_metrics is None or self._fit_results is None: + return None + total_chi2 = self.classical_chi2 + total_points = sum(metric['n_classical_points'] for metric in self._classical_fit_metrics) + n_params = self._fit_results[0].n_pars + return _compute_reduced_chi2(total_chi2, total_points, n_params) + + @property + def objective_chi2(self) -> float | None: + """Objective-space chi-squared returned by the minimizer.""" + return self.chi2 + + @property + def objective_reduced_chi(self) -> float | None: + """Objective-space reduced chi-squared returned by the minimizer.""" + return self.reduced_chi + def switch_minimizer(self, minimizer: AvailableMinimizers) -> None: """ Switch the minimizer for the fitting. diff --git a/src/easyreflectometry/limits.py b/src/easyreflectometry/limits.py new file mode 100644 index 00000000..691f86e3 --- /dev/null +++ b/src/easyreflectometry/limits.py @@ -0,0 +1,44 @@ +import numpy as np +from easyscience.variable import Parameter + +# Fixed-range limit definitions +SLD_LIMITS = (-1.0, 10.0) +SCALE_LIMITS = (0.0, 10.0) + + +def apply_default_limits(parameter: Parameter, kind: str) -> None: + """Apply default min/max to a parameter if current bounds are infinite. + + :param parameter: The parameter to adjust. + :type parameter: Parameter + :param kind: One of 'thickness', 'roughness', 'sld', 'isld', 'scale'. + :type kind: str + """ + if not parameter.independent: + return + + if kind in ('thickness', 'roughness'): + _apply_percentage_limits(parameter) + elif kind in ('sld', 'isld'): + _apply_fixed_limits(parameter, *SLD_LIMITS) + elif kind == 'scale': + _apply_fixed_limits(parameter, *SCALE_LIMITS) + + +def _apply_percentage_limits(parameter: Parameter) -> None: + """Set min to 50% and max to 200% of the current value, only if current bounds are inf.""" + value = parameter.value + if value == 0.0: + return + if np.isinf(parameter.min): + parameter.min = 0.5 * value + if np.isinf(parameter.max): + parameter.max = 2.0 * value + + +def _apply_fixed_limits(parameter: Parameter, low: float, high: float) -> None: + """Set fixed min/max, only if current bounds are inf.""" + if np.isinf(parameter.min) and low <= parameter.value: + parameter.min = low + if np.isinf(parameter.max) and high >= parameter.value: + parameter.max = high diff --git a/src/easyreflectometry/model/model.py b/src/easyreflectometry/model/model.py index e4bdaac5..7f651fa2 100644 --- a/src/easyreflectometry/model/model.py +++ b/src/easyreflectometry/model/model.py @@ -12,6 +12,7 @@ from easyscience import global_object from easyscience.variable import Parameter +from easyreflectometry.limits import apply_default_limits from easyreflectometry.sample import BaseAssembly from easyreflectometry.sample import Sample from easyreflectometry.utils import get_as_parameter @@ -86,6 +87,7 @@ def __init__( resolution_function = PercentageFwhm(DEFAULTS['resolution']['value']) scale = get_as_parameter('scale', scale, DEFAULTS) + apply_default_limits(scale, 'scale') background = get_as_parameter('background', background, DEFAULTS) self.color = color self._is_default = False diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py index 6f7096c1..7e1ab3c9 100644 --- a/src/easyreflectometry/project.py +++ b/src/easyreflectometry/project.py @@ -21,6 +21,7 @@ from easyreflectometry.data.measurement import extract_orso_title from easyreflectometry.data.measurement import load_data_from_orso_file from easyreflectometry.fitting import MultiFitter +from easyreflectometry.limits import apply_default_limits from easyreflectometry.model import Model from easyreflectometry.model import ModelCollection from easyreflectometry.model import PercentageFwhm @@ -91,6 +92,52 @@ def parameters(self) -> List[Parameter]: parameters.append(param) return parameters + def _sync_parameter_states(self) -> None: + """Apply project-level parameter enablement and default limits. + + Superphase thickness/roughness and subphase thickness are physically + meaningless and are marked as disabled. Thickness and roughness default + ranges are then applied only to enabled parameters created from project + defaults, leaving explicit user-provided bounds untouched. + """ + if self._models is None: + return + + disabled_ids: set[int] = set() + for model in self._models: + sample = model.sample + if sample is None or len(sample) == 0: + continue + superphase = sample.superphase + if superphase is not None: + disabled_ids.add(id(superphase.thickness)) + disabled_ids.add(id(superphase.roughness)) + subphase = sample.subphase + if subphase is not None: + disabled_ids.add(id(subphase.thickness)) + + for model in self._models: + sample = model.sample + if sample is None or len(sample) == 0: + continue + for assembly in sample: + for layer in assembly.layers: + self._sync_layer_parameter_state(layer.thickness, 'thickness', disabled_ids) + self._sync_layer_parameter_state(layer.roughness, 'roughness', disabled_ids) + + def _sync_layer_parameter_state(self, parameter: Parameter, kind: str, disabled_ids: set[int]) -> None: + """Update a layer parameter's enabled state and pending default limits.""" + if id(parameter) in disabled_ids: + parameter.enabled = False + return + + if getattr(parameter, 'default_limits_pending', False): + delattr(parameter, 'default_limits_pending') + if getattr(parameter, 'enabled', True): + parameter.min = -np.inf + parameter.max = np.inf + apply_default_limits(parameter, kind) + @property def q_min(self): if self._q_min is None: @@ -204,6 +251,7 @@ def models(self, models: ModelCollection) -> None: self._materials.extend(self._get_materials_in_models()) for model in self._models: model.interface = self._calculator + self._sync_parameter_states() @property def fitter(self) -> MultiFitter: @@ -220,7 +268,17 @@ def calculator(self) -> str: @calculator.setter def calculator(self, calculator: str) -> None: + if calculator == self._calculator.current_interface_name: + return + self._calculator.switch(calculator) + self._calculator.reset_storage() + + for model in self._models: + model.generate_bindings() + + self._fitter = None + self._fitter_model_index = None @property def minimizer(self) -> AvailableMinimizers: @@ -324,6 +382,7 @@ def add_sample_from_orso(self, sample: Sample) -> None: model.interface = self._calculator # Extract materials from the new model and add to project materials self._materials.extend(self._get_materials_from_model(model)) + self._sync_parameter_states() # Switch to the newly added model so its data is visible in the UI self.current_model_index = len(self._models) - 1 diff --git a/src/easyreflectometry/sample/elements/layers/layer.py b/src/easyreflectometry/sample/elements/layers/layer.py index 28f13a38..513b18f9 100644 --- a/src/easyreflectometry/sample/elements/layers/layer.py +++ b/src/easyreflectometry/sample/elements/layers/layer.py @@ -65,18 +65,23 @@ def __init__( if unique_name is None: unique_name = global_object.generate_unique_name(self.__class__.__name__) + thickness_value = thickness thickness = get_as_parameter( name='thickness', value=thickness, default_dict=DEFAULTS, unique_name_prefix=f'{unique_name}_Thickness', ) + thickness.default_limits_pending = not isinstance(thickness_value, Parameter) + + roughness_value = roughness roughness = get_as_parameter( name='roughness', value=roughness, default_dict=DEFAULTS, unique_name_prefix=f'{unique_name}_Roughness', ) + roughness.default_limits_pending = not isinstance(roughness_value, Parameter) super().__init__( name=name, diff --git a/src/easyreflectometry/sample/elements/materials/material.py b/src/easyreflectometry/sample/elements/materials/material.py index 249cd160..8c030031 100644 --- a/src/easyreflectometry/sample/elements/materials/material.py +++ b/src/easyreflectometry/sample/elements/materials/material.py @@ -7,6 +7,7 @@ from easyscience import global_object from easyscience.variable import Parameter +from easyreflectometry.limits import apply_default_limits from easyreflectometry.utils import get_as_parameter from ...base_core import BaseCore @@ -62,12 +63,15 @@ def __init__( default_dict=DEFAULTS, unique_name_prefix=f'{unique_name}_Sld', ) + apply_default_limits(sld, 'sld') + isld = get_as_parameter( name='isld', value=isld, default_dict=DEFAULTS, unique_name_prefix=f'{unique_name}_Isld', ) + apply_default_limits(isld, 'isld') super().__init__( name=name, diff --git a/tests/model/test_model.py b/tests/model/test_model.py index 5745501e..49ce60fc 100644 --- a/tests/model/test_model.py +++ b/tests/model/test_model.py @@ -37,7 +37,7 @@ def test_default(self): assert_equal(str(p.scale.unit), 'dimensionless') assert_equal(p.scale.value, 1.0) assert_equal(p.scale.min, 0.0) - assert_equal(p.scale.max, np.inf) + assert_equal(p.scale.max, 10.0) assert_equal(p.scale.fixed, True) assert_equal(p.background.display_name, 'background') assert_equal(str(p.background.unit), 'dimensionless') @@ -73,7 +73,7 @@ def test_from_pars(self): assert_equal(str(mod.scale.unit), 'dimensionless') assert_equal(mod.scale.value, 2.0) assert_equal(mod.scale.min, 0.0) - assert_equal(mod.scale.max, np.inf) + assert_equal(mod.scale.max, 10.0) assert_equal(mod.scale.fixed, True) assert_equal(mod.background.display_name, 'background') assert_equal(str(mod.background.unit), 'dimensionless') diff --git a/tests/sample/elements/materials/test_material.py b/tests/sample/elements/materials/test_material.py index a9ff1dde..c07a2217 100644 --- a/tests/sample/elements/materials/test_material.py +++ b/tests/sample/elements/materials/test_material.py @@ -5,7 +5,6 @@ __author__ = 'github.com/arm61' __version__ = '0.0.1' -import numpy as np from easyscience import global_object from easyreflectometry.sample.elements.materials.material import DEFAULTS @@ -21,14 +20,14 @@ def test_no_arguments(self): assert p.sld.display_name == 'sld' assert str(p.sld.unit) == '1/Å^2' assert p.sld.value == 4.186 - assert p.sld.min == -np.inf - assert p.sld.max == np.inf + assert p.sld.min == -1.0 + assert p.sld.max == 10.0 assert p.sld.fixed is True assert p.isld.display_name == 'isld' assert str(p.isld.unit) == '1/Å^2' assert p.isld.value == 0.0 - assert p.isld.min == -np.inf - assert p.isld.max == np.inf + assert p.isld.min == -1.0 + assert p.isld.max == 10.0 assert p.isld.fixed is True def test_shuffled_arguments(self): @@ -38,14 +37,14 @@ def test_shuffled_arguments(self): assert p.sld.display_name == 'sld' assert str(p.sld.unit) == '1/Å^2' assert p.sld.value == 6.908 - assert p.sld.min == -np.inf - assert p.sld.max == np.inf + assert p.sld.min == -1.0 + assert p.sld.max == 10.0 assert p.sld.fixed is True assert p.isld.display_name == 'isld' assert str(p.isld.unit) == '1/Å^2' assert p.isld.value == -0.278 - assert p.isld.min == -np.inf - assert p.isld.max == np.inf + assert p.isld.min == -1.0 + assert p.isld.max == 10.0 assert p.isld.fixed is True def test_only_sld_key(self): @@ -53,8 +52,8 @@ def test_only_sld_key(self): assert p.sld.display_name == 'sld' assert str(p.sld.unit) == '1/Å^2' assert p.sld.value == 10 - assert p.sld.min == -np.inf - assert p.sld.max == np.inf + assert p.sld.min == -1.0 + assert p.sld.max == 10.0 assert p.sld.fixed is True def test_only_sld_key_parameter(self): @@ -69,8 +68,8 @@ def test_only_isld_key(self): assert p.isld.display_name == 'isld' assert str(p.isld.unit) == '1/Å^2' assert p.isld.value == 10 - assert p.isld.min == -np.inf - assert p.isld.max == np.inf + assert p.isld.min == -1.0 + assert p.isld.max == 10.0 assert p.isld.fixed is True def test_only_isld_key_parameter(self): diff --git a/tests/test_fitting.py b/tests/test_fitting.py index 446f10b9..2a03a98c 100644 --- a/tests/test_fitting.py +++ b/tests/test_fitting.py @@ -5,6 +5,7 @@ import numpy as np import pytest +import scipp as sc from easyscience.fitting.minimizers.factory import AvailableMinimizers import easyreflectometry @@ -12,6 +13,8 @@ from easyreflectometry.data import DataSet1D from easyreflectometry.data.measurement import load from easyreflectometry.fitting import MultiFitter +from easyreflectometry.fitting import _prepare_fit_arrays +from easyreflectometry.fitting import _validate_objective from easyreflectometry.model import Model from easyreflectometry.model import PercentageFwhm from easyreflectometry.sample import Layer @@ -76,7 +79,7 @@ def test_fitting(minimizer): def test_fitting_with_zero_variance(): - """Test that zero variance points are properly detected and masked during fitting when present in the data.""" + """Test that zero variance points are handled via Mighell substitution (hybrid default).""" import warnings import numpy as np @@ -129,26 +132,24 @@ def test_fitting_with_zero_variance(): model.interface = interface fitter = MultiFitter(model) - # Capture warnings during fitting - check if zero variance points still exist in the data - # and are properly handled by the fitting method + # Capture warnings during fitting with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') analysed = fitter.fit(data) - # Check if any zero variance warnings were issued during fitting - fitting_warnings = [str(warning.message) for warning in w if 'zero variance during fitting' in str(warning.message)] + # Under hybrid default, zero variance points trigger Mighell substitution warnings + mighell_warnings = [str(warning.message) for warning in w if 'Mighell substitution' in str(warning.message)] + mask_warnings = [str(warning.message) for warning in w if 'Masked' in str(warning.message)] + + # Hybrid mode should NOT produce mask warnings + assert len(mask_warnings) == 0, f'Unexpected mask warnings under hybrid: {mask_warnings}' - # The fitting method should handle zero variance points gracefully - # If there are any zero variance points remaining in the data, they should be masked - # and a warning should be issued - if len(fitting_warnings) > 0: - # Verify the warning message format and that it mentions masking points - for warning_msg in fitting_warnings: - assert 'Masked' in warning_msg and 'zero variance during fitting' in warning_msg - print(f'Info: {warning_msg}') # Log for debugging + # If there are zero-variance points in the loaded data, Mighell warnings should appear + if len(mighell_warnings) > 0: + for warning_msg in mighell_warnings: + assert 'zero-variance point(s)' in warning_msg # Basic checks that fitting completed - # The keys will be based on the filename, not just '0' model_keys = [k for k in analysed.keys() if k.endswith('_model')] sld_keys = [k for k in analysed.keys() if k.startswith('SLD_')] assert len(model_keys) > 0, f'No model keys found in {list(analysed.keys())}' @@ -157,7 +158,7 @@ def test_fitting_with_zero_variance(): def test_fitting_with_manual_zero_variance(): - """Test the fit method with manually created zero variance points.""" + """Test the fit method with manually created zero variance points using hybrid (default).""" import warnings import numpy as np @@ -217,12 +218,12 @@ def test_fitting_with_manual_zero_variance(): warnings.simplefilter('always') analysed = fitter.fit(data) - # Check that warnings were issued about zero variance points - fitting_warnings = [str(warning.message) for warning in w if 'zero variance during fitting' in str(warning.message)] + # Under hybrid default, should get Mighell substitution warning, not masking + mighell_warnings = [str(warning.message) for warning in w if 'Mighell substitution' in str(warning.message)] + + assert len(mighell_warnings) == 1, f'Expected 1 Mighell warning, got {len(mighell_warnings)}: {mighell_warnings}' + assert '7 zero-variance point(s)' in mighell_warnings[0], f'Unexpected warning content: {mighell_warnings[0]}' - # Should have one warning about the 7 zero variance points (5 + 2) - assert len(fitting_warnings) == 1, f'Expected 1 warning, got {len(fitting_warnings)}: {fitting_warnings}' - assert 'Masked 7 data point(s)' in fitting_warnings[0], f'Unexpected warning content: {fitting_warnings[0]}' # Basic checks that fitting completed despite zero variance points assert 'R_0_model' in analysed.keys() assert 'SLD_0' in analysed.keys() @@ -230,9 +231,10 @@ def test_fitting_with_manual_zero_variance(): def test_fit_single_data_set_1d_masks_zero_variance_points(): + """Legacy mask mode: zero-variance points are dropped.""" model = Model() model.interface = CalculatorFactory() - fitter = MultiFitter(model) + fitter = MultiFitter(model, objective='legacy_mask') captured = {} mock_result = MagicMock() @@ -255,7 +257,7 @@ def _fake_fit(*, x, y, weights): ye=np.array([0.01, 0.0, 0.04]), ) - with pytest.warns(UserWarning, match='Masked 1 data point\(s\) in single-dataset fit'): + with pytest.warns(UserWarning, match='Masked 1 data point\\(s\\) in single-dataset fit'): result = fitter.fit_single_data_set_1d(data) assert result is mock_result @@ -286,9 +288,10 @@ def test_reduced_chi_uses_global_dof_across_fit_results(): def test_fit_single_data_set_1d_all_zero_variance_raises(): + """Legacy mask mode raises when all points have zero variance.""" model = Model() model.interface = CalculatorFactory() - fitter = MultiFitter(model) + fitter = MultiFitter(model, objective='legacy_mask') data = DataSet1D( name='all_zero', @@ -376,3 +379,408 @@ def _fake_fit(*, x, y, weights): assert result is mock_result assert np.allclose(captured['x'][0], np.array([0.01, 0.02, 0.03])) assert np.allclose(captured['y'][0], np.array([1.0, 0.8, 0.6])) + + +# --- New tests for objective-based zero-variance handling --- + + +def test_objective_validation_rejects_unknown_value(): + with pytest.raises(ValueError, match='Unknown objective'): + _validate_objective('bad_value') + + +def test_objective_validation_resolves_auto(): + assert _validate_objective('auto') == 'hybrid' + assert _validate_objective('hybrid') == 'hybrid' + assert _validate_objective('legacy_mask') == 'legacy_mask' + assert _validate_objective('mighell') == 'mighell' + + +def test_prepare_fit_arrays_weights_always_positive_and_finite(): + """Weights must be strictly positive and finite for all inputs and objectives.""" + test_cases = [ + # (y_vals, variances, description) + (np.array([0.0]), np.array([0.0]), 'y=0, var=0'), + (np.array([-0.5]), np.array([0.0]), 'y=-0.5, var=0'), + (np.array([-1.0]), np.array([0.0]), 'y=-1, var=0'), + (np.array([1e6]), np.array([0.0]), 'y=1e6, var=0'), + (np.array([0.5, 0.3, 0.1]), np.array([0.0, 0.0, 0.0]), 'all-zero variances'), + (np.array([0.5, 0.3, 0.1]), np.array([0.01, 0.0, 0.04]), 'mixed variances'), + (np.array([0.0, -0.5, -1.0, 1e6]), np.array([0.0, 0.0, 0.0, 0.0]), 'edge y values'), + ] + + for objective in ('hybrid', 'mighell'): + for y_vals, variances, desc in test_cases: + x = np.arange(len(y_vals), dtype=float) + _, _, weights, _ = _prepare_fit_arrays(x, y_vals, variances, objective) + assert len(weights) == len(y_vals), f'Wrong length for {desc}, {objective}' + assert np.all(weights > 0), f'Non-positive weight for {desc}, {objective}: {weights}' + assert np.all(np.isfinite(weights)), f'Non-finite weight for {desc}, {objective}: {weights}' + + +def test_prepare_fit_arrays_legacy_mask_drops_zero_variance(): + x = np.array([0.01, 0.02, 0.03]) + y = np.array([1.0, 0.8, 0.6]) + var = np.array([0.01, 0.0, 0.04]) + + x_out, y_eff, weights, stats = _prepare_fit_arrays(x, y, var, 'legacy_mask') + + assert np.allclose(x_out, [0.01, 0.03]) + assert np.allclose(y_eff, [1.0, 0.6]) + assert np.allclose(weights, [1.0 / np.sqrt(0.01), 1.0 / np.sqrt(0.04)]) + assert stats == {'valid': 2, 'mighell_substituted': 0, 'masked': 1, 'transformed_all_points': False} + + +def test_prepare_fit_arrays_hybrid_transforms_zero_variance(): + x = np.array([0.01, 0.02, 0.03]) + y = np.array([1.0, 0.8, 0.6]) + var = np.array([0.01, 0.0, 0.04]) + + x_out, y_eff, weights, stats = _prepare_fit_arrays(x, y, var, 'hybrid') + + # x unchanged + assert np.allclose(x_out, x) + # Index 0 and 2: standard WLS (unchanged y) + assert y_eff[0] == pytest.approx(1.0) + assert y_eff[2] == pytest.approx(0.6) + assert weights[0] == pytest.approx(1.0 / np.sqrt(0.01)) + assert weights[2] == pytest.approx(1.0 / np.sqrt(0.04)) + # Index 1: Mighell transform — y_eff = y + min(y, 1) = 0.8 + 0.8 = 1.6 + assert y_eff[1] == pytest.approx(0.8 + 0.8) + # sigma = sqrt(y + 1) = sqrt(1.8) + assert weights[1] == pytest.approx(1.0 / np.sqrt(1.8)) + assert stats == {'valid': 2, 'mighell_substituted': 1, 'masked': 0, 'transformed_all_points': False} + + +def test_prepare_fit_arrays_mighell_transforms_all(): + x = np.array([0.01, 0.02]) + y = np.array([0.5, 0.3]) + var = np.array([0.01, 0.04]) # All valid, but mighell transforms everything + + x_out, y_eff, weights, stats = _prepare_fit_arrays(x, y, var, 'mighell') + + assert np.allclose(x_out, x) + # y_eff = y + min(y, 1) = y + y (since y < 1) + assert y_eff[0] == pytest.approx(0.5 + 0.5) + assert y_eff[1] == pytest.approx(0.3 + 0.3) + # sigma = sqrt(y + 1) + assert weights[0] == pytest.approx(1.0 / np.sqrt(1.5)) + assert weights[1] == pytest.approx(1.0 / np.sqrt(1.3)) + assert stats == {'valid': 0, 'mighell_substituted': 2, 'masked': 0, 'transformed_all_points': True} + + +def test_fit_single_data_set_1d_hybrid_keeps_zero_variance_points(): + """Hybrid mode keeps all points (transforms zero-variance ones).""" + model = Model() + model.interface = CalculatorFactory() + fitter = MultiFitter(model) # default objective='hybrid' + + captured = {} + mock_result = MagicMock() + mock_result.chi2 = 1.0 + mock_result.n_pars = 1 + + def _fake_fit(*, x, y, weights): + captured['x'] = x + captured['y'] = y + captured['weights'] = weights + return [mock_result] + + fitter.easy_science_multi_fitter = MagicMock() + fitter.easy_science_multi_fitter.fit = MagicMock(side_effect=_fake_fit) + + data = DataSet1D( + name='hybrid_test', + x=np.array([0.01, 0.02, 0.03]), + y=np.array([1.0, 0.8, 0.6]), + ye=np.array([0.01, 0.0, 0.04]), + ) + + with pytest.warns(UserWarning, match='Mighell substitution'): + result = fitter.fit_single_data_set_1d(data) + + assert result is mock_result + # All 3 points should be passed through (not masked) + assert len(captured['x'][0]) == 3 + assert len(captured['y'][0]) == 3 + assert len(captured['weights'][0]) == 3 + + +def test_fit_single_data_set_1d_mighell_warning_mentions_all_points(): + model = Model() + model.interface = CalculatorFactory() + fitter = MultiFitter(model, objective='mighell') + + mock_result = MagicMock() + mock_result.chi2 = 1.0 + mock_result.reduced_chi = 0.5 + mock_result.n_pars = 1 + + fitter.easy_science_multi_fitter = MagicMock() + fitter.easy_science_multi_fitter.fit = MagicMock(return_value=[mock_result]) + fitter._fit_func = [lambda x: np.zeros_like(x)] + + data = DataSet1D( + name='mighell_warning', + x=np.array([0.01, 0.02, 0.03]), + y=np.array([1.0, 0.8, 0.6]), + ye=np.array([0.01, 0.02, 0.04]), + ) + + with pytest.warns(UserWarning, match=r'Applied Mighell transform to all 3 point\(s\)'): + fitter.fit_single_data_set_1d(data) + + +def test_classical_and_objective_chi_are_split_for_fit_results(): + model = Model() + model.interface = CalculatorFactory() + fitter = MultiFitter(model, objective='mighell') + + fit_result = MagicMock() + fit_result.chi2 = 0.25 + fit_result.reduced_chi = 0.125 + fit_result.n_pars = 1 + fit_result.x = np.array([0.01, 0.02, 0.03]) + + fitter.easy_science_multi_fitter = MagicMock() + fitter.easy_science_multi_fitter.fit = MagicMock(return_value=[fit_result]) + fitter.easy_science_multi_fitter._fit_objects = [MagicMock(interface=MagicMock())] + fitter.easy_science_multi_fitter._fit_objects[0].interface.sld_profile.return_value = ( + np.array([0.0, 1.0]), + np.array([1.0, 2.0]), + ) + + fitter._models = [MagicMock(unique_name='model_0', as_dict=MagicMock(return_value={'name': 'model_0'}))] + fitter._fit_func = [lambda x: np.array([0.8, 0.75, 0.7])] + + data = sc.DataGroup( + { + 'coords': {'Qz_0': sc.array(dims=['Qz_0'], values=np.array([0.01, 0.02, 0.03]), unit=sc.Unit('1/angstrom'))}, + 'data': {'R_0': sc.array(dims=['Qz_0'], values=np.array([1.0, 0.9, 0.7]), variances=np.array([0.01, 0.0, 0.04]))}, + 'attrs': {}, + } + ) + + analysed = fitter.fit(data) + + expected_classical_chi2 = ((1.0 - 0.8) / 0.1) ** 2 + ((0.7 - 0.7) / 0.2) ** 2 + expected_classical_reduced = expected_classical_chi2 / (2 - fit_result.n_pars) + + assert analysed['objective_chi2'] == pytest.approx(0.25) + assert analysed['objective_reduced_chi'] == pytest.approx(0.125) + assert analysed['classical_chi2'] == pytest.approx(expected_classical_chi2) + assert analysed['classical_reduced_chi'] == pytest.approx(expected_classical_reduced) + assert fitter.objective_chi2 == pytest.approx(0.25) + assert fitter.objective_reduced_chi == pytest.approx(0.125) + assert fitter.classical_chi2 == pytest.approx(expected_classical_chi2) + assert fitter.classical_reduced_chi == pytest.approx(expected_classical_reduced) + + +def test_fit_single_data_set_1d_all_zero_variance_hybrid_does_not_raise(): + """Hybrid mode handles all-zero-variance data without raising.""" + model = Model() + model.interface = CalculatorFactory() + fitter = MultiFitter(model) # default objective='hybrid' + + captured = {} + mock_result = MagicMock() + mock_result.chi2 = 1.0 + mock_result.n_pars = 1 + + def _fake_fit(*, x, y, weights): + captured['x'] = x + captured['y'] = y + captured['weights'] = weights + return [mock_result] + + fitter.easy_science_multi_fitter = MagicMock() + fitter.easy_science_multi_fitter.fit = MagicMock(side_effect=_fake_fit) + + data = DataSet1D( + name='all_zero_hybrid', + x=np.array([0.01, 0.02, 0.03]), + y=np.array([1.0, 0.8, 0.6]), + ye=np.array([0.0, 0.0, 0.0]), + ) + + with pytest.warns(UserWarning, match='Mighell substitution'): + result = fitter.fit_single_data_set_1d(data) + + assert result is mock_result + assert len(captured['x'][0]) == 3 + + +def test_fit_single_data_set_1d_legacy_mask_preserves_old_behavior(): + """Legacy mask mode drops zero-variance points and warns with old message.""" + model = Model() + model.interface = CalculatorFactory() + fitter = MultiFitter(model, objective='legacy_mask') + + captured = {} + mock_result = MagicMock() + mock_result.chi2 = 1.0 + mock_result.n_pars = 1 + + def _fake_fit(*, x, y, weights): + captured['x'] = x + captured['y'] = y + captured['weights'] = weights + return [mock_result] + + fitter.easy_science_multi_fitter = MagicMock() + fitter.easy_science_multi_fitter.fit = MagicMock(side_effect=_fake_fit) + + data = DataSet1D( + name='legacy_test', + x=np.array([0.01, 0.02, 0.03]), + y=np.array([1.0, 0.8, 0.6]), + ye=np.array([0.01, 0.0, 0.04]), + ) + + with pytest.warns(UserWarning, match='Masked 1 data point'): + result = fitter.fit_single_data_set_1d(data) + + assert result is mock_result + assert np.allclose(captured['x'][0], np.array([0.01, 0.03])) + assert np.allclose(captured['y'][0], np.array([1.0, 0.6])) + + +def test_fit_multi_dataset_hybrid_uses_transformed_y_and_weights(): + """Multi-dataset fit with hybrid objective transforms zero-variance points.""" + import scipp as sc + + qz_values = np.linspace(0.01, 0.3, 10) + r_values = np.exp(-qz_values * 50) + variances = np.ones_like(r_values) * 0.01 + variances[3:5] = 0.0 # 2 zero-variance points + + data = sc.DataGroup( + { + 'coords': {'Qz_0': sc.array(dims=['Qz_0'], values=qz_values)}, + 'data': {'R_0': sc.array(dims=['Qz_0'], values=r_values, variances=variances)}, + } + ) + + model = Model() + model.interface = CalculatorFactory() + fitter = MultiFitter(model) + + captured = {} + + def _fake_fit(x, y, weights): + captured['x'] = x + captured['y'] = y + captured['weights'] = weights + mock_r = MagicMock() + mock_r.reduced_chi = 1.0 + mock_r.success = True + mock_r.chi2 = 1.0 + mock_r.n_pars = 1 + mock_r.x = x[0] + return [mock_r] + + fitter.easy_science_multi_fitter = MagicMock() + fitter.easy_science_multi_fitter.fit = MagicMock(side_effect=_fake_fit) + fitter.easy_science_multi_fitter._fit_objects = [MagicMock()] + fitter.easy_science_multi_fitter._fit_objects[0].interface.sld_profile.return_value = ( + np.linspace(0, 100, 5), + np.ones(5), + ) + + import warnings + + with warnings.catch_warnings(record=True) as w: + warnings.simplefilter('always') + fitter.fit(data) + + # All 10 points should be present (not masked) + assert len(captured['x'][0]) == 10 + assert len(captured['y'][0]) == 10 + assert len(captured['weights'][0]) == 10 + + # Zero-variance points should have Mighell-transformed y + for idx in [3, 4]: + y_orig = r_values[idx] + expected_y_eff = y_orig + min(y_orig, 1.0) + assert captured['y'][0][idx] == pytest.approx(expected_y_eff) + + # Check that Mighell warning was emitted + mighell_warnings = [str(ww.message) for ww in w if 'Mighell substitution' in str(ww.message)] + assert len(mighell_warnings) == 1 + assert '2 zero-variance point(s)' in mighell_warnings[0] + + +def test_fit_warnings_objective_specific(): + """Verify that each objective mode produces the correct warning type.""" + import warnings + + model = Model() + model.interface = CalculatorFactory() + + mock_result = MagicMock() + mock_result.chi2 = 1.0 + mock_result.n_pars = 1 + + data = DataSet1D( + name='warn_test', + x=np.array([0.01, 0.02, 0.03]), + y=np.array([1.0, 0.8, 0.6]), + ye=np.array([0.01, 0.0, 0.04]), + ) + + for obj, expected_fragment in [ + ('legacy_mask', 'Masked 1 data point(s)'), + ('hybrid', 'Mighell substitution'), + ('mighell', 'Applied Mighell transform to all 3 point(s)'), + ]: + fitter = MultiFitter(model, objective=obj) + fitter.easy_science_multi_fitter = MagicMock() + fitter.easy_science_multi_fitter.fit = MagicMock(return_value=[mock_result]) + + with warnings.catch_warnings(record=True) as w: + warnings.simplefilter('always') + fitter.fit_single_data_set_1d(data) + + matching = [str(ww.message) for ww in w if expected_fragment in str(ww.message)] + assert len(matching) > 0, f'No warning containing {expected_fragment!r} for objective={obj}' + + +def test_multifitter_constructor_rejects_bad_objective(): + model = Model() + model.interface = CalculatorFactory() + with pytest.raises(ValueError, match='Unknown objective'): + MultiFitter(model, objective='nonsense') + + +def test_fit_per_call_objective_override(): + """Per-call objective override in fit_single_data_set_1d works.""" + model = Model() + model.interface = CalculatorFactory() + fitter = MultiFitter(model, objective='hybrid') # default + + captured = {} + mock_result = MagicMock() + mock_result.chi2 = 1.0 + mock_result.n_pars = 1 + + def _fake_fit(*, x, y, weights): + captured['x'] = x + captured['y'] = y + captured['weights'] = weights + return [mock_result] + + fitter.easy_science_multi_fitter = MagicMock() + fitter.easy_science_multi_fitter.fit = MagicMock(side_effect=_fake_fit) + + data = DataSet1D( + name='override_test', + x=np.array([0.01, 0.02, 0.03]), + y=np.array([1.0, 0.8, 0.6]), + ye=np.array([0.01, 0.0, 0.04]), + ) + + # Override to legacy_mask — should drop the zero-variance point + with pytest.warns(UserWarning, match='Masked 1 data point'): + fitter.fit_single_data_set_1d(data, objective='legacy_mask') + + assert len(captured['x'][0]) == 2 # one point dropped diff --git a/tests/test_limits.py b/tests/test_limits.py new file mode 100644 index 00000000..e8320eb7 --- /dev/null +++ b/tests/test_limits.py @@ -0,0 +1,150 @@ +import numpy as np +import pytest +from easyscience import global_object +from easyscience.variable import Parameter + +from easyreflectometry.limits import SCALE_LIMITS +from easyreflectometry.limits import SLD_LIMITS +from easyreflectometry.limits import apply_default_limits + + +class TestApplyDefaultLimits: + def test_sld_with_inf_bounds(self): + param = Parameter('sld', 4.186, min=-np.inf, max=np.inf) + apply_default_limits(param, 'sld') + assert param.min == SLD_LIMITS[0] + assert param.max == SLD_LIMITS[1] + + def test_isld_with_inf_bounds(self): + param = Parameter('isld', 0.0, min=-np.inf, max=np.inf) + apply_default_limits(param, 'isld') + assert param.min == SLD_LIMITS[0] + assert param.max == SLD_LIMITS[1] + + def test_sld_preserves_finite_bounds(self): + param = Parameter('sld', 4.0, min=-2.0, max=8.0) + apply_default_limits(param, 'sld') + assert param.min == -2.0 + assert param.max == 8.0 + + def test_scale_with_inf_bounds(self): + param = Parameter('scale', 1.0, min=0, max=np.inf) + apply_default_limits(param, 'scale') + assert param.min == SCALE_LIMITS[0] + assert param.max == SCALE_LIMITS[1] + + def test_scale_preserves_finite_bounds(self): + param = Parameter('scale', 1.0, min=0.5, max=2.0) + apply_default_limits(param, 'scale') + assert param.min == 0.5 + assert param.max == 2.0 + + def test_thickness_percentage_limits(self): + param = Parameter('thickness', 10.0, min=0.0, max=np.inf) + apply_default_limits(param, 'thickness') + assert param.min == 0.0 # 0.0 is finite, not overwritten + assert param.max == 20.0 # 2.0 * 10.0 + + def test_thickness_both_inf(self): + param = Parameter('thickness', 10.0, min=-np.inf, max=np.inf) + apply_default_limits(param, 'thickness') + assert param.min == 5.0 # 0.5 * 10.0 + assert param.max == 20.0 # 2.0 * 10.0 + + def test_roughness_percentage_limits(self): + param = Parameter('roughness', 3.3, min=0.0, max=np.inf) + apply_default_limits(param, 'roughness') + assert param.min == 0.0 # 0.0 is finite, not overwritten + assert param.max == pytest.approx(6.6) # 2.0 * 3.3 + + def test_thickness_zero_value_unchanged(self): + param = Parameter('thickness', 0.0, min=0.0, max=np.inf) + apply_default_limits(param, 'thickness') + assert param.min == 0.0 + assert param.max == np.inf # unchanged, zero-valued skip + + def test_roughness_zero_value_unchanged(self): + param = Parameter('roughness', 0.0, min=-np.inf, max=np.inf) + apply_default_limits(param, 'roughness') + assert param.min == -np.inf + assert param.max == np.inf + + def test_thickness_preserves_finite_bounds(self): + param = Parameter('thickness', 10.0, min=2.0, max=25.0) + apply_default_limits(param, 'thickness') + assert param.min == 2.0 + assert param.max == 25.0 + + def test_dependent_parameter_skipped(self): + independent_param = Parameter('sld_main', 4.0, min=-np.inf, max=np.inf) + dependent_param = Parameter('sld_dep', 4.0, min=-np.inf, max=np.inf) + dependent_param.make_dependent_on(dependency_expression='a', dependency_map={'a': independent_param}) + apply_default_limits(dependent_param, 'sld') + assert np.isinf(dependent_param.min) + assert np.isinf(dependent_param.max) + + def test_unknown_kind_is_noop(self): + param = Parameter('foo', 5.0, min=-np.inf, max=np.inf) + apply_default_limits(param, 'unknown') + assert np.isinf(param.min) + assert np.isinf(param.max) + + +class TestIntegrationWithConstructors: + def setup_method(self): + global_object.map._clear() + + def test_material_gets_sld_limits(self): + from easyreflectometry.sample.elements.materials.material import Material + + mat = Material(sld=6.36, isld=0.0) + assert mat.sld.min == SLD_LIMITS[0] + assert mat.sld.max == SLD_LIMITS[1] + assert mat.isld.min == SLD_LIMITS[0] + assert mat.isld.max == SLD_LIMITS[1] + + def test_layer_gets_percentage_limits(self): + from easyreflectometry.project import Project + + project = Project() + project.default_model() + layer = project.models[0].sample[1].layers[0] + assert layer.thickness.min == 50.0 + assert layer.thickness.max == 200.0 + assert layer.roughness.min == 1.5 + assert layer.roughness.max == 6.0 + + def test_layer_constructor_keeps_default_bounds_until_project_sync(self): + from easyreflectometry.sample.elements.layers.layer import Layer + + layer = Layer(thickness=20.0, roughness=5.0) + assert layer.thickness.min == 0.0 + assert layer.thickness.max == np.inf + assert layer.roughness.min == 0.0 + assert layer.roughness.max == np.inf + + def test_layer_zero_thickness_unchanged(self): + from easyreflectometry.project import Project + + project = Project() + project.default_model() + layer = project.models[0].sample[0].layers[0] + assert layer.thickness.min == 0.0 + assert layer.thickness.max == np.inf + assert layer.roughness.min == 0.0 + assert layer.roughness.max == np.inf + + def test_model_gets_scale_limits(self): + from easyreflectometry.model.model import Model + + model = Model(scale=1.0) + assert model.scale.min == SCALE_LIMITS[0] + assert model.scale.max == SCALE_LIMITS[1] + + def test_existing_parameter_bounds_preserved(self): + from easyreflectometry.sample.elements.materials.material import Material + + custom_sld = Parameter('sld', 4.0, min=-0.5, max=7.0) + mat = Material(sld=custom_sld) + assert mat.sld.min == -0.5 + assert mat.sld.max == 7.0 diff --git a/tests/test_ort_file.py b/tests/test_ort_file.py index c547b1f5..8ef1de16 100644 --- a/tests/test_ort_file.py +++ b/tests/test_ort_file.py @@ -123,6 +123,7 @@ def fit_model(load_data): fitter1 = MultiFitter(multi_layer_model) fitter1.switch_minimizer(AvailableMinimizers.Bumps_simplex) + fitter1.easy_science_multi_fitter.max_evaluations = 3000 analysed = fitter1.fit(data) return analysed diff --git a/tests/test_project.py b/tests/test_project.py index b93df068..3c390960 100644 --- a/tests/test_project.py +++ b/tests/test_project.py @@ -268,6 +268,20 @@ def test_fitter_new_model_index(self): # Expect assert fitter_0 is not fitter_1 + def test_switch_calculator_rebuilds_model_bindings(self): + # When + project = Project() + project.default_model() + + # Then + project.calculator = 'refl1d' + reflectivity = project.model_data_for_model_at_index(0, np.array([0.01, 0.05, 0.1, 0.5])) + + # Expect + assert project.calculator == 'refl1d' + assert len(reflectivity.y) == 4 + assert np.all(np.isfinite(reflectivity.y)) + def test_experiments(self): # When project = Project() @@ -706,6 +720,35 @@ def test_parameters(self): assert len(parameters) == 14 assert isinstance(parameters[0], Parameter) + def test_parameters_enabled_flags(self): + global_object.map._clear() + project = Project() + project.default_model() + + sample = project.models[0].sample + superphase = sample.superphase + subphase = sample.subphase + middle_layer = sample[1].front_layer + + assert superphase.thickness.enabled is False + assert superphase.roughness.enabled is False + assert subphase.thickness.enabled is False + assert getattr(subphase.roughness, 'enabled', True) is True + assert getattr(middle_layer.thickness, 'enabled', True) is True + assert getattr(middle_layer.roughness, 'enabled', True) is True + + def test_parameters_read_does_not_overwrite_enabled_flag(self): + global_object.map._clear() + project = Project() + project.default_model() + + parameter = project.models[0].sample[0].layers[0].thickness + parameter.enabled = True + + _ = project.parameters + + assert parameter.enabled is True + def test_current_experiment_index_getter_and_setter(self): global_object.map._clear() project = Project() From e23adc3a35df67f9c350b5a81c7d86f2eb6e86c7 Mon Sep 17 00:00:00 2001 From: rozyczko Date: Thu, 7 May 2026 13:31:14 +0200 Subject: [PATCH 02/20] initial commit up to and including `pixi run check` step --- .badgery.yaml | 72 + .codecov.yml | 10 +- .copier-answers.yml | 30 +- .gitattributes | 2 + .github/actions/download-artifact/action.yml | 50 + .github/actions/github-script/action.yml | 19 + .../actions/setup-easyscience-bot/action.yml | 40 + .github/actions/setup-pixi/action.yml | 44 + .github/actions/upload-artifact/action.yml | 49 + .github/actions/upload-codecov/action.yml | 42 + .github/configs/pages-deployment.json | 6 + .github/configs/rulesets-develop.json | 37 + .github/configs/rulesets-gh-pages.json | 19 + .github/configs/rulesets-master.json | 30 + .github/copilot-instructions.md | 53 +- .github/release-drafter.yml | 32 +- .github/scripts/backmerge-conflict-issue.js | 69 + .github/scripts/publish-dashboard.sh | 77 + .github/workflows/backmerge.yml | 109 + .github/workflows/cleanup.yml | 84 + .github/workflows/codeql-analysis.yml | 72 +- .github/workflows/coverage.yml | 94 + .github/workflows/dashboard.yml | 111 + .github/workflows/docs.yml | 188 + .github/workflows/documentation-build.yml | 66 +- .github/workflows/issues-labels.yml | 149 + .github/workflows/lint-format.yml | 124 + .github/workflows/ossar-analysis.yml | 62 +- .github/workflows/pr-labels.yml | 63 + .github/workflows/pypi-publish.yml | 46 + .github/workflows/pypi-test.yml | 80 + .github/workflows/python-ci.yml | 84 +- .github/workflows/python-package.yml | 42 +- .github/workflows/python-publish.yml | 28 +- .../release-drafter-verify-pr-labels.yml | 18 +- .github/workflows/release-drafter.yml | 1 - .github/workflows/release-notes.yml | 71 + .github/workflows/release-pr.yml | 55 + .github/workflows/security.yml | 93 + .github/workflows/test-trigger.yml | 40 + .github/workflows/test.yml | 302 + .github/workflows/tutorial-tests-trigger.yml | 40 + .github/workflows/tutorial-tests.yml | 60 + .gitignore | 59 +- .pre-commit-config.yaml | 61 + .prettierignore | 32 + CHANGELOG.md | 17 +- CONTRIBUTING.md | 446 + LICENSE | 3 +- README.md | 56 +- codecov.yml | 13 + docs/docs/api-reference/index.md | 8 + docs/docs/assets/images/logo_dark.svg | 25 + docs/docs/assets/images/logo_light.svg | 25 + docs/docs/assets/javascripts/extra.js | 27 + docs/docs/assets/javascripts/mathjax.js | 33 + docs/docs/assets/stylesheets/extra.css | 359 + docs/docs/index.md | 21 + docs/docs/installation-and-setup/index.md | 282 + docs/docs/introduction/index.md | 68 + docs/docs/tutorials/index.md | 21 + docs/docs/tutorials/tutorial.ipynb | 63 + docs/docs/user-guide/index.md | 24 + docs/includes/abbreviations.md | 15 + docs/mkdocs.yml | 180 + docs/overrides/.icons/app.svg | 4 + docs/overrides/.icons/easyscience.svg | 20 + docs/overrides/.icons/google-colab.svg | 7 + docs/overrides/main.html | 39 + docs/overrides/partials/logo.html | 15 + package-lock.json | 65 + package.json | 6 + pixi.lock | 10397 ++++++++++++++++ pixi.toml | 274 + prettierrc.toml | 22 + pyproject.toml | 434 +- src/easyreflectometry/__init__.py | 16 +- src/easyreflectometry/__version__.py | 3 + src/easyreflectometry/calculators/__init__.py | 3 + .../calculators/bornagain/calculator.py | 97 +- .../calculators/bornagain/wrapper.py | 243 +- .../calculators/calculator_base.py | 118 +- src/easyreflectometry/calculators/factory.py | 8 + .../calculators/refl1d/calculator.py | 8 +- .../calculators/refl1d/wrapper.py | 179 +- .../calculators/refnx/calculator.py | 8 +- .../calculators/refnx/wrapper.py | 165 +- .../calculators/wrapper_base.py | 190 +- src/easyreflectometry/data/__init__.py | 3 + src/easyreflectometry/data/data_store.py | 21 + src/easyreflectometry/data/measurement.py | 14 +- src/easyreflectometry/fitting.py | 159 +- src/easyreflectometry/limits.py | 13 +- src/easyreflectometry/main.py | 4 + src/easyreflectometry/model/__init__.py | 3 + src/easyreflectometry/model/model.py | 93 +- .../model/model_collection.py | 32 +- .../model/resolution_functions.py | 30 +- src/easyreflectometry/orso_utils.py | 42 +- src/easyreflectometry/plot.py | 20 +- src/easyreflectometry/project.py | 210 +- src/easyreflectometry/sample/__init__.py | 3 + .../sample/assemblies/base_assembly.py | 39 +- .../sample/assemblies/bilayer.py | 135 +- .../sample/assemblies/gradient_layer.py | 50 +- .../sample/assemblies/multilayer.py | 55 +- .../sample/assemblies/repeating_multilayer.py | 24 +- .../sample/assemblies/surfactant_layer.py | 63 +- src/easyreflectometry/sample/base_core.py | 13 +- .../sample/collections/base_collection.py | 55 +- .../sample/collections/layer_collection.py | 15 +- .../sample/collections/material_collection.py | 16 +- .../sample/collections/sample.py | 54 +- .../sample/elements/layers/layer.py | 27 +- .../layers/layer_area_per_molecule.py | 65 +- .../sample/elements/materials/material.py | 19 +- .../elements/materials/material_density.py | 30 +- .../elements/materials/material_mixture.py | 64 +- .../elements/materials/material_solvated.py | 46 +- src/easyreflectometry/special/calculations.py | 97 +- src/easyreflectometry/special/parsing.py | 65 +- src/easyreflectometry/summary/__init__.py | 3 + .../summary/html_templates.py | 15 +- src/easyreflectometry/summary/summary.py | 14 + src/easyreflectometry/utils.py | 27 +- .../bornagain/test_bornagain_calculator.py | 3 + .../bornagain/test_bornagain_wrapper.py | 3 + .../refl1d/test_refl1d_calculator.py | 3 + .../calculators/refl1d/test_refl1d_wrapper.py | 3 + .../refnx/test_refnx_calculator.py | 3 + tests/calculators/refnx/test_refnx_wrapper.py | 37 +- tests/data/test_data_store.py | 11 +- tests/functional/test_dummy.py | 8 + tests/integration/fitting/test_dummy.py | 17 + .../integration/scipp-analysis/test_dummy.py | 17 + tests/model/test_model.py | 3 + tests/model/test_model_collection.py | 8 +- tests/model/test_resolution_functions.py | 12 +- tests/sample/assemblies/test_base_assembly.py | 3 + tests/sample/assemblies/test_bilayer.py | 3 + .../sample/assemblies/test_gradient_layer.py | 9 +- tests/sample/assemblies/test_multilayer.py | 3 + .../assemblies/test_repeating_multilayer.py | 3 + .../assemblies/test_surfactant_layer.py | 10 +- .../collections/test_base_collection.py | 3 + .../collections/test_layer_collection.py | 3 + .../collections/test_material_collection.py | 3 + tests/sample/collections/test_sample.py | 3 + tests/sample/elements/layers/test_layer.py | 3 + .../layers/test_layer_area_per_molecule.py | 3 + .../elements/materials/test_material.py | 3 + .../materials/test_material_density.py | 3 + .../materials/test_material_mixture.py | 3 + .../materials/test_material_solvated.py | 3 + tests/special/test_calculations.py | 3 + tests/summary/test_summary.py | 3 + tests/test_data.py | 8 +- tests/test_fitting.py | 62 +- tests/test_limits.py | 3 + tests/test_measurement_comprehensive.py | 34 +- tests/test_orso_utils.py | 16 +- tests/test_ort_file.py | 3 +- tests/test_parameter_utils.py | 3 + tests/test_project.py | 36 +- tests/test_topmost_nesting.py | 5 +- tests/test_utils.py | 16 +- tests/unit/test_dummy.py | 8 + tools/license_headers.py | 321 + tools/update_docs_assets.py | 91 + tools/update_github_labels.py | 341 + vscode-template/settings.json | 22 +- 171 files changed, 18455 insertions(+), 1269 deletions(-) create mode 100644 .badgery.yaml create mode 100644 .gitattributes create mode 100644 .github/actions/download-artifact/action.yml create mode 100644 .github/actions/github-script/action.yml create mode 100644 .github/actions/setup-easyscience-bot/action.yml create mode 100644 .github/actions/setup-pixi/action.yml create mode 100644 .github/actions/upload-artifact/action.yml create mode 100644 .github/actions/upload-codecov/action.yml create mode 100644 .github/configs/pages-deployment.json create mode 100644 .github/configs/rulesets-develop.json create mode 100644 .github/configs/rulesets-gh-pages.json create mode 100644 .github/configs/rulesets-master.json create mode 100644 .github/scripts/backmerge-conflict-issue.js create mode 100644 .github/scripts/publish-dashboard.sh create mode 100644 .github/workflows/backmerge.yml create mode 100644 .github/workflows/cleanup.yml create mode 100644 .github/workflows/coverage.yml create mode 100644 .github/workflows/dashboard.yml create mode 100644 .github/workflows/docs.yml create mode 100644 .github/workflows/issues-labels.yml create mode 100644 .github/workflows/lint-format.yml create mode 100644 .github/workflows/pr-labels.yml create mode 100644 .github/workflows/pypi-publish.yml create mode 100644 .github/workflows/pypi-test.yml create mode 100644 .github/workflows/release-notes.yml create mode 100644 .github/workflows/release-pr.yml create mode 100644 .github/workflows/security.yml create mode 100644 .github/workflows/test-trigger.yml create mode 100644 .github/workflows/test.yml create mode 100644 .github/workflows/tutorial-tests-trigger.yml create mode 100644 .github/workflows/tutorial-tests.yml create mode 100644 .pre-commit-config.yaml create mode 100644 .prettierignore create mode 100644 CONTRIBUTING.md create mode 100644 codecov.yml create mode 100644 docs/docs/api-reference/index.md create mode 100644 docs/docs/assets/images/logo_dark.svg create mode 100644 docs/docs/assets/images/logo_light.svg create mode 100644 docs/docs/assets/javascripts/extra.js create mode 100644 docs/docs/assets/javascripts/mathjax.js create mode 100644 docs/docs/assets/stylesheets/extra.css create mode 100644 docs/docs/index.md create mode 100644 docs/docs/installation-and-setup/index.md create mode 100644 docs/docs/introduction/index.md create mode 100644 docs/docs/tutorials/index.md create mode 100644 docs/docs/tutorials/tutorial.ipynb create mode 100644 docs/docs/user-guide/index.md create mode 100644 docs/includes/abbreviations.md create mode 100644 docs/mkdocs.yml create mode 100644 docs/overrides/.icons/app.svg create mode 100644 docs/overrides/.icons/easyscience.svg create mode 100644 docs/overrides/.icons/google-colab.svg create mode 100644 docs/overrides/main.html create mode 100644 docs/overrides/partials/logo.html create mode 100644 package-lock.json create mode 100644 package.json create mode 100644 pixi.lock create mode 100644 pixi.toml create mode 100644 prettierrc.toml create mode 100644 tests/functional/test_dummy.py create mode 100644 tests/integration/fitting/test_dummy.py create mode 100644 tests/integration/scipp-analysis/test_dummy.py create mode 100644 tests/unit/test_dummy.py create mode 100644 tools/license_headers.py create mode 100644 tools/update_docs_assets.py create mode 100644 tools/update_github_labels.py diff --git a/.badgery.yaml b/.badgery.yaml new file mode 100644 index 00000000..99bcdc1c --- /dev/null +++ b/.badgery.yaml @@ -0,0 +1,72 @@ +default_branch: master +develop_branch: develop + +cards: + - group: Tests + type: gh_action + title: Code/package tests (GitHub) + file: test.yml + enabled: true + - group: Tests + type: gh_action + title: Tutorial tests (GitHub) + file: tutorial-tests.yml + enabled: true + + - group: Tests + type: gh_action + title: Package tests (PyPI) + file: pypi-test.yml + enabled: true + + - group: Code Quality + type: codefactor + title: Code quality (CodeFactor) + enabled: true + + - group: Code Quality + type: radon_mi + title: Maintainability index (radon) + report: reports/{branch}/maintainability-index.json + enabled: true + + - group: Code Quality + type: radon_cc + title: Cyclomatic complexity (radon) + report: reports/{branch}/cyclomatic-complexity.json + enabled: true + + - group: Size + type: radon_loc + title: Source/Logical lines of code (radon) + report: reports/{branch}/raw-metrics.json + enabled: true + + - group: Size + type: radon_ff + title: Functions/Files count (radon) + report: reports/{branch}/cyclomatic-complexity.json + enabled: true + + - group: Coverage + type: codecov + title: Unit test coverage (Codecov) + flag: unittests + enabled: true + + - group: Coverage + type: interrogate + title: Docstring coverage (interrogate) + report: reports/{branch}/coverage-docstring.txt + enabled: true + - group: Build & Release + type: gh_action + title: Publishing (PyPI) + workflow: pypi-publish.yml + enabled: true + + - group: Build & Release + type: gh_action + title: Docs build/deployment + workflow: docs.yml + enabled: true diff --git a/.codecov.yml b/.codecov.yml index 9c9abf0b..e17376e8 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -1,8 +1,8 @@ github_checks: - annotations: true + annotations: true comment: - layout: "reach, diff, flags, files" + layout: 'reach, diff, flags, files' behavior: default - require_changes: false # if true: only post the comment if coverage changes - require_base: no # [yes :: must have a base report to post] - require_head: yes # [yes :: must have a head report to post] + require_changes: false # if true: only post the comment if coverage changes + require_base: no # [yes :: must have a base report to post] + require_head: yes # [yes :: must have a head report to post] diff --git a/.copier-answers.yml b/.copier-answers.yml index 867a00e8..727e2511 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,11 +1,19 @@ -# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY -_commit: 8bdcedc -_src_path: gh:/EasyScience/EasyProjectTemplate -description: A reflectometry python package built on the EasyScience framework. -max_python: '3.13' -min_python: '3.9' -orgname: EasyScience -packagename: easyreflectometry -prettyname: Easy Reflectometry Library -projectname: easyreflectometry -year: 2024 +# WARNING: Do not edit this file manually. +# Any changes will be overwritten by Copier. +_commit: v0.11.2 +_src_path: gh:easyscience/templates +lib_docs_url: https://easyscience.github.io/reflectometry-lib +lib_doi: 10.5281/zenodo.18163581 +lib_package_name: easyreflectometry +lib_python_max: '3.13' +lib_python_min: '3.11' +lib_repo_name: reflectometry-lib +project_contact_email: support@easyreflectometry.org +project_copyright_years: 2021-2026 +project_extended_description: A software for performing reflectometry calculations + based on a layer model and refining its parameters against reflectometry data +project_name: EasyReflectometry +project_short_description: Reflectometry data analysis +project_shortcut: ER +project_type: lib +template_type: lib diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..997504b4 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/.github/actions/download-artifact/action.yml b/.github/actions/download-artifact/action.yml new file mode 100644 index 00000000..d1fff1a0 --- /dev/null +++ b/.github/actions/download-artifact/action.yml @@ -0,0 +1,50 @@ +name: 'Download artifact' +description: 'Wrapper for actions/download-artifact' +inputs: + name: + description: 'Name of the artifact to download' + required: true + + path: + description: 'Destination path' + required: false + default: '.' + + pattern: + description: 'Glob pattern to match artifact names (optional)' + required: false + default: '' + + merge-multiple: + description: 'Merge multiple artifacts into the same directory' + required: false + default: 'false' + + github-token: + description: 'GitHub token for cross-repo download (optional)' + required: false + default: '' + + repository: + description: 'owner/repo for cross-repo download (optional)' + required: false + default: '' + + run-id: + description: 'Workflow run ID for cross-run download (optional)' + required: false + default: '' + +runs: + using: 'composite' + steps: + - name: Download artifact + uses: actions/download-artifact@v8 + with: + name: ${{ inputs.name }} + path: ${{ inputs.path }} + pattern: ${{ inputs.pattern }} + merge-multiple: ${{ inputs.merge-multiple }} + github-token: ${{ inputs.github-token }} + repository: ${{ inputs.repository }} + run-id: ${{ inputs.run-id }} diff --git a/.github/actions/github-script/action.yml b/.github/actions/github-script/action.yml new file mode 100644 index 00000000..50de89b7 --- /dev/null +++ b/.github/actions/github-script/action.yml @@ -0,0 +1,19 @@ +name: 'GitHub Script' +description: 'Wrapper for actions/github-script' +inputs: + script: + description: 'JavaScript to run' + required: true + + github-token: + description: 'GitHub token (defaults to github.token)' + required: false + default: ${{ github.token }} + +runs: + using: 'composite' + steps: + - uses: actions/github-script@v9 + with: + script: ${{ inputs.script }} + github-token: ${{ inputs.github-token }} diff --git a/.github/actions/setup-easyscience-bot/action.yml b/.github/actions/setup-easyscience-bot/action.yml new file mode 100644 index 00000000..e51eb01a --- /dev/null +++ b/.github/actions/setup-easyscience-bot/action.yml @@ -0,0 +1,40 @@ +name: 'Setup EasyScience bot for pushing' +description: 'Create GitHub App token and configure git identity + origin remote' +inputs: + app-id: + description: 'GitHub App ID' + required: true + private-key: + description: 'GitHub App private key (PEM)' + required: true + repositories: + description: 'Additional repositories to grant access to (newline-separated)' + required: false + default: '' + +outputs: + token: + description: 'Installation access token' + value: ${{ steps.app-token.outputs.token }} + +runs: + using: 'composite' + steps: + - name: Create GitHub App installation token + id: app-token + uses: actions/create-github-app-token@v3 + with: + client-id: ${{ inputs.app-id }} + private-key: ${{ inputs.private-key }} + repositories: ${{ inputs.repositories }} + + - name: Configure git for pushing + shell: bash + run: | + git config user.name "easyscience[bot]" + git config user.email "${{ inputs.app-id }}+easyscience[bot]@users.noreply.github.com" + + - name: Configure origin remote to use the bot token + shell: bash + run: | + git remote set-url origin https://x-access-token:${{ steps.app-token.outputs.token }}@github.com/${{ github.repository }}.git diff --git a/.github/actions/setup-pixi/action.yml b/.github/actions/setup-pixi/action.yml new file mode 100644 index 00000000..ec7d7ba7 --- /dev/null +++ b/.github/actions/setup-pixi/action.yml @@ -0,0 +1,44 @@ +name: 'Setup Pixi Environment' +description: 'Wrapper for prefix-dev/setup-pixi' +inputs: + environments: + description: 'Pixi environments to setup' + required: false + default: 'default' + activate-environment: + description: 'Environment to activate' + required: false + default: 'default' + run-install: + description: 'Whether to run pixi install' + required: false + default: 'true' + locked: + description: 'Whether to run pixi install --locked' + required: false + default: 'false' + frozen: + description: 'Whether to run pixi install --frozen' + required: false + default: 'true' + cache: + description: 'Whether to use cache' + required: false + default: 'false' + post-cleanup: + description: 'Whether to run post cleanup' + required: false + default: 'false' + +runs: + using: 'composite' + steps: + - uses: prefix-dev/setup-pixi@v0.9.4 + with: + environments: ${{ inputs.environments }} + activate-environment: ${{ inputs.activate-environment }} + run-install: ${{ inputs.run-install }} + locked: ${{ inputs.locked }} + frozen: ${{ inputs.frozen }} + cache: ${{ inputs.cache }} + post-cleanup: ${{ inputs.post-cleanup }} diff --git a/.github/actions/upload-artifact/action.yml b/.github/actions/upload-artifact/action.yml new file mode 100644 index 00000000..fe8e4680 --- /dev/null +++ b/.github/actions/upload-artifact/action.yml @@ -0,0 +1,49 @@ +name: 'Upload artifact' +description: 'Wrapper for actions/upload-artifact' +inputs: + name: + description: 'Artifact name' + required: true + + path: + description: 'File(s)/dir(s)/glob(s) to upload (newline-separated)' + required: true + + include-hidden-files: + description: 'Include hidden files' + required: false + default: 'true' + + if-no-files-found: + description: 'warn | error | ignore' + required: false + default: 'error' + + compression-level: + description: '0-9 (0 = no compression)' + required: false + default: '0' + + retention-days: + description: 'Retention in days (optional)' + required: false + default: '' + + overwrite: + description: 'Overwrite an existing artifact with the same name' + required: false + default: 'false' + +runs: + using: 'composite' + steps: + - name: Upload artifact + uses: actions/upload-artifact@v7 + with: + name: ${{ inputs.name }} + path: ${{ inputs.path }} + include-hidden-files: ${{ inputs.include-hidden-files }} + if-no-files-found: ${{ inputs.if-no-files-found }} + compression-level: ${{ inputs.compression-level }} + retention-days: ${{ inputs.retention-days }} + overwrite: ${{ inputs.overwrite }} diff --git a/.github/actions/upload-codecov/action.yml b/.github/actions/upload-codecov/action.yml new file mode 100644 index 00000000..0cb15d1f --- /dev/null +++ b/.github/actions/upload-codecov/action.yml @@ -0,0 +1,42 @@ +name: 'Upload coverage to Codecov' +description: 'Wrapper for codecov/codecov-action' + +inputs: + name: + description: 'Codecov upload name' + required: true + + flags: + description: 'Codecov flags' + required: false + default: '' + + files: + description: 'Coverage report files' + required: true + + fail_ci_if_error: + description: 'Fail CI if upload fails' + required: false + default: 'true' + + verbose: + description: 'Enable verbose output' + required: false + default: 'true' + + token: + description: 'Codecov token' + required: true + +runs: + using: composite + steps: + - uses: codecov/codecov-action@v6 + with: + name: ${{ inputs.name }} + flags: ${{ inputs.flags }} + files: ${{ inputs.files }} + fail_ci_if_error: ${{ inputs.fail_ci_if_error }} + verbose: ${{ inputs.verbose }} + token: ${{ inputs.token }} diff --git a/.github/configs/pages-deployment.json b/.github/configs/pages-deployment.json new file mode 100644 index 00000000..c0d3fbee --- /dev/null +++ b/.github/configs/pages-deployment.json @@ -0,0 +1,6 @@ +{ + "source": { + "branch": "gh-pages", + "path": "/" + } +} diff --git a/.github/configs/rulesets-develop.json b/.github/configs/rulesets-develop.json new file mode 100644 index 00000000..04489e52 --- /dev/null +++ b/.github/configs/rulesets-develop.json @@ -0,0 +1,37 @@ +{ + "name": "develop branch", + "target": "branch", + "enforcement": "active", + "conditions": { + "ref_name": { + "include": ["refs/heads/develop"], + "exclude": [] + } + }, + "bypass_actors": [ + { + "actor_id": 2476259, + "actor_type": "Integration", + "bypass_mode": "always" + } + ], + "rules": [ + { + "type": "non_fast_forward" + }, + { + "type": "deletion" + }, + { + "type": "pull_request", + "parameters": { + "allowed_merge_methods": ["squash"], + "dismiss_stale_reviews_on_push": false, + "require_code_owner_review": false, + "require_last_push_approval": false, + "required_approving_review_count": 0, + "required_review_thread_resolution": false + } + } + ] +} diff --git a/.github/configs/rulesets-gh-pages.json b/.github/configs/rulesets-gh-pages.json new file mode 100644 index 00000000..ebf38928 --- /dev/null +++ b/.github/configs/rulesets-gh-pages.json @@ -0,0 +1,19 @@ +{ + "name": "gh-pages branch", + "target": "branch", + "enforcement": "active", + "conditions": { + "ref_name": { + "include": ["refs/heads/gh-pages"], + "exclude": [] + } + }, + "rules": [ + { + "type": "non_fast_forward" + }, + { + "type": "deletion" + } + ] +} diff --git a/.github/configs/rulesets-master.json b/.github/configs/rulesets-master.json new file mode 100644 index 00000000..f658a5c6 --- /dev/null +++ b/.github/configs/rulesets-master.json @@ -0,0 +1,30 @@ +{ + "name": "master branch", + "target": "branch", + "enforcement": "active", + "conditions": { + "ref_name": { + "include": ["~DEFAULT_BRANCH"], + "exclude": [] + } + }, + "rules": [ + { + "type": "non_fast_forward" + }, + { + "type": "deletion" + }, + { + "type": "pull_request", + "parameters": { + "allowed_merge_methods": ["merge"], + "dismiss_stale_reviews_on_push": false, + "require_code_owner_review": false, + "require_last_push_approval": false, + "required_approving_review_count": 0, + "required_review_thread_resolution": false + } + } + ] +} diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md index 881b2c53..533cae79 100644 --- a/.github/copilot-instructions.md +++ b/.github/copilot-instructions.md @@ -2,32 +2,40 @@ ## Project Overview -EasyReflectometryLib is a reflectometry Python package built on the EasyScience framework. It provides tools for reflectometry analysis and modeling. +EasyReflectometryLib is a reflectometry Python package built on the +EasyScience framework. It provides tools for reflectometry analysis and +modeling. ## Development Environment - **Python Versions**: 3.11, 3.12 -- **Supported Platforms**: Linux (ubuntu-latest), macOS (macos-latest), Windows (windows-latest) +- **Supported Platforms**: Linux (ubuntu-latest), macOS (macos-latest), + Windows (windows-latest) - **Package Manager**: pip - **Build System**: hatchling with setuptools-git-versioning ## Code Style and Formatting ### Ruff Configuration -- Use **Ruff** for linting and formatting (configured in `pyproject.toml`) + +- Use **Ruff** for linting and formatting (configured in + `pyproject.toml`) - Maximum line length: 127 characters - Quote style: single quotes for strings - Import style: force single-line imports - To fix issues automatically: `python -m ruff . --fix` ### Code Quality Standards + - Follow PEP 8 guidelines - Use type hints where appropriate - Write clear, self-documenting code with meaningful variable names - Maintain consistency with existing code patterns in the repository ### Linting Rules + The project uses Ruff with the following rule sets: + - `E9`, `F63`, `F7`, `F82`: Critical flake8 rules - `E`: pycodestyle errors - `F`: Pyflakes @@ -35,6 +43,7 @@ The project uses Ruff with the following rule sets: - `S`: flake8-bandit (security checks) Special notes: + - Asserts are allowed in test files (`*test_*.py`) - Init module imports are ignored - Exclude `docs` directory from linting @@ -42,12 +51,14 @@ Special notes: ## Testing ### Test Framework + - Use **pytest** for all tests - Test coverage should be tracked with **pytest-cov** - Aim for comprehensive test coverage - Tests are located in the `tests/` directory ### Running Tests + ```bash # Install dev dependencies pip install -e '.[dev]' @@ -61,6 +72,7 @@ tox ``` ### Test Guidelines + - Write unit tests for all new functionality - Include tests when fixing bugs to prevent regression - Test files should match the pattern `test_*.py` @@ -77,11 +89,14 @@ tox ## Documentation ### Docstring Style + - Include docstrings for all public modules, classes, and functions -- Use **Sphinx/reStructuredText style** docstrings (`:param`, `:type`, `:return`, `:rtype`) +- Use **Sphinx/reStructuredText style** docstrings (`:param`, `:type`, + `:return`, `:rtype`) - Use clear, concise descriptions - Document parameters, return values, and exceptions - Example format: + ```python """ Brief description of the function. @@ -94,6 +109,7 @@ tox ``` ### Documentation Build + - Documentation is built using Sphinx (version 8.1.3) - Source files are in the `docs/` directory - Use `myst_parser` (MyST parser) for Markdown support @@ -102,6 +118,7 @@ tox ## Dependencies ### Core Dependencies + - easyscience (EasyScience framework) - scipp (Scientific computing) - refnx, refl1d (Reflectometry calculations) @@ -109,6 +126,7 @@ tox - bumps (Optimization) ### Adding New Dependencies + - Only add dependencies when absolutely necessary - Add to appropriate section in `pyproject.toml`: - `dependencies` for core runtime dependencies @@ -119,13 +137,16 @@ tox ## Git and Version Control ### Commit Messages + - Write clear, descriptive commit messages - Use present tense ("Add feature" not "Added feature") - Reference issue numbers when applicable ### Branch Workflow + - Create feature branches from the main branch -- Use descriptive branch names (e.g., `feature/add-new-calculator`, `bugfix/fix-reflection-calculation`) +- Use descriptive branch names (e.g., `feature/add-new-calculator`, + `bugfix/fix-reflection-calculation`) - Keep changes focused and atomic ## Pull Request Guidelines @@ -157,17 +178,24 @@ docs/ # Documentation source ## Best Practices -1. **Minimal Changes**: Make the smallest possible changes to accomplish the task -2. **Don't Break Existing Code**: Maintain backward compatibility unless explicitly required -3. **Test Before Committing**: Always run tests and linting before pushing -4. **Follow Existing Patterns**: Look at similar code in the repository for guidance -5. **Ask When Uncertain**: If unsure about an approach, ask for clarification +1. **Minimal Changes**: Make the smallest possible changes to accomplish + the task +2. **Don't Break Existing Code**: Maintain backward compatibility unless + explicitly required +3. **Test Before Committing**: Always run tests and linting before + pushing +4. **Follow Existing Patterns**: Look at similar code in the repository + for guidance +5. **Ask When Uncertain**: If unsure about an approach, ask for + clarification ## CI/CD Pipeline The project uses GitHub Actions for continuous integration: + - **Code Consistency**: Runs Ruff linting on all pushes and PRs -- **Code Testing**: Runs pytest across multiple Python versions and platforms +- **Code Testing**: Runs pytest across multiple Python versions and + platforms - **Package Testing**: Validates package building and installation - **Coverage**: Uploads test coverage to Codecov @@ -177,5 +205,6 @@ All CI checks must pass before merging PRs. - The project is part of the EasyScience ecosystem - Built on top of established reflectometry libraries (refnx, refl1d) -- Focuses on providing a user-friendly interface for reflectometry analysis +- Focuses on providing a user-friendly interface for reflectometry + analysis - Maintains compatibility with multiple calculator backends diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml index cc95caf6..4f0d1964 100644 --- a/.github/release-drafter.yml +++ b/.github/release-drafter.yml @@ -4,30 +4,30 @@ name-template: v$NEXT_PATCH_VERSION 🌈 tag-template: v$NEXT_PATCH_VERSION categories: -- title: 🚀 Features - labels: - - feature - - enhancement -- title: 🐛 Bug Fixes - labels: - - fix - - bugfix - - bug -- title: 🧰 Maintenance - labels: - - chore - - documentation + - title: 🚀 Features + labels: + - feature + - enhancement + - title: 🐛 Bug Fixes + labels: + - fix + - bugfix + - bug + - title: 🧰 Maintenance + labels: + - chore + - documentation change-template: '- $TITLE @$AUTHOR (#$NUMBER)' version-resolver: major: labels: - - major + - major minor: labels: - - minor + - minor patch: labels: - - patch + - patch default: patch template: | ## Changes diff --git a/.github/scripts/backmerge-conflict-issue.js b/.github/scripts/backmerge-conflict-issue.js new file mode 100644 index 00000000..f6bd98b5 --- /dev/null +++ b/.github/scripts/backmerge-conflict-issue.js @@ -0,0 +1,69 @@ +module.exports = async ({ github, context, core }) => { + // Repo context + const owner = context.repo.owner + const repo = context.repo.repo + + // Link to the exact workflow run that detected the conflict + const runUrl = `${context.serverUrl}/${owner}/${repo}/actions/runs/${context.runId}` + + // We use a *stable title* so we can find/reuse the same "conflict tracker" issue + // instead of creating a new issue on every failed run. + const title = 'Backmerge conflict: master → develop' + + // Comment/issue body includes the run URL so maintainers can jump straight to logs. + const body = [ + 'Automatic backmerge failed due to merge conflicts.', + '', + `Workflow run: ${runUrl}`, + '', + 'Manual resolution required.', + ].join('\n') + + // Label applied to the tracker issue (assumed to already exist in the repo). + const label = '[bot] backmerge' + + // Search issues by title across *open and closed* issues. + // Why: if the conflict was resolved previously and the issue was closed, + // we prefer to reopen it and append a new comment instead of creating duplicates. + const q = `repo:${owner}/${repo} is:issue in:title "${title}"` + const search = await github.rest.search.issuesAndPullRequests({ + q, + per_page: 10, + }) + + // Pick the first exact-title match (search can return partial matches). + const existing = search.data.items.find((i) => i.title === title) + + if (existing) { + // If a tracker issue exists, reuse it: + // - reopen it if needed + // - add a comment with the new run URL + if (existing.state === 'closed') { + await github.rest.issues.update({ + owner, + repo, + issue_number: existing.number, + state: 'open', + }) + } + + await github.rest.issues.createComment({ + owner, + repo, + issue_number: existing.number, + body, + }) + + core.notice(`Conflict issue updated: #${existing.number}`) + return + } + + // No tracker issue exists yet -> create the first one. + await github.rest.issues.create({ + owner, + repo, + title, + body, + labels: [label], + }) +} diff --git a/.github/scripts/publish-dashboard.sh b/.github/scripts/publish-dashboard.sh new file mode 100644 index 00000000..dcbd0b32 --- /dev/null +++ b/.github/scripts/publish-dashboard.sh @@ -0,0 +1,77 @@ +#!/usr/bin/env bash + +set -euo pipefail + +remote_repository="${DASHBOARD_REMOTE_REPOSITORY:?}" +publish_branch="${DASHBOARD_PUBLISH_BRANCH:-master}" +source_dir="${DASHBOARD_SOURCE_DIR:?}" +token="${DASHBOARD_TOKEN:?}" +git_user_name="${DASHBOARD_GIT_USER_NAME:-easyscience[bot]}" +git_user_email="${DASHBOARD_GIT_USER_EMAIL:?}" +commit_message="${DASHBOARD_COMMIT_MESSAGE:?}" +max_attempts="${DASHBOARD_PUSH_ATTEMPTS:-3}" +delay_seconds="${DASHBOARD_PUSH_DELAY_SECONDS:-15}" + +workspace_dir="$(mktemp -d)" +repo_dir="${workspace_dir}/dashboard" +remote_url="https://x-access-token:${token}@github.com/${remote_repository}.git" + +cleanup() { + rm -rf "${workspace_dir}" +} + +prepare_worktree() { + if [[ ! -d "${repo_dir}/.git" ]]; then + git clone --branch "${publish_branch}" --depth 1 "${remote_url}" "${repo_dir}" + else + git -C "${repo_dir}" fetch origin "${publish_branch}" + git -C "${repo_dir}" checkout "${publish_branch}" + git -C "${repo_dir}" reset --hard "origin/${publish_branch}" + git -C "${repo_dir}" clean -fd + fi + + git -C "${repo_dir}" config user.name "${git_user_name}" + git -C "${repo_dir}" config user.email "${git_user_email}" +} + +sync_publish_dir() { + cp -R "${source_dir}/." "${repo_dir}/" + git -C "${repo_dir}" add . + + if git -C "${repo_dir}" diff --cached --quiet; then + return 1 + fi + + git -C "${repo_dir}" commit -m "${commit_message}" +} + +trap cleanup EXIT + +prepare_worktree + +if ! sync_publish_dir; then + echo "No dashboard changes to publish." + exit 0 +fi + +for ((attempt = 1; attempt <= max_attempts; attempt += 1)); do + if git -C "${repo_dir}" push origin "HEAD:${publish_branch}"; then + echo "Dashboard published on attempt ${attempt}." + exit 0 + fi + + if ((attempt == max_attempts)); then + echo "Dashboard publish failed after ${max_attempts} attempts." >&2 + exit 1 + fi + + echo "Dashboard push attempt ${attempt} failed. Retrying in ${delay_seconds}s." >&2 + sleep "${delay_seconds}" + + prepare_worktree + + if ! sync_publish_dir; then + echo "Dashboard changes already exist in the target repository." + exit 0 + fi +done \ No newline at end of file diff --git a/.github/workflows/backmerge.yml b/.github/workflows/backmerge.yml new file mode 100644 index 00000000..36ce6f54 --- /dev/null +++ b/.github/workflows/backmerge.yml @@ -0,0 +1,109 @@ +# This workflow automatically merges `master` into `develop` whenever a +# new version release with a tag is published. It can also be triggered +# manually via workflow_dispatch for cases where an automatic backmerge +# is needed outside of the standard release process. +# If a merge conflict occurs, the workflow creates an issue to notify +# maintainers for manual resolution. + +name: Backmerge (master → develop) + +on: + release: + types: [published, prereleased] + workflow_dispatch: + +permissions: + contents: write + issues: write + +concurrency: + group: backmerge-master-into-develop + cancel-in-progress: false + +jobs: + backmerge: + runs-on: ubuntu-latest + timeout-minutes: 10 + + steps: + - name: Checkout repository (for local actions) + uses: actions/checkout@v6 + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + repositories: ${{ github.event.repository.name }} + + - name: Checkout repository (with bot token) + uses: actions/checkout@v6 + with: + fetch-depth: 0 + token: ${{ steps.bot.outputs.token }} + + - name: Configure git identity + run: | + git config user.name "easyscience[bot]" + git config user.email "${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com" + + - name: Set merge message + run: | + if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then + MESSAGE="Backmerge: master into develop (manual) [skip ci]" + else + TAG="${{ github.event.release.tag_name }}" + MESSAGE="Backmerge: master (${TAG}) into develop [skip ci]" + fi + + echo "MESSAGE=$MESSAGE" >> "$GITHUB_ENV" + echo "message=$MESSAGE" >> "$GITHUB_OUTPUT" + echo "📝 Merge message: $MESSAGE" | tee -a "$GITHUB_STEP_SUMMARY" + + - name: Prepare branches + run: | + git fetch origin master develop + git checkout -B develop origin/develop + + - name: Check if develop is already up-to-date + id: up_to_date + run: | + if git merge-base --is-ancestor origin/master develop; then + echo "value=true" >> "$GITHUB_OUTPUT" + echo "ℹ️ Develop is already up-to-date with master" | tee -a "$GITHUB_STEP_SUMMARY" + else + echo "value=false" >> "$GITHUB_OUTPUT" + fi + + - name: Try merge master into develop + id: merge + if: steps.up_to_date.outputs.value == 'false' + continue-on-error: true + run: | + if ! git merge origin/master --no-ff -m "${MESSAGE}"; then + echo "conflict=true" >> "$GITHUB_OUTPUT" + echo "❌ Backmerge conflict detected." | tee -a "$GITHUB_STEP_SUMMARY" + git status --porcelain || true + exit 0 + fi + + echo "conflict=false" >> "$GITHUB_OUTPUT" + echo "✅ Merge commit created." | tee -a "$GITHUB_STEP_SUMMARY" + + - name: Push to develop (if merge succeeded) + if: + steps.up_to_date.outputs.value == 'false' && steps.merge.outputs.conflict == + 'false' + run: | + git push origin develop + echo "🚀 Backmerge successful: master → develop" | tee -a "$GITHUB_STEP_SUMMARY" + + - name: Create issue (if merge failed with conflicts) + if: steps.merge.outputs.conflict == 'true' + uses: ./.github/actions/github-script + with: + github-token: ${{ steps.bot.outputs.token }} + script: | + const run = require('./.github/scripts/backmerge-conflict-issue.js') + await run({ github, context, core }) diff --git a/.github/workflows/cleanup.yml b/.github/workflows/cleanup.yml new file mode 100644 index 00000000..21c72b38 --- /dev/null +++ b/.github/workflows/cleanup.yml @@ -0,0 +1,84 @@ +# This workflow will delete old workflow runs based on the input +# parameters. +# https://github.com/Mattraks/delete-workflow-runs + +name: Old workflow runs cleanup + +on: + # Run monthly, at 00:00 on the 1st day of month. + schedule: + - cron: '0 0 1 * *' + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + inputs: + days: + description: 'Number of days.' + required: true + default: '30' + minimum_runs: + description: 'The minimum runs to keep for each workflow.' + required: true + default: '6' + delete_workflow_pattern: + description: + 'The name or filename of the workflow. if not set then it will target all + workflows.' + required: false + delete_workflow_by_state_pattern: + description: + 'Remove workflow by state: active, deleted, disabled_fork, + disabled_inactivity, disabled_manually' + required: true + default: 'All' + type: choice + options: + - 'All' + - active + - deleted + - disabled_inactivity + - disabled_manually + delete_run_by_conclusion_pattern: + description: + 'Remove workflow by conclusion: action_required, cancelled, failure, skipped, + success' + required: true + default: 'All' + type: choice + options: + - 'All' + - action_required + - cancelled + - failure + - skipped + - success + dry_run: + description: 'Only log actions, do not perform any delete operations (dry run).' + required: false + default: 'false' + type: choice + options: + - 'false' + - 'true' + +jobs: + del-runs: + runs-on: ubuntu-latest + + permissions: + actions: write + + steps: + - name: Delete workflow runs + uses: Mattraks/delete-workflow-runs@v2 + with: + token: ${{ github.token }} + repository: ${{ github.repository }} + retain_days: ${{ github.event.inputs.days }} + keep_minimum_runs: ${{ github.event.inputs.minimum_runs }} + delete_workflow_pattern: ${{ github.event.inputs.delete_workflow_pattern }} + delete_workflow_by_state_pattern: + ${{ github.event.inputs.delete_workflow_by_state_pattern }} + delete_run_by_conclusion_pattern: + ${{ github.event.inputs.delete_run_by_conclusion_pattern }} + dry_run: ${{ github.event.inputs.dry_run }} diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml index b388f884..238dc354 100644 --- a/.github/workflows/codeql-analysis.yml +++ b/.github/workflows/codeql-analysis.yml @@ -1,11 +1,11 @@ -name: "CodeQL" +name: 'CodeQL' on: push: - branches: [ master, pre-release, develop ] + branches: [master, pre-release, develop] pull_request: # The branches below must be a subset of the branches above - branches: [ master ] + branches: [master] schedule: - cron: '0 16 * * 5' @@ -24,43 +24,43 @@ jobs: # https://docs.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#overriding-automatic-language-detection steps: - - name: Checkout repository - uses: actions/checkout@v4 - with: - # We must fetch at least the immediate parents so that if this is - # a pull request then we can checkout the head. - fetch-depth: 2 + - name: Checkout repository + uses: actions/checkout@v4 + with: + # We must fetch at least the immediate parents so that if this is + # a pull request then we can checkout the head. + fetch-depth: 2 - # If this run was triggered by a pull request event, then checkout - # the head of the pull request instead of the merge commit. - - run: git checkout HEAD^2 - if: ${{ github.event_name == 'pull_request' }} + # If this run was triggered by a pull request event, then checkout + # the head of the pull request instead of the merge commit. + - run: git checkout HEAD^2 + if: ${{ github.event_name == 'pull_request' }} - # Initializes the CodeQL tools for scanning. - - name: Initialize CodeQL - uses: github/codeql-action/init@v3 - with: - languages: ${{ matrix.language }} - # If you wish to specify custom queries, you can do so here or in a config file. - # By default, queries listed here will override any specified in a config file. - # Prefix the list here with "+" to use these queries and those in the config file. - # queries: ./path/to/local/query, your-org/your-repo/queries@master + # Initializes the CodeQL tools for scanning. + - name: Initialize CodeQL + uses: github/codeql-action/init@v3 + with: + languages: ${{ matrix.language }} + # If you wish to specify custom queries, you can do so here or in a config file. + # By default, queries listed here will override any specified in a config file. + # Prefix the list here with "+" to use these queries and those in the config file. + # queries: ./path/to/local/query, your-org/your-repo/queries@master - # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). - # If this step fails, then you should remove it and run the build manually (see below) - - name: Autobuild - uses: github/codeql-action/autobuild@v3 + # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). + # If this step fails, then you should remove it and run the build manually (see below) + - name: Autobuild + uses: github/codeql-action/autobuild@v3 - # ℹ️ Command-line programs to run using the OS shell. - # 📚 https://git.io/JvXDl + # ℹ️ Command-line programs to run using the OS shell. + # 📚 https://git.io/JvXDl - # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines - # and modify them (or add more) to build your code if your project - # uses a compiled language + # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines + # and modify them (or add more) to build your code if your project + # uses a compiled language - #- run: | - # make bootstrap - # make release + #- run: | + # make bootstrap + # make release - - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v3 \ No newline at end of file + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v3 diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml new file mode 100644 index 00000000..d96e5b87 --- /dev/null +++ b/.github/workflows/coverage.yml @@ -0,0 +1,94 @@ +name: Coverage checks + +on: + # Trigger the workflow on push to develop + push: + branches: + - develop + # Trigger the workflow on pull request + pull_request: + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Need permissions to trigger the dashboard build workflow +permissions: + actions: write + contents: read + +# Allow only one concurrent workflow per PR or branch ref. +# Cancel in-progress runs only for pull requests, but let branch push runs finish. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: ${{ github.event_name == 'pull_request' }} + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + +jobs: + # Job 1: Run docstring coverage + docstring-coverage: + runs-on: ubuntu-latest + + steps: + - name: Check-out repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Run docstring coverage + run: pixi run docstring-coverage + + # Job 2: Run unit tests with coverage and upload to Codecov + unit-tests-coverage: + runs-on: ubuntu-latest + + steps: + - name: Check-out repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Run unit tests with coverage + run: pixi run unit-tests-coverage --cov-report=xml:coverage-unit.xml + + - name: Upload unit tests coverage to Codecov + if: ${{ !cancelled() }} + uses: ./.github/actions/upload-codecov + with: + name: unit-tests-job + flags: unittests + files: ./coverage-unit.xml + token: ${{ secrets.CODECOV_TOKEN }} + + # Job 2: Run integration tests with coverage and upload to Codecov + integration-tests-coverage: + runs-on: ubuntu-latest + + steps: + - name: Check-out repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Run integration tests with coverage + run: + pixi run integration-tests-coverage --cov-report=xml:coverage-integration.xml + + - name: Upload integration tests coverage to Codecov + if: ${{ !cancelled() }} + uses: ./.github/actions/upload-codecov + with: + name: integration-tests-job + flags: integration + files: ./coverage-integration.xml + token: ${{ secrets.CODECOV_TOKEN }} + + # Job 4: Build and publish dashboard (reusable workflow) + run-reusable-workflows: + needs: [docstring-coverage, unit-tests-coverage, integration-tests-coverage] # depend on the previous jobs + uses: ./.github/workflows/dashboard.yml + secrets: inherit diff --git a/.github/workflows/dashboard.yml b/.github/workflows/dashboard.yml new file mode 100644 index 00000000..9d1f2b0b --- /dev/null +++ b/.github/workflows/dashboard.yml @@ -0,0 +1,111 @@ +name: Dashboard build and publish + +on: + workflow_dispatch: + workflow_call: + +permissions: + contents: read + +concurrency: + group: dashboard-publish-${{ github.repository }} + cancel-in-progress: false + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} + DEVELOP_BRANCH: develop + REPO_OWNER: ${{ github.repository_owner }} + REPO_NAME: ${{ github.event.repository.name }} + +jobs: + dashboard: + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + with: + fetch-depth: 0 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Install badgery + shell: bash + run: pixi add --pypi --git https://github.com/enhantica/badgery badgery + + - name: Run docstring coverage and code complexity/maintainability checks + run: | + for BRANCH in $DEFAULT_BRANCH $DEVELOP_BRANCH $CI_BRANCH; do + echo + echo "🔹🔸🔹🔸🔹 Processing branch $BRANCH 🔹🔸🔹🔸🔹" + if [ -d "../$BRANCH" ]; then + echo "Branch $BRANCH already processed, skipping" + continue + fi + + git worktree add ../$BRANCH origin/$BRANCH + mkdir -p reports/$BRANCH + + echo "Docstring coverage for branch $BRANCH" + pixi run interrogate -c pyproject.toml --fail-under=0 ../$BRANCH/src > reports/$BRANCH/coverage-docstring.txt + + echo "Cyclomatic complexity for branch $BRANCH" + pixi run radon cc -s -j ../$BRANCH/src > reports/$BRANCH/cyclomatic-complexity.json + + echo "Maintainability index for branch $BRANCH" + pixi run radon mi -j ../$BRANCH/src > reports/$BRANCH/maintainability-index.json + + echo "Raw metrics for branch $BRANCH" + pixi run radon raw -s -j ../$BRANCH/src > reports/$BRANCH/raw-metrics.json + done + + - name: Generate dashboard HTML + run: > + pixi run python -m badgery --config .badgery.yaml --repo ${{ github.repository + }} --branch ${{ env.CI_BRANCH }} --output index.html + + - name: Prepare publish directory + run: | + mkdir -p _dashboard_publish/${{ env.REPO_NAME }}/${{ env.CI_BRANCH }} + cp index.html _dashboard_publish/${{ env.REPO_NAME }}/${{ env.CI_BRANCH }} + + # Create GitHub App token for pushing to external dashboard repo. + # The 'repositories' parameter is required to grant access to repos + # other than the one where the workflow is running. + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + repositories: | + ${{ github.event.repository.name }} + dashboard + + # Push to external dashboard repository with retry logic. + # Retry is needed to handle transient GitHub API/authentication issues + # that occasionally cause 403 errors when multiple workflows push concurrently. + # Uses personal_token (not github_token) as GITHUB_TOKEN cannot access external repos. + - name: + Push to ${{ env.REPO_OWNER }}/dashboard/${{ env.REPO_NAME }}/${{ env.CI_BRANCH + }} + shell: bash + env: + DASHBOARD_COMMIT_MESSAGE: ${{ env.CI_BRANCH }} + DASHBOARD_GIT_USER_EMAIL: + ${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com + DASHBOARD_PUSH_ATTEMPTS: '3' + DASHBOARD_PUSH_DELAY_SECONDS: '15' + DASHBOARD_PUBLISH_BRANCH: master + DASHBOARD_REMOTE_REPOSITORY: ${{ env.REPO_OWNER }}/dashboard + DASHBOARD_SOURCE_DIR: ./_dashboard_publish + DASHBOARD_TOKEN: ${{ steps.bot.outputs.token }} + run: bash ./.github/scripts/publish-dashboard.sh + + - name: Add dashboard link to summary + run: | + URL="https://${{ env.REPO_OWNER }}.github.io/dashboard/${{ env.REPO_NAME }}/${{ env.CI_BRANCH }}" + echo "Dashboard link: [$URL]($URL)" >> $GITHUB_STEP_SUMMARY diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 00000000..d8622c29 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,188 @@ +# This workflow builds and deploys documentation for the project. +# +# Overview: +# - Converts tutorial Python scripts to Jupyter notebooks and executes them. +# - Builds the documentation site using MkDocs with the Material theme. +# - Uploads the built site as an artifact for local inspection. +# - Deploys versioned documentation to the gh-pages branch using Mike: +# - For release tags (v*): deploys to a versioned folder (e.g., /0.9.1/) and updates /latest/. +# - For branches: deploys to /dev/. +# +# The action summary page will contain a link to the built artifact for downloading +# and inspecting, as well as a link to the deployed documentation site. + +name: Docs build and deployment + +on: + # Trigger the workflow on push + push: + # Selected branches + branches: [develop] # master and main are already verified in PR + # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3' + tags: ['v*'] + # Trigger the workflow on pull request + pull_request: + # Selected branches + branches: [master, main, develop] + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# - Non-tagged pushes and pull requests all use `docs-dev` group, so +# they cancel each other. +# - Tagged pushes use their own group like docs-v1.2.3, so they do not +# cancel non-tagged runs, and non-tagged runs do not cancel them. +concurrency: + group: >- + ${{ startsWith(github.ref, 'refs/tags/v') + && format('docs-{0}', github.ref_name) + || 'docs-dev' }} + cancel-in-progress: true + +# Set the environment variables to be used in all jobs defined in this workflow +env: + # CI_BRANCH - the branch name (used in mkdocs.yml) + # For PRs: github.head_ref is the source branch + # For pushes: github.ref_name is the branch + # For tags: github.ref_name is the tag name + # GITHUB_REPOSITORY - the repository name (used in mkdocs.yml) + # NOTEBOOKS_DIR - the directory containing the Jupyter notebooks (used in mkdocs.yml) + DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} + DEVELOP_BRANCH: develop + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + IS_RELEASE_TAG: ${{ startsWith(github.ref, 'refs/tags/v') }} + GITHUB_REPOSITORY: ${{ github.repository }} + NOTEBOOKS_DIR: tutorials + +jobs: + # Single job that builds and deploys documentation. + # Uses macOS runner for consistent Plotly chart rendering. + build-deploy-docs: + runs-on: ubuntu-latest # macos-latest + + permissions: + contents: write # Required for pushing to the gh-pages branch + + steps: + # Setting DOCS_VERSION to be used in mkdocs.yml, and then in the + # main.html template. It defines the versioned docs subfolder name + # in the gh-pages branch. If it's a release tag, use the version + # number without the 'v' prefix, otherwise use 'dev'. + # Setting RELEASE_VERSION to be used in mkdocs.yml to show + # the latest release version in the index.md file. If it's a + # release tag, use the tag name, otherwise use the branch name + # for development builds. + - name: Set extra env variables + shell: bash + run: | + if [[ "${IS_RELEASE_TAG}" == "true" ]]; then + RELEASE_VERSION="${GITHUB_REF_NAME}" + DOCS_VERSION="${RELEASE_VERSION#v}" + else + RELEASE_VERSION="${CI_BRANCH}" + DOCS_VERSION="dev" + fi + echo "RELEASE_VERSION=${RELEASE_VERSION}" >> "$GITHUB_ENV" + echo "DOCS_VERSION=${DOCS_VERSION}" >> "$GITHUB_ENV" + + # Check out the repository source code. + # Note: The gh-pages branch is fetched separately later for mike deployment. + - name: Checkout repository + uses: actions/checkout@v6 + + # Activate dark mode to create documentation with Plotly charts in dark mode + # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher + # Something similar to mkdocs_plotly_plugin https://haoda-li.github.io/mkdocs-plotly-plugin/, + # but for generating documentation from notepads + #- name: Activate dark mode + # run: | + # brew install dark-mode + # dark-mode status + # dark-mode on + # dark-mode status + + # Set up the pixi package manager and install dependencies from pixi.toml. + # Uses frozen lockfile to ensure reproducible builds. + - name: Set up pixi + uses: ./.github/actions/setup-pixi + # Pre-import the main package to exclude info messages from the docs + # E.g., Matplotlib may print messages to stdout/stderr when first + # imported. This step allows to avoid "Matplotlib is building the font + # cache" messages during notebook execution. + - name: Pre-build site step + run: pixi run python -c "import easyreflectometry" + + # Prepare the Jupyter notebooks for documentation (strip output, etc.). + - name: Prepare notebooks + run: pixi run notebook-prepare + + # Execute all Jupyter notebooks to generate output cells (plots, tables, etc.). + # Uses multiple cores for parallel execution to speed up the process. + - name: Run notebooks + # if: false # Temporarily disabled to speed up the docs build + run: pixi run notebook-exec + + # Build the static files for the documentation site for local inspection + # Input: docs/ directory containing the Markdown files + # Output: site/ directory containing the generated HTML files + - name: Build site for local check + run: pixi run docs-build-local + + # Upload the static files from the site/ directory to be used for + # local check + - name: Upload built site as artifact + uses: ./.github/actions/upload-artifact + with: + name: site-local_easyreflectometry-lib-${{ env.RELEASE_VERSION }} + path: docs/site/ + + # Create GitHub App token for pushing to gh-pages as easyscience[bot]. + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + # Configure git identity and remote URL so mike pushes as easyscience[bot]. + - name: Configure git for pushing + run: | + set -euo pipefail + git config user.name "easyscience[bot]" + git config user.email "${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com" + git remote set-url origin "https://x-access-token:${{ steps.bot.outputs.token }}@github.com/${{ github.repository }}.git" + + # Fetch the gh-pages branch to ensure mike has the latest remote state. + # This is required because the checkout step only fetches the source branch, + # not the gh-pages branch that mike needs to update. + - name: Fetch gh-pages branch + run: | + git fetch origin gh-pages:gh-pages 2>/dev/null || true + + # Deploy versioned documentation using mike (MkDocs plugin for versioning). + # - For release tags (v*): deploys to versioned folder (e.g., /0.9.1/) and aliases to /latest/. + # - For branches: deploys to /dev/. + # The "${RELEASE_VERSION#v}" syntax strips the 'v' prefix (v0.9.1 -> 0.9.1). + # Also sets 'latest' as the default version for the version selector. + - name: Rebuild and deploy docs with mike + run: | + # Exit on error (-e), undefined vars (-u), and pipeline failures (pipefail) + set -euo pipefail + + REPO_NAME="${{ github.event.repository.name }}" + BASE_URL="https://easyscience.github.io/${REPO_NAME}" + + # Deploy the release version and update the "latest" alias + if [[ "${IS_RELEASE_TAG}" == "true" ]]; then + pixi run docs-deploy-pre "${RELEASE_VERSION#v}" latest + pixi run docs-set-default-pre latest + DEPLOYMENT_URL="${BASE_URL}/latest" + + # Deploy/update the "dev" alias (or whatever your convention is) + else + pixi run docs-deploy-pre dev + DEPLOYMENT_URL="${BASE_URL}/dev" + + fi + + # Add links to the action summary page for easy access + echo "🔗 deployment url [${DEPLOYMENT_URL}](${DEPLOYMENT_URL})" >> "${GITHUB_STEP_SUMMARY}" diff --git a/.github/workflows/documentation-build.yml b/.github/workflows/documentation-build.yml index f447b491..b3477bb6 100644 --- a/.github/workflows/documentation-build.yml +++ b/.github/workflows/documentation-build.yml @@ -29,40 +29,40 @@ jobs: # Grant GITHUB_TOKEN the permissions required to make a Pages deployment permissions: - contents: read # to clone the repository - pages: write # to deploy to Pages - id-token: write # to verify the deployment originates from an appropriate source + contents: read # to clone the repository + pages: write # to deploy to Pages + id-token: write # to verify the deployment originates from an appropriate source steps: - - name: Checkout - uses: actions/checkout@master - with: - fetch-depth: 0 # otherwise, you will failed to push refs to dest repo - - name: Upgrade pip - run: | - python -m pip install --upgrade pip - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: 3.12 - - name: Install Pandoc, repo and dependencies - run: | - sudo apt install pandoc - sudo apt install libcairo2-dev - pip install sphinx==8.1.3 - pip install . '.[dev,docs]' + - name: Checkout + uses: actions/checkout@master + with: + fetch-depth: 0 # otherwise, you will failed to push refs to dest repo + - name: Upgrade pip + run: | + python -m pip install --upgrade pip + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: 3.12 + - name: Install Pandoc, repo and dependencies + run: | + sudo apt install pandoc + sudo apt install libcairo2-dev + pip install sphinx==8.1.3 + pip install . '.[dev,docs]' - - name: Install Jupyter kernel - run: | - python -m ipykernel install --user --name=python3 + - name: Install Jupyter kernel + run: | + python -m ipykernel install --user --name=python3 - - name: Build and Commit - uses: sphinx-notes/pages@v3 - with: - sphinx_version: 8.1.3 - documentation_path: docs/src - - name: Push changes - uses: ad-m/github-push-action@master - continue-on-error: true - with: - branch: gh-pages \ No newline at end of file + - name: Build and Commit + uses: sphinx-notes/pages@v3 + with: + sphinx_version: 8.1.3 + documentation_path: docs/src + - name: Push changes + uses: ad-m/github-push-action@master + continue-on-error: true + with: + branch: gh-pages diff --git a/.github/workflows/issues-labels.yml b/.github/workflows/issues-labels.yml new file mode 100644 index 00000000..56ab5b19 --- /dev/null +++ b/.github/workflows/issues-labels.yml @@ -0,0 +1,149 @@ +# Verifies if the current issue has at least one real `[scope]` label and one +# real `[priority]` label. If either is missing, the workflow adds a reminder +# label with a warning emoji. + +name: Issue labels check + +on: + issues: + types: [opened, labeled, unlabeled] + +permissions: + issues: write + +jobs: + check-labels: + runs-on: ubuntu-latest + + concurrency: + group: issue-labels-${{ github.event.issue.number }} + cancel-in-progress: true + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Sync missing-label reminders + uses: ./.github/actions/github-script + with: + script: | + const fs = require('fs'); + + const issueNumber = context.issue.number; + const action = context.payload.action; + const changedLabel = context.payload.label?.name ?? null; + const labels = context.payload.issue.labels.map(({ name }) => name); + const requirements = [ + { + prefix: '[scope] ', + reminder: '[scope] ⚠️ label needed', + }, + { + prefix: '[priority] ', + reminder: '[priority] ⚠️ label needed', + }, + ]; + + const labelsToAdd = []; + const labelsToRemove = []; + const evaluations = []; + + console.log(`::group::Issue label check for #${issueNumber}`); + console.log(`Event action: ${action}`); + if (changedLabel) { + console.log(`Event label: ${changedLabel}`); + } + console.log( + `Current labels: ${labels.length > 0 ? labels.join(', ') : '(none)'}`, + ); + + for (const { prefix, reminder } of requirements) { + const matchingRealLabels = labels.filter( + (name) => name.startsWith(prefix) && name !== reminder, + ); + const hasRealLabel = matchingRealLabels.length > 0; + const hasReminderLabel = labels.includes(reminder); + + evaluations.push({ + prefix, + reminder, + matchingRealLabels, + hasReminderLabel, + }); + + if (hasRealLabel && hasReminderLabel) { + labelsToRemove.push(reminder); + } else if (!hasRealLabel && !hasReminderLabel) { + labelsToAdd.push(reminder); + } + } + + for (const evaluation of evaluations) { + if (evaluation.matchingRealLabels.length > 0) { + console.log( + `Found required ${evaluation.prefix}label(s): ${evaluation.matchingRealLabels.join(', ')}`, + ); + } else { + console.log(`Missing required ${evaluation.prefix}label.`); + } + + if (evaluation.hasReminderLabel) { + console.log(`Reminder label already present: ${evaluation.reminder}`); + } + } + + if (labelsToAdd.length > 0) { + console.log(`Adding reminder labels: ${labelsToAdd.join(', ')}`); + await github.rest.issues.addLabels({ + owner: context.repo.owner, + repo: context.repo.repo, + issue_number: context.issue.number, + labels: labelsToAdd, + }); + } + + for (const name of labelsToRemove) { + console.log(`Removing reminder label: ${name}`); + await github.rest.issues.removeLabel({ + owner: context.repo.owner, + repo: context.repo.repo, + issue_number: context.issue.number, + name, + }); + } + + if (labelsToAdd.length === 0 && labelsToRemove.length === 0) { + console.log('No label changes required.'); + } + + console.log('::endgroup::'); + + if (process.env.GITHUB_STEP_SUMMARY) { + const summaryLines = [ + '### Issue Label Check', + `- Issue: #${issueNumber}`, + `- Event: ${action}`, + `- Trigger label: ${changedLabel ?? '(none)'}`, + `- Current labels: ${labels.length > 0 ? labels.join(', ') : '(none)'}`, + '', + '#### Requirement status', + ...evaluations.map((evaluation) => { + const status = + evaluation.matchingRealLabels.length > 0 + ? `found ${evaluation.matchingRealLabels.join(', ')}` + : 'missing'; + const reminder = evaluation.hasReminderLabel + ? `reminder present: ${evaluation.reminder}` + : `reminder absent: ${evaluation.reminder}`; + return `- ${evaluation.prefix}: ${status}; ${reminder}`; + }), + '', + `- Labels to add: ${labelsToAdd.length > 0 ? labelsToAdd.join(', ') : '(none)'}`, + `- Labels to remove: ${labelsToRemove.length > 0 ? labelsToRemove.join(', ') : '(none)'}`, + ]; + + fs.appendFileSync( + process.env.GITHUB_STEP_SUMMARY, + `${summaryLines.join('\n')}\n`, + ); + } diff --git a/.github/workflows/lint-format.yml b/.github/workflows/lint-format.yml new file mode 100644 index 00000000..16dd95c9 --- /dev/null +++ b/.github/workflows/lint-format.yml @@ -0,0 +1,124 @@ +# The workflow checks +# - the validity of pyproject.toml, +# - the presence and correctness of SPDX license headers, +# - linting and formatting of Python code, +# - linting and formatting of docstrings in Python code, +# - formatting of non-Python files (like markdown and toml). +# - linting of Python code in Jupyter notebooks (for library template). +# +# A summary of the checks is added to the GitHub Actions summary. + +name: Lint and format checks + +on: + # Trigger the workflow on push + push: + branches-ignore: [master, main] # Already verified in PR + # Do not run this workflow on creating a new tag starting with + # 'v', e.g. 'v1.0.3' (see publish-pypi.yml) + tags-ignore: ['v*'] + # Trigger the workflow on pull request + pull_request: + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +permissions: + contents: read + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + +jobs: + lint-format: + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Run post-install developer steps + run: pixi run post-install + + - name: Check validity of pyproject.toml + id: pyproject + continue-on-error: true + shell: bash + run: pixi run pyproject-check + + - name: Check SPDX license headers + id: license_headers + continue-on-error: true + shell: bash + run: pixi run license-check + + - name: Check linting of Python code + id: py_lint + continue-on-error: true + shell: bash + run: pixi run py-lint-check + + - name: Check formatting of Python code + id: py_format + continue-on-error: true + shell: bash + run: pixi run py-format-check + + - name: Check linting of docstrings in Python code + id: docstring_lint + continue-on-error: true + shell: bash + run: pixi run docstring-lint-check + + - name: Check formatting of non-Python files (md, toml, etc.) + id: nonpy_format + continue-on-error: true + shell: bash + run: pixi run nonpy-format-check + + - name: Check linting of Python code in Jupyter notebooks (ipynb) + id: notebook_lint + continue-on-error: true + shell: bash + run: pixi run notebook-lint-check + + # Add summary + - name: Add quality checks summary + if: always() + shell: bash + run: | + { + echo "## 🧪 Checks Summary" + echo "" + echo "| Check | Status |" + echo "|-------|--------|" + echo "| pyproject.toml | ${{ steps.pyproject.outcome == 'success' && '✅' || '❌' }} |" + echo "| license headers | ${{ steps.license_headers.outcome == 'success' && '✅' || '❌' }} |" + echo "| py lint | ${{ steps.py_lint.outcome == 'success' && '✅' || '❌' }} |" + echo "| py format | ${{ steps.py_format.outcome == 'success' && '✅' || '❌' }} |" + echo "| docstring lint | ${{ steps.docstring_lint.outcome == 'success' && '✅' || '❌' }} |" + echo "| nonpy format | ${{ steps.nonpy_format.outcome == 'success' && '✅' || '❌' }} |" + echo "| notebooks lint | ${{ steps.notebook_lint.outcome == 'success' && '✅' || '❌' }} |" + } >> "$GITHUB_STEP_SUMMARY" + + # Fail job if any check failed + - name: Fail job if any check failed + if: | + steps.pyproject.outcome == 'failure' + || steps.license_headers.outcome == 'failure' + || steps.py_lint.outcome == 'failure' + || steps.py_format.outcome == 'failure' + || steps.docstring_lint.outcome == 'failure' + || steps.nonpy_format.outcome == 'failure' + || steps.notebook_lint.outcome == 'failure' + shell: bash + run: exit 1 diff --git a/.github/workflows/ossar-analysis.yml b/.github/workflows/ossar-analysis.yml index a2c77306..94859565 100644 --- a/.github/workflows/ossar-analysis.yml +++ b/.github/workflows/ossar-analysis.yml @@ -3,7 +3,6 @@ # # For more information see: https://github.com/github/ossar-action - name: OSSAR on: @@ -17,35 +16,34 @@ jobs: steps: # Checkout your code repository to scan - - name: Checkout repository - uses: actions/checkout@v4 - with: - # We must fetch at least the immediate parents so that if this is - # a pull request then we can checkout the head. - fetch-depth: 2 - - # If this run was triggered by a pull request event, then checkout - # the head of the pull request instead of the merge commit. - - run: git checkout HEAD^2 - if: ${{ github.event_name == 'pull_request' }} - - # Ensure a compatible version of dotnet is installed. - # The [Microsoft Security Code Analysis CLI](https://aka.ms/mscadocs) is built with dotnet v3.1.201. - # A version greater than or equal to v3.1.201 of dotnet must be installed on the agent in order to run this action. - # Remote agents already have a compatible version of dotnet installed and this step may be skipped. - # For local agents, ensure dotnet version 3.1.201 or later is installed by including this action: - # - name: Install .NET - # uses: actions/setup-dotnet@v1 - # with: - # dotnet-version: '3.1.x' - + - name: Checkout repository + uses: actions/checkout@v4 + with: + # We must fetch at least the immediate parents so that if this is + # a pull request then we can checkout the head. + fetch-depth: 2 + + # If this run was triggered by a pull request event, then checkout + # the head of the pull request instead of the merge commit. + - run: git checkout HEAD^2 + if: ${{ github.event_name == 'pull_request' }} + + # Ensure a compatible version of dotnet is installed. + # The [Microsoft Security Code Analysis CLI](https://aka.ms/mscadocs) is built with dotnet v3.1.201. + # A version greater than or equal to v3.1.201 of dotnet must be installed on the agent in order to run this action. + # Remote agents already have a compatible version of dotnet installed and this step may be skipped. + # For local agents, ensure dotnet version 3.1.201 or later is installed by including this action: + # - name: Install .NET + # uses: actions/setup-dotnet@v1 + # with: + # dotnet-version: '3.1.x' # Run open source static analysis tools - - name: Run OSSAR - uses: github/ossar-action@v2.0.0 - id: ossar - - # Upload results to the Security tab - - name: Upload OSSAR results - uses: github/codeql-action/upload-sarif@v3 - with: - sarif_file: ${{ steps.ossar.outputs.sarifFile }} \ No newline at end of file + - name: Run OSSAR + uses: github/ossar-action@v2.0.0 + id: ossar + + # Upload results to the Security tab + - name: Upload OSSAR results + uses: github/codeql-action/upload-sarif@v3 + with: + sarif_file: ${{ steps.ossar.outputs.sarifFile }} diff --git a/.github/workflows/pr-labels.yml b/.github/workflows/pr-labels.yml new file mode 100644 index 00000000..25710633 --- /dev/null +++ b/.github/workflows/pr-labels.yml @@ -0,0 +1,63 @@ +# Verifies if a pull request has at least one label from a set of valid +# labels before it can be merged. +# +# NOTE: +# This workflow may be triggered twice in quick succession when a PR is +# created: +# 1) `opened` — when the pull request is initially created +# 2) `labeled` — if labels are added immediately after creation +# (e.g. by manual labeling, another workflow, or GitHub App). +# +# These are separate GitHub events, so two workflow runs can be started. +# The `concurrency` configuration below ensures that only the latest run +# for the same PR remains active, canceling any previous in-progress +# run. + +name: PR labels check + +on: + pull_request_target: + types: [opened, labeled, unlabeled, synchronize] + +concurrency: + group: pr-labels-${{ github.event.pull_request.number }} + cancel-in-progress: true + +permissions: + pull-requests: read + +jobs: + check-labels: + runs-on: ubuntu-latest + + steps: + - name: Check for valid labels + run: | + PR_LABELS=$(echo '${{ toJson(github.event.pull_request.labels.*.name) }}' | jq -r '.[]') + + echo "Current PR labels: $PR_LABELS" + VALID_LABELS=( + "[bot] release" + "[scope] bug" + "[scope] documentation" + "[scope] enhancement" + "[scope] maintenance" + "[scope] significant" + ) + + found=false + for label in "${VALID_LABELS[@]}"; do + if echo "$PR_LABELS" | grep -Fxq "$label"; then + echo "✅ Found valid label: $label" + found=true + break + fi + done + + if [ "$found" = false ]; then + echo "ERROR: PR must have at least one of the following labels:" + for label in "${VALID_LABELS[@]}"; do + echo " - $label" + done + exit 1 + fi diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml new file mode 100644 index 00000000..0b431717 --- /dev/null +++ b/.github/workflows/pypi-publish.yml @@ -0,0 +1,46 @@ +# Builds a Python package and publish it to PyPI when a new tag is +# created. + +name: PyPI publishing + +on: + # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3' + push: + tags: ['v*'] + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +jobs: + pypi-publish: + runs-on: ubuntu-latest + + permissions: + contents: read + id-token: write # IMPORTANT: this permission is mandatory for trusted publishing + + steps: + - name: Check-out repository + uses: actions/checkout@v6 + with: + fetch-depth: 0 # full history with tags to get the version number by versioningit + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + # Build the Python package (to dist/ folder) + - name: Create Python package + run: pixi run default-build + + # Publish the package to PyPI (from dist/ folder) + # Instead of publishing with personal access token, we use + # GitHub Actions OIDC to get a short-lived token from PyPI. + # New publisher must be previously configured in PyPI at + # https://pypi.org/manage/project/easyreflectometry/settings/publishing/ + # Use the following data: + # Owner: easyscience + # Repository name: reflectometry-lib + # Workflow name: pypi-publish.yml + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + packages-dir: 'dist' diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml new file mode 100644 index 00000000..2f4f58ac --- /dev/null +++ b/.github/workflows/pypi-test.yml @@ -0,0 +1,80 @@ +name: PyPI package tests + +on: + # Run daily, at 00:00. + schedule: + - cron: '0 0 * * *' + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +permissions: + contents: read + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} + +jobs: + # Job 1: Test installation from PyPI on multiple OS + pypi-package-tests: + strategy: + matrix: + os: [ubuntu-latest, windows-latest, macos-latest] + + runs-on: ${{ matrix.os }} + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + with: + environments: '' + activate-environment: '' + run-install: false + frozen: false + + - name: Init pixi project + run: pixi init easyreflectometry + + - name: Set the minimum system requirements + working-directory: easyreflectometry + run: pixi project system-requirements add macos 14.0 + + - name: Add Python 3.13 from Conda + working-directory: easyreflectometry + run: pixi add "python=3.13" + + - name: Add other Conda dependencies + working-directory: easyreflectometry + run: pixi add gsl + + - name: Add easyreflectometry (with dev dependencies) from PyPI + working-directory: easyreflectometry + run: pixi add --pypi "easyreflectometry[dev]" + + - name: Run unit tests to verify the installation + working-directory: easyreflectometry + run: pixi run python -m pytest ../tests/unit/ --color=yes -v + + - name: Run functional tests to verify the installation + working-directory: easyreflectometry + run: pixi run python -m pytest ../tests/functional/ --color=yes -v + + - name: Run integration tests to verify the installation + working-directory: easyreflectometry + run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto + + # Job 2: Build and publish dashboard (reusable workflow) + run-reusable-workflows: + needs: pypi-package-tests # depend on previous job + uses: ./.github/workflows/dashboard.yml + secrets: inherit diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 1d33313f..ea40ee70 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -1,4 +1,4 @@ -# This workflow will for a variety of Python versions +# This workflow will for a variety of Python versions # - install the code base # - lint the code base # - test the code base @@ -21,8 +21,8 @@ jobs: - name: Suggestion to fix issues if: ${{ failure() }} run: | - echo "::notice::In project root run 'python.exe -m ruff . --fix' and commit changes to fix issues." - exit 1 + echo "::notice::In project root run 'python.exe -m ruff . --fix' and commit changes to fix issues." + exit 1 Code_Testing: strategy: @@ -35,56 +35,54 @@ jobs: if: "!contains(github.event.head_commit.message, '[ci skip]')" steps: - - uses: actions/checkout@v4 - - - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Upgrade pip - run: | - python -m pip install --upgrade pip + - uses: actions/checkout@v4 - - name: Install dependencies - run: pip install -e '.[dev]' + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} - - name: Test with pytest and coverage - run: | - pip install pytest pytest-cov - pytest --cov=src/easyreflectometry tests --cov-branch --cov-report=xml:coverage-unit.xml + - name: Upgrade pip + run: | + python -m pip install --upgrade pip - - name: Upload coverage reports to Codecov - # only on ubuntu to avoid multiple uploads - if: runner.os == 'Linux' - uses: codecov/codecov-action@v5 - with: - name: unit-tests-job - flags: unittests - files: ./coverage-unit.xml - fail_ci_if_error: false - verbose: true - token: ${{ secrets.CODECOV_TOKEN }} - slug: EasyScience/EasyReflectometryLib + - name: Install dependencies + run: pip install -e '.[dev]' + - name: Test with pytest and coverage + run: | + pip install pytest pytest-cov + pytest --cov=src/easyreflectometry tests --cov-branch --cov-report=xml:coverage-unit.xml + + - name: Upload coverage reports to Codecov + # only on ubuntu to avoid multiple uploads + if: runner.os == 'Linux' + uses: codecov/codecov-action@v5 + with: + name: unit-tests-job + flags: unittests + files: ./coverage-unit.xml + fail_ci_if_error: false + verbose: true + token: ${{ secrets.CODECOV_TOKEN }} + slug: EasyScience/EasyReflectometryLib Package_Testing: - runs-on: ubuntu-latest if: "!contains(github.event.head_commit.message, '[ci skip]')" steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - with: - python-version: 3.11 + - uses: actions/setup-python@v5 + with: + python-version: 3.11 - - name: Install dependencies and build - run: | - pip install -e '.[dev]' - python -m build + - name: Install dependencies and build + run: | + pip install -e '.[dev]' + python -m build - - name: Check Build - run: | - cd ./dist - pytest ../ + - name: Check Build + run: | + cd ./dist + pytest ../ diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 3a4d1036..c0717847 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -9,34 +9,34 @@ name: Create Python Package on: push: - branches: [ master, pre-release ] + branches: [master, pre-release] pull_request: - branches: [ master, pre-release ] + branches: [master, pre-release] jobs: build: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.11','3.12','3.13'] + python-version: ['3.11', '3.12', '3.13'] if: "!contains(github.event.head_commit.message, '[ci skip]')" steps: - - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies and build - run: | - pip install -e '.[dev]' - python -m build - - name: Test with pytest - run: | - cd ./dist - pytest ../ - - uses: actions/upload-artifact@v4 - with: - name: EasyReflectometrys - Python ${{ matrix.python-version }} - path: ${{ github.workspace }}/dist/* - overwrite: true \ No newline at end of file + - uses: actions/checkout@v4 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies and build + run: | + pip install -e '.[dev]' + python -m build + - name: Test with pytest + run: | + cd ./dist + pytest ../ + - uses: actions/upload-artifact@v4 + with: + name: EasyReflectometrys - Python ${{ matrix.python-version }} + path: ${{ github.workspace }}/dist/* + overwrite: true diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index dce167b2..38133fd1 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -4,7 +4,6 @@ # # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries - name: Publish Python Package # Controls when the workflow will run @@ -19,24 +18,23 @@ on: jobs: deploy: - runs-on: ubuntu-latest permissions: id-token: write - + steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - with: - python-version: 3.12 + - uses: actions/setup-python@v5 + with: + python-version: 3.12 - - name: Install dependencies and build - run: | - pip install -e '.[dev]' - python -m build + - name: Install dependencies and build + run: | + pip install -e '.[dev]' + python -m build - - name: Publish distribution 📦 to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - #with: - # password: ${{ secrets.PYPI_PASSWORD }} + - name: Publish distribution 📦 to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + #with: + # password: ${{ secrets.PYPI_PASSWORD }} diff --git a/.github/workflows/release-drafter-verify-pr-labels.yml b/.github/workflows/release-drafter-verify-pr-labels.yml index b024955b..3a8dbb4b 100644 --- a/.github/workflows/release-drafter-verify-pr-labels.yml +++ b/.github/workflows/release-drafter-verify-pr-labels.yml @@ -5,7 +5,6 @@ # # For more information see: https://github.com/marketplace/actions/release-drafter - name: Verify PR labels on: pull_request_target: @@ -16,11 +15,12 @@ jobs: runs-on: ubuntu-latest name: Verify that the PR has a valid label steps: - - name: Verify PR label action - uses: jesusvasquez333/verify-pr-label-action@v1.4.0 - id: verify-pr-label - with: - github-token: ${{ secrets.GITHUB_TOKEN }} - valid-labels: chore, fix, bugfix, bug, enhancement, feature, dependencies, documentation - pull-request-number: ${{ github.event.pull_request.number }} - disable-reviews: false + - name: Verify PR label action + uses: jesusvasquez333/verify-pr-label-action@v1.4.0 + id: verify-pr-label + with: + github-token: ${{ secrets.GITHUB_TOKEN }} + valid-labels: + chore, fix, bugfix, bug, enhancement, feature, dependencies, documentation + pull-request-number: ${{ github.event.pull_request.number }} + disable-reviews: false diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml index 31308447..51cd0d22 100644 --- a/.github/workflows/release-drafter.yml +++ b/.github/workflows/release-drafter.yml @@ -4,7 +4,6 @@ # Uses the release-drafter.yml configuration file in the .github directory. # https://github.com/marketplace/actions/release-drafter - name: Release Drafter on: diff --git a/.github/workflows/release-notes.yml b/.github/workflows/release-notes.yml new file mode 100644 index 00000000..b6d8205c --- /dev/null +++ b/.github/workflows/release-notes.yml @@ -0,0 +1,71 @@ +# Drafts your next Release notes as pull requests are merged into +# default branch + +name: Release draft update + +on: + # Runs on pushes targeting the default branch (updates the real draft release) + push: + branches: [master, main] + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +jobs: + draft-release-notes: + permissions: + # write permission is required to create a github release + contents: write + + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + with: + fetch-depth: 0 # full history with tags to get the version number + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + - name: Drafts the next release notes + id: draft + uses: enhantica/drafterino@v2 + with: + config: | + title: 'easyreflectometry $COMPUTED_VERSION' + tag: 'v$COMPUTED_VERSION' + note-template: '- $PR_TITLE (#$PR_NUMBER)' + + default-bump: post + + major-bump-labels: ['[scope] significant'] + minor-bump-labels: ['[scope] enhancement'] + patch-bump-labels: ['[scope] bug', '[scope] maintenance'] + post-bump-labels: ['[scope] documentation'] + + release-notes: + - title: 'Added' + labels: ['[scope] significant', '[scope] enhancement'] + - title: 'Fixed' + labels: ['[scope] bug'] + - title: 'Changed' + labels: ['[scope] maintenance', '[scope] documentation'] + env: + GITHUB_TOKEN: ${{ steps.bot.outputs.token }} + + - name: Create GitHub draft release + uses: softprops/action-gh-release@v3 + with: + draft: true + tag_name: ${{ steps.draft.outputs.tag_name }} + name: ${{ steps.draft.outputs.release_name }} + body: ${{ steps.draft.outputs.release_notes }} + env: + GITHUB_TOKEN: ${{ steps.bot.outputs.token }} diff --git a/.github/workflows/release-pr.yml b/.github/workflows/release-pr.yml new file mode 100644 index 00000000..3fa073b9 --- /dev/null +++ b/.github/workflows/release-pr.yml @@ -0,0 +1,55 @@ +# This workflow creates an automated release PR from a source branch into the default branch. +# +# Usage: +# - Triggered manually via workflow_dispatch. +# - Creates a PR titled "Release: merge into ". +# - Adds the label "[bot] release" so it is excluded from changelogs. +# - The PR body makes clear that this is automation only (no review needed). + +name: 'Release PR (develop → master)' + +on: + workflow_dispatch: + inputs: + source_branch: + description: 'Source branch to create PR from' + required: false + default: 'develop' + type: string + +permissions: + contents: read + pull-requests: write + +env: + DEFAULT_BRANCH: ${{ github.event.repository.default_branch }} + SOURCE_BRANCH: ${{ inputs.source_branch || 'develop' }} + +jobs: + create-pull-request: + runs-on: ubuntu-latest + steps: + - name: Checkout ${{ env.SOURCE_BRANCH }} branch + uses: actions/checkout@v6 + with: + ref: ${{ env.SOURCE_BRANCH }} + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + - name: Create PR from ${{ env.SOURCE_BRANCH }} to ${{ env.DEFAULT_BRANCH }} + env: + GH_TOKEN: ${{ steps.bot.outputs.token }} + run: | + gh pr create \ + --base ${{ env.DEFAULT_BRANCH }} \ + --head ${{ env.SOURCE_BRANCH }} \ + --title "🎉 Release: merge ${{ env.SOURCE_BRANCH }} into ${{ env.DEFAULT_BRANCH }}" \ + --label "[bot] release" \ + --body "This PR is created automatically to trigger the release pipeline. It merges the accumulated changes from \`${{ env.SOURCE_BRANCH }}\` into \`${{ env.DEFAULT_BRANCH }}\`. + + ⚠️ It is labeled \`[bot] release\` and is excluded from release notes and version bump logic." diff --git a/.github/workflows/security.yml b/.github/workflows/security.yml new file mode 100644 index 00000000..0f43db35 --- /dev/null +++ b/.github/workflows/security.yml @@ -0,0 +1,93 @@ +# Code scanning (CodeQL) for vulnerabilities and insecure coding patterns. +# +# What this workflow does +# - Runs GitHub CodeQL analysis and uploads results to your repository's Security tab. +# - Triggers on PRs (so findings appear as PR checks) and on pushes to `develop`. +# - Runs on a weekly schedule. +# +# Where to find results on GitHub +# - Repository → Security → Code scanning alerts +# (You can filter by tool = CodeQL and by branch.) +# +# Where to configure on GitHub +# - Repository → Settings → Advanced Security +# Enable "GitHub Advanced Security" (if available) and configure CodeQL there. +# - Repository → Security → Code scanning alerts +# This page shows findings produced by this workflow. +# +# Notes about the scheduled run +# - Scheduled workflows are triggered from the repository's *default branch*. +# If your default branch is `master` but you want the scheduled scan to analyze +# `develop`, this workflow checks out `develop` explicitly for scheduled runs. +# +# References +# - CodeQL Action: https://github.com/github/codeql-action +# - Advanced setup docs: https://docs.github.com/en/code-security/code-scanning + +name: Security scans with CodeQL + +on: + # Run on pull requests so results show up as PR checks and code + # scanning alerts. + pull_request: + branches: [master, main, develop] + + # Run on pushes (e.g., after merging PRs). + push: + branches: [master, main, develop] + + # Run weekly. (Cron is in UTC.) + schedule: + - cron: '0 3 * * 1' + +permissions: + contents: read + security-events: write + +jobs: + codeql: + name: Code scanning + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + # Keep this list tight to avoid noise and speed up runs. + language: [python, actions] + + steps: + # Scheduled workflows run from the default branch. + # We explicitly analyze `develop` on the schedule to keep the scan + # focused on the active dev branch. + - name: Checkout repository (scheduled → develop) + if: ${{ github.event_name == 'schedule' }} + uses: actions/checkout@v6 + with: + ref: develop + + - name: Checkout repository + if: ${{ github.event_name != 'schedule' }} + uses: actions/checkout@v6 + + - name: Initialize CodeQL + uses: github/codeql-action/init@v4 + with: + languages: ${{ matrix.language }} + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v4 + + print-link: + name: Print results link + runs-on: ubuntu-latest + + needs: codeql + permissions: {} # no special perms needed just to print links + + steps: + - name: Add Code Scanning link to job summary + run: | + echo "## 🔎 CodeQL Results" >> $GITHUB_STEP_SUMMARY + echo "" >> $GITHUB_STEP_SUMMARY + echo "View Code Scanning alerts here:" >> $GITHUB_STEP_SUMMARY + echo "${{ github.server_url }}/${{ github.repository }}/security/code-scanning" >> $GITHUB_STEP_SUMMARY diff --git a/.github/workflows/test-trigger.yml b/.github/workflows/test-trigger.yml new file mode 100644 index 00000000..440bae3c --- /dev/null +++ b/.github/workflows/test-trigger.yml @@ -0,0 +1,40 @@ +name: Scheduled code tests trigger + +on: + # Run daily, at 00:00. + schedule: + - cron: '0 0 * * *' + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +permissions: + contents: read + +jobs: + code-tests-trigger: + runs-on: ubuntu-latest + + steps: + - name: Checkout develop branch + uses: actions/checkout@v6 + with: + ref: develop + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + - name: Dispatch code tests workflow + uses: ./.github/actions/github-script + with: + github-token: ${{ steps.bot.outputs.token }} + script: | + await github.rest.actions.createWorkflowDispatch({ + owner: context.repo.owner, + repo: context.repo.repo, + workflow_id: "test.yml", + ref: "develop" + }); diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 00000000..f75ac8be --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,302 @@ +# This is the main workflow for testing the code before and after +# packaging it. +# The workflow is divided into three jobs: +# 1. env-prepare: +# - Prepare the environment for testing +# 2. source-test: +# - Test the code base against the latest code in the repository +# - Create the Python package +# - Upload the Python package for the next job +# 3. package-test: +# - Download the Python package (including extra files) from the previous job +# - Install the downloaded Python package +# - Test the code base against the installed package +# 4. dashboard-build-trigger: +# - Trigger the dashboard build workflow to update the code quality +# metrics on the dashboard + +name: Code and package tests + +on: + # Trigger the workflow on push + push: + branches-ignore: [master, main] # Already verified in PR + # But do not run this workflow on creating a new tag starting with + # 'v', e.g. 'v1.0.3' (see publish-pypi.yml) + tags-ignore: ['v*'] + # Trigger the workflow on pull request + pull_request: + branches: ['**'] + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Need permissions to trigger the dashboard build workflow +permissions: + actions: write + contents: read + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + PY_VERSIONS: '3.11 3.13' + PIXI_ENVS: 'py-311-env py-313-env' + +jobs: + # Job 1: Set up environment variables + env-prepare: + runs-on: [ubuntu-latest] + + outputs: + pytest-marks: ${{ steps.set-mark.outputs.pytest_marks }} + + steps: + # Determine if integration tests should be run fully or only the fast ones + # (to save time on branches other than master and develop) + - name: Set mark for integration tests + id: set-mark + run: | + if [[ "${{ env.CI_BRANCH }}" == "master" || "${{ env.CI_BRANCH }}" == "develop" ]]; then + echo "pytest_marks=" >> $GITHUB_OUTPUT + else + echo "pytest_marks=-m fast" >> $GITHUB_OUTPUT + fi + + # Job 2: Test code + source-test: + needs: env-prepare # depend on previous job + + strategy: + fail-fast: false + matrix: + os: [ubuntu-24.04, macos-15, windows-2022] + + runs-on: ${{ matrix.os }} + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + with: + environments: ${{ env.PIXI_ENVS }} + + - name: Run unit tests + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env + + echo "Running tests in environment: $env" + pixi run --environment $env unit-tests + done + + - name: Run functional tests + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env + + echo "Running tests in environment: $env" + pixi run --environment $env functional-tests + done + + - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }} + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env + + echo "Running tests in environment: $env" + pixi run --environment $env integration-tests ${{ needs.env-prepare.outputs.pytest-marks }} + done + + # Delete all local tags when not on a tagged commit to force versioningit + # to fall back to the configured default-tag, which is '999.0.0' in our case. + # This is needed for testing the package in the next job, as its version + # must be higher than the PyPI version for pip to prefer the local version. + - name: Force using versioningit default tag (non tagged release) + if: startsWith(github.ref , 'refs/tags/v') != true + run: git tag --delete $(git tag) + + - name: Build package wheels for all Python versions + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env + + echo "Building wheel in environment: $env" + pixi run --environment $env dist-build + + echo "Moving built wheel to dist/py$py_ver/" + pixi run mkdir -p dist/py$py_ver + pixi run mv dist/*.whl dist/py$py_ver/ + done + + - name: Remove Python cache files before uploading + shell: bash + run: pixi run clean-pycache + + # More than one file/dir need to be specified in 'path', to preserve the + # structure of the dist/ directory, not only its contents. + - name: Upload package (incl. extras) for next job + uses: ./.github/actions/upload-artifact + with: + name: easyreflectometry_${{ matrix.os }}_${{ runner.arch }} + path: dist/ + + # Job 3: Test the package + package-test: + needs: source-test # depend on previous job + + strategy: + fail-fast: false + matrix: + os: [ubuntu-24.04, macos-15, windows-2022] + + runs-on: ${{ matrix.os }} + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Download package (incl. extras) from previous job + uses: ./.github/actions/download-artifact + with: + # name and path should be taken from the upload step of the previous job + name: easyreflectometry_${{ matrix.os }}_${{ runner.arch }} + path: dist/ + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + with: + environments: '' + activate-environment: '' + run-install: false + frozen: false + + - name: Install easyreflectometry from the built wheel + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + echo "Initializing pixi project" + pixi init easyreflectometry_py$py_ver + cd easyreflectometry_py$py_ver + + echo "Adding Python $py_ver" + pixi add "python=$py_ver" + + echo "Setting macOS 14.0 as minimum required" + pixi project system-requirements add macos 14.0 + + echo "Looking for wheel in ../dist/py$py_ver/" + ls -l "../dist/py$py_ver/" + + whl_path=(../dist/"py$py_ver"/*.whl) + if [[ ! -f "${whl_path[0]}" ]]; then + echo "❌ No wheel found in ../dist/py$py_ver/" + exit 1 + fi + + whl_url="file://$(python -c 'import os,sys; print(os.path.abspath(sys.argv[1]))' "${whl_path[0]}")" + + echo "Adding easyreflectometry from: $whl_url" + pixi add --pypi "easyreflectometry[dev] @ ${whl_url}" + + echo "Exiting pixi project directory" + cd .. + done + + - name: Run unit tests + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + echo "Entering pixi project directory easyreflectometry_py$py_ver" + cd easyreflectometry_py$py_ver + + echo "Running tests" + pixi run python -m pytest ../tests/unit/ --color=yes -v + + echo "Exiting pixi project directory" + cd .. + done + + - name: Run functional tests + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + echo "Entering pixi project directory easyreflectometry_py$py_ver" + cd easyreflectometry_py$py_ver + + echo "Running tests" + pixi run python -m pytest ../tests/functional/ --color=yes -v + + echo "Exiting pixi project directory" + cd .. + done + + - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }} + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹" + + echo "Entering pixi project directory easyreflectometry_py$py_ver" + cd easyreflectometry_py$py_ver + + echo "Running tests" + pixi run python -m pytest ../tests/integration/ --color=yes -n auto -v ${{ needs.env-prepare.outputs.pytest-marks }} + + echo "Exiting pixi project directory" + cd .. + done + + # Job 4: Build and publish dashboard (reusable workflow) + run-reusable-workflows: + needs: package-test # depend on previous job + uses: ./.github/workflows/dashboard.yml + secrets: inherit diff --git a/.github/workflows/tutorial-tests-trigger.yml b/.github/workflows/tutorial-tests-trigger.yml new file mode 100644 index 00000000..4b160d87 --- /dev/null +++ b/.github/workflows/tutorial-tests-trigger.yml @@ -0,0 +1,40 @@ +name: Scheduled tutorial tests trigger + +on: + # Run daily, at 00:00. + schedule: + - cron: '0 0 * * *' + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +permissions: + contents: read + +jobs: + tutorial-tests-trigger: + runs-on: ubuntu-latest + + steps: + - name: Checkout develop branch + uses: actions/checkout@v6 + with: + ref: develop + + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + - name: Dispatch tutorial tests workflow + uses: ./.github/actions/github-script + with: + github-token: ${{ steps.bot.outputs.token }} + script: | + await github.rest.actions.createWorkflowDispatch({ + owner: context.repo.owner, + repo: context.repo.repo, + workflow_id: "tutorial-tests.yml", + ref: "develop" + }); diff --git a/.github/workflows/tutorial-tests.yml b/.github/workflows/tutorial-tests.yml new file mode 100644 index 00000000..a4fc940c --- /dev/null +++ b/.github/workflows/tutorial-tests.yml @@ -0,0 +1,60 @@ +name: Tutorial tests + +on: + # Trigger the workflow on push + push: + # Selected branches + branches: [develop] # master and main are already verified in PR + # Trigger the workflow on pull request + pull_request: + branches: ['**'] + # Trigger the workflow on workflow_call (to be called from other workflows) + # Needed, as standard schedule triggers the master branch only, but we want + # to run this workflow on develop branch. + workflow_call: + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +permissions: + contents: read + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + +jobs: + # Job 1: Test tutorials as scripts and notebooks on multiple OS + tutorial-tests: + strategy: + fail-fast: false + matrix: + os: [ubuntu-latest, macos-latest, windows-latest] + + runs-on: ${{ matrix.os }} + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Prepare notebooks + shell: bash + run: pixi run notebook-prepare + + - name: Test tutorials as notebooks + shell: bash + run: pixi run notebook-tests + + # Job 2: Build and publish dashboard (reusable workflow) + run-reusable-workflows: + needs: tutorial-tests # depend on previous job + uses: ./.github/workflows/dashboard.yml + secrets: inherit diff --git a/.gitignore b/.gitignore index ff5a50d4..6dc595c7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,49 +1,46 @@ -# QtCreator -*.autosave - -# QtCreator Qml -*.qmlproject.user -*.qmlproject.user.* - -# QtCreator Python -*.pyproject.user -*.pyproject.user.* - -# QtCreator CMake -CMakeLists.txt.user* - # Python -__pycache__ -.venv +__pycache__/ +.venv/ .coverage .pyc -# Poetry -dist -poetry.lock -*.egg-info +# Pixi +.pixi/ # PyInstaller -build +dist/ +build/ *.spec -# Jupyter +# MkDocs +docs/site/ + +# Jupyter Notebooks .ipynb_checkpoints +# Node +node_modules/ + +# QtCreator +*.autosave +*.qmlproject.user +*.qmlproject.user.* +*.pyproject.user +*.pyproject.user.* +CMakeLists.txt.user* + +# PyCharm +.idea/ + +# VS Code +.vscode/ + # macOS .DS_Store *.app *.dmg -# Docs -docs/_build - -# VSCode -.vscode - # Misc -..* +.cache/ *.log *.zip -.ci/ -.idea/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..9a3855f4 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,61 @@ +repos: + - repo: local + hooks: + # ------------- + # Manual checks + # ------------- + - id: pixi-pyproject-check + name: pixi run pyproject-check + entry: pixi run pyproject-check + language: system + pass_filenames: false + stages: [manual] + + - id: license-headers-check + name: pixi run license-check + entry: pixi run license-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-py-lint-check + name: pixi run py-lint-check + entry: pixi run py-lint-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-py-format-check + name: pixi run py-format-check + entry: pixi run py-format-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-docstring-lint-check + name: pixi run docstring-lint-check + entry: pixi run docstring-lint-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-nonpy-format-check + name: pixi run nonpy-format-check + entry: pixi run nonpy-format-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-notebook-lint-check + name: pixi run notebook-lint-check + entry: pixi run notebook-lint-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-unit-tests + name: pixi run unit-tests + entry: pixi run unit-tests + language: system + pass_filenames: false + stages: [manual] diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 00000000..a08c3c48 --- /dev/null +++ b/.prettierignore @@ -0,0 +1,32 @@ +# Git +.git/ + +# Copier +.copier-answers*.yml + +# Pixi +.pixi +pixi.lock + +# MkDocs +docs/overrides/ +docs/site/ +docs/docs/assets/ + +# Python +.pytest_cache/ + +# MyPy +.mypy_cache/ + +# Ruff +.ruff_cache/ + +# Node +node_modules + +# Misc +.benchmarks +.cache +deps/ +tmp/ diff --git a/CHANGELOG.md b/CHANGELOG.md index 69077f1c..bb888bf6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,13 +1,14 @@ # Version 1.6.0 (1 May 2026) -Add Mighell-based handling of non-positive-variance points in fitting (issue #256). -Non-positive-variance data points are no longer forcibly discarded; instead, a -hybrid objective applies a Mighell substitution for non-positive-variance points -while using standard weighted least squares for the rest. The previous masking -behavior is available via `objective='legacy_mask'`. New `objective` parameter on -`MultiFitter`, `fit()`, and `fit_single_data_set_1d()`. +Add Mighell-based handling of non-positive-variance points in fitting +(issue #256). Non-positive-variance data points are no longer forcibly +discarded; instead, a hybrid objective applies a Mighell substitution +for non-positive-variance points while using standard weighted least +squares for the rest. The previous masking behavior is available via +`objective='legacy_mask'`. New `objective` parameter on `MultiFitter`, +`fit()`, and `fit_single_data_set_1d()`. # Version 1.3.3 (17 June 2025) -Added Chi^2 and fit status to fitting results. -Added explicit dependency on bumps version. +Added Chi^2 and fit status to fitting results. Added explicit dependency +on bumps version. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..a4ac1fbc --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,446 @@ +# Contributing to EasyReflectometry + +Thank you for your interest in contributing to **EasyReflectometry**! + +This guide explains how you can: + +- Report issues +- Contribute code +- Improve documentation +- Suggest enhancements +- Interact with the EasyScience community + +Whether you are an experienced developer or contributing for the first +time, this document walks you through the entire process step by step. + +Please make sure you follow the EasyScience organization-wide +[Code of Conduct](https://github.com/easyscience/.github/blob/master/CODE_OF_CONDUCT.md). + +--- + +## Table of Contents + +- [How to Interact With This Project](#how-to-interact-with-this-project) +- [1. Understanding the Development Model](#1-understanding-the-development-model) +- [2. Getting the Code](#2-getting-the-code) +- [3. Setting Up the Development Environment](#3-setting-up-the-development-environment) +- [4. Creating a Branch](#4-creating-a-branch) +- [5. Implementing Your Changes](#5-implementing-your-changes) +- [6. Code Quality Checks](#6-code-quality-checks) +- [7. Opening a Pull Request](#7-opening-a-pull-request) +- [8. Continuous Integration (CI)](#8-continuous-integration-ci) +- [9. Code Review](#9-code-review) +- [10. Documentation Contributions](#10-documentation-contributions) +- [11. Reporting Issues](#11-reporting-issues) +- [12. Security Issues](#12-security-issues) +- [13. Releases](#13-releases) + +--- + +## How to Interact With This Project + +If you are not planning to contribute code, you may want to: + +- 🐞 Report a bug — see [Reporting Issues](#11-reporting-issues) +- 🛡 Report a security issue — see + [Security Issues](#12-security-issues) +- 💬 Ask a question or start a discussion at + [Project Discussions](https://github.com/easyscience/reflectometry-lib/discussions) + +If you plan to contribute code or documentation, continue below. + +--- + +## 1. Understanding the Development Model + +Before you start coding, it is important to understand how development +works in this project. + +### Branching Strategy + +We use the following branches: + +- `master` — stable releases only +- `develop` — active development branch +- Short-lived branches — feature or fix branches created for a single + contribution and deleted after merge + +> [!IMPORTANT] +> +> All normal contributions must target the `develop` branch. +> +> - Do **not** open Pull Requests against `master` +> - Always create your branch from `develop` +> - Always target `develop` when opening a Pull Request + +See ADR easyscience/.github#12 for more details on the branching +strategy. + +--- + +## 2. Getting the Code + +### 2.1. If You Are an External Contributor + +If you are not a core maintainer of this repository, follow these steps. + +1. Open the repository page: + `https://github.com/easyscience/reflectometry-lib` + +2. Click the **Fork** button (top-right corner). This creates your own + copy of the repository. + +3. Clone your fork locally: + + ```bash + git clone https://github.com//reflectometry-lib.git + cd reflectometry-lib + ``` + +4. Add the original repository as `upstream`: + + ```bash + git remote add upstream https://github.com/easyscience/reflectometry-lib.git + ``` + +5. Switch to the `develop` branch and update it: + + ```bash + git fetch upstream + git checkout develop + git pull upstream develop + ``` + +If you have contributed before, make sure your local `develop` branch is +up to date before starting new work. You can update it with: + +```bash +git fetch upstream +git pull upstream develop +``` + +This ensures you are working on the latest version of the project. + +### 2.2. If You Are a Core Team Member + +Core team members can create branches directly in this repository and +therefore do not need to fork it, but the rest of the workflow remains +the same. + +--- + +## 3. Setting Up the Development Environment + +You need: + +- Git +- Pixi + +EasyScience projects use **Pixi** to manage the development environment. + +To install Pixi, follow the official instructions: +https://pixi.prefix.dev/latest/installation/ + +You do **not** need to manually install Python. Pixi automatically: + +- Creates the correct Python environment +- Installs all required dependencies +- Installs development tools (linters, formatters, test tools) + +Set up the environment: + +```bash +pixi install +pixi run post-install # Install additional tooling +``` + +After this step, your development environment is ready. + +See ADR easyscience/.github#63 for more details about using Pixi for +development. + +--- + +## 4. Creating a Branch + +Never work directly on `develop`. + +Create a new branch: + +```bash +git checkout -b my-change develop +``` + +> [!IMPORTANT] +> +> Use a clear and descriptive name, for example: +> +> - `improve-solver-speed` +> - `fix-boundary-condition` +> - `add-tutorial-example` + +Clear branch names make reviews and history easier to understand. + +--- + +## 5. Implementing Your Changes + +While developing, make small, logical commits with clear messages. + +Example: + +```bash +git add . +git commit -m "Improve performance of time integrator for large systems" +``` + +--- + +## 6. Code Quality Checks + +> [!IMPORTANT] +> +> When adding new functionality or making changes, make sure to add or +> update the following as needed: +> +> - 📘 docstrings +> - 🧪 unit tests + +Before opening a Pull Request, always run: + +```bash +pixi run check +``` + +This command: + +- Validates the pyproject.toml file +- Checks for licence headers in code files +- Identifies linting and formatting issues in Python code +- Checks docstring linting and formatting issues in Python code +- Detects formatting issues in non-Python files (MD, YAML, TOML etc.) +- Checks linting issues in Jupyter notebooks (if applicable) +- Runs unit tests + +A successful run should look like this: + +```bash +pixi run pyproject-check.......................Passed +pixi run license-check.........................Passed +pixi run py-lint-check.........................Passed +pixi run py-format-check.......................Passed +pixi run docstring-lint-check..................Passed +pixi run nonpy-format-check....................Passed +pixi run notebook-lint-check...................Passed +pixi run unit-tests............................Passed +``` + +If something fails, read the error message carefully and fix the issue. + +You can run individual checks, for example, to run only unit tests: + +```bash +pixi run unit-tests +``` + +or to run only Python linting checks: + +```bash +pixi run py-lint-check +``` + +Some formatting issues can be fixed automatically: + +```bash +pixi run fix +``` + +If everything is correctly formatted, you will see: + +```text +✅ All auto-formatting steps completed successfully! +``` + +This indicates that the auto-formatting pipeline completed successfully. +If you do not see this message and no error messages appear, try running +the command again. + +If errors are reported, resolve them and re-run: + +```bash +pixi run check +``` + +> [!IMPORTANT] +> +> All checks must pass before your Pull Request can be merged. + +If you are unsure how to fix an issue, ask for help in your Pull Request +discussion. + +--- + +## 7. Opening a Pull Request + +Push your branch: + +```bash +git push origin my-change +``` + +On GitHub: + +- Click **Compare & Pull Request** +- Ensure the base branch is `develop` +- Write a clear and concise title +- Add a description explaining what changed and why +- Add the required `[scope]` label + +### Pull Request Title + +> [!IMPORTANT] +> +> The PR title appears in release notes and changelogs. It should be +> concise and informative. + +Good examples: + +- Improve performance of time integrator for large systems +- Fix incorrect boundary condition handling in solver +- Add adaptive step-size control to ODE solver +- Add tutorial for custom model configuration +- Refactor solver API for improved readability + +### Required `[scope]` Label + +> [!IMPORTANT] +> +> Each Pull Request must include a `[scope]` label, which is used for +> automatically suggesting version bumps when preparing a new release. + +The available scopes are: + +| Label | Description | +| ----------------------- | ----------------------------------------------------------------------- | +| `[scope] bug` | Bug report or fix (major.minor.**PATCH**) | +| `[scope] documentation` | Documentation-only changes (major.minor.patch.**POST**) | +| `[scope] enhancement` | Adds or improves features (major.**MINOR**.patch) | +| `[scope] maintenance` | Code/tooling cleanup without feature or bug fix (major.minor.**PATCH**) | +| `[scope] significant` | Breaking or major changes (**MAJOR**.minor.patch) | + +See ADR easyscience/.github#33 for more details on the standardized +labeling scheme. + +--- + +## 8. Continuous Integration (CI) + +After opening a Pull Request: + +- Automated checks run automatically +- You will see green checkmarks or red crosses + +If checks fail: + +1. Open the failing check +2. Read the logs +3. Fix the issue locally +4. Run `pixi run check` +5. Push your changes + +The Pull Request updates automatically. + +--- + +## 9. Code Review + +All Pull Requests are reviewed by at least one core team member. + +Code review is collaborative and aims to improve quality. + +Do not take comments personally — they are meant to help. + +To update your PR: + +```bash +git add . +git commit -m "Address review comments" +git push +``` + +--- + +## 10. Documentation Contributions + +> [!IMPORTANT] +> +> If your change affects user-facing functionality, update the project +> documentation accordingly — specifically the `nav:` (navigation) +> structure in `mkdocs.yml` and the relevant documentation Markdown +> files in `docs/docs/`. +> +> ```text +> 📁 docs +> ├── 📁 docs - Markdown files for documentation +> │ └── ... +> └── 📄 mkdocs.yml - Configuration file (navigation, theme, etc.) +> ``` + +This may include: + +- API documentation +- Examples +- Tutorials +- Jupyter notebooks + +Preview documentation locally: + +```bash +pixi run docs-serve +``` + +Open the URL shown in the terminal to review your changes. + +--- + +## 11. Reporting Issues + +If you find a bug but cannot work on a fix, please consider opening an +issue. + +When reporting an issue, it helps to: + +- Search existing issues first. +- Provide clear reproduction steps. +- Include logs, screenshots, and environment details. + +Clear and detailed reports help maintainers investigate and resolve +issues more effectively. + +--- + +## 12. Security Issues + +> [!IMPORTANT] +> +> Please do **not** report security vulnerabilities publicly. + +If you discover a potential vulnerability, please contact the +maintainers privately so the issue can be investigated and addressed +responsibly. + +--- + +## 13. Releases + +Once your contribution is merged into `develop`, it will eventually be +included in the next stable release. + +When enough changes have accumulated in `develop`, core team members +merge `develop` into `master` to prepare a new release. The release is +then tagged and published on GitHub and PyPI. + +--- + +Thank you for contributing to EasyReflectometry and the EasyScience +ecosystem! diff --git a/LICENSE b/LICENSE index c1ee0cf3..c4e3e48e 100644 --- a/LICENSE +++ b/LICENSE @@ -1,7 +1,6 @@ BSD 3-Clause License -Copyright (c) 2024, Easyscience contributors (https://github.com/EasyScience) -All rights reserved. +Copyright (c) 2021-2026 EasyScience contributors. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: diff --git a/README.md b/README.md index 1e53cdf4..01da1ff1 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,48 @@ -![Logo](https://github.com/easyScience/EasyReflectometryLib/raw/master/docs/src/_static/logo.png) -[![CI badge](https://github.com/easyScience/EasyReflectometryLib/actions/workflows/python-ci.yml/badge.svg)](https://github.com/easyScience/easyReflectometryLib/actions/workflows/python-ci.yml) -[![PyPI badge](https://img.shields.io/pypi/v/easyreflectometry.svg)](https://pypi.python.org/pypi/easyreflectometry) -[![Quality badge](https://www.codefactor.io/repository/github/easyscience/easyreflectometrylib/badge)](https://www.codefactor.io/repository/github/easyscience/easyreflectometrylib) -[![Docs badge](https://img.shields.io/badge/docs-built-blue)](http://docs.easyreflectometry.org) +

+ + + + + + + EasyReflectometry + +

-# About +**EasyReflectometry** is a software for performing reflectometry +calculations based on a layer model and refining its parameters against +reflectometry data. -A reflectometry python package and an application. + -This repo and documentation is for the `easyreflectometry` Python package that is built on the `easyscience` [framework](https://easyscience.software). -To get more information about the application visit [`easyreflectometry.org`](https://easyreflectometry.org) +**EasyReflectometry** is developed as a Python library. -# Installation +License: +[BSD 3-Clause](https://github.com/easyscience/reflectometry-lib/blob/master/LICENSE) -```sh -python -m pip install easyreflectometry -``` +## Useful Links + +### For Users + +- 📖 + [Documentation](https://easyscience.github.io/reflectometry-lib/latest) +- 🚀 + [Getting Started](https://easyscience.github.io/reflectometry-lib/latest/introduction) +- 🧪 + [Tutorials](https://easyscience.github.io/reflectometry-lib/latest/tutorials) +- 💬 + [Get in Touch](https://easyscience.github.io/reflectometry-lib/latest/introduction/#get-in-touch) +- 🧾 + [Citation](https://easyscience.github.io/reflectometry-lib/latest/introduction/#citation) + +### For Contributors + +- 🧑‍💻 [Source Code](https://github.com/easyscience/reflectometry-lib) +- 🐞 + [Issue Tracker](https://github.com/easyscience/reflectometry-lib/issues) +- 💡 + [Discussions](https://github.com/easyscience/reflectometry-lib/discussions) +- 🤝 + [Contributing Guide](https://github.com/easyscience/reflectometry-lib/blob/master/CONTRIBUTING.md) +- 🛡 + [Code of Conduct](https://github.com/easyscience/.github/blob/master/CODE_OF_CONDUCT.md) diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 00000000..f62b13ab --- /dev/null +++ b/codecov.yml @@ -0,0 +1,13 @@ +# Codecov configuration +# https://docs.codecov.com/docs/codecovyml-reference + +coverage: + status: + project: + default: + # Make project coverage informational (won't block PR) + informational: true + patch: + default: + # Require patch coverage but with threshold + threshold: 1% diff --git a/docs/docs/api-reference/index.md b/docs/docs/api-reference/index.md new file mode 100644 index 00000000..a639b377 --- /dev/null +++ b/docs/docs/api-reference/index.md @@ -0,0 +1,8 @@ +--- +icon: material/code-braces-box +--- + +# :material-code-braces-box: API Reference + +This section contains the reference detailing the functions and modules +available in EasyReflectometry. diff --git a/docs/docs/assets/images/logo_dark.svg b/docs/docs/assets/images/logo_dark.svg new file mode 100644 index 00000000..1006baa6 --- /dev/null +++ b/docs/docs/assets/images/logo_dark.svg @@ -0,0 +1,25 @@ + + + + + + + + + + + + Logo + + + + + + + + Text + + + + + \ No newline at end of file diff --git a/docs/docs/assets/images/logo_light.svg b/docs/docs/assets/images/logo_light.svg new file mode 100644 index 00000000..4fb06ddb --- /dev/null +++ b/docs/docs/assets/images/logo_light.svg @@ -0,0 +1,25 @@ + + + + + + + + + + + + Logo + + + + + + + + Text + + + + + \ No newline at end of file diff --git a/docs/docs/assets/javascripts/extra.js b/docs/docs/assets/javascripts/extra.js new file mode 100644 index 00000000..9596ee07 --- /dev/null +++ b/docs/docs/assets/javascripts/extra.js @@ -0,0 +1,27 @@ +;(function () { + 'use strict' + + // Variables + const header = document.getElementsByTagName('header')[0] + + console.log(window.pageYOffset) + + // Hide-show header shadow + function toggleHeaderShadow() { + if (window.pageYOffset <= 0) { + header.classList.remove('md-header--shadow') + } else { + header.classList.add('md-header--shadow') + } + } + + // Onload + window.onload = function () { + toggleHeaderShadow() + } + + // Onscroll + window.onscroll = function () { + toggleHeaderShadow() + } +})() diff --git a/docs/docs/assets/javascripts/mathjax.js b/docs/docs/assets/javascripts/mathjax.js new file mode 100644 index 00000000..333524ec --- /dev/null +++ b/docs/docs/assets/javascripts/mathjax.js @@ -0,0 +1,33 @@ +window.MathJax = { + tex: { + //inlineMath: [['\\(', '\\)']], + //displayMath: [['\\[', '\\]']], + // Add support for $...$ and \(...\) delimiters + inlineMath: [ + ['$', '$'], + ['\\(', '\\)'], + ], + // Add support for $$...$$ and \[...]\ delimiters + displayMath: [ + ['$$', '$$'], + ['\\[', '\\]'], + ], + processEscapes: true, + processEnvironments: true, + }, + options: { + //ignoreHtmlClass: ".*|", + //processHtmlClass: "arithmatex" + // Skip code blocks only + skipHtmlTags: ['script', 'noscript', 'style', 'textarea', 'pre', 'code'], + // Only ignore explicit opt-out + ignoreHtmlClass: 'no-mathjax|tex2jax_ignore', + }, +} + +document$.subscribe(() => { + MathJax.startup.output.clearCache() + MathJax.typesetClear() + MathJax.texReset() + MathJax.typesetPromise() +}) diff --git a/docs/docs/assets/stylesheets/extra.css b/docs/docs/assets/stylesheets/extra.css new file mode 100644 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var(--sz-body-text-color--lightmode); /* E.g., Copy icon in code */ + --md-default-bg-color: var(--sz-body-background-color--lightmode); + + /* Code color shades */ + --md-code-bg-color: var(--sz-code-background-color--lightmode); + + /* Typeset color shades */ + --md-typeset-color: var(--sz-body-text-color--lightmode); + + /* Typeset `a` color shades */ + --md-typeset-a-color: var(--sz-link-color--lightmode); + + /* Footer color shades */ + --md-footer-fg-color: var(--sz-body-text-color--lightmode); /* E.g., Next -> */ + --md-footer-fg-color--light: var(--sz-body-text-color--lightmode); /* E.g., © 2022 EasyDiffraction, Material for MkDocs */ + --md-footer-fg-color--lighter: var(--sz-body-text-color--lightmode); /* E.g. 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+ word-break: break-word !important; +} +*/ + +/* Custom styles for the CIF files */ + +.cif { + padding-left: 1em; + padding-right: 1em; + padding-top: 1px; + padding-bottom: 1px; + background-color: var(--md-code-bg-color); + font-size: small; +} +.red { + color: var(--sz-red-color); +} +.green { + color: var(--sz-green-color); +} +.blue { + color: var(--sz-blue-color); +} +.orange { + color: var(--sz-orange-color); +} +.grey { + color: grey; +} + +/**********/ +/* Labels */ +/**********/ + +.label-cif { + padding-top: 0.5ex; + padding-bottom: 0.5ex; + padding-left: 0.9ex; + padding-right: 0.9ex; + border-radius: 1ex; + color: var(--md-default-fg-color) !important; + background-color: var(--md-code-bg-color); +} + +p .label-cif, li .label-cif { + vertical-align: 5%; + font-size: 12px; +} + +.label-cif:hover { + color: white !important; +} + +.label-experiment { + padding-top: 0.25ex; + padding-bottom: 0.6ex; + padding-left: 0.9ex; + padding-right: 0.9ex; + border-radius: 1ex; + color: var(--md-default-fg-color) !important; + background-color: rgba(55, 189, 249, 0.1); +} + +p .label-experiment, li .label-experiment { + vertical-align: 5%; + font-size: 12px; +} + +h1 .label-experiment { + padding-top: 0.05ex; + padding-bottom: 0.4ex; + padding-left: 0.9ex; + padding-right: 0.9ex; + border-radius: 0.75ex; + color: var(--md-default-fg-color) !important; + background-color: rgba(55, 189, 249, 0.1); +} + +.label-experiment:hover { + color: white !important; +} diff --git a/docs/docs/index.md b/docs/docs/index.md new file mode 100644 index 00000000..f11ef87f --- /dev/null +++ b/docs/docs/index.md @@ -0,0 +1,21 @@ +![](assets/images/logo_dark.svg#gh-dark-mode-only)![](assets/images/logo_light.svg#gh-light-mode-only) + +# Reflectometry data analysis + +Here is a brief overview of the main documentation sections: + +- [:material-information-slab-circle: Introduction](introduction/index.md) + – Provides a description of EasyReflectometry, including its purpose, + licensing, latest release details, and contact information. +- [:material-cog-box: Installation & Setup](installation-and-setup/index.md) + – Guides users through system requirements, environment configuration, + and the installation process. +- [:material-book-open-variant: User Guide](user-guide/index.md) – + Covers core concepts, key terminology, workflow steps, and essential + parameters for effective use of EasyReflectometry. +- [:material-school: Tutorials](tutorials/index.md) – Offers practical, + step-by-step examples demonstrating common workflows and data analysis + tasks. +- [:material-code-braces-box: API Reference](api-reference/index.md) – + An auto-generated reference detailing the available functions and + modules in EasyReflectometry. diff --git a/docs/docs/installation-and-setup/index.md b/docs/docs/installation-and-setup/index.md new file mode 100644 index 00000000..4baef822 --- /dev/null +++ b/docs/docs/installation-and-setup/index.md @@ -0,0 +1,282 @@ +--- +icon: material/cog-box +--- + +# :material-cog-box: Installation & Setup + +**EasyReflectometry** is a cross-platform Python library compatible with +**Python 3.11** through **3.13**. + +To install and set up EasyReflectometry, we recommend using +[**Pixi**](https://pixi.prefix.dev), a modern package manager for +Windows, macOS, and Linux. + +??? note "Main benefits of using Pixi" + + - **Ease of use**: Pixi simplifies the installation process, making it + accessible even for users with limited experience in package management. + - **Python version control**: Pixi allows specifying and managing different + Python versions for each project, ensuring compatibility. + - **Isolated environments**: Pixi creates isolated environments for each + project, preventing conflicts between different package versions. + - **PyPI and Conda support**: Pixi can install packages from both PyPI and + Conda repositories, providing access to a wide range of libraries. + +An alternative installation method using the traditional **pip** package +manager is also provided. + +## Installing with Pixi recommended { #installing-with-pixi data-toc-label="Installing with Pixi" } + +This section describes the simplest way to set up EasyReflectometry +using **Pixi**. + +#### Installing Pixi + +- Install Pixi by following the instructions on the + [official Pixi Installation Guide](https://pixi.prefix.dev/latest/installation). + +#### Setting up EasyReflectometry with Pixi + + + +- Choose a project location (local drive recommended). + + ??? warning ":fontawesome-brands-windows: Windows + OneDrive" + + We **do not recommend creating a Pixi project inside OneDrive or other + synced folders**. + + By default, Pixi creates the virtual environment inside the project + directory (in `.pixi/`). On Windows, synced folders such as OneDrive + may cause file‑system issues (e.g., path-length limitations or + restricted link operations), which can lead to unexpected install + errors or environments being recreated. + + Instead, create your project in a **local directory on your drive** + where you have full write permissions. + + + +- Initialize a new Pixi project and navigate into it: + ```txt + pixi init easyreflectometry + cd easyreflectometry + ``` +- Set the Python version for the Pixi environment (e.g., 3.13): + ```txt + pixi add python=3.13 + ``` +- Add EasyReflectometry to the Pixi environment from PyPI: + ```txt + pixi add --pypi easyreflectometry + ``` +- Add a Pixi task to run EasyReflectometry commands easily: + ```txt + pixi task add easyreflectometry "python -m easyreflectometry" + ``` + +#### Updating Pixi and EasyReflectometry + +- To update all packages in the Pixi environment, including + EasyReflectometry: + ```txt + pixi update + ``` +- To update Pixi itself to the latest version: + ```txt + pixi self-update + ``` + +#### Uninstalling Pixi + +- Follow the + [official Pixi Guide](https://pixi.prefix.dev/latest/installation/#uninstall). + +## Classical Installation + +This section describes how to install EasyReflectometry using the +traditional method with **pip**. It is assumed that you are familiar +with Python package management and virtual environments. + +### Environment Setup optional { #environment-setup data-toc-label="Environment Setup" } + +We recommend using a **virtual environment** to isolate dependencies and +avoid conflicts with system-wide packages. If any issues arise, you can +simply delete and recreate the environment. + +#### Creating and Activating a Virtual Environment: + + + +- Create a new virtual environment: + ```txt + python3 -m venv venv + ``` +- Activate the environment: + + === ":material-apple: macOS" + ```txt + . venv/bin/activate + ``` + === ":material-linux: Linux" + ```txt + . venv/bin/activate + ``` + === ":fontawesome-brands-windows: Windows" + ```txt + . venv/Scripts/activate # Windows with Unix-like shells + .\venv\Scripts\activate.bat # Windows with CMD + .\venv\Scripts\activate.ps1 # Windows with PowerShell + ``` + +- The terminal should now show `(venv)`, indicating that the virtual environment + is active. + + + +#### Deactivating and Removing the Virtual Environment: + + + +- Exit the environment: + ```txt + deactivate + ``` +- If this environment is no longer needed, delete it: + + === ":material-apple: macOS" + ```txt + rm -rf venv + ``` + === ":material-linux: Linux" + ```txt + rm -rf venv + ``` + === ":fontawesome-brands-windows: Windows" + ```txt + rmdir /s /q venv + ``` + + + +### Installing from PyPI { #from-pypi } + +EasyReflectometry is available on **PyPI (Python Package Index)** and +can be installed using `pip`. To do so, use the following command: + +```txt +pip install easyreflectometry +``` + +To install a specific version of EasyReflectometry, e.g., 1.0.3: + +```txt +pip install 'easyreflectometry==1.0.3' +``` + +To upgrade to the latest version: + +```txt +pip install --upgrade easyreflectometry +``` + +To upgrade to the latest version and force reinstallation of all +dependencies (useful if files are corrupted): + +```txt +pip install --upgrade --force-reinstall easyreflectometry +``` + +To check the installed version: + +```txt +pip show easyreflectometry +``` + +### Installing from GitHub alternative { #from-github data-toc-label="Installing from GitHub" } + +Installing unreleased versions is generally not recommended but may be +useful for testing. + +To install EasyReflectometry from the `develop` branch of GitHub, for +example: + +```txt +pip install git+https://github.com/easyscience/reflectometry-lib@develop +``` + +To include extra dependencies (e.g., dev): + +```txt +pip install 'easyreflectometry[dev] @ git+https://github.com/easyscience/reflectometry-lib@develop' +``` + +## How to Run Tutorials + +EasyReflectometry includes a collection of **Jupyter Notebook examples** +that demonstrate key functionality. These tutorials serve as +**step-by-step guides** to help users understand the data analysis +workflow. They are available as **static HTML pages** in the +[:material-school: Tutorials](../tutorials/index.md) section. + +In the next sections, we explain how to set up Jupyter and run the +tutorials interactively in two different ways: locally or online via +Google Colab. + +If you decide to run the tutorials locally, you need to download them +first. This can be done individually via the :material-download: +**Download Notebook** button available on each tutorial page, or all at +once using the command line, as shown below. + +### Run Tutorials Locally with Pixi recommended { #running-with-pixi data-toc-label="Run Tutorials Locally with Pixi" } + +- Navigate to your existing Pixi project, created as described in the + [Installing with Pixi](#installing-with-pixi) section. +- Add JupyterLab, Interactive Python shell and the Pixi kernel for + Jupyter: + ```txt + pixi add --pypi jupyterlab ipython pixi-kernel + ``` +- Download all the EasyReflectometry tutorials to the `tutorials/` + directory. +- Start the JupyterLab server in the `tutorials/` directory to access + the notebooks: + ```txt + pixi run jupyter lab tutorials/ + ``` +- Your web browser should open automatically. Click on one of the + `*.ipynb` files and select the `Python (Pixi)` kernel to get started. + +### Classical Run Tutorials Locally + +- Install Jupyter Notebook, Interactive Python shell and the IPython + kernel: + ```txt + pip install notebook ipython ipykernel + ``` +- Add the virtual environment as a Jupyter kernel: + ```txt + python -m ipykernel install --user --name=venv --display-name "EasyReflectometry Python kernel" + ``` +- Download all the EasyReflectometry tutorials to the `tutorials/` + directory. +- Start the Jupyter Notebook server in the `tutorials/` directory to + access the notebooks: + ```txt + jupyter notebook tutorials/ + ``` +- Your web browser should open automatically. Click on one of the + `*.ipynb` files and select the `EasyReflectometry Python kernel` to + get started. + +### Run Tutorials via Google Colab + +**Google Colab** lets you run Jupyter Notebooks in the cloud without any +local installation. This is the fastest way to start experimenting with +EasyReflectometry. + +- Ensure you have a **Google account**. +- Go to the **[:material-school: Tutorials](../tutorials/index.md)** + section. +- Click the :google-colab: **Open in Google Colab** button on any + tutorial. diff --git a/docs/docs/introduction/index.md b/docs/docs/introduction/index.md new file mode 100644 index 00000000..4335dfdf --- /dev/null +++ b/docs/docs/introduction/index.md @@ -0,0 +1,68 @@ +--- +icon: material/information-slab-circle +--- + +# :material-information-slab-circle: Introduction + +## Description + +**EasyReflectometry** is a software for performing reflectometry +calculations based on a layer model and refining its parameters against +reflectometry data. + +**EasyReflectometry** is developed as a Python library. + + + +## License + +**EasyReflectometry** library is released under the +[BSD 3-Clause License](https://raw.githubusercontent.com/easyscience/reflectometry-lib/master/LICENSE). + +## Releases + +The latest version of the **EasyReflectometry** library is +[{{ vars.release_version }}](https://github.com/easyscience/reflectometry-lib/releases/latest). + +For a complete list of new features, bug fixes, and improvements, see +the +[GitHub Releases page](https://github.com/easyscience/reflectometry-lib/releases). + +## Citation + +If you use **EasyReflectometry** library in your work, please cite the +specific version you used. + +All official releases of the **EasyReflectometry** library are archived +on Zenodo, each with a version-specific Digital Object Identifier (DOI). + +Citation details in various styles (e.g., APA, MLA) and formats (e.g., +BibTeX, JSON) are available on the +[Zenodo archive page](https://doi.org/10.5281/zenodo.18163581). + +## Contributing + +We welcome contributions of any kind! + +**EasyReflectometry** is intended to be a community-driven, open-source +project supported by a diverse group of contributors. + +The project is maintained by the +[European Spallation Source (ESS)](https://ess.eu). + +If you would like to report a bug or request a new feature, please use +the +[GitHub Issue Tracker](https://github.com/easyscience/reflectometry-lib/issues) +(A free GitHub account is required.) + +To contribute code, documentation, or tests, please see our +[:material-account-plus: Contributing Guidelines](https://github.com/easyscience/reflectometry-lib/blob/master/CONTRIBUTING.md) +for detailed development instructions. + +## Get in Touch + +For general questions or feedback, please contact us at +[support@easyreflectometry.org](mailto:support@easyreflectometry.org). diff --git a/docs/docs/tutorials/index.md b/docs/docs/tutorials/index.md new file mode 100644 index 00000000..e0ed567a --- /dev/null +++ b/docs/docs/tutorials/index.md @@ -0,0 +1,21 @@ +--- +icon: material/school +--- + +# :material-school: Tutorials + +This section presents a collection of **Jupyter Notebook** tutorials +that demonstrate how to use EasyReflectometry for various tasks. These +tutorials serve as self-contained, step-by-step **guides** to help users +grasp the workflow of data analysis using EasyReflectometry. + +Instructions on how to run the tutorials are provided in the +[:material-cog-box: Installation & Setup](../installation-and-setup/index.md#how-to-run-tutorials) +section of the documentation. + +The tutorials are organized into the following categories: + +## Getting Started + +- [Dummy tutorial](tutorial.ipynb) – A dummy tutorial to ensure the + tutorial infrastructure is working correctly. diff --git a/docs/docs/tutorials/tutorial.ipynb b/docs/docs/tutorials/tutorial.ipynb new file mode 100644 index 00000000..0ff94f42 --- /dev/null +++ b/docs/docs/tutorials/tutorial.ipynb @@ -0,0 +1,63 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "# Dummy Tutorial\n", + "\n", + "This is a dummy tutorial file to ensure that the tutorials section is\n", + "not empty. You can replace this file with actual tutorial content as\n", + "needed." + ] + }, + { + "cell_type": "markdown", + "id": "1", + "metadata": {}, + "source": [ + "## Import Library" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2", + "metadata": {}, + "outputs": [], + "source": [ + "import easyreflectometry" + ] + }, + { + "cell_type": "markdown", + "id": "3", + "metadata": {}, + "source": [ + "## Step 1: Blah Blah Blah" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4", + "metadata": {}, + "outputs": [], + "source": [ + "# This is a placeholder for tutorial content.\n", + "print('This is a dummy tutorial.')\n", + "print('Imported library:', easyreflectometry)" + ] + } + ], + "metadata": { + "jupytext": { + "cell_metadata_filter": "-all", + "main_language": "python", + "notebook_metadata_filter": "-all" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/docs/user-guide/index.md b/docs/docs/user-guide/index.md new file mode 100644 index 00000000..2f8ac219 --- /dev/null +++ b/docs/docs/user-guide/index.md @@ -0,0 +1,24 @@ +--- +icon: material/book-open-variant +--- + +# :material-book-open-variant: User Guide + +This section provides an overview of the **core concepts**, **key +parameters** and **workflow steps** required for using EasyReflectometry +effectively. + +Here is a brief overview of the User Guide sections: + +- [Glossary](#) – Defines common terms and labels used throughout the + documentation. +- [Concept](#) – Introduces the overall idea behind data analysis in + EasyReflectometry. +- [Data Format](#) – Explains the data structures and file formats used + by EasyReflectometry. +- [Parameters](#) – Describes how parameters are structured, named, and + accessed within the EasyReflectometry. +- [First Steps](#) – Shows how to begin using EasyReflectometry in + Python or Jupyter notebooks. +- [Analysis Workflow](#) – Breaks down the data analysis pipeline into + practical, sequential steps. diff --git a/docs/includes/abbreviations.md b/docs/includes/abbreviations.md new file mode 100644 index 00000000..682f16ff --- /dev/null +++ b/docs/includes/abbreviations.md @@ -0,0 +1,15 @@ + + +*[CIF]: Crystallographic Information File. +*[curl]: Command-line tool for transferring data with URLs. +*[GitHub]: A web-based platform for version control and collaboration. +*[Google Colab]: Cloud service that allows you to run Jupyter Notebooks in the cloud. +*[IUCr]: International Union of Crystallography. +*[Jupyter Notebook]: An open-source web application that allows you to create and share documents that contain live code, equations, visualizations, and narrative text. +*[JupyterLab]: Web-based interactive development environment for notebooks, code, and data. +*[pip]: Package installer for Python. +*[PyPI]: The Python Package Index is a repository of software for the Python programming language. +*[Conda]: Conda is a cross-platform, language-agnostic binary package manager. +*[Pixi]: A modern package manager for Windows, macOS, and Linux. + + diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml new file mode 100644 index 00000000..295600cf --- /dev/null +++ b/docs/mkdocs.yml @@ -0,0 +1,180 @@ +# Project information +site_name: EasyReflectometry Library +site_url: https://easyscience.github.io/reflectometry-lib + +# Repository +repo_url: https://github.com/easyscience/reflectometry-lib +edit_uri: edit/develop/docs/ + +# Copyright +copyright: © 2021-2026 EasyReflectometry + +# Sets the theme and theme-specific configuration +theme: + name: material + custom_dir: overrides + features: + #- content.action.edit # Temporary disable edit button (until decided on which branch to use and where to host the notebooks) + #- content.action.view + - content.code.annotate + - content.code.copy # Auto generated button to copy a code block's content + - content.tooltips + - navigation.footer + - navigation.indexes + #- navigation.instant # Instant loading, but it causes issues with rendering equations + #- navigation.sections + - navigation.top # Back-to-top button + - navigation.tracking # Anchor tracking + - search.highlight + - search.share + - search.suggest + - toc.follow + palette: + # Palette toggle for light mode + - media: '(prefers-color-scheme: light)' + scheme: default + primary: custom + toggle: + icon: fontawesome/solid/sun + name: Switch to dark mode + # Palette toggle for dark mode + - media: '(prefers-color-scheme: dark)' + scheme: slate + primary: custom + toggle: + icon: fontawesome/solid/moon + name: Switch to light mode + font: + text: Mulish + code: Roboto Mono + icon: + edit: material/file-edit-outline + favicon: assets/images/favicon.png + logo_dark_mode: assets/images/logo_dark.svg + logo_light_mode: assets/images/logo_light.svg + +# A set of key-value pairs, where the values can be any valid YAML +# construct, that will be passed to the template +extra: + generator: false # Disable `Made with Material for MkDocs` (bottom left) + social: # Extra icons in the bottom right corner + - icon: easyscience # File: overrides/.icons/easyscience.svg + link: https://easyscience.org + name: EasyScience Framework Webpage + - icon: easyreflectometry # File: overrides/.icons/easyreflectometry.svg + link: https://easyscience.github.io/reflectometry + name: EasyReflectometry Main Webpage + - icon: fontawesome/brands/github # Name as in Font Awesome + link: https://github.com/easyscience/reflectometry-lib + name: EasyReflectometry Library Source Code on GitHub + # Set custom variables to be used in Markdown and HTML files + vars: + ci_branch: !ENV CI_BRANCH + github_repository: !ENV GITHUB_REPOSITORY + release_version: !ENV RELEASE_VERSION + docs_version: !ENV DOCS_VERSION + notebooks_dir: !ENV NOTEBOOKS_DIR + # Renders a version selector in the header + version: + provider: mike + +# Customization to be included by the theme +extra_css: + - assets/stylesheets/extra.css + +extra_javascript: + - assets/javascripts/extra.js + # MathJax for rendering mathematical expressions + - assets/javascripts/mathjax.js # Custom MathJax config to ensure compatibility with mkdocs-jupyter + - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js # Official MathJax CDN + +# A list of extensions beyond the ones that MkDocs uses by default (meta, toc, tables, and fenced_code) +markdown_extensions: + - abbr + - admonition + - attr_list + - def_list + - footnotes + - pymdownx.arithmatex: # rendering of equations and integrates with MathJax or KaTeX + generic: true + - pymdownx.blocks.caption + - pymdownx.details + - pymdownx.emoji: + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg + options: + custom_icons: + - docs/overrides/.icons + - pymdownx.highlight: # whether highlighting should be carried out during build time by Pygments + use_pygments: true + pygments_lang_class: true + - pymdownx.snippets: + auto_append: + - docs/includes/abbreviations.md + - pymdownx.superfences: # whether highlighting should be carried out during build time by Pygments + custom_fences: + - name: mermaid + class: mermaid + format: !!python/name:pymdownx.superfences.fence_code_format + - pymdownx.tabbed: # enables content tabs + alternate_style: true + - pymdownx.tasklist: + custom_checkbox: true + - toc: + toc_depth: 3 + +# A list of plugins (with optional configuration settings) to use when building the site +plugins: + - autorefs + - inline-svg + - markdownextradata # Plugin that injects the mkdocs.yml extra variables into the Markdown template + - mike # Plugin that makes it easy to deploy multiple versions of the docs + - mkdocs-jupyter: + include: ['*.ipynb'] # Default: ['*.py', '*.ipynb'] + execute: false # Do not execute notebooks during build. They are expected to be pre-executed. + allow_errors: false + include_source: true + include_requirejs: true # Required for Plotly + #custom_mathjax_url: 'https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js' # See 'extra_javascript' above + ignore_h1_titles: true # Use titles defined in the nav section below + remove_tag_config: + remove_input_tags: + - hide-in-docs + - mkdocstrings: + handlers: + python: + paths: ['src'] # Change 'src' to your actual sources directory + options: + docstring_style: numpy + group_by_category: false + heading_level: 1 + show_root_heading: true + show_root_full_path: false + show_submodules: true + show_source: true + - search + +# Determines additional directories to watch when running mkdocs serve +watch: + - includes + - overrides + - ../src + +# Exclude files and folders from the global navigation +not_in_nav: | + index.md + +# Format and layout of the global navigation for the site +nav: + - Introduction: + - Introduction: introduction/index.md + - Installation & Setup: + - Installation & Setup: installation-and-setup/index.md + - User Guide: + - User Guide: user-guide/index.md + - Tutorials: + - Tutorials: tutorials/index.md + - Getting Started: + - Dummy tutorial: tutorials/tutorial.ipynb + - API Reference: + - API Reference: api-reference/index.md diff --git a/docs/overrides/.icons/app.svg b/docs/overrides/.icons/app.svg new file mode 100644 index 00000000..b4fdd4f3 --- /dev/null +++ b/docs/overrides/.icons/app.svg @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/docs/overrides/.icons/easyscience.svg b/docs/overrides/.icons/easyscience.svg new file mode 100644 index 00000000..fb514912 --- /dev/null +++ b/docs/overrides/.icons/easyscience.svg @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/overrides/.icons/google-colab.svg b/docs/overrides/.icons/google-colab.svg new file mode 100644 index 00000000..9cd9d1b0 --- /dev/null +++ b/docs/overrides/.icons/google-colab.svg @@ -0,0 +1,7 @@ + + + + + + + diff --git a/docs/overrides/main.html b/docs/overrides/main.html new file mode 100644 index 00000000..2e146827 --- /dev/null +++ b/docs/overrides/main.html @@ -0,0 +1,39 @@ +{% extends "base.html" %} + +{% block content %} + +{% if page.nb_url %} + {# Parse notebook path/URL #} + {% set parts = page.nb_url.split('/') %} + {% set tutorial_name = parts[-2] %} + {% set filename = parts[-1] %} + + {# Colab url #} + {% set base_colab_url = "https://colab.research.google.com/github/" %} + {% set colab_url = + base_colab_url ~ config.extra.vars.github_repository ~ + "/blob/gh-pages/" ~ config.extra.vars.docs_version ~ + "/tutorials/" ~ tutorial_name ~ "/" ~ filename + %} + + {# Download link: relative to the current page #} + {% set file_url = filename %} + + {# Open in Colab (absolute GitHub URL; works anywhere) #} + + {% include ".icons/google-colab.svg" %} + + + {# Download: use a RELATIVE link to the file next to this page #} + + {% include ".icons/material/download.svg" %} + +{% endif %} + +{{ super() }} +{% endblock content %} diff --git a/docs/overrides/partials/logo.html b/docs/overrides/partials/logo.html new file mode 100644 index 00000000..78fa69ca --- /dev/null +++ b/docs/overrides/partials/logo.html @@ -0,0 +1,15 @@ +{% if ( config.theme.logo_light_mode and config.theme.logo_dark_mode ) %} +logo +logo +{% elif config.theme.logo %} +logo +{% else %} {% set icon = config.theme.icon.logo or "material/library" %} {% +include ".icons/" ~ icon ~ ".svg" %} {% endif %} diff --git a/package-lock.json b/package-lock.json new file mode 100644 index 00000000..1b7139b3 --- /dev/null +++ b/package-lock.json @@ -0,0 +1,65 @@ +{ + "name": "reflectometry-lib", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "devDependencies": { + "prettier": "^3.8.3", + "prettier-plugin-toml": "^2.0.6" + } + }, + "node_modules/@taplo/core": { + "version": "0.2.0", + "resolved": "https://registry.npmjs.org/@taplo/core/-/core-0.2.0.tgz", + "integrity": "sha512-r8bl54Zj1In3QLkiW/ex694bVzpPJ9EhwqT9xkcUVODnVUGirdB1JTsmiIv0o1uwqZiwhi8xNnTOQBRQCpizrQ==", + "dev": true, + "license": "MIT" + }, + "node_modules/@taplo/lib": { + "version": "0.5.0", + "resolved": "https://registry.npmjs.org/@taplo/lib/-/lib-0.5.0.tgz", + "integrity": "sha512-+xIqpQXJco3T+VGaTTwmhxLa51qpkQxCjRwezjFZgr+l21ExlywJFcDfTrNmL6lG6tqb0h8GyJKO3UPGPtSCWg==", + "dev": true, + "license": "MIT", + "dependencies": { + "@taplo/core": "^0.2.0" + } + }, + "node_modules/prettier": { + "version": "3.8.3", + "resolved": "https://registry.npmjs.org/prettier/-/prettier-3.8.3.tgz", + "integrity": "sha512-7igPTM53cGHMW8xWuVTydi2KO233VFiTNyF5hLJqpilHfmn8C8gPf+PS7dUT64YcXFbiMGZxS9pCSxL/Dxm/Jw==", + "dev": true, + "license": "MIT", + "bin": { + "prettier": "bin/prettier.cjs" + }, + "engines": { + "node": ">=14" + }, + "funding": { + "url": "https://github.com/prettier/prettier?sponsor=1" + } + }, + "node_modules/prettier-plugin-toml": { + "version": "2.0.6", + "resolved": "https://registry.npmjs.org/prettier-plugin-toml/-/prettier-plugin-toml-2.0.6.tgz", + "integrity": "sha512-12N/wBuHa9jd/KVy9pRP20NMKxQfQLMseQCt66lIbLaPLItvGUcSIryE1eZZMJ7loSws6Ig3M2Elc2EreNh76w==", + "dev": true, + "license": "MIT", + "dependencies": { + "@taplo/lib": "^0.5.0" + }, + "engines": { + "node": ">=16.0.0" + }, + "funding": { + "url": "https://opencollective.com/unts" + }, + "peerDependencies": { + "prettier": "^3.0.3" + } + } + } +} diff --git a/package.json b/package.json new file mode 100644 index 00000000..80724263 --- /dev/null +++ b/package.json @@ -0,0 +1,6 @@ +{ + "devDependencies": { + "prettier": "^3.8.3", + "prettier-plugin-toml": "^2.0.6" + } +} diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 00000000..be073a9e --- /dev/null +++ b/pixi.lock @@ -0,0 +1,10397 @@ +version: 6 +environments: + default: + channels: + - 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This is a workaround for +# Pixi, see https://github.com/prefix-dev/pixi/issues/5667 +macos = '14.0' + +# Non-default features: + +# Set specific Python versions to be used in CI testing. + +[feature.py-min.dependencies] +python = '3.11.*' + +[feature.py-max.dependencies] +python = '3.13.*' + +# Development dependencies for local development and testing with +# editable installations. + +[feature.dev.dependencies] +nodejs = '*' # Required for Prettier (non-Python formatting) +jupyterlab = '*' # Jupyter notebooks +ipython = '*' # Interactive Python shell +pixi-kernel = '*' # Pixi Jupyter kernel + +[feature.dev.pypi-dependencies] +pip = '*' +easyreflectometry = { path = '.', editable = true, extras = ['dev'] } + +# User-like behavior for testing with pip-installed dependencies instead +# of editable installations. + +[feature.user.dependencies] +jupyterlab = '*' # Jupyter notebooks +ipython = '*' # Interactive Python shell +pixi-kernel = '*' # Pixi Jupyter kernel + +[feature.user.pypi-dependencies] +pip = '*' +easydiffraction = '*' + +############## +# ENVIRONMENTS +############## + +[environments] + +# The `default` feature is always included in all environments. +# Additional features can be specified per environment. + +# Specific environments for CI testing with different Python versions. +py-311-env = { features = ['py-min', 'dev'] } +py-313-env = { features = ['py-max', 'dev'] } + +# The `default` environment is developer-oriented for local development +# and testing with editable installation of the current package. +default = { features = ['py-max', 'dev'] } + +# The `user` environment allows testing with pip-installed dependencies +# instead of editable installation of the current package. +user = { features = ['py-max', 'user'] } + +####### +# TASKS +####### + +[tasks] + +################## +# 🧪 Testing Tasks +################## + +unit-tests = 'python -m pytest tests/unit/ --color=yes -v' +functional-tests = 'python -m pytest tests/functional/ --color=yes -v' +integration-tests = 'python -m pytest tests/integration/ --color=yes -n auto -v' +notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --color=yes -n auto -v' + +test = { depends-on = ['unit-tests'] } + +########### +# ✔️ Checks +########### + +pyproject-check = 'python -m validate_pyproject pyproject.toml' +docstring-lint-check = 'pydoclint --quiet src/' +notebook-lint-check = 'nbqa ruff docs/docs/tutorials/' +py-lint-check = 'ruff check src/ tests/ docs/docs/tutorials/' +py-format-check = 'ruff format --check src/ tests/ docs/docs/tutorials/' +nonpy-format-check = 'npx prettier --list-different --config=prettierrc.toml --ignore-unknown .' +nonpy-format-check-modified = 'python tools/nonpy_prettier_modified.py' + +check = 'pre-commit run --hook-stage manual --all-files' + +########## +# 🛠️ Fixes +########## + +docstring-transform = 'pixi run docstripy src/ -s=numpy -w' +docstring-format-fix = 'format-docstring src/' +notebook-lint-fix = 'nbqa ruff --fix docs/docs/tutorials/' +py-lint-fix = 'ruff check --fix src/ tests/ docs/docs/tutorials/' +py-lint-fix-unsafe = 'ruff check --fix --unsafe-fixes src/ tests/ docs/docs/tutorials/' +py-format-fix = 'ruff format src/ tests/ docs/docs/tutorials/' +nonpy-format-fix = 'npx prettier --write --list-different --config=prettierrc.toml --ignore-unknown .' +nonpy-format-fix-modified = 'python tools/nonpy_prettier_modified.py --write' +success-message = 'echo "✅ All auto-formatting steps completed successfully!"' + +fix = { depends-on = [ + 'docstring-format-fix', + 'py-format-fix', + 'py-lint-fix', + 'nonpy-format-fix', + 'notebook-lint-fix', + 'success-message', +] } + +#################### +# 🧮 Code Complexity +#################### + +complexity-check = 'radon cc -s src/' +complexity-check-json = 'radon cc -s -j src/' +maintainability-check = 'radon mi src/' +maintainability-check-json = 'radon mi -j src/' +raw-metrics = 'radon raw -s src/' +raw-metrics-json = 'radon raw -s -j src/' + +############# +# 📊 Coverage +############# + +unit-tests-coverage = 'pixi run unit-tests --cov=src/easyreflectometry --cov-report=term-missing' +functional-tests-coverage = 'pixi run functional-tests --cov=src/easyreflectometry --cov-report=term-missing' +integration-tests-coverage = 'pixi run integration-tests --cov=src/easyreflectometry --cov-report=term-missing' +docstring-coverage = 'interrogate -c pyproject.toml src/easyreflectometry' + +cov = { depends-on = [ + 'docstring-coverage', + 'unit-tests-coverage', + 'integration-tests-coverage', +] } + +######################## +# 📓 Notebook Management +######################## + +notebook-convert = 'jupytext docs/docs/tutorials/*.py --from py:percent --to ipynb' +notebook-strip = 'nbstripout docs/docs/tutorials/*.ipynb' +notebook-tweak = 'python tools/tweak_notebooks.py docs/docs/tutorials/' +notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --overwrite --color=yes -n auto -v' + +notebook-prepare = { depends-on = [ + #'notebook-convert', + 'notebook-strip', + #'notebook-tweak', +] } + +######################## +# 📚 Documentation Tasks +######################## + +docs-vars = "JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS='ignore::RuntimeWarning'" +docs-pre = 'pixi run docs-vars python -m mkdocs' +docs-serve = 'pixi run docs-pre serve -f docs/mkdocs.yml' +docs-serve-dirty = 'pixi run docs-serve --dirty' +docs-build = 'pixi run docs-pre build -f docs/mkdocs.yml' +docs-build-local = 'pixi run docs-build --no-directory-urls' + +docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type redirect' +docs-set-default-pre = 'mike set-default -F docs/mkdocs.yml --push --branch gh-pages' + +docs-update-assets = 'python tools/update_docs_assets.py' + +############################## +# 📦 Template Management Tasks +############################## + +copier-copy = 'copier copy gh:easyscience/templates . --data-file .copier-answers.yml --data template_type=lib' +copier-recopy = 'copier recopy --data-file .copier-answers.yml --data template_type=lib' +copier-update = 'copier update --data-file .copier-answers.yml --data template_type=lib' + +##################### +# 🪝 Pre-commit Hooks +##################### + +pre-commit-clean = 'pre-commit clean' +pre-commit-install = 'pre-commit install --hook-type pre-commit --hook-type pre-push --overwrite' +pre-commit-uninstall = 'pre-commit uninstall --hook-type pre-commit --hook-type pre-push' +pre-commit-setup = { depends-on = [ + 'pre-commit-clean', + 'pre-commit-uninstall', + 'pre-commit-install', +] } + +################# +# 🐙️ GitHub Tasks +################# + +repo-wiki = 'gh api -X PATCH repos/easyscience/reflectometry-lib -f has_wiki=false' +repo-discussions = 'gh api -X PATCH repos/easyscience/reflectometry-lib -f has_discussions=true' +repo-description = "gh api -X PATCH repos/easyscience/reflectometry-lib -f description='Reflectometry data analysis'" +repo-homepage = "gh api -X PATCH repos/easyscience/reflectometry-lib -f homepage='https://easyscience.github.io/reflectometry-lib'" +repo-config = { depends-on = [ + 'repo-wiki', + 'repo-discussions', + 'repo-description', + 'repo-homepage', +] } + +master-protection = 'gh api -X POST repos/easyscience/reflectometry-lib/rulesets --input .github/configs/rulesets-master.json' +develop-protection = 'gh api -X POST repos/easyscience/reflectometry-lib/rulesets --input .github/configs/rulesets-develop.json' +gh-pages-protection = 'gh api -X POST repos/easyscience/reflectometry-lib/rulesets --input .github/configs/rulesets-gh-pages.json' +branch-protection = { depends-on = [ + 'master-protection', + 'develop-protection', + 'gh-pages-protection', +] } + +pages-deployment = 'gh api -X POST repos/easyscience/reflectometry-lib/pages --input .github/configs/pages-deployment.json' + +github-labels = 'python tools/update_github_labels.py' + +######################### +# ⚖️ SPDX License Headers +######################### + +license-remove = 'python tools/license_headers.py remove src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude' +license-add = 'python tools/license_headers.py add src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude' +license-check = 'python tools/license_headers.py check src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude' + +#################################### +# 🚀 Other Development & Build Tasks +#################################### + +default-build = 'python -m build' +dist-build = 'python -m build --wheel --outdir dist' + +npm-config = 'npm config set registry https://registry.npmjs.org/' +prettier-install = 'npm install --no-save --no-audit --no-fund prettier prettier-plugin-toml' + +clean-pycache = "find . -type d -name '__pycache__' -prune -exec rm -rf '{}' +" + +post-install = { depends-on = [ + 'npm-config', + 'prettier-install', + #'pre-commit-setup', +] } + +########################## +# 🔗 Main Package Shortcut +########################## +easyreflectometry = 'python -m easyreflectometry' diff --git a/prettierrc.toml b/prettierrc.toml new file mode 100644 index 00000000..b98c86eb --- /dev/null +++ b/prettierrc.toml @@ -0,0 +1,22 @@ +plugins = [ + "prettier-plugin-toml", # use the TOML plugin +] + +endOfLine = 'lf' # change line endings to LF +proseWrap = 'always' # change wrapping in Markdown files +semi = false # remove semicolons +singleQuote = true # use single quotes instead of double quotes +tabWidth = 2 # change tab width to 2 spaces +useTabs = false # use spaces instead of tabs + +printWidth = 79 # wrap lines at 79 characters + +[[overrides]] +files = ["*.md"] +[overrides.options] +printWidth = 72 # wrap Markdown files at 72 characters + +[[overrides]] +files = ["*.yml", "*.yaml"] +[overrides.options] +printWidth = 88 # wrap YAML files at 88 characters diff --git a/pyproject.toml b/pyproject.toml index ec3df724..b103ef8c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,164 +1,338 @@ -[build-system] -requires = [ - "hatchling<=1.21.0", - "setuptools-git-versioning", -] -build-backend = "hatchling.build" - -[tool.setuptools-git-versioning] -enabled = true +############################### +# Configuration for the project +############################### [project] -name = "easyreflectometry" -dynamic = ["version"] -description = "A reflectometry python package built on the EasyScience framework." -readme = "README.md" -authors = [{name = "EasyScience contributors"}] -license = { file = "LICENSE" } +name = 'easyreflectometry' +dynamic = ['version'] # Use versioningit to manage the version +description = 'Reflectometry data analysis' +authors = [{ name = 'EasyScience contributors' }] +readme = 'README.md' +license = 'BSD-3-Clause' +license-files = ['LICENSE'] classifiers = [ - "License :: OSI Approved :: BSD License", - "Operating System :: OS Independent", - "Topic :: Scientific/Engineering", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "Programming Language :: Python :: 3.13", - "Development Status :: 3 - Alpha" + 'Intended Audience :: Science/Research', + 'Topic :: Scientific/Engineering', + 'License :: OSI Approved :: BSD License', + 'Operating System :: OS Independent', + 'Programming Language :: Python :: 3 :: Only', + 'Programming Language :: Python :: 3', + 'Programming Language :: Python :: 3.11', + 'Programming Language :: Python :: 3.12', + 'Programming Language :: Python :: 3.13', ] - -requires-python = ">=3.11,<3.14" - +requires-python = '>=3.11' dependencies = [ - "easyscience", - "scipp", - "refnx", - "refl1d>=1.0.0", - "orsopy", - "svglib<1.6 ; platform_system=='Linux' or sys_platform == 'darwin'", - "xhtml2pdf", - "bumps", + #'easyscience', # The base library of the EasyScience framework + 'pooch', # Data downloader ] [project.optional-dependencies] dev = [ - "build", - "codecov", - "coverage", - "coveralls", - "flake8", - "ipykernel", - "jupyter", - "jupyterlab", - "plopp", - "pooch", - "pytest", - "pytest-cov", - "ruff", - "toml", - "yapf", -] - -docs = [ - "myst_parser", - "nbsphinx", - "plopp", - "sphinx<=8.1.3", - "sphinx_autodoc_typehints", - "sphinx_book_theme", - "sphinx-copybutton", - "toml" + 'GitPython', # Interact with Git repositories + 'build', # Building the package + 'pre-commit', # Pre-commit hooks + 'jinja2', # Templating + 'nbmake', # Building notebooks + 'nbstripout', # Strip output from notebooks + 'nbqa', # Linting and formatting notebooks + 'pytest', # Testing + 'pytest-cov', # Test coverage + 'pytest-xdist', # Enable parallel testing + 'ruff', # Linting and formatting code + 'radon', # Code complexity and maintainability + 'validate-pyproject[all]', # Validate pyproject.toml + 'versioningit', # Automatic versioning from git tags + 'jupytext', # Jupyter notebook text format support + 'jupyterquiz', # Quizzes in Jupyter notebooks + 'pydoclint', # Docstring linter + 'format-docstring', # Docstring formatter + 'docstripy', # Convert docstrings to other formats + 'interrogate', # Docstring coverage checker + 'copier', # Template management + 'mike', # MkDocs: Versioned documentation support + 'mkdocs', # Static site generator + 'mkdocs-material', # Documentation framework on top of MkDocs + 'mkdocs-autorefs', # MkDocs: Auto-references support + 'mkdocs-jupyter', # MkDocs: Jupyter notebook support + 'mkdocs-plugin-inline-svg', # MkDocs: Inline SVG support + 'mkdocs-markdownextradata-plugin', # MkDocs: Markdown extra data support, such as global variables + 'mkdocstrings-python', # MkDocs: Python docstring support + 'pyyaml', # YAML parser + 'spdx-headers', # SPDX license header validation ] [project.urls] -homepage = "https://docs.easyreflectometry.org" -documentation = "https://docs.easyreflectometry.org" +Documentation = 'https://easyscience.github.io/reflectometry-lib' +'Release Notes' = 'https://github.com/easyscience/reflectometry-lib/releases' +'Source Code' = 'https://github.com/easyscience/reflectometry-lib' +'Issue Tracker' = 'https://github.com/easyscience/reflectometry-lib/issues' -[tool.hatch.version] -path = "src/easyreflectometry/__version__.py" +############################ +# Build system configuration +############################ + +[build-system] +build-backend = 'hatchling.build' +requires = ['hatchling', 'versioningit'] + +############################# +# Configuration for hatchling +############################# + +# 'hatch' -- Build system for Python +# https://hatch.pypa.io/ + +[tool.hatch.build.targets.wheel] +packages = ['src/easyreflectometry'] [tool.hatch.metadata] allow-direct-references = true -[tool.hatch.build.targets.sdist] -packages = ["src"] +[tool.hatch.version] +source = 'versioningit' # Use versioningit to manage the version -[tool.hatch.build.targets.wheel] -packages = ["src/easyreflectometry"] +################################ +# Configuration for versioningit +################################ + +# 'versioningit' -- Versioning from git tags +# https://versioningit.readthedocs.io/ + +# Versioningit generates versions from git tags, so we don't need to +# either specify them statically in pyproject.toml or save them in the +# source code. Do not use {distance} in the version format, as it +# forces a version bump for every commit, which triggers unnecessary +# pixi.lock update without any changes to the source code. + +[tool.versioningit.format] +distance = '{base_version}+dev{distance}' # example: 1.2.3.post4+dev3 +dirty = '{base_version}+dirty{distance}' # example: 0.5.8+dirty3 +distance-dirty = '{base_version}+devdirty{distance}' # example: 0.5.8+devdirty3 + +# Configure how versioningit detects versions from Git +# - 'match' ensures it only considers tags starting with 'v' +# - 'default-tag' is used as a fallback when no matching tag is found +[tool.versioningit.vcs] +method = 'git' +match = ['v*'] +default-tag = 'v999.0.0' + +################################ +# Configuration for interrogate +################################ + +# 'interrogate' -- Docstring coverage checker +# https://interrogate.readthedocs.io/en/latest/ + +[tool.interrogate] +fail-under = 0 # Minimum docstring coverage percentage to pass +verbose = 1 +#exclude = ['src/**/__init__.py'] + +####################################### +# Configuration for coverage/pytest-cov +####################################### + +# 'coverage' -- Code coverage measurement tool +# https://coverage.readthedocs.io/en/latest/ [tool.coverage.run] -source = ["src/easyreflectometry"] +branch = true # Measure branch coverage as well +source = ['src'] # Limit coverage to the source code directory + +[tool.coverage.report] +show_missing = true # Show missing lines +skip_covered = false # Skip files with 100% coverage in the report +fail_under = 0 # Minimum coverage percentage to pass + +########################## +# Configuration for pytest +########################## -[tool.github.info] -organization = 'easyScience' -repo = "easyreflectometry" +# 'pytest' -- Testing framework +# https://docs.pytest.org/en/stable/ + +[tool.pytest.ini_options] +addopts = '--import-mode=importlib' +markers = ['fast: mark test as fast (should be run on every push)'] +testpaths = ['tests'] + +######################## +# Configuration for ruff +######################## + +# 'ruff' -- Python linter and code formatter +# https://docs.astral.sh/ruff/rules/ [tool.ruff] -line-length = 127 -exclude = [ - "docs", -] +exclude = ['tmp'] +indent-width = 4 +# line-length = 99 # See also `max-line-length` in [tool.ruff.lint.pycodestyle] +line-length = 128 # See also `max-line-length` in [tool.ruff.lint.pycodestyle] +preview = true # Enable new rules that are not yet stable, like DOC + +# Formatting options for Ruff [tool.ruff.format] -quote-style = "single" +docstring-code-format = true # Whether to format code snippets in docstrings +docstring-code-line-length = 99 # Line length for code snippets in docstrings +# docstring-code-line-length = 72 # Line length for code snippets in docstrings +indent-style = 'space' # PEP 8 recommends using spaces over tabs +quote-style = 'single' # But double quotes in docstrings (PEP 8, PEP 257) -[tool.ruff.lint.per-file-ignores] -# allow asserts in test files -"*test_*.py" = ["S101"] +# Linting rules to use with Ruff [tool.ruff.lint] select = [ - # flake8 settings from existing CI setup - "E9", "F63", "F7", "F82", - # Code should be polished to fulfill all cases below - # https://docs.astral.sh/ruff/rules/ - # pycodestyle - "E", - # Pyflakes - "F", - # pyupgrade -# "UP", - # flake8-bugbear -# "B", - # flake8-simplify -# "SIM", - # isort - "I", - # flake8-bandit - "S", + # Various rules + #'C90', # https://docs.astral.sh/ruff/rules/#mccabe-c90 + #'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d + 'F', # https://docs.astral.sh/ruff/rules/#pyflakes-f + #'FLY', # https://docs.astral.sh/ruff/rules/#flynt-fly + #'FURB', # https://docs.astral.sh/ruff/rules/#refurb-furb + 'I', # https://docs.astral.sh/ruff/rules/#isort-i + #'N', # https://docs.astral.sh/ruff/rules/#pep8-naming-n + #'NPY', # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy + #'PGH', # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh + #'PERF', # https://docs.astral.sh/ruff/rules/#perflint-perf + #'RUF', # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf + #'TRY', # https://docs.astral.sh/ruff/rules/#tryceratops-try + #'UP', # https://docs.astral.sh/ruff/rules/#pyupgrade-up + # pycodestyle (E, W) rules + 'E', # https://docs.astral.sh/ruff/rules/#error-e + 'W', # https://docs.astral.sh/ruff/rules/#warning-w + # Pylint (PL) rules + #'PLC', # https://docs.astral.sh/ruff/rules/#convention-plc + #'PLE', # https://docs.astral.sh/ruff/rules/#error-ple + #'PLR', # https://docs.astral.sh/ruff/rules/#refactor-plr + #'PLW', # https://docs.astral.sh/ruff/rules/#warning-plw + # flake8 rules + #'A', # https://docs.astral.sh/ruff/rules/#flake8-builtins-a + #'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann + #'ARG', # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg + #'ASYNC', # https://docs.astral.sh/ruff/rules/#flake8-async-async + #'B', # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b + #'BLE', # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble + #'C4', # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4 + #'COM', # https://docs.astral.sh/ruff/rules/#flake8-commas-com + #'DTZ', # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz + #'EM', # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em + #'FA', # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa + #'FBT', # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt + #'FIX', # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix + #'G', # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g + #'ICN', # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn + #'INP', # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp + #'ISC', # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc + #'LOG', # https://docs.astral.sh/ruff/rules/#flake8-logging-log + #'PIE', # https://docs.astral.sh/ruff/rules/#flake8-pie-pie + #'PT', # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt + #'PTH', # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth + #'PYI', # https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi + #'RET', # https://docs.astral.sh/ruff/rules/#flake8-return-ret + #'RSE', # https://docs.astral.sh/ruff/rules/#flake8-raise-rse + 'S', # https://docs.astral.sh/ruff/rules/#flake8-bandit-s + #'SIM', # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim + #'SLF', # https://docs.astral.sh/ruff/rules/#flake8-self-slf + #'SLOT', # https://docs.astral.sh/ruff/rules/#flake8-slots-slot + #'T20', # https://docs.astral.sh/ruff/rules/#flake8-print-t20 + #'TC', # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc + #'TD', # https://docs.astral.sh/ruff/rules/#flake8-todos-td + #'TID', # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid +] + +# Exceptions to the linting rules + +# Ignore specific rules globally +ignore = [ + 'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/ + # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint] + 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc + # Disable, as [tool.format_docstring] split one-line docstrings into the canonical multi-line layout + 'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/ +] + +# Ignore specific rules in certain files or directories +[tool.ruff.lint.per-file-ignores] +'*/__init__.py' = [ + 'F401', # re-exports are intentional in __init__.py +] +'tests/**' = [ + 'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann + 'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d + 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc + 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ + 'S101', # https://docs.astral.sh/ruff/rules/assert/ ] +'docs/**' = [ + 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ + 'T201', # https://docs.astral.sh/ruff/rules/print/ +] + +# Specific options for certain rules + +[tool.ruff.lint.flake8-tidy-imports] +# Disallow all relative imports +ban-relative-imports = 'all' [tool.ruff.lint.isort] +# Forces all from imports to appear on their own line force-single-line = true -[tool.tox] -legacy_tox_ini = """ -[tox] -isolated_build = True -envlist = py{3.11,3.12,3.13} -[gh-actions] -python = - 3.11: py311 - 3.12: py312 - 3.13: py313 -[gh-actions:env] -PLATFORM = - ubuntu-latest: linux - macos-latest: macos - windows-latest: 2022 -[testenv] -passenv = - CI - GITHUB_ACTIONS - GITHUB_ACTION - GITHUB_REF - GITHUB_REPOSITORY - GITHUB_HEAD_REF - GITHUB_RUN_ID - GITHUB_SHA - COVERAGE_FILE -deps = coverage -commands = - pip install -e '.[dev]' - pytest --cov --cov-report=xml -""" +[tool.ruff.lint.mccabe] +# Cyclomatic complexity threshold (default is 10) +max-complexity = 10 + +[tool.ruff.lint.pycodestyle] +# PEP 8 line length guidance: +# https://peps.python.org/pep-0008/#maximum-line-length +# Use 99 characters as the project-wide maximum for regular code lines. +# Use 72 characters for docstrings. +max-line-length = 128 # See also `line-length` in [tool.ruff] +max-doc-length = 128 +# max-doc-length = 72 + +[tool.ruff.lint.pydocstyle] +convention = 'numpy' + +[tool.ruff.lint.pylint] +# Ruff counts `self`/`cls` in max-args; traditional pylint does not. +# Setting 6 here matches pylint's default of 5 (excluding self). +max-args = 6 +max-positional-args = 6 + +############################# +# Configuration for pydoclint +############################# + +# 'pydoclint' -- Docstring linter, a faster alternative to +# 'darglint' or 'darglint2'. +# https://pypi.org/project/pydoclint/ + +# This is a more advanced docstring linter compared to Ruff's built-in +# docstring check rules D or DOC. For example, among many other things, +# it can check that arguments in the docstring, which are used by MkDocs +# and IDEs to render parameter documentation, remain synchronized with +# the parameter declarations in the code (in function's signature). + +[tool.pydoclint] +exclude = '\.' # Temporarily disable pydoclint until we are ready +style = 'numpy' +check-style-mismatch = true +check-arg-defaults = true +allow-init-docstring = true + +#################################### +# Configuration for format-docstring +#################################### + +# 'format-docstring' -- Code formatter for docstrings +# https://github.com/jsh9/format-docstring + +[tool.format_docstring] +exclude = '\.' # Temporarily disable format-docstring until we are ready +docstring_style = 'numpy' +line_length = 72 +fix_rst_backticks = true +verbose = 'default' diff --git a/src/easyreflectometry/__init__.py b/src/easyreflectometry/__init__.py index 6de988ac..7046227e 100644 --- a/src/easyreflectometry/__init__.py +++ b/src/easyreflectometry/__init__.py @@ -1,13 +1,3 @@ -from importlib import metadata - -from .project import Project - -try: - __version__ = metadata.version(__package__ or __name__) -except metadata.PackageNotFoundError: - __version__ = '0.0.0' - -__all__ = [ - Project, - __version__, -] +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""EasyReflectometry library.""" diff --git a/src/easyreflectometry/__version__.py b/src/easyreflectometry/__version__.py index bcd8d54e..a39a2412 100644 --- a/src/easyreflectometry/__version__.py +++ b/src/easyreflectometry/__version__.py @@ -1 +1,4 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __version__ = '1.6.0' diff --git a/src/easyreflectometry/calculators/__init__.py b/src/easyreflectometry/calculators/__init__.py index 2411a89f..0df164c1 100644 --- a/src/easyreflectometry/calculators/__init__.py +++ b/src/easyreflectometry/calculators/__init__.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import traceback from .calculator_base import CalculatorBase diff --git a/src/easyreflectometry/calculators/bornagain/calculator.py b/src/easyreflectometry/calculators/bornagain/calculator.py index 06d86986..27fcfff3 100644 --- a/src/easyreflectometry/calculators/bornagain/calculator.py +++ b/src/easyreflectometry/calculators/bornagain/calculator.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' from easyscience.fitting.calculators.interface_factory import ItemContainer @@ -18,9 +21,7 @@ class BornAgain(CalculatorBase): - """ - Calculator for BornAgain - """ + """Calculator for BornAgain.""" name = 'BornAgain' @@ -45,23 +46,26 @@ class BornAgain(CalculatorBase): } def __init__(self): + """Init function.""" super().__init__() self._wrapper = BornAgainWrapper() def reset_storage(self) -> None: - """ - Reset the storage area of the calculator - """ + """Reset the storage area of the calculator.""" self._wrapper.reset_storage() def create(self, model: Material | Layer | Multilayer | Model) -> list[ItemContainer]: - """ - Creation function + """Creation function. - :param model: Object to be created - :type model: Union[Material, Layer, Item, Model] - :return: Item containers of the objects - :rtype: List[ItemContainer] + Parameters + ---------- + model : Material | Layer | Multilayer | Model + Object to be created. + + Returns + ------- + List[ItemContainer] + Item containers of the objects. """ r_list = [] t_ = type(model) @@ -130,52 +134,61 @@ def create(self, model: Material | Layer | Multilayer | Model) -> list[ItemConta return r_list def assign_material_to_layer(self, material_id: int, layer_id: int) -> None: - """ - Assign a material to a layer. - - :param material_name: The material name - :type material_name: str - :param layer_name: The layer name - :type layer_name: str + """Assign a material to a layer. + + Parameters + ---------- + layer_id : int + material_id : int + material_name : str + The material name. + layer_name : str + The layer name. """ self._wrapper.assign_material_to_layer(material_id, layer_id) def add_layer_to_item(self, layer_id: int, item_id: int) -> None: - """ - Add a layer to the item stack - - :param item_id: The item id - :type item_id: int - :param layer_id: The layer id - :type layer_id: int + """Add a layer to the item stack. + + Parameters + ---------- + item_id : int + The item id. + layer_id : int + The layer id. """ self._wrapper.add_layer_to_item(layer_id, item_id) def remove_layer_from_item(self, layer_id: int, item_id: int) -> None: - """ - Remove a layer from an item stack - - :param item_id: The item id - :param layer_id: The layer id + """Remove a layer from an item stack. + + Parameters + ---------- + item_id : int + The item id. + layer_id : int + The layer id. """ self._wrapper.remove_layer_from_item(layer_id, item_id) def add_item_to_model(self, item_id: int) -> None: - """ - Add a layer to the item stack + """Add a layer to the item stack. - :param item_id: The item id - :type item_id: int + Parameters + ---------- + item_id : int + The item id. """ self._wrapper.add_item(item_id) def remove_item_from_model(self, item_id: int) -> None: - """ - Remove a layer from the item stack - - :param item_id: The item id - :type item_id: int - :param layer_id: The layer id - :type layer_id: int + """Remove a layer from the item stack. + + Parameters + ---------- + item_id : int + The item id. + layer_id : int + The layer id. """ self._wrapper.remove_item(item_id) diff --git a/src/easyreflectometry/calculators/bornagain/wrapper.py b/src/easyreflectometry/calculators/bornagain/wrapper.py index 5ad3b985..8dc2fe33 100644 --- a/src/easyreflectometry/calculators/bornagain/wrapper.py +++ b/src/easyreflectometry/calculators/bornagain/wrapper.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' import bornagain as ba @@ -14,6 +17,7 @@ class BornAgainWrapper(WrapperBase): def __init__(self): + """Init function.""" super().__init__() self.storage = { 'layer_material': {}, @@ -24,9 +28,7 @@ def __init__(self): } def reset_storage(self): - """ - Reset the storage area to blank. - """ + """Reset the storage area to blank.""" super().reset_storage() self.storage = { 'layer_material': {}, @@ -37,20 +39,23 @@ def reset_storage(self): } def create_material(self, name): - """ - Create a material using SLD. + """Create a material using SLD. - :param name: The name of the material - :type name: str + Parameters + ---------- + name : str + The name of the material. """ self.storage['material'][name] = ba.MaterialBySLD(str(name), 0.0, 0.0) def update_material(self, name, **kwargs): - """ - Update a material. + """Update a material. - :param name: The name of the material - :type name: str + Parameters + ---------- + **kwargs : + name : str + The name of the material. """ current_value = self.storage['material'][name].materialData() real = current_value.real @@ -64,40 +69,48 @@ def update_material(self, name, **kwargs): self.storage['material'][name] = ba.MaterialBySLD(str(name), real, imag) def get_material_value(self, name, key): - """ - A function to get a given material value - - :param name: The material name - :type name: str - :param key: The given value keys - :type name: str - :return: The desired value - :rtype: float + """A function to get a given material value. + + Parameters + ---------- + name : str + The material name. + key : str + The given value keys. + + Returns + ------- + float + The desired value. """ current_value = self.storage['material'][name].materialData() return getattr(current_value, key) / 1e-6 def create_layer(self, name): - """ - Create a layer using Slab. + """Create a layer using Slab. - :param name: The name of the layer - :type name: str + Parameters + ---------- + name : str + The name of the layer. """ self.storage['layer'][name] = ba.Layer(ba.MaterialBySLD('A', 0, 0)) self.storage['roughness'][name] = ba.LayerRoughness() def update_layer(self, name, **kwargs): - """ - Update a layer in a given item. + """Update a layer in a given item. - :param name: The layer name - :type name: str + Parameters + ---------- + **kwargs : + name : str + The layer name. """ if 'thickness' in kwargs.keys(): thickness = kwargs['thickness'] self.storage['layer'][name] = ba.Layer( - self.storage['material'][self.storage['layer_material'][name]], thickness * ba.angstrom + self.storage['material'][self.storage['layer_material'][name]], + thickness * ba.angstrom, ) if 'sigma' in kwargs.keys(): sigma = kwargs['sigma'] @@ -105,15 +118,19 @@ def update_layer(self, name, **kwargs): self.storage['roughness'][name].setSigma(sigma * ba.angstrom) def get_layer_value(self, name, key): - """ - A function to get a given layer value - - :param name: The layer name - :type name: str - :param key: The given value keys - :type name: str - :return: The desired value - :rtype: float + """A function to get a given layer value. + + Parameters + ---------- + name : str + The layer name. + key : str + The given value keys. + + Returns + ------- + float + The desired value. """ layer = self.storage['layer'][name] roughness = self.storage['roughness'][name] @@ -123,43 +140,48 @@ def get_layer_value(self, name, key): return roughness.getSigma() / ba.angstrom def create_item(self, name): - """ - Create an item. + """Create an item. - :param name: The name of the item - :type name: str + Parameters + ---------- + name : str + The name of the item. """ self.storage['item'][name] = [] self.storage['item_repeats'][name] = 1 def update_item(self, name, **kwargs): - """ - Update a layer. + """Update a layer. - :param name: The item name - :type name: str + Parameters + ---------- + **kwargs : + name : str + The item name. """ if 'repeats' in kwargs.keys(): self.storage['item_repeats'][name] = kwargs['repeats'] def get_item_value(self, name, key): - """ - A function to get a given item value - - :param name: The item name - :type name: str - :param key: The given value keys - :type name: str - :return: The desired value - :rtype: float + """A function to get a given item value. + + Parameters + ---------- + name : str + The item name. + key : str + The given value keys. + + Returns + ------- + float + The desired value. """ if key == 'repeats': return self.storage['item_repeats'][name] def create_model(self): - """ - Create a model for analysis - """ + """Create a model for analysis.""" self.storage['model'] = ba.Multilayer() self.storage['model'].setRoughnessModel(ba.RoughnessModel.NEVOT_CROCE) self.storage['model_items'] = [] @@ -168,65 +190,72 @@ def create_model(self): self.storage['model_parameters']['resolution'] = 0 def update_model(self, name, **kwargs): - """ - Update the non-structural parameters of the model - """ + """Update the non-structural parameters of the model.""" model = self.storage[name + '_parameters'] for key in kwargs.keys(): model[key] = kwargs[key] def get_model_value(self, name, key): - """ - A function to get a given model value + """A function to get a given model value. + + Parameters + ---------- + name : + key : str + The given value keys. - :param key: The given value keys - :type name: str - :return: The desired value - :rtype: float + Returns + ------- + float + The desired value. """ model = self.storage[name + '_parameters'] return model[key] def assign_material_to_layer(self, material_name, layer_name): - """ - Assign a material to a layer. + """Assign a material to a layer. - :param material_name: The material name - :type material_name: str - :param layer_name: The layer name - :type layer_name: str + Parameters + ---------- + material_name : str + The material name. + layer_name : str + The layer name. """ self.storage['layer_material'][layer_name] = material_name def add_layer_to_item(self, layer_name, item_name): - """ - Create a layer from the material of the same name, in a given item. + """Create a layer from the material of the same name, in a given item. - :param layer_name: The layer name - :type layer_name: int - :param item_name: The item name - :type item_name: int + Parameters + ---------- + layer_name : int + The layer name. + item_name : int + The item name. """ item = self.storage['item'][item_name] item.append(layer_name) def add_item(self, item_name): - """ - Add an item to the model. + """Add an item to the model. - :param item_name: items to add to model - :type item_name: str + Parameters + ---------- + item_name : str + Items to add to model. """ self.storage['model_items'].append(item_name) def remove_layer_from_item(self, layer_name, item_name): - """ - Remove a layer in a given item. + """Remove a layer in a given item. - :param layer_name: The layer name - :type layer_name: int - :param item_name: The item name - :type item_name: int + Parameters + ---------- + layer_name : int + The layer name. + item_name : int + The item name. """ layers_idx = self.storage['item'][item_name].index(layer_name) del self.storage['layer'][layer_name] @@ -234,11 +263,12 @@ def remove_layer_from_item(self, layer_name, item_name): del self.storage['layer_material'][layer_name] def remove_item(self, item_name): - """ - Remove a given item. + """Remove a given item. - :param item_name: The item name - :type item_name: int + Parameters + ---------- + item_name : int + The item name. """ item_idx = self.storage['model_items'].index(item_name) del self.storage['model_items'][item_idx] @@ -250,9 +280,17 @@ def remove_item(self, item_name): def calculate(self, q_array: np.ndarray) -> np.ndarray: """For a given q array calculate the corresponding reflectivity. - :param q_array: array of data points to be calculated - :param model_name: the model name - :return: reflectivity calculated at q + Parameters + ---------- + q_array : np.ndarray + Array of data points to be calculated. + model_name : + The model name. + + Returns + ------- + np.ndarray + Reflectivity calculated at q. """ # 3.5 sigma to sync with refnx n_sig = 3.5 @@ -261,7 +299,8 @@ def calculate(self, q_array: np.ndarray) -> np.ndarray: scan = ba.QSpecScan(q_array / ba.angstrom) scan.setAbsoluteQResolution( - distr, q_array / ba.angstrom * (self.storage['model_parameters']['resolution'] * 0.5 / 100) + distr, + q_array / ba.angstrom * (self.storage['model_parameters']['resolution'] * 0.5 / 100), ) simulation = ba.SpecularSimulation() @@ -286,13 +325,14 @@ def calculate(self, q_array: np.ndarray) -> np.ndarray: ) def sld_profile(self) -> np.ndarray: - """ - Return the scattering length density profile. + """Return the scattering length density profile. This is borrowed from the refnx implementation of the scattering length density. - :return: z and sld(z) - :rtype: tuple[np.ndarray, np.ndarray] + Returns + ------- + tuple[np.ndarray, np.ndarray] + Z and sld(z). """ number_of_layers = 0 for i in self.storage['model_items']: @@ -331,6 +371,7 @@ def sld_profile(self) -> np.ndarray: # use erf for roughness function, but step if the roughness is zero def step(z, scale=1, loc=0): + """Step function.""" new_z = z - loc f = np.ones_like(new_z) * 0.5 f[new_z <= -scale] = 0 diff --git a/src/easyreflectometry/calculators/calculator_base.py b/src/easyreflectometry/calculators/calculator_base.py index 7d1314cd..57d30224 100644 --- a/src/easyreflectometry/calculators/calculator_base.py +++ b/src/easyreflectometry/calculators/calculator_base.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from __future__ import annotations from abc import ABCMeta @@ -19,9 +22,7 @@ class CalculatorBase(SerializerComponent, metaclass=ABCMeta): - """ - This class is a template and defines all properties that a calculator should have. - """ + """This class is a template and defines all properties that a calculator should have.""" _calculators: list[CalculatorBase] = [] # class variable to store all calculators _material_link: dict[str, str] @@ -30,27 +31,36 @@ class CalculatorBase(SerializerComponent, metaclass=ABCMeta): _model_link: dict[str, str] def __init_subclass__(cls, is_abstract: bool = False, **kwargs) -> None: - r"""Initialise all subclasses so that they can be created in the factory - - :param is_abstract: Is this a subclass which shouldn't be dded - :param kwargs: key word arguments + r"""Initialise all subclasses so that they can be created in the factory. + + Parameters + ---------- + cls : + is_abstract : bool, optional + Is this a subclass which shouldn't be dded. By default, False. + **kwargs : + Key word arguments. """ super().__init_subclass__(**kwargs) if not is_abstract: cls._calculators.append(cls) def __init__(self): + """Init function.""" self._namespace = {} self._wrapper: WrapperBase def reset_storage(self) -> None: - """Reset the storage area of the calculator""" + r"""Reset the storage area of the calculato.""" self._wrapper.reset_storage() def create(self, model: Material | Layer | Multilayer | Model) -> list[ItemContainer]: - """Creation function + """Creation function. - :param model: Object to be created + Parameters + ---------- + model : Material | Layer | Multilayer | Model + Object to be created. """ r_list = [] t_ = type(model) @@ -122,72 +132,106 @@ def create(self, model: Material | Layer | Multilayer | Model) -> list[ItemConta def assign_material_to_layer(self, material_id: str, layer_id: str) -> None: """Assign a material to a layer. - :param material_id: The material name - :param layer_id: The layer name + Parameters + ---------- + material_id : str + The material name. + layer_id : str + The layer name. """ self._wrapper.assign_material_to_layer(material_id, layer_id) def add_layer_to_item(self, layer_id: str, item_id: str) -> None: - """Add a layer to the item stack - - :param item_id: The item id - :param layer_id: The layer id + """Add a layer to the item stack. + + Parameters + ---------- + item_id : str + The item id. + layer_id : str + The layer id. """ self._wrapper.add_layer_to_item(layer_id, item_id) def remove_layer_from_item(self, layer_id: str, item_id: str) -> None: - """Remove a layer from an item stack - - :param item_id: The item id - :param layer_id: The layer id + """Remove a layer from an item stack. + + Parameters + ---------- + item_id : str + The item id. + layer_id : str + The layer id. """ self._wrapper.remove_layer_from_item(layer_id, item_id) def add_item_to_model(self, item_id: str, model_id: str) -> None: - """Add a layer to the item stack - - :param item_id: The item id - :param model_id: The model id + """Add a layer to the item stack. + + Parameters + ---------- + item_id : str + The item id. + model_id : str + The model id. """ self._wrapper.add_item(item_id, model_id) def remove_item_from_model(self, item_id: str, model_id: str) -> None: - """Remove an item from the model - - :param item_id: The item id - :param model_id: The model id + """Remove an item from the model. + + Parameters + ---------- + item_id : str + The item id. + model_id : str + The model id. """ self._wrapper.remove_item(item_id, model_id) def reflectity_profile(self, x_array: np.ndarray, model_id: str) -> np.ndarray: """Determines the reflectivity profile for the given range and model. - :param x_array: points to be calculated at - :param model_id: The model id + Parameters + ---------- + x_array : np.ndarray + Points to be calculated at. + model_id : str + The model id. """ return self._wrapper.calculate(x_array, model_id) def sld_profile(self, model_id: str) -> tuple[np.ndarray, np.ndarray]: - """ - Return the scattering length density profile. + """Return the scattering length density profile. - :param model_id: The model id - :return: z and sld(z) + Parameters + ---------- + model_id : str + The model id. + + Returns + ------- + tuple[np.ndarray, np.ndarray] + Z and sld(z). """ return self._wrapper.sld_profile(model_id) def set_resolution_function(self, resolution_function: Callable[[np.array], np.array]) -> None: + """Set resolution function.""" return self._wrapper.set_resolution_function(resolution_function) @property def include_magnetism(self): + """Include magnetism.""" return self._wrapper.magnetism @include_magnetism.setter def include_magnetism(self, magnetism: bool): - """ - Set the magnetism flag for the calculator + """Set the magnetism flag for the calculator. - :param magnetism: True if the calculator should include magnetism + Parameters + ---------- + magnetism : bool + True if the calculator should include magnetism. """ self._wrapper.magnetism = magnetism diff --git a/src/easyreflectometry/calculators/factory.py b/src/easyreflectometry/calculators/factory.py index 15e996fd..c3e1479c 100644 --- a/src/easyreflectometry/calculators/factory.py +++ b/src/easyreflectometry/calculators/factory.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/wardsimon' from typing import Callable @@ -8,16 +11,20 @@ class CalculatorFactory(InterfaceFactoryTemplate): def __init__(self): + """Init function.""" super().__init__(interface_list=CalculatorBase._calculators) def reset_storage(self) -> None: + """Reset storage.""" return self().reset_storage() def sld_profile(self, model_id: str) -> tuple: + """Sld profile.""" return self().sld_profile(model_id) @property def fit_func(self) -> Callable: + """Fit func.""" """ Pass through to the underlying interfaces fitting function. @@ -32,6 +39,7 @@ def fit_func(self) -> Callable: #""" def __fit_func(*args, **kwargs): + """Fit func.""" return self().reflectity_profile(*args, **kwargs) return __fit_func diff --git a/src/easyreflectometry/calculators/refl1d/calculator.py b/src/easyreflectometry/calculators/refl1d/calculator.py index a472b7b5..5532a0fd 100644 --- a/src/easyreflectometry/calculators/refl1d/calculator.py +++ b/src/easyreflectometry/calculators/refl1d/calculator.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' from ..calculator_base import CalculatorBase @@ -5,9 +8,7 @@ class Refl1d(CalculatorBase): - """ - Calculator for refl1 - """ + """Calculator for refl1.""" name = 'refl1d' @@ -31,5 +32,6 @@ class Refl1d(CalculatorBase): } def __init__(self): + """Init function.""" super().__init__() self._wrapper = Refl1dWrapper() diff --git a/src/easyreflectometry/calculators/refl1d/wrapper.py b/src/easyreflectometry/calculators/refl1d/wrapper.py index e47cf052..78cac9a8 100644 --- a/src/easyreflectometry/calculators/refl1d/wrapper.py +++ b/src/easyreflectometry/calculators/refl1d/wrapper.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' from typing import Tuple @@ -17,18 +20,22 @@ class Refl1dWrapper(WrapperBase): def create_material(self, name: str): - """ - Create a material using SLD. + """Create a material using SLD. - :param name: The name of the material + Parameters + ---------- + name : str + The name of the material. """ self.storage['material'][name] = names.SLD(str(name)) def create_layer(self, name: str): - """ - Create a layer using Slab. + """Create a layer using Slab. - :param name: The name of the layer + Parameters + ---------- + name : str + The name of the layer. """ if self._magnetism: magnetism = names.Magnetism(rhoM=0.0, thetaM=0.0) @@ -37,10 +44,12 @@ def create_layer(self, name: str): self.storage['layer'][name] = names.Slab(name=str(name), magnetism=magnetism) def create_item(self, name: str): - """ - Create an item using Repeat. + """Create an item using Repeat. - :param name: The name of the item + Parameters + ---------- + name : str + The name of the item. """ self.storage['item'][name] = Repeat(names.Stack(names.Slab(names.SLD(), thickness=0, interface=0)), name=str(name)) del self.storage['item'][name].stack[0] @@ -48,8 +57,11 @@ def create_item(self, name: str): def update_layer(self, name: str, **kwargs): """Update a layer in a given item. - :param name: The layer name. - :param kwargs: + Parameters + ---------- + name : str + The layer name. + **kwargs : """ kwargs_no_magnetism = {k: v for k, v in kwargs.items() if k != 'magnetism_rhoM' and k != 'magnetism_thetaM'} super().update_layer(name, **kwargs_no_magnetism) @@ -58,10 +70,14 @@ def update_layer(self, name: str, **kwargs): self.storage['layer'][name].magnetism = magnetism def get_layer_value(self, name: str, key: str) -> float: - """A function to get a given layer value - - :param name: The layer name - :param key: The given value keys + """A function to get a given layer value. + + Parameters + ---------- + name : str + The layer name. + key : str + The given value keys. """ if key in ['magnetism_rhoM', 'magnetism_thetaM']: return getattr( @@ -70,78 +86,105 @@ def get_layer_value(self, name: str, key: str) -> float: return super().get_layer_value(name, key) def create_model(self, name: str): - """ - Create a model for analysis + """Create a model for analysis. - :param name: Name for the model + Parameters + ---------- + name : str + Name for the model. """ self.storage['model'][name] = {'scale': 1, 'bkg': 0, 'items': []} def update_model(self, name: str, **kwargs): - """ - Update the non-structural parameters of the model + """Update the non-structural parameters of the model. - :param name: Name of the model + Parameters + ---------- + **kwargs : + name : str + Name of the model. """ model = self.storage['model'][name] for key in kwargs.keys(): model[key] = kwargs[key] def get_model_value(self, name: str, key: str) -> float: - """ - A function to get a given model value - - :param name: Name of the model - :param key: The given value keys - :return: The desired value + """A function to get a given model value. + + Parameters + ---------- + name : str + Name of the model. + key : str + The given value keys. + + Returns + ------- + float + The desired value. """ model = self.storage['model'][name] return model[key] def assign_material_to_layer(self, material_name: str, layer_name: str): - """ - Assign a material to a layer. - - :param material_name: The material name - :param layer_name: The layer name + """Assign a material to a layer. + + Parameters + ---------- + material_name : str + The material name. + layer_name : str + The layer name. """ self.storage['layer'][layer_name].material = self.storage['material'][material_name] def add_layer_to_item(self, layer_name: str, item_name: str): - """ - Create a layer from the material of the same name, in a given item. - - :param layer_name: The layer name - :param item_name: The item name + """Create a layer from the material of the same name, in a given item. + + Parameters + ---------- + layer_name : str + The layer name. + item_name : str + The item name. """ item = self.storage['item'][item_name] item.stack.add(self.storage['layer'][layer_name]) def add_item(self, item_name: str, model_name: str): - """ - Add an item to the model. - - :param item_name: items to add to model - :param model_name: name for the model + """Add an item to the model. + + Parameters + ---------- + item_name : str + Items to add to model. + model_name : str + Name for the model. """ self.storage['model'][model_name]['items'].append(self.storage['item'][item_name]) def remove_layer_from_item(self, layer_name: str, item_name: str): - """ - Remove a layer in a given item. - - :param layer_name: The layer name - :param item_name: The item name + """Remove a layer in a given item. + + Parameters + ---------- + layer_name : str + The layer name. + item_name : str + The item name. """ layer_idx = list(self.storage['item'][item_name].stack).index(self.storage['layer'][layer_name]) del self.storage['item'][item_name].stack[layer_idx] def remove_item(self, item_name: str, model_name: str): - """ - Remove a given item. - - :param item_name: The item name - :param model_name: The model name + """Remove a given item. + + Parameters + ---------- + item_name : str + The item name. + model_name : str + The model name. """ item_idx = self.storage['model'][model_name]['items'].index(self.storage['item'][item_name]) del self.storage['model'][model_name]['items'][item_idx] @@ -150,9 +193,17 @@ def remove_item(self, item_name: str, model_name: str): def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray: """For a given q array calculate the corresponding reflectivity. - :param q_array: array of data points to be calculated - :param model_name: the model name - :return: reflectivity calculated at q + Parameters + ---------- + q_array : np.ndarray + Array of data points to be calculated. + model_name : str + The model name. + + Returns + ------- + np.ndarray + Reflectivity calculated at q. """ sample = _build_sample(self.storage, model_name) dq_array = self._resolution_function.smearing(q_array) @@ -197,11 +248,17 @@ def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray: return reflectivity def sld_profile(self, model_name: str) -> Tuple[np.ndarray, np.ndarray]: - """ - Return the scattering length density profile. + """Return the scattering length density profile. + + Parameters + ---------- + model_name : str + The model name. + + Returns + ------- - :param model_name: the model name - :return: z and sld(z) + Z and sld(z). """ sample = _build_sample(self.storage, model_name) probe = _get_probe( @@ -216,6 +273,7 @@ def sld_profile(self, model_name: str) -> Tuple[np.ndarray, np.ndarray]: def _get_oversampling_q(q_array: np.ndarray, dq_array: np.ndarray, oversampling_factor: int) -> np.ndarray: + """Get oversampling q.""" argmin = np.argmin(q_array) # index of the smallest q element argmax = np.argmax(q_array) # index of the largest q element return np.linspace( @@ -233,6 +291,7 @@ def _get_probe( oversampling_factor: int = 1, magnetism: bool = False, ) -> names.QProbe: + """Get probe.""" probe = names.QProbe( Q=q_array, dQ=dq_array, @@ -258,6 +317,7 @@ def _get_polarized_probe( oversampling_factor: int = 1, all_polarizations: bool = False, ) -> names.PolarizedNeutronQProbe: + """Get polarized probe.""" four_probes = [] for i in range(4): if i == 0 or all_polarizations: @@ -281,6 +341,7 @@ def _get_polarized_probe( def _build_sample(storage: dict, model_name: str) -> names.Stack: + """Build sample.""" sample = names.Stack() # -1 to reverse the order for i in storage['model'][model_name]['items'][::-1]: diff --git a/src/easyreflectometry/calculators/refnx/calculator.py b/src/easyreflectometry/calculators/refnx/calculator.py index 2a5b45b0..defe40ae 100644 --- a/src/easyreflectometry/calculators/refnx/calculator.py +++ b/src/easyreflectometry/calculators/refnx/calculator.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' from ..calculator_base import CalculatorBase @@ -5,9 +8,7 @@ class Refnx(CalculatorBase): - """ - Calculator for refnx - """ + """Calculator for refnx.""" name = 'refnx' @@ -31,5 +32,6 @@ class Refnx(CalculatorBase): } def __init__(self): + """Init function.""" super().__init__() self._wrapper = RefnxWrapper() diff --git a/src/easyreflectometry/calculators/refnx/wrapper.py b/src/easyreflectometry/calculators/refnx/wrapper.py index d2290877..345e902a 100644 --- a/src/easyreflectometry/calculators/refnx/wrapper.py +++ b/src/easyreflectometry/calculators/refnx/wrapper.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' from typing import Tuple @@ -13,53 +16,68 @@ class RefnxWrapper(WrapperBase): @property def include_magnetism(self) -> bool: + """Include magnetism.""" return self._magnetism @include_magnetism.setter def include_magnetism(self, magnetism: bool) -> None: """Set the magnetism flag. - :param magnetism: The magnetism flag + Parameters + ---------- + magnetism : bool + The magnetism flag. """ raise NotImplementedError('Magnetism is not supported by refnx') def create_material(self, name: str): - """ - Create a material using SLD. + """Create a material using SLD. - :param name: The name of the material + Parameters + ---------- + name : str + The name of the material. """ self.storage['material'][name] = reflect.SLD(0, name=name) def create_layer(self, name: str): - """ - Create a layer using Slab. + """Create a layer using Slab. - :param name: The name of the layer + Parameters + ---------- + name : str + The name of the layer. """ self.storage['layer'][name] = reflect.Slab(0, 0, 0, name=name) def create_item(self, name: str): - """ - Create an item using Stack. + """Create an item using Stack. - :param name: The name of the item + Parameters + ---------- + name : str + The name of the item. """ self.storage['item'][name] = reflect.Stack(name=name) def create_model(self, name: str): - """ - Create a model for analysis + """Create a model for analysis. - :param name: Name for the model + Parameters + ---------- + name : str + Name for the model. """ self.storage['model'][name] = reflect.ReflectModel(reflect.Structure()) def update_model(self, name: str, **kwargs): - """ - Update the non-structural parameters of the model + """Update the non-structural parameters of the model. - :param name: Name for the model + Parameters + ---------- + **kwargs : + name : str + Name for the model. """ model = self.storage['model'][name] for key in kwargs.keys(): @@ -67,61 +85,83 @@ def update_model(self, name: str, **kwargs): setattr(item, 'value', kwargs[key]) def get_model_value(self, name: str, key: str) -> float: - """ - A function to get a given model value + """A function to get a given model value. + + Parameters + ---------- + name : str + Name for the model. + key : str + The given value keys. - :param name: Name for the model - :param key: The given value keys - :return: The desired value + Returns + ------- + float + The desired value. """ model = self.storage['model'][name] item = getattr(model, key) return getattr(item, 'value') def assign_material_to_layer(self, material_name: str, layer_name: str): - """ - Assign a material to a layer. + """Assign a material to a layer. - :param material_name: The material name - :param layer_name: The layer name + Parameters + ---------- + material_name : str + The material name. + layer_name : str + The layer name. """ self.storage['layer'][layer_name].sld = self.storage['material'][material_name] def add_layer_to_item(self, layer_name: str, item_name: str): - """ - Create a layer from the material of the same name, in a given item. + """Create a layer from the material of the same name, in a given item. - :param layer_name: The layer name - :param item_name: The item name + Parameters + ---------- + layer_name : str + The layer name. + item_name : str + The item name. """ item = self.storage['item'][item_name] item.append(self.storage['layer'][layer_name]) def add_item(self, item_name: str, model_name: str): - """ - Add an item to the model. + """Add an item to the model. - :param item_name: items to add to model - :param model_name: Name for the model + Parameters + ---------- + item_name : str + Items to add to model. + model_name : str + Name for the model. """ self.storage['model'][model_name].structure.components.append(self.storage['item'][item_name]) def remove_layer_from_item(self, layer_name: str, item_name: str): - """ - Remove a layer in a given item. + """Remove a layer in a given item. - :param layer_name: The layer name - :param item_name: The item name + Parameters + ---------- + layer_name : str + The layer name. + item_name : str + The item name. """ layer_idx = self.storage['item'][item_name].components.index(self.storage['layer'][layer_name]) del self.storage['item'][item_name].components[layer_idx] def remove_item(self, item_name: str, model_name: str): - """ - Remove a given item. + """Remove a given item. - :param item_name: The item name - :param model_name: Name of the model + Parameters + ---------- + item_name : str + The item name. + model_name : str + Name of the model. """ item_idx = self.storage['model'][model_name].structure.components.index(self.storage['item'][item_name]) del self.storage['model'][model_name].structure.components[item_idx] @@ -130,9 +170,17 @@ def remove_item(self, item_name: str, model_name: str): def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray: """For a given q array calculate the corresponding reflectivity. - :param q_array: array of data points to be calculated - :param model_name: the model name - :return: reflectivity calculated at q + Parameters + ---------- + q_array : np.ndarray + Array of data points to be calculated. + model_name : str + The model name. + + Returns + ------- + np.ndarray + Reflectivity calculated at q. """ structure = _remove_unecessary_stacks(self.storage['model'][model_name].structure) model = reflect.ReflectModel( @@ -151,22 +199,33 @@ def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray: return model(x=q_array, x_err=dq_vector) def sld_profile(self, model_name: str) -> Tuple[np.ndarray, np.ndarray]: - """ - Return the scattering length density profile. + """Return the scattering length density profile. - :param model_name: Name for the model - :return: z and sld(z) + Parameters + ---------- + model_name : str + Name for the model. + + Returns + ------- + + Z and sld(z). """ return _remove_unecessary_stacks(self.storage['model'][model_name].structure).sld_profile() def _remove_unecessary_stacks(current_structure: reflect.Structure) -> reflect.Structure: - """ - Removed unnecessary reflect.Stack objects from the structure. + """Removed unnecessary reflect.Stack objects from the structure. + + Parameters + ---------- + current_structure : reflect.Structure + The current structure. - :param current_structure: The current structure - :return: The structre without the unnecessary Stacks - :rtype: reflect.structure + Returns + ------- + reflect.structure + The structre without the unnecessary Stacks. """ structure = [] for i in current_structure.components: diff --git a/src/easyreflectometry/calculators/wrapper_base.py b/src/easyreflectometry/calculators/wrapper_base.py index 0755ff64..1ad872d8 100644 --- a/src/easyreflectometry/calculators/wrapper_base.py +++ b/src/easyreflectometry/calculators/wrapper_base.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from abc import abstractmethod import numpy as np @@ -31,7 +34,10 @@ def reset_storage(self): def create_material(self, name: str): """Create a material using SLD. - :param name: The name of the material + Parameters + ---------- + name : str + The name of the material. """ ... @@ -39,7 +45,10 @@ def create_material(self, name: str): def create_layer(self, name: str): """Create a layer using Slab. - :param name: The name of the layer + Parameters + ---------- + name : str + The name of the layer. """ ... @@ -47,34 +56,46 @@ def create_layer(self, name: str): def create_item(self, name: str): """Create an item using Stack. - :param name: The name of the item + Parameters + ---------- + name : str + The name of the item. """ ... @abstractmethod def create_model(self, name: str): - """Create a model for analysis + """Create a model for analysis. - :param name: Name for the model + Parameters + ---------- + name : str + Name for the model. """ ... @abstractmethod def update_model(self, name: str, **kwargs): - """Update the non-structural parameters of the model - - :param name: Name for the model - :param kwargs: + """Update the non-structural parameters of the model. + Parameters + ---------- + name : str + Name for the model. + **kwargs : """ ... @abstractmethod def get_model_value(self, name: str, key: str) -> float: - """A function to get a given model value - - :param name: Name for the model - :param key: The given value keys + """A function to get a given model value. + + Parameters + ---------- + name : str + Name for the model. + key : str + The given value keys. """ ... @@ -82,8 +103,12 @@ def get_model_value(self, name: str, key: str) -> float: def assign_material_to_layer(self, material_name: str, layer_name: str): """Assign a material to a layer. - :param material_name: The material name - :param layer_name: The layer name + Parameters + ---------- + material_name : str + The material name. + layer_name : str + The layer name. """ ... @@ -91,8 +116,12 @@ def assign_material_to_layer(self, material_name: str, layer_name: str): def add_layer_to_item(self, layer_name: str, item_name: str): """Create a layer from the material of the same name, in a given item. - :param layer_name: The layer name - :param item_name: The item name + Parameters + ---------- + layer_name : str + The layer name. + item_name : str + The item name. """ ... @@ -100,8 +129,12 @@ def add_layer_to_item(self, layer_name: str, item_name: str): def add_item(self, item_name: str, model_name: str): """Add an item to the model. - :param item_name: items to add to model - :param model_name: Name for the model + Parameters + ---------- + item_name : str + Items to add to model. + model_name : str + Name for the model. """ ... @@ -109,8 +142,12 @@ def add_item(self, item_name: str, model_name: str): def remove_layer_from_item(self, layer_name: str, item_name: str): """Remove a layer in a given item. - :param layer_name: The layer name - :param item_name: The item name + Parameters + ---------- + layer_name : str + The layer name. + item_name : str + The item name. """ ... @@ -118,8 +155,12 @@ def remove_layer_from_item(self, layer_name: str, item_name: str): def remove_item(self, item_name: str, model_name: str): """Remove a given item. - :param item_name: The item name - :param model_name: Name of the model + Parameters + ---------- + item_name : str + The item name. + model_name : str + Name of the model. """ ... @@ -127,9 +168,17 @@ def remove_item(self, item_name: str, model_name: str): def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray: """For a given q array calculate the corresponding reflectivity. - :param q_array: array of data points to be calculated - :param model_name: the model name - :return: reflectivity calculated at q + Parameters + ---------- + q_array : np.ndarray + Array of data points to be calculated. + model_name : str + The model name. + + Returns + ------- + np.ndarray + Reflectivity calculated at q. """ ... @@ -137,15 +186,26 @@ def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray: def sld_profile(self, model_name: str) -> tuple[np.ndarray, np.ndarray]: """Return the scattering length density profile. - :param model_name: Name for the model - :return: z and sld(z) + Parameters + ---------- + model_name : str + Name for the model. + + Returns + ------- + tuple[np.ndarray, np.ndarray] + Z and sld(z). """ ... def update_material(self, name: str, **kwargs): """Update a material. - :param name: The name of the material + Parameters + ---------- + **kwargs : + name : str + The name of the material. """ material = self.storage['material'][name] for key in kwargs.keys(): @@ -153,11 +213,19 @@ def update_material(self, name: str, **kwargs): setattr(item, 'value', kwargs[key]) def get_material_value(self, name: str, key: str) -> float: - """A function to get a given material value - - :param name: The material name - :param key: The given value keys - :return: The desired value + """A function to get a given material value. + + Parameters + ---------- + name : str + The material name. + key : str + The given value keys. + + Returns + ------- + float + The desired value. """ material = self.storage['material'][name] item = getattr(material, key) @@ -166,8 +234,11 @@ def get_material_value(self, name: str, key: str) -> float: def update_layer(self, name: str, **kwargs): """Update a layer in a given item. - :param name: The layer name. - :param kwargs: + Parameters + ---------- + name : str + The layer name. + **kwargs : """ layer = self.storage['layer'][name] for key in kwargs.keys(): @@ -175,10 +246,14 @@ def update_layer(self, name: str, **kwargs): setattr(ii, 'value', kwargs[key]) def get_layer_value(self, name: str, key: str) -> float: - """A function to get a given layer value - - :param name: The layer name - :param key: The given value keys + """A function to get a given layer value. + + Parameters + ---------- + name : str + The layer name. + key : str + The given value keys. """ layer = self.storage['layer'][name] ii = getattr(layer, key) @@ -187,7 +262,11 @@ def get_layer_value(self, name: str, key: str) -> float: def update_item(self, name: str, **kwargs): """Update a layer. - :param name: The item name + Parameters + ---------- + **kwargs : + name : str + The item name. """ item = self.storage['item'][name] for key in kwargs.keys(): @@ -195,11 +274,19 @@ def update_item(self, name: str, **kwargs): setattr(ii, 'value', kwargs[key]) def get_item_value(self, name: str, key: str) -> float: - """A function to get a given item value - - :param name: The item name - :param key: The given value keys - :return: The desired value + """A function to get a given item value. + + Parameters + ---------- + name : str + The item name. + key : str + The given value keys. + + Returns + ------- + float + The desired value. """ item = self.storage['item'][name] item = getattr(item, key) @@ -208,18 +295,25 @@ def get_item_value(self, name: str, key: str) -> float: def set_resolution_function(self, resolution_function: ResolutionFunction) -> None: """Set the resolution function for the calculator. - :param resolution_function: The resolution function + Parameters + ---------- + resolution_function : ResolutionFunction + The resolution function. """ self._resolution_function = resolution_function @property def magnetism(self) -> bool: + """Magnetism function.""" return self._magnetism @magnetism.setter def magnetism(self, magnetism: bool) -> None: """Set the magnetism flag. - :param magnetism: The magnetism flag + Parameters + ---------- + magnetism : bool + The magnetism flag. """ self._magnetism = magnetism diff --git a/src/easyreflectometry/data/__init__.py b/src/easyreflectometry/data/__init__.py index 194f0d31..0d058120 100644 --- a/src/easyreflectometry/data/__init__.py +++ b/src/easyreflectometry/data/__init__.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from .data_store import DataSet1D from .data_store import ProjectData from .measurement import load diff --git a/src/easyreflectometry/data/data_store.py b/src/easyreflectometry/data/data_store.py index 948382d7..b0cf001f 100644 --- a/src/easyreflectometry/data/data_store.py +++ b/src/easyreflectometry/data/data_store.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/wardsimon' from collections.abc import Sequence @@ -16,6 +19,7 @@ class ProjectData(SerializerComponent): def __init__(self, name='DataStore', exp_data=None, sim_data=None): + """Init function.""" self.name = name if exp_data is None: exp_data = DataStore(name='Exp Datastore') @@ -27,31 +31,39 @@ def __init__(self, name='DataStore', exp_data=None, sim_data=None): class DataStore(Sequence, SerializerComponent): def __init__(self, *args, name='DataStore'): + """Init function.""" self.name = name self.items = list(args) self.show_legend = False def __getitem__(self, i: int) -> T: + """Getitem function.""" return self.items.__getitem__(i) def __len__(self) -> int: + """Len function.""" return len(self.items) def __setitem__(self, key, value): + """Setitem function.""" self.items[key] = value def __delitem__(self, key): + """Delitem function.""" del self.items[key] def append(self, *args): + """Append function.""" self.items.append(*args) def as_dict(self, skip: list = []) -> dict: + """As dict.""" this_dict = super(DataStore, self).as_dict(self, skip=skip) this_dict['items'] = [item.as_dict() for item in self.items if hasattr(item, 'as_dict')] @classmethod def from_dict(cls, d): + """From dict.""" items = d['items'] del d['items'] obj = cls.from_dict(d) @@ -61,10 +73,12 @@ def from_dict(cls, d): @property def experiments(self): + """Experiments function.""" return [self[idx] for idx in range(len(self)) if self[idx].is_experiment] @property def simulations(self): + """Simulations function.""" return [self[idx] for idx in range(len(self)) if self[idx].is_simulation] @@ -81,6 +95,7 @@ def __init__( y_label: str = 'y', auto_background: bool = True, ): + """Init function.""" self._model = model if y is not None and model is not None and auto_background: self._model.background = max(np.min(y), 1e-10) @@ -119,22 +134,28 @@ def __init__( @property def model(self) -> 'Model': # delay type checking until runtime (quotes) + """Model function.""" return self._model @model.setter def model(self, new_model: 'Model') -> None: + """Model function.""" self._model = new_model @property def is_experiment(self) -> bool: + """Is experiment.""" return self._model is not None @property def is_simulation(self) -> bool: + """Is simulation.""" return self._model is None def data_points(self) -> tuple[float, float, float, float]: + """Data points.""" return zip(self.x, self.y, self.ye, self.xe) def __repr__(self) -> str: + """Repr function.""" return "1D DataStore of '{:s}' Vs '{:s}' with {} data points".format(self.x_label, self.y_label, len(self.x)) diff --git a/src/easyreflectometry/data/measurement.py b/src/easyreflectometry/data/measurement.py index df4064b6..5de8df1f 100644 --- a/src/easyreflectometry/data/measurement.py +++ b/src/easyreflectometry/data/measurement.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' import os @@ -14,7 +17,10 @@ def load(fname: Union[TextIO, str]) -> sc.DataGroup: """Load data from an ORSO .ort file. - :param fname: The file to be read. + Parameters + ---------- + fname : Union[TextIO, str] + The file to be read. """ try: return load_data_from_orso_file(fname) @@ -40,6 +46,7 @@ def load_as_dataset(fname: Union[TextIO, str]) -> DataSet1D: def extract_orso_title(data_group: sc.DataGroup, data_name: str) -> str | None: + """Extract orso title.""" try: header = data_group['attrs'][data_name]['orso_header'] title = header.values.get('data_source', {}).get('experiment', {}).get('title') @@ -54,7 +61,10 @@ def extract_orso_title(data_group: sc.DataGroup, data_name: str) -> str | None: def _load_txt(fname: Union[TextIO, str]) -> sc.DataGroup: """Load data from a simple txt file. - :param fname: The path for the file to be read. + Parameters + ---------- + fname : Union[TextIO, str] + The path for the file to be read. """ # fname can have either a space or a comma as delimiter # Determine the delimiter used in the file diff --git a/src/easyreflectometry/fitting.py b/src/easyreflectometry/fitting.py index 0750beb5..83e5efed 100644 --- a/src/easyreflectometry/fitting.py +++ b/src/easyreflectometry/fitting.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' import warnings @@ -18,11 +21,20 @@ def _validate_objective(objective: str) -> str: """Validate and resolve the objective string. - :param objective: The objective mode string. - :type objective: str - :return: Resolved objective string ('auto' becomes 'hybrid'). - :rtype: str - :raises ValueError: If the objective is not one of the valid options. + Parameters + ---------- + objective : str + The objective mode string. + + Raises + ------ + ValueError : + If the objective is not one of the valid options. + + Returns + ------- + str + Resolved objective string ('auto' becomes 'hybrid'). """ if objective not in _VALID_OBJECTIVES: raise ValueError(f'Unknown objective {objective!r}. Valid options: {_VALID_OBJECTIVES}') @@ -46,17 +58,22 @@ def _prepare_fit_arrays( Note: ``variances`` here means σ² (the scipp convention), not σ. - :param x_vals: Independent variable values. - :type x_vals: np.ndarray - :param y_vals: Observed dependent variable values. - :type y_vals: np.ndarray - :param variances: Variance (σ²) of each observed point. - :type variances: np.ndarray - :param objective: One of 'legacy_mask', 'hybrid', 'mighell'. - :type objective: str - :return: Tuple of (x_out, y_eff, weights, stats) where stats is a dict - with keys 'valid', 'mighell_substituted', 'masked'. - :rtype: tuple[np.ndarray, np.ndarray, np.ndarray, dict] + Parameters + ---------- + x_vals : np.ndarray + Independent variable values. + y_vals : np.ndarray + Observed dependent variable values. + variances : np.ndarray + Variance (σ²) of each observed point. + objective : str + One of 'legacy_mask', 'hybrid', 'mighell'. + + Returns + ------- + tuple[np.ndarray, np.ndarray, np.ndarray, dict] + Tuple of (x_out, y_eff, weights, stats) where stats is a dict + with keys 'valid', 'mighell_substituted', 'masked'. """ n = len(y_vals) zero_mask = variances <= 0.0 @@ -71,7 +88,12 @@ def _prepare_fit_arrays( weights = 1.0 / np.sqrt(variances[valid]) else: weights = np.array([]) - stats = {'valid': n_valid, 'mighell_substituted': 0, 'masked': n_zero, 'transformed_all_points': False} + stats = { + 'valid': n_valid, + 'mighell_substituted': 0, + 'masked': n_zero, + 'transformed_all_points': False, + } return x_out, y_eff, weights, stats # hybrid or mighell @@ -143,18 +165,24 @@ def __init__(self, *args: Model, objective: str = 'hybrid'): which will populate the :py:class:`sc.DataGroup` appropriately after the fitting is performed. - :param args: Reflectometry model(s). - :param objective: Zero-variance handling strategy. One of + Parameters + ---------- + *args : Model + Reflectometry model(s). + objective : str, optional + Zero-variance handling strategy. One of ``'hybrid'`` (default, Mighell for zero-variance, WLS otherwise), ``'mighell'`` (Mighell transform for all points), ``'legacy_mask'`` (drop zero-variance points), - ``'auto'`` (alias for ``'hybrid'``). - :type objective: str + ``'auto'`` (alias for ``'hybrid'``). By default, 'hybrid'. """ # This lets the unique_name be passed with the fit_func. def func_wrapper(func, unique_name): + """Func wrapper.""" + def wrapped(*args, **kwargs): + """Wrapped function.""" return func(*args, unique_name, **kwargs) return wrapped @@ -169,21 +197,20 @@ def wrapped(*args, **kwargs): def fit(self, data: sc.DataGroup, id: int = 0, objective: str | None = None) -> sc.DataGroup: """Perform the fitting and populate the DataGroups with the result. - :param data: DataGroup to be fitted to and populated. - :type data: sc.DataGroup - :param id: Unused parameter kept for backward compatibility. - :type id: int - :param objective: Per-call override for the zero-variance objective. - If ``None``, uses the instance default set at construction. - :type objective: str or None - :return: A new DataGroup with fitted model curves, SLD profiles, and fit statistics. - :rtype: sc.DataGroup - - :note: Under the ``mighell`` objective all points are transformed, - so ``reduced_chi`` is not a classical chi-square statistic. - Under ``hybrid``, only zero-variance points are transformed; - when they are a small fraction of the data the chi-square - remains approximately classical. + Parameters + ---------- + data : sc.DataGroup + DataGroup to be fitted to and populated. + id : int, optional + Unused parameter kept for backward compatibility. By default, 0. + objective : str | None, optional + Per-call override for the zero-variance objective. + If ``None``, uses the instance default set at construction. By default, None. + + Returns + ------- + sc.DataGroup + A new DataGroup with fitted model curves, SLD profiles, and fit statistics. """ obj = _validate_objective(objective) if objective is not None else self._objective @@ -236,7 +263,9 @@ def fit(self, data: sc.DataGroup, id: int = 0, objective: str | None = None) -> if 'attrs' in new_data: new_data['attrs'][f'R_{id}_model'] = {'model': sc.scalar(self._models[i].as_dict())} new_data['coords'][f'z_{id}'] = sc.array( - dims=[f'z_{id}'], values=sld_profile[0], unit=(1 / new_data['coords'][f'Qz_{id}'].unit).unit + dims=[f'z_{id}'], + values=sld_profile[0], + unit=(1 / new_data['coords'][f'Qz_{id}'].unit).unit, ) original = original_arrays[i] sigma_classical = np.sqrt(np.clip(original['variances'], 0.0, None)) @@ -246,15 +275,13 @@ def fit(self, data: sc.DataGroup, id: int = 0, objective: str | None = None) -> objective_chi2 = float(result[i].chi2) objective_reduced_chi = _fit_result_reduced_chi(result[i], np.size(result[i].x)) - self._classical_fit_metrics.append( - { - 'classical_chi2': classical_chi2, - 'classical_reduced_chi': classical_reduced_chi, - 'objective_chi2': objective_chi2, - 'objective_reduced_chi': objective_reduced_chi, - 'n_classical_points': n_classical_points, - } - ) + self._classical_fit_metrics.append({ + 'classical_chi2': classical_chi2, + 'classical_reduced_chi': classical_reduced_chi, + 'objective_chi2': objective_chi2, + 'objective_reduced_chi': objective_reduced_chi, + 'n_classical_points': n_classical_points, + }) new_data['objective_chi2'] = objective_chi2 new_data['objective_reduced_chi'] = objective_reduced_chi @@ -267,14 +294,19 @@ def fit(self, data: sc.DataGroup, id: int = 0, objective: str | None = None) -> def fit_single_data_set_1d(self, data: DataSet1D, objective: str | None = None) -> FitResults: """Perform fitting on a single 1D dataset. - :param data: The 1D dataset to fit. Note that ``data.ye`` stores + Parameters + ---------- + data : DataSet1D + The 1D dataset to fit. Note that ``data.ye`` stores variances (σ²), not standard deviations. - :type data: DataSet1D - :param objective: Per-call override for the zero-variance objective. - If ``None``, uses the instance default set at construction. - :type objective: str or None - :return: Fit results from the minimizer. - :rtype: FitResults + objective : str | None, optional + Per-call override for the zero-variance objective. + If ``None``, uses the instance default set at construction. By default, None. + + Returns + ------- + FitResults + Fit results from the minimizer. """ obj = _validate_objective(objective) if objective is not None else self._objective @@ -372,20 +404,27 @@ def objective_reduced_chi(self) -> float | None: return self.reduced_chi def switch_minimizer(self, minimizer: AvailableMinimizers) -> None: - """ - Switch the minimizer for the fitting. + """Switch the minimizer for the fitting. - :param minimizer: Minimizer to be switched to + Parameters + ---------- + minimizer : AvailableMinimizers + Minimizer to be switched to. """ self.easy_science_multi_fitter.switch_minimizer(minimizer) def _flatten_list(this_list: list) -> list: - """ - Flatten nested lists. + """Flatten nested lists. - :param this_list: List to be flattened + Parameters + ---------- + this_list : list + List to be flattened. - :return: Flattened list + Returns + ------- + list + Flattened list. """ return np.array([item for sublist in this_list for item in sublist]) diff --git a/src/easyreflectometry/limits.py b/src/easyreflectometry/limits.py index 691f86e3..001bba64 100644 --- a/src/easyreflectometry/limits.py +++ b/src/easyreflectometry/limits.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import numpy as np from easyscience.variable import Parameter @@ -9,10 +12,12 @@ def apply_default_limits(parameter: Parameter, kind: str) -> None: """Apply default min/max to a parameter if current bounds are infinite. - :param parameter: The parameter to adjust. - :type parameter: Parameter - :param kind: One of 'thickness', 'roughness', 'sld', 'isld', 'scale'. - :type kind: str + Parameters + ---------- + parameter : Parameter + The parameter to adjust. + kind : str + One of 'thickness', 'roughness', 'sld', 'isld', 'scale'. """ if not parameter.independent: return diff --git a/src/easyreflectometry/main.py b/src/easyreflectometry/main.py index 043d72c1..2f7737e0 100644 --- a/src/easyreflectometry/main.py +++ b/src/easyreflectometry/main.py @@ -1,7 +1,11 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from easyreflectometry.calculators import CalculatorFactory def main(): + """Main function.""" factory = CalculatorFactory() print(f'Available calculators: {factory.available_interfaces}') diff --git a/src/easyreflectometry/model/__init__.py b/src/easyreflectometry/model/__init__.py index 6246b2d8..698b5a0c 100644 --- a/src/easyreflectometry/model/__init__.py +++ b/src/easyreflectometry/model/__init__.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from .model import Model from .model_collection import ModelCollection from .resolution_functions import LinearSpline diff --git a/src/easyreflectometry/model/model.py b/src/easyreflectometry/model/model.py index 7f651fa2..aa67a043 100644 --- a/src/easyreflectometry/model/model.py +++ b/src/easyreflectometry/model/model.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from __future__ import annotations __author__ = 'github.com/arm61' @@ -43,11 +46,23 @@ }, } -COLORS = ['#0173B2', '#DE8F05', '#029E73', '#D55E00', '#CC78BC', '#CA9161', '#FBAFE4', '#949494', '#ECE133', '#56B4E9'] +COLORS = [ + '#0173B2', + '#DE8F05', + '#029E73', + '#D55E00', + '#CC78BC', + '#CA9161', + '#FBAFE4', + '#949494', + '#ECE133', + '#56B4E9', +] class Model(BaseObj): """Model is the class that represents the experiment. + It is used to store the information about the experiment and to perform the calculations. """ @@ -70,13 +85,24 @@ def __init__( ): """Constructor. - :param sample: The sample being modelled. - :param scale: Scaling factor of profile. - :param background: Linear background magnitude. - :param name: Name of the model, defaults to 'Model'. - :param resolution_function: Resolution function, defaults to PercentageFwhm. - :param interface: Calculator interface, defaults to `None`. - + Parameters + ---------- + unique_name : Optional[str], optional + By default, None. + color : str, optional + By default, COLORS[0]. + sample : Union[Sample, None], optional + The sample being modelled. By default, None. + scale : Union[Parameter, Number, None], optional + Scaling factor of profile. By default, None. + background : Union[Parameter, Number, None], optional + Linear background magnitude. By default, None. + name : str, optional + Name of the model. By default, 'Model'. + resolution_function : Union[ResolutionFunction, None], optional + Resolution function. By default, None. + interface : + Calculator interface. By default, None. """ if unique_name is None: unique_name = global_object.generate_unique_name(self.__class__.__name__) @@ -107,7 +133,10 @@ def __init__( def add_assemblies(self, *assemblies: list[BaseAssembly]) -> None: """Add assemblies to the model sample. - :param assemblies: Assemblies to add to model sample. + Parameters + ---------- + *assemblies : list[BaseAssembly] + Assemblies to add to model sample. """ if not assemblies: self.sample.add_assembly() @@ -125,7 +154,11 @@ def add_assemblies(self, *assemblies: list[BaseAssembly]) -> None: def duplicate_assembly(self, index: int) -> None: """Duplicate a given item or layer in a sample. - :param idx: Index of the item or layer to duplicate + Parameters + ---------- + index : int + idx : + Index of the item or layer to duplicate. """ self.sample.duplicate_assembly(index) if self.interface is not None: @@ -134,7 +167,11 @@ def duplicate_assembly(self, index: int) -> None: def remove_assembly(self, index: int) -> None: """Remove an assembly from the model. - :param idx: Index of the item to remove. + Parameters + ---------- + index : int + idx : + Index of the item to remove. """ assembly_unique_name = self.sample[index].unique_name self.sample.remove_assembly(index) @@ -150,8 +187,10 @@ def is_default(self) -> bool: def is_default(self, value: bool) -> None: """Set whether this model is a default placeholder. - :param value: True if the model is a default placeholder. - :type value: bool + Parameters + ---------- + value : bool + True if the model is a default placeholder. """ self._is_default = value @@ -169,9 +208,7 @@ def resolution_function(self, resolution_function: ResolutionFunction) -> None: @property def interface(self): - """ - Get the current interface of the object - """ + """Get the current interface of the object.""" return self._interface @interface.setter @@ -209,9 +246,13 @@ def __repr__(self) -> str: def as_dict(self, skip: Optional[list[str]] = None) -> dict: """Produces a cleaned dict using a custom as_dict method to skip necessary things. + The resulting dict matches the parameters in __init__ - :param skip: List of keys to skip, defaults to `None`. + Parameters + ---------- + skip : Optional[list[str]], optional + List of keys to skip. By default, None. """ if skip is None: skip = [] @@ -233,11 +274,19 @@ def as_orso(self) -> dict: @classmethod def from_dict(cls, passed_dict: dict) -> Model: - """ - Create a Model from a dictionary. - - :param this_dict: dictionary of the Model - :return: Model + """Create a Model from a dictionary. + + Parameters + ---------- + passed_dict : dict + cls : + this_dict : + Dictionary of the Model. + + Returns + ------- + Model + Model. """ # Causes circular import if imported at the top from easyreflectometry.calculators import CalculatorFactory diff --git a/src/easyreflectometry/model/model_collection.py b/src/easyreflectometry/model/model_collection.py index b3c0bd2d..a8ef1577 100644 --- a/src/easyreflectometry/model/model_collection.py +++ b/src/easyreflectometry/model/model_collection.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from __future__ import annotations from typing import List @@ -12,6 +15,7 @@ # Needs to be a function, elements are added to the global_object.map def DEFAULT_ELEMENTS(interface): + """Default elements.""" return (Model(interface),) @@ -26,6 +30,7 @@ def __init__( next_color_index: Optional[int] = None, **kwargs, ): + """Init function.""" if not models: if populate_if_none: models = DEFAULT_ELEMENTS(interface) @@ -49,7 +54,10 @@ def __init__( def add_model(self, model: Optional[Model] = None): """Add a model to the collection. - :param model: Model to add. + Parameters + ---------- + model : Optional[Model], optional + Model to add. By default, None. """ if model is None: model = Model(name='Model', interface=self.interface, color=self._current_color()) @@ -58,7 +66,10 @@ def add_model(self, model: Optional[Model] = None): def duplicate_model(self, index: int): """Duplicate a model in the collection. - :param index: Model to duplicate. + Parameters + ---------- + index : int + Model to duplicate. """ to_be_duplicated = self[index] duplicate = Model.from_dict(to_be_duplicated.as_dict(skip=['unique_name'])) @@ -66,6 +77,7 @@ def duplicate_model(self, index: int): self.append(duplicate) def as_dict(self, skip: List[str] | None = None) -> dict: + """As dict.""" this_dict = super().as_dict(skip=skip) this_dict['populate_if_none'] = self.populate_if_none this_dict['next_color_index'] = self._next_color_index @@ -73,10 +85,14 @@ def as_dict(self, skip: List[str] | None = None) -> dict: @classmethod def from_dict(cls, this_dict: dict) -> ModelCollection: - """ - Create an instance of a collection from a dictionary. - - :param data: The dictionary for the collection + """Create an instance of a collection from a dictionary. + + Parameters + ---------- + this_dict : dict + cls : + data : + The dictionary for the collection. """ collection_dict = this_dict.copy() # We need to call from_dict on the base class to get the models @@ -102,14 +118,17 @@ def from_dict(cls, this_dict: dict) -> ModelCollection: return collection def append(self, model: Model) -> None: # type: ignore[override] + """Append function.""" self._append_internal(model, advance=True) def _append_internal(self, model: Model, advance: bool) -> None: + """Append internal.""" super().append(model) if advance: self._advance_color_index() def _advance_color_index(self) -> None: + """Advance color index.""" if not COLORS: self._next_color_index = 0 return @@ -119,6 +138,7 @@ def _advance_color_index(self) -> None: self._next_color_index = (self._next_color_index + 1) % len(COLORS) def _current_color(self) -> str: + """Current color.""" if not COLORS: raise ValueError('No colors defined for models.') if self._next_color_index is None: diff --git a/src/easyreflectometry/model/resolution_functions.py b/src/easyreflectometry/model/resolution_functions.py index 2a6e5c8c..ee0933e2 100644 --- a/src/easyreflectometry/model/resolution_functions.py +++ b/src/easyreflectometry/model/resolution_functions.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """Resolution functions for the resolution of the experiment. When a percentage is provided we assume that the resolution is a Gaussian distribution with a FWHM of the percentage of the q value. @@ -26,51 +29,68 @@ def as_dict(self, skip: Optional[List[str]] = None) -> dict: ... @classmethod def from_dict(cls, data: dict) -> ResolutionFunction: + """Smearing function.""" if data['smearing'] == 'PercentageFwhm': return PercentageFwhm(data['constant']) if data['smearing'] == 'LinearSpline': return LinearSpline(data['q_data_points'], data['fwhm_values']) if data['smearing'] == 'Pointwise': - return Pointwise([data['q_data_points'], data['R_data_points'], data['sQz_data_points']]) + return Pointwise([ + data['q_data_points'], + data['R_data_points'], + data['sQz_data_points'], + ]) raise ValueError('Unknown resolution function type') class PercentageFwhm(ResolutionFunction): def __init__(self, constant: Union[None, float] = None): + """Init function.""" if constant is None: constant = DEFAULT_RESOLUTION_FWHM_PERCENTAGE self.constant = constant def smearing(self, q: Union[np.array, float]) -> np.array: + """Smearing function.""" return np.ones(np.array(q).size) * self.constant def as_dict( self, skip: Optional[List[str]] = None ) -> dict[str, str]: # skip is kept for consistency of the as_dict signature + """As dict.""" return {'smearing': 'PercentageFwhm', 'constant': self.constant} class LinearSpline(ResolutionFunction): def __init__(self, q_data_points: np.array, fwhm_values: np.array): + """Init function.""" self.q_data_points = q_data_points self.fwhm_values = fwhm_values def smearing(self, q: Union[np.array, float]) -> np.array: + """Smearing function.""" return np.interp(q, self.q_data_points, self.fwhm_values) def as_dict( self, skip: Optional[List[str]] = None ) -> dict[str, str]: # skip is kept for consistency of the as_dict signature - return {'smearing': 'LinearSpline', 'q_data_points': list(self.q_data_points), 'fwhm_values': list(self.fwhm_values)} + """As dict.""" + return { + 'smearing': 'LinearSpline', + 'q_data_points': list(self.q_data_points), + 'fwhm_values': list(self.fwhm_values), + } # add pointwise smearing funtion class Pointwise(ResolutionFunction): def __init__(self, q_data_points: list[np.ndarray]): + """Init function.""" self.q_data_points = q_data_points self.q = None def smearing(self, q: Union[np.ndarray, float] = None) -> np.ndarray: + """Smearing function.""" Qz = self.q_data_points[0] R = self.q_data_points[1] sQz = self.q_data_points[2] @@ -87,6 +107,7 @@ def smearing(self, q: Union[np.ndarray, float] = None) -> np.ndarray: def as_dict( self, skip: Optional[List[str]] = None ) -> dict[str, str]: # skip is kept for consistency of the as_dict signature + """As dict.""" return { 'smearing': 'Pointwise', 'q_data_points': list(self.q_data_points[0]), @@ -95,6 +116,7 @@ def as_dict( } def gaussian_smearing(self, qt, Qz, R, sQz): + """Gaussian smearing.""" weights = np.exp(-0.5 * ((qt - Qz) / sQz) ** 2) if np.sum(weights) == 0 or not np.isfinite(np.sum(weights)): return np.sum(R) @@ -102,9 +124,7 @@ def gaussian_smearing(self, qt, Qz, R, sQz): return np.sum(R * weights) / np.sum(weights) def apply_smooth_smearing(self, Qz, R, sQzs): - """ - Apply smooth resolution smearing using convolution with Gaussian kernel. - """ + """Apply smooth resolution smearing using convolution with Gaussian kernel.""" if self.q is None: R_smeared = np.zeros_like(Qz) else: diff --git a/src/easyreflectometry/orso_utils.py b/src/easyreflectometry/orso_utils.py index 494ed248..aa320933 100644 --- a/src/easyreflectometry/orso_utils.py +++ b/src/easyreflectometry/orso_utils.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2025 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import logging import warnings @@ -49,8 +52,7 @@ def load_data_from_orso_file(fname: str) -> sc.DataGroup: def load_orso_model(orso_data) -> Sample: - """ - Load a model from an ORSO file and return a Sample object. + """Load a model from an ORSO file and return a Sample object. The ORSO file .ort contains information about the sample, saved as a simple "stack" string, e.g. 'air | m1 | SiO2 | Si'. @@ -61,11 +63,20 @@ def load_orso_model(orso_data) -> Sample: - Middle layers -> 'Loaded layer' Multilayer assembly (parameters enabled) - Last layer -> Subphase assembly (thickness=0 fixed, roughness enabled) - :param orso_data: Parsed ORSO dataset list (as returned by ``orso.load_orso``). - :type orso_data: list - :return: An EasyReflectometry Sample object. - :rtype: Sample - :raises ValueError: If ORSO layers could not be resolved or fewer than 2 layers. + Parameters + ---------- + orso_data : list + Parsed ORSO dataset list (as returned by ``orso.load_orso``). + + Raises + ------ + ValueError : + If ORSO layers could not be resolved or fewer than 2 layers. + + Returns + ------- + Sample + An EasyReflectometry Sample object. """ # Extract stack string and layer definitions from ORSO sample model sample_model = orso_data[0].info.data_source.sample.model @@ -134,7 +145,7 @@ def load_orso_model(orso_data) -> Sample: def _convert_orso_layer_to_erl(layer): - """Helper function to convert an ORSO layer to an EasyReflectometry layer""" + r"""Helper function to convert an ORSO layer to an EasyReflectometry laye.""" material = layer.material # Prefer original_name for material name, fall back to formula if available m_name = layer.original_name if layer.original_name is not None else material.formula @@ -157,7 +168,7 @@ def _get_sld_values(material, material_name): Note: ORSO stores SLD in absolute units (A^-2), but the internal representation uses 10^-6 A^-2. When reading directly from ORSO, we multiply by 1e6 to convert. - When calculating from mass density, MaterialDensity already returns the correct units. + When calculating from mass density, MaterialDensity already returns the correct units.. """ if material.sld is None and material.mass_density is not None: # Calculate SLD from mass density @@ -196,10 +207,15 @@ def _get_sld_values(material, material_name): def load_orso_data(orso_data) -> DataSet1D: """Convert parsed ORSO dataset objects into a scipp DataGroup. - :param orso_data: Parsed ORSO dataset list (as returned by ``orso.load_orso``). - :type orso_data: list - :return: A scipp DataGroup with data, coords, and attrs. - :rtype: sc.DataGroup + Parameters + ---------- + orso_data : list + Parsed ORSO dataset list (as returned by ``orso.load_orso``). + + Returns + ------- + sc.DataGroup + A scipp DataGroup with data, coords, and attrs. """ data = {} coords = {} diff --git a/src/easyreflectometry/plot.py b/src/easyreflectometry/plot.py index a88a89bf..28285e24 100644 --- a/src/easyreflectometry/plot.py +++ b/src/easyreflectometry/plot.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' import matplotlib.pyplot as plt @@ -8,10 +11,12 @@ def plot(data: sc.DataGroup) -> None: - """ - A general plotting function for easyreflectometry. + """A general plotting function for easyreflectometry. - :param data: the DataGroup to be plotted. + Parameters + ---------- + data : sc.DataGroup + The DataGroup to be plotted. """ if len([i for i in list(data.keys()) if 'SLD' in i]) == 0: plot_sld = False @@ -41,7 +46,14 @@ def plot(data: sc.DataGroup) -> None: ) plot_model_data.data *= sc.scalar(10.0**i, unit=plot_model_data.unit) plot_model_data.coords[f'Qz_{refl_num}'].variances = None - sc.plot(plot_model_data, ax=ax1, norm='log', linestyle='--', color=color_cycle[i], marker='') + sc.plot( + plot_model_data, + ax=ax1, + norm='log', + linestyle='--', + color=color_cycle[i], + marker='', + ) except KeyError: pass ax1.autoscale(True) diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py index 7e1ab3c9..5127ad16 100644 --- a/src/easyreflectometry/project.py +++ b/src/easyreflectometry/project.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import datetime import json import logging @@ -43,6 +46,7 @@ class Project: def __init__(self): + """Init function.""" self._info = self._default_info() self._path_project_parent = Path(os.path.expanduser('~')) self._models = ModelCollection(populate_if_none=False, unique_name='project_models') @@ -68,6 +72,7 @@ def __init__(self): self._with_experiments = False def reset(self): + """Reset function.""" del self._models del self._materials global_object.map._clear() @@ -140,40 +145,48 @@ def _sync_layer_parameter_state(self, parameter: Parameter, kind: str, disabled_ @property def q_min(self): + """Q min.""" if self._q_min is None: return Q_MIN return self._q_min @q_min.setter def q_min(self, value: float) -> None: + """Q min.""" self._q_min = value @property def q_max(self): + """Q max.""" if self._q_max is None: return Q_MAX return self._q_max @q_max.setter def q_max(self, value: float) -> None: + """Q max.""" self._q_max = value @property def q_resolution(self): + """Q resolution.""" if self._q_resolution is None: return Q_RESOLUTION return self._q_resolution @q_resolution.setter def q_resolution(self, value: int) -> None: + """Q resolution.""" self._q_resolution = value @property def current_material_index(self) -> Optional[int]: + """Current material index.""" return self._current_material_index @current_material_index.setter def current_material_index(self, value: int) -> None: + """Current material index.""" if value < 0 or value >= len(self._materials): raise ValueError(f'Index {value} out of range') if self._current_material_index != value: @@ -181,10 +194,12 @@ def current_material_index(self, value: int) -> None: @property def current_model_index(self) -> Optional[int]: + """Current model index.""" return self._current_model_index @current_model_index.setter def current_model_index(self, value: int) -> None: + """Current model index.""" if value < 0 or value >= len(self._models): raise ValueError(f'Index {value} out of range') if self._current_model_index != value: @@ -194,10 +209,12 @@ def current_model_index(self, value: int) -> None: @property def current_assembly_index(self) -> Optional[int]: + """Current assembly index.""" return self._current_assembly_index @current_assembly_index.setter def current_assembly_index(self, value: int) -> None: + """Current assembly index.""" if value < 0 or value >= len(self._models[self._current_model_index].sample): raise ValueError(f'Index {value} out of range') if self._current_assembly_index != value: @@ -206,10 +223,12 @@ def current_assembly_index(self, value: int) -> None: @property def current_layer_index(self) -> Optional[int]: + """Current layer index.""" return self._current_layer_index @current_layer_index.setter def current_layer_index(self, value: int) -> None: + """Current layer index.""" if value < 0 or value >= len(self._models[self._current_model_index].sample[self._current_assembly_index].layers): raise ValueError(f'Index {value} out of range') if self._current_layer_index != value: @@ -217,10 +236,12 @@ def current_layer_index(self, value: int) -> None: @property def current_experiment_index(self) -> Optional[int]: + """Current experiment index.""" return self._current_experiment_index @current_experiment_index.setter def current_experiment_index(self, value: int) -> None: + """Current experiment index.""" if value < 0 or value >= len(self._experiments): raise ValueError(f'Index {value} out of range') if self._current_experiment_index != value: @@ -230,21 +251,26 @@ def current_experiment_index(self, value: int) -> None: @property def created(self) -> bool: + """Created function.""" return self._created @property def path(self): + """Path function.""" return self._path_project_parent / self._info['name'] def set_path_project_parent(self, path: Union[Path, str]): + """Set path project parent.""" self._path_project_parent = Path(path) @property def models(self) -> ModelCollection: + """Models function.""" return self._models @models.setter def models(self, models: ModelCollection) -> None: + """Models function.""" self._replace_collection(models, self._models) # Use setter to update indicies for current model, assembly and layer self.current_model_index = 0 @@ -255,6 +281,7 @@ def models(self, models: ModelCollection) -> None: @property def fitter(self) -> MultiFitter: + """Fitter function.""" if len(self._models): if (self._fitter is None) or (self._fitter_model_index != self._current_model_index): self._fitter = MultiFitter(self._models[self._current_model_index]) @@ -264,10 +291,12 @@ def fitter(self) -> MultiFitter: @property def calculator(self) -> str: + """Calculator function.""" return self._calculator.current_interface_name @calculator.setter def calculator(self, calculator: str) -> None: + """Calculator function.""" if calculator == self._calculator.current_interface_name: return @@ -282,47 +311,61 @@ def calculator(self, calculator: str) -> None: @property def minimizer(self) -> AvailableMinimizers: + """Minimizer function.""" if self._fitter is not None: return self._fitter.easy_science_multi_fitter.minimizer.enum return self._minimizer_selection @minimizer.setter def minimizer(self, minimizer: AvailableMinimizers) -> None: + """Minimizer function.""" old_name = getattr(self._minimizer_selection, 'name', str(self._minimizer_selection)) new_name = getattr(minimizer, 'name', str(minimizer)) - logger.info('Minimizer changed from %s to %s (fitter active: %s)', old_name, new_name, self._fitter is not None) + logger.info( + 'Minimizer changed from %s to %s (fitter active: %s)', + old_name, + new_name, + self._fitter is not None, + ) self._minimizer_selection = minimizer if self._fitter is not None: self._fitter.easy_science_multi_fitter.switch_minimizer(minimizer) @property def experiments(self) -> Dict[int, DataSet1D]: + """Experiments function.""" return self._experiments @experiments.setter def experiments(self, experiments: Dict[int, DataSet1D]) -> None: + """Experiments function.""" self._experiments = experiments @property def path_json(self): + """Path json.""" return self.path / 'project.json' def get_index_air(self) -> int: + """Get index air.""" if 'Air' not in [material.name for material in self._materials]: self._materials.add_material(Material(name='Air', sld=0.0, isld=0.0)) return [material.name for material in self._materials].index('Air') def get_index_si(self) -> int: + """Get index si.""" if 'Si' not in [material.name for material in self._materials]: self._materials.add_material(Material(name='Si', sld=2.07, isld=0.0)) return [material.name for material in self._materials].index('Si') def get_index_sio2(self) -> int: + """Get index sio2.""" if 'SiO2' not in [material.name for material in self._materials]: self._materials.add_material(Material(name='SiO2', sld=3.47, isld=0.0)) return [material.name for material in self._materials].index('SiO2') def get_index_d2o(self) -> int: + """Get index d2o.""" if 'D2O' not in [material.name for material in self._materials]: self._materials.add_material(Material(name='D2O', sld=6.36, isld=0.0)) return [material.name for material in self._materials].index('D2O') @@ -351,10 +394,15 @@ def set_sample_from_orso(self, sample: Sample) -> None: This is a convenience helper for the ORSO import pipeline where a complete :class:`~easyreflectometry.sample.Sample` is constructed elsewhere. - :param sample: Sample to set as the project's (single) model. - :type sample: easyreflectometry.sample.Sample - :return: ``None``. - :rtype: None + Parameters + ---------- + sample : Sample + Sample to set as the project's (single) model. + + Returns + ------- + None + ``None``. """ model = Model(sample=sample) self.models = ModelCollection([model]) @@ -369,10 +417,15 @@ def add_sample_from_orso(self, sample: Sample) -> None: After adding the model, :attr:`current_model_index` is updated to point to the newly added model. - :param sample: Sample to add as a new model. - :type sample: easyreflectometry.sample.Sample - :return: ``None``. - :rtype: None + Parameters + ---------- + sample : Sample + Sample to add as a new model. + + Returns + ------- + None + ``None``. """ if sample is None: raise ValueError('The ORSO file does not contain a valid sample model definition.') @@ -393,10 +446,15 @@ def replace_models_from_orso(self, sample: Sample) -> None: model is created from *sample*, assigned to the project's calculator, and the material collection is rebuilt from the new model only. - :param sample: Sample to set as the project's only model. - :type sample: easyreflectometry.sample.Sample - :return: ``None``. - :rtype: None + Parameters + ---------- + sample : Sample + Sample to set as the project's only model. + + Returns + ------- + None + ``None``. """ if sample is None: raise ValueError('The ORSO file does not contain a valid sample model definition.') @@ -427,11 +485,18 @@ def _apply_experiment_metadata( ) -> None: """Set experiment name from ORSO title and configure the resolution function. - :param path: Path to the experiment data file. - :param experiment: The loaded experiment dataset to configure. - :param fallback_name: Name to use when no ORSO title is available. - :param data_group: Pre-loaded scipp DataGroup (avoids reloading the file). - :param data_key: Specific dataset key to use for title extraction (e.g. ``'R_1'``). + Parameters + ---------- + path : Union[Path, str] + Path to the experiment data file. + experiment : DataSet1D + The loaded experiment dataset to configure. + fallback_name : str + Name to use when no ORSO title is available. + data_group : + Pre-loaded scipp DataGroup (avoids reloading the file). By default, None. + data_key : Optional[str], optional + Specific dataset key to use for title extraction (e.g. ``'R_1'``). By default, None. """ # Prefer ORSO title when available (keeps UI descriptive) title = None @@ -456,8 +521,12 @@ def _apply_resolution_function( ) -> None: """Set the resolution function on *model* based on variance data in *experiment*. - :param experiment: The experiment whose variance data drives the choice. - :param model: The model whose resolution function is set. + Parameters + ---------- + experiment : DataSet1D + The experiment whose variance data drives the choice. + model : Model + The model whose resolution function is set. """ model.resolution_function = PercentageFwhm(5.0) @@ -468,6 +537,7 @@ def _auto_set_background(experiment: DataSet1D) -> None: experiment.model.background = max(np.min(experiment.y), 1e-10) def load_new_experiment(self, path: Union[Path, str]) -> None: + """Load new experiment.""" new_experiment = load_as_dataset(str(path)) new_index = len(self._experiments) @@ -485,8 +555,15 @@ def load_new_experiment(self, path: Union[Path, str]) -> None: def count_datasets_in_file(self, path: Union[Path, str]) -> int: """Return the number of datasets contained in the file at *path*. - :param path: Path to the data file. - :return: Number of datasets found; 1 if the file cannot be introspected. + Parameters + ---------- + path : Union[Path, str] + Path to the data file. + + Returns + ------- + int + Number of datasets found; 1 if the file cannot be introspected. """ try: data_group = load_data_from_orso_file(str(path)) @@ -502,8 +579,15 @@ def load_all_experiments_from_file(self, path: Union[Path, str]) -> int: currently selected. Falls back to :meth:`load_new_experiment` for single-dataset files or on any loading error. - :param path: Path to the data file. - :return: Number of experiments that were added. + Parameters + ---------- + path : Union[Path, str] + Path to the data file. + + Returns + ------- + int + Number of experiments that were added. """ try: data_group = load_data_from_orso_file(str(path)) @@ -547,6 +631,7 @@ def load_all_experiments_from_file(self, path: Union[Path, str]) -> int: return len(data_keys) def load_experiment_for_model_at_index(self, path: Union[Path, str], index: Optional[int] = 0) -> None: + """Load experiment for model at index.""" experiment = load_as_dataset(str(path)) self._apply_experiment_metadata(path, experiment, f'Experiment {index}') @@ -557,6 +642,7 @@ def load_experiment_for_model_at_index(self, path: Union[Path, str], index: Opti self._apply_resolution_function(experiment, self._models[index]) def sld_data_for_model_at_index(self, index: int = 0) -> DataSet1D: + """Sld data for model at index.""" self.models[index].interface = self._calculator sld = self.models[index].interface().sld_profile(self._models[index].unique_name) return DataSet1D( @@ -566,6 +652,7 @@ def sld_data_for_model_at_index(self, index: int = 0) -> DataSet1D: ) def sample_data_for_model_at_index(self, index: int = 0, q_range: Optional[np.array] = None) -> DataSet1D: + """Sample data for model at index.""" original_resolution_function = self.models[index].resolution_function self.models[index].resolution_function = PercentageFwhm(0) reflectivity_data = self.model_data_for_model_at_index(index, q_range) @@ -574,6 +661,7 @@ def sample_data_for_model_at_index(self, index: int = 0, q_range: Optional[np.ar return reflectivity_data def model_data_for_model_at_index(self, index: int = 0, q_range: Optional[np.array] = None) -> DataSet1D: + """Model data for model at index.""" if q_range is None: q_range = np.linspace(self.q_min, self.q_max, self.q_resolution) self.models[index].interface = self._calculator @@ -585,18 +673,38 @@ def model_data_for_model_at_index(self, index: int = 0, q_range: Optional[np.arr ) def experimental_data_for_model_at_index(self, index: int = 0) -> DataSet1D: + """Experimental data for model at index.""" if index in self._experiments.keys(): return self._experiments[index] else: raise IndexError(f'No experiment data for model at index {index}') def default_model(self): + """Default model.""" self._replace_collection(MaterialCollection(interface=self._calculator), self._materials) layers = [ - Layer(material=self._materials[0], thickness=0.0, roughness=0.0, name='Vacuum Layer', interface=self._calculator), - Layer(material=self._materials[1], thickness=100.0, roughness=3.0, name='D2O Layer', interface=self._calculator), - Layer(material=self._materials[2], thickness=0.0, roughness=1.2, name='Si Layer', interface=self._calculator), + Layer( + material=self._materials[0], + thickness=0.0, + roughness=0.0, + name='Vacuum Layer', + interface=self._calculator, + ), + Layer( + material=self._materials[1], + thickness=100.0, + roughness=3.0, + name='D2O Layer', + interface=self._calculator, + ), + Layer( + material=self._materials[2], + thickness=0.0, + roughness=1.2, + name='Si Layer', + interface=self._calculator, + ), ] assemblies = [ Multilayer(layers[0], name='Superphase', interface=self._calculator), @@ -611,10 +719,15 @@ def default_model(self): def is_default_model(self, index: int) -> bool: """Check if the model at the given index is a default model. - :param index: Index of the model to check. - :type index: int - :return: True if the model was created as a default placeholder. - :rtype: bool + Parameters + ---------- + index : int + Index of the model to check. + + Returns + ------- + bool + True if the model was created as a default placeholder. """ if index < 0 or index >= len(self._models): return False @@ -630,10 +743,17 @@ def remove_model_at_index(self, index: int) -> None: Adjusts the current model index if necessary. - :param index: Index of the model to remove. - :type index: int - :raises IndexError: If the index is out of range. - :raises ValueError: If trying to remove the last remaining model. + Parameters + ---------- + index : int + Index of the model to remove. + + Raises + ------ + IndexError : + If the index is out of range. + ValueError : + If trying to remove the last remaining model. """ if index < 0 or index >= len(self._models): raise IndexError(f'Model index {index} out of range') @@ -668,18 +788,21 @@ def remove_model_at_index(self, index: int) -> None: self._current_layer_index = 0 def add_material(self, material: MaterialCollection) -> None: + """Add material.""" if material in self._materials: print(f'WARNING: Material {material} is already in material collection') else: self._materials.append(material) def remove_material(self, index: int) -> None: + """Remove material.""" if self._materials[index] in self._get_materials_in_models(): print(f'ERROR: Material {self._materials[index]} is used in models') else: self._materials.pop(index) def _default_info(self): + """Default info.""" return dict( name='DefaultEasyReflectometryProject', short_description='Reflectometry, 1D', @@ -687,6 +810,7 @@ def _default_info(self): ) def create(self): + """Create function.""" if not os.path.exists(self.path): os.makedirs(self.path) os.makedirs(self.path / 'experiments') @@ -696,6 +820,7 @@ def create(self): print(f'ERROR: Directory {self.path} already exists') def save_as_json(self, overwrite=False): + """Save as json.""" if self.path_json.exists() and overwrite: print(f'File already exists {self.path_json}. Overwriting...') self.path_json.unlink() @@ -708,6 +833,7 @@ def save_as_json(self, overwrite=False): print(exception) def load_from_json(self, path: Optional[Union[Path, str]] = None): + """Load from json.""" if path is None: path = self.path_json path = Path(path) @@ -722,6 +848,7 @@ def load_from_json(self, path: Optional[Union[Path, str]] = None): print(f'ERROR: File {path} does not exist') def as_dict(self, include_materials_not_in_model=False): + """As dict.""" project_dict = {} project_dict['info'] = self._info project_dict['with_experiments'] = self._with_experiments @@ -743,6 +870,7 @@ def as_dict(self, include_materials_not_in_model=False): return project_dict def _as_dict_add_materials_not_in_model_dict(self, project_dict: dict): + """As dict add materials not in model dict.""" materials_not_in_model = [] for material in self._materials: if material not in self._get_materials_in_models(): @@ -751,18 +879,24 @@ def _as_dict_add_materials_not_in_model_dict(self, project_dict: dict): project_dict['materials_not_in_model'] = MaterialCollection(materials_not_in_model).as_dict(skip=['interface']) def _as_dict_add_experiments(self, project_dict: dict): + """As dict add experiments.""" project_dict['experiments'] = {} project_dict['experiments_models'] = {} project_dict['experiments_names'] = {} for key, experiment in self._experiments.items(): - project_dict['experiments'][key] = [list(experiment.x), list(experiment.y), list(experiment.ye)] + project_dict['experiments'][key] = [ + list(experiment.x), + list(experiment.y), + list(experiment.ye), + ] if experiment.xe is not None: project_dict['experiments'][key].append(list(experiment.xe)) project_dict['experiments_models'][key] = experiment.model.name project_dict['experiments_names'][key] = experiment.name def from_dict(self, project_dict: dict): + """From dict.""" keys = list(project_dict.keys()) self._info = project_dict['info'] self._with_experiments = project_dict['with_experiments'] @@ -786,6 +920,7 @@ def from_dict(self, project_dict: dict): resolve_all_parameter_dependencies(self) def _from_dict_extract_experiments(self, project_dict: dict) -> Dict[int, DataSet1D]: + """From dict extract experiments.""" experiments = {} for key in project_dict['experiments'].keys(): experiments[int(key)] = DataSet1D( @@ -800,6 +935,7 @@ def _from_dict_extract_experiments(self, project_dict: dict) -> Dict[int, DataSe return experiments def _get_materials_in_models(self) -> MaterialCollection: + """Get materials in models.""" materials_in_model = MaterialCollection(populate_if_none=False) for model in self._models: for assembly in model.sample: @@ -808,6 +944,7 @@ def _get_materials_in_models(self) -> MaterialCollection: return materials_in_model def _replace_collection(self, src_collection: BaseCollection, dst_collection: BaseCollection) -> None: + """Replace collection.""" # Clear the destination collection for i in range(len(dst_collection)): dst_collection.pop(0) @@ -816,4 +953,5 @@ def _replace_collection(self, src_collection: BaseCollection, dst_collection: Ba dst_collection.append(element) def _timestamp_modification(self): + """Timestamp modification.""" self._info['modified'] = datetime.datetime.now().strftime('%d.%m.%Y %H:%M') diff --git a/src/easyreflectometry/sample/__init__.py b/src/easyreflectometry/sample/__init__.py index 4991b975..e6f347ad 100644 --- a/src/easyreflectometry/sample/__init__.py +++ b/src/easyreflectometry/sample/__init__.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from .assemblies.base_assembly import BaseAssembly from .assemblies.bilayer import Bilayer from .assemblies.gradient_layer import GradientLayer diff --git a/src/easyreflectometry/sample/assemblies/base_assembly.py b/src/easyreflectometry/sample/assemblies/base_assembly.py index 68486805..39cb2b18 100644 --- a/src/easyreflectometry/sample/assemblies/base_assembly.py +++ b/src/easyreflectometry/sample/assemblies/base_assembly.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from typing import Any from typing import Optional @@ -8,6 +11,7 @@ class BaseAssembly(BaseCore): """Assembly of layers. + The front layer (front_layer) is the layer the neutron beam starts in, it has an index of 0. The back layer (back_layer) is the final layer from which the unreflected neutron beam is transmitted, its index number depends on the number of finite layers in the system, but it might be accessed at index -1. @@ -38,6 +42,7 @@ def __init__( @property def type(self) -> str: """Get type of the assembly. + Needed by the GUI. """ return self._type @@ -53,7 +58,10 @@ def front_layer(self) -> Optional[Layer]: def front_layer(self, layer: Layer) -> None: """Set the front layer in the assembly. - :param layer: Layer to set as the front layer. + Parameters + ---------- + layer : Layer + Layer to set as the front layer. """ if len(self.layers) == 0: self.layers.append(layer) @@ -72,7 +80,10 @@ def back_layer(self) -> Optional[Layer]: def back_layer(self, layer: Layer) -> None: """Set the back layer in the assembly. - :param layer: Layer to set as the back layer. + Parameters + ---------- + layer : Layer + Layer to set as the back layer. """ if len(self.layers) == 0: @@ -83,18 +94,14 @@ def back_layer(self, layer: Layer) -> None: self.layers[-1] = layer def _setup_thickness_constraints(self) -> None: - """ - Setup thickness constraint, front layer is the deciding layer - """ + """Setup thickness constraint, front layer is the deciding layer.""" independent_param = self.front_layer.thickness for i in range(1, len(self.layers)): self.layers[i].thickness.make_dependent_on(dependency_expression='a', dependency_map={'a': independent_param}) self._thickness_constraints_setup = True def _enable_thickness_constraints(self): - """ - Enable the thickness constraint. - """ + """Enable the thickness constraint.""" if self._thickness_constraints_setup: # Make sure that the thickness constraint is enabled self._setup_thickness_constraints() @@ -103,9 +110,7 @@ def _enable_thickness_constraints(self): raise Exception('Thickness constraints not setup') def _disable_thickness_constraints(self): - """ - Disable the thickness constraint. - """ + """Disable the thickness constraint.""" if self._thickness_constraints_setup: for i in range(1, len(self.layers)): self.layers[i].thickness.make_independent() @@ -113,25 +118,19 @@ def _disable_thickness_constraints(self): raise Exception('Thickness constraints not setup') def _setup_roughness_constraints(self) -> None: - """ - Setup roughness constraint, front layer is the deciding layer - """ + """Setup roughness constraint, front layer is the deciding layer.""" independent_parameter = self.front_layer.roughness for i in range(1, len(self.layers)): self.layers[i].roughness.make_dependent_on(dependency_expression='a', dependency_map={'a': independent_parameter}) self._roughness_constraints_setup = True def _enable_roughness_constraints(self): - """ - Enable the roughness constraint. - """ + """Enable the roughness constraint.""" independent_parameter = self.front_layer.roughness for i in range(1, len(self.layers)): self.layers[i].roughness.make_dependent_on(dependency_expression='a', dependency_map={'a': independent_parameter}) def _disable_roughness_constraints(self): - """ - Disable the roughness constraint. - """ + """Disable the roughness constraint.""" for i in range(1, len(self.layers)): self.layers[i].roughness.make_independent() diff --git a/src/easyreflectometry/sample/assemblies/bilayer.py b/src/easyreflectometry/sample/assemblies/bilayer.py index 21c428f6..5409d359 100644 --- a/src/easyreflectometry/sample/assemblies/bilayer.py +++ b/src/easyreflectometry/sample/assemblies/bilayer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from __future__ import annotations from typing import Any @@ -64,19 +67,29 @@ def __init__( ): """Constructor. - :param front_head_layer: Layer representing the front head part of the bilayer. - :param front_tail_layer: Layer representing the front tail part of the bilayer. + Parameters + ---------- + front_head_layer : LayerAreaPerMolecule | None, optional + Layer representing the front head part of the bilayer. By default, None. + front_tail_layer : LayerAreaPerMolecule | None, optional + Layer representing the front tail part of the bilayer. A back tail layer is created internally with its thickness, area per molecule, - and solvent fraction constrained to match this layer. - :param back_head_layer: Layer representing the back head part of the bilayer. - :param name: Name for bilayer, defaults to 'EasyBilayer'. - :param unique_name: Unique name for internal object tracking, defaults to `None`. - :param constrain_heads: When `True`, the back head layer thickness and area per + and solvent fraction constrained to match this layer. By default, None. + back_head_layer : LayerAreaPerMolecule | None, optional + Layer representing the back head part of the bilayer. By default, None. + name : str, optional + Name for bilayer. By default, 'EasyBilayer'. + unique_name : str | None, optional + Unique name for internal object tracking. By default, None. + constrain_heads : bool, optional + When `True`, the back head layer thickness and area per molecule are constrained to match the front head layer. Solvent fraction - (hydration) remains independent on each side. Defaults to `True`. - :param conformal_roughness: When `True`, all four layer interfaces share - the same roughness value, controlled by the front head layer. Defaults to `True`. - :param interface: Calculator interface, defaults to `None`. + (hydration) remains independent on each side. By default, True. + conformal_roughness : bool, optional + When `True`, all four layer interfaces share + the same roughness value, controlled by the front head layer. By default, True. + interface : Any, optional + Calculator interface. By default, None. """ # Generate unique name for nested objects if unique_name is None: @@ -154,10 +167,19 @@ def _create_default_head_layer( ) -> LayerAreaPerMolecule: """Create a default head layer with DPPC head group parameters. - :param unique_name: Base unique name for internal object tracking. - :param name_suffix: Suffix for layer name ('Front' or 'Back'). - :param interface: Calculator interface, defaults to `None`. - :return: A new LayerAreaPerMolecule for the head group. + Parameters + ---------- + unique_name : str + Base unique name for internal object tracking. + name_suffix : str + Suffix for layer name ('Front' or 'Back'). + interface : Any, optional + Calculator interface. By default, None. + + Returns + ------- + LayerAreaPerMolecule + A new LayerAreaPerMolecule for the head group. """ solvent = Material( sld=DEFAULTS['solvent']['sld'], @@ -185,9 +207,17 @@ def _create_default_tail_layer( ) -> LayerAreaPerMolecule: """Create a default tail layer with DPPC tail group parameters. - :param unique_name: Base unique name for internal object tracking. - :param interface: Calculator interface, defaults to `None`. - :return: A new LayerAreaPerMolecule for the tail group. + Parameters + ---------- + unique_name : str + Base unique name for internal object tracking. + interface : Any, optional + Calculator interface. By default, None. + + Returns + ------- + LayerAreaPerMolecule + A new LayerAreaPerMolecule for the tail group. """ solvent = Material( sld=DEFAULTS['solvent']['sld'], @@ -216,10 +246,19 @@ def _create_back_tail_layer( ) -> LayerAreaPerMolecule: """Create a back tail layer with initial values copied from the front tail layer. - :param front_tail_layer: The front tail layer to copy initial values from. - :param unique_name: Base unique name for internal object tracking. - :param interface: Calculator interface, defaults to `None`. - :return: A new LayerAreaPerMolecule for the back tail. + Parameters + ---------- + front_tail_layer : LayerAreaPerMolecule + The front tail layer to copy initial values from. + unique_name : str + Base unique name for internal object tracking. + interface : Any, optional + Calculator interface. By default, None. + + Returns + ------- + LayerAreaPerMolecule + A new LayerAreaPerMolecule for the back tail. """ solvent = Material( sld=DEFAULTS['solvent']['sld'], @@ -312,7 +351,10 @@ def constrain_heads(self, status: bool) -> None: are constrained to match the front head layer. Solvent fraction (hydration) remains independent. - :param status: Boolean for the constraint status. + Parameters + ---------- + status : bool + Boolean for the constraint status. """ if status: self._enable_head_constraints() @@ -354,7 +396,10 @@ def conformal_roughness(self, status: bool) -> None: When enabled, all layers share the same roughness parameter (controlled by the front head layer). - :param status: Boolean for the constraint status. + Parameters + ---------- + status : bool + Boolean for the constraint status. """ if status: self._setup_roughness_constraints() @@ -367,7 +412,10 @@ def conformal_roughness(self, status: bool) -> None: def constrain_solvent_roughness(self, solvent_roughness: Parameter) -> None: """Add the constraint to the solvent roughness. - :param solvent_roughness: The solvent roughness parameter. + Parameters + ---------- + solvent_roughness : Parameter + The solvent roughness parameter. """ if not self.conformal_roughness: raise ValueError('Roughness must be conformal to use this function.') @@ -395,16 +443,28 @@ def constrain_multiple_contrast( Makes this bilayer's parameters dependent on another_contrast's parameters, so that changes to another_contrast propagate to this bilayer. - :param another_contrast: The bilayer to constrain to. - :param front_head_thickness: Constrain front head thickness. - :param back_head_thickness: Constrain back head thickness. - :param tail_thickness: Constrain tail thickness. - :param front_head_area_per_molecule: Constrain front head area per molecule. - :param back_head_area_per_molecule: Constrain back head area per molecule. - :param tail_area_per_molecule: Constrain tail area per molecule. - :param front_head_fraction: Constrain front head solvent fraction. - :param back_head_fraction: Constrain back head solvent fraction. - :param tail_fraction: Constrain tail solvent fraction. + Parameters + ---------- + another_contrast : Bilayer + The bilayer to constrain to. + front_head_thickness : bool, optional + Constrain front head thickness. By default, True. + back_head_thickness : bool, optional + Constrain back head thickness. By default, True. + tail_thickness : bool, optional + Constrain tail thickness. By default, True. + front_head_area_per_molecule : bool, optional + Constrain front head area per molecule. By default, True. + back_head_area_per_molecule : bool, optional + Constrain back head area per molecule. By default, True. + tail_area_per_molecule : bool, optional + Constrain tail area per molecule. By default, True. + front_head_fraction : bool, optional + Constrain front head solvent fraction. By default, True. + back_head_fraction : bool, optional + Constrain back head solvent fraction. By default, True. + tail_fraction : bool, optional + Constrain tail solvent fraction. By default, True. """ if front_head_thickness: self.front_head_layer.thickness.make_dependent_on( @@ -479,7 +539,10 @@ def as_dict(self, skip: list[str] | None = None) -> dict: The resulting dict matches the parameters in __init__ - :param skip: List of keys to skip, defaults to `None`. + Parameters + ---------- + skip : list[str] | None, optional + List of keys to skip. By default, None. """ this_dict = super().as_dict(skip=skip) this_dict['front_head_layer'] = self.front_head_layer.as_dict(skip=skip) diff --git a/src/easyreflectometry/sample/assemblies/gradient_layer.py b/src/easyreflectometry/sample/assemblies/gradient_layer.py index 38771e80..1e08bb2e 100644 --- a/src/easyreflectometry/sample/assemblies/gradient_layer.py +++ b/src/easyreflectometry/sample/assemblies/gradient_layer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from typing import Optional from easyscience import global_object @@ -11,8 +14,8 @@ class GradientLayer(BaseAssembly): """A set of discrete gradient layers changing from the front to the back material. - The front layer is where the neutron beam starts in, it has an index of 0. + The front layer is where the neutron beam starts in, it has an index of 0. """ def __init__( @@ -28,13 +31,24 @@ def __init__( ): """Constructor. - :param front_material: Material of front of the layer - :param back_material: Material of back of the layer - :param thickness: Thicknkess of the layer - :param roughness: Roughness of the layer - :param discretisation_elements: Number of discrete layers - :param name: Name for gradient layer, defaults to 'EasyGradienLayer'. - :param interface: Calculator interface, defaults to `None`. + Parameters + ---------- + unique_name : Optional[str], optional + By default, None. + front_material : Optional[Material], optional + Material of front of the layer. By default, None. + back_material : Optional[Material], optional + Material of back of the layer. By default, None. + thickness : Optional[float], optional + Thicknkess of the layer. By default, 2.0. + roughness : Optional[float], optional + Roughness of the layer. By default, 0.2. + discretisation_elements : int, optional + Number of discrete layers. By default, 10. + name : str, optional + Name for gradient layer. By default, 'EasyGradienLayer'. + interface : + Calculator interface. By default, None. """ if front_material is None: @@ -82,7 +96,10 @@ def thickness(self) -> float: def thickness(self, thickness: float) -> None: """Set the thickness of the gradient layer. - :param thickness: Thickness of the gradient layer in Angstroms. + Parameters + ---------- + thickness : float + Thickness of the gradient layer in Angstroms. """ self.front_layer.thickness.value = thickness / self._discretisation_elements @@ -95,7 +112,10 @@ def roughness(self) -> float: def roughness(self, roughness: float) -> None: """Set the roughness of the gradient layer. - :param roughness: Roughness of the gradient layer in Angstroms. + Parameters + ---------- + roughness : float + Roughness of the gradient layer in Angstroms. """ self.front_layer.roughness.value = roughness @@ -103,7 +123,7 @@ def roughness(self, roughness: float) -> None: def _dict_repr(self) -> dict[str, str]: """A simplified dict representation.""" return { - 'thickness': float(self.thickness), # Conversion to float is necessary to prevent property reference in dict + 'thickness': float(self.thickness), # Conversion to float is necessary to prevent property reference in dict 'discretisation_elements': int(self._discretisation_elements), # Same as above 'back_layer': self.back_layer._dict_repr, 'front_layer': self.front_layer._dict_repr, @@ -111,9 +131,13 @@ def _dict_repr(self) -> dict[str, str]: def as_dict(self, skip: Optional[list[str]] = None) -> dict: """Produces a cleaned dict using a custom as_dict method to skip necessary things. + The resulting dict matches the parameters in __init__ - :param skip: List of keys to skip, defaults to `None`. + Parameters + ---------- + skip : Optional[list[str]], optional + List of keys to skip. By default, None. """ this_dict = super().as_dict(skip=skip) # Determined in __init__ @@ -126,6 +150,7 @@ def _linear_gradient( back_value: float, discretisation_elements: int, ) -> list[float]: + """Linear gradient.""" discrete_step = (back_value - front_value) / discretisation_elements if discrete_step != 0: # Both front and back values are included @@ -141,6 +166,7 @@ def _prepare_gradient_layers( discretisation_elements: int, interface=None, ) -> LayerCollection: + """Prepare gradient layers.""" gradient_sld = _linear_gradient( front_value=front_material.sld.value, back_value=back_material.sld.value, diff --git a/src/easyreflectometry/sample/assemblies/multilayer.py b/src/easyreflectometry/sample/assemblies/multilayer.py index 360db10a..0238f3ae 100644 --- a/src/easyreflectometry/sample/assemblies/multilayer.py +++ b/src/easyreflectometry/sample/assemblies/multilayer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from __future__ import annotations from typing import Optional @@ -10,6 +13,7 @@ class Multilayer(BaseAssembly): """A multi layer is build from a single or a list of `Layer` or `LayerCollection`. + The multi layer will arrange the layers as slabs, allowing the reflectometry to be determined from them. The front layer is where the neutron beam starts in, it has an index of 0. @@ -30,10 +34,20 @@ def __init__( ): """Constructor. - :param layers: The layers that make up the multi-layer. - :param name: Name for multi layer, defaults to 'EasyMultilayer'. - :param interface: Calculator interface, defaults to `None`. - :param type: Type of the constructed instance, defaults to 'Multi-layer' + Parameters + ---------- + populate_if_none : Optional[bool], optional + By default, True. + unique_name : Optional[str], optional + By default, None. + layers : Union[Layer, list[Layer], LayerCollection, None], optional + The layers that make up the multi-layer. By default, None. + name : str, optional + Name for multi layer. By default, 'EasyMultilayer'. + interface : + Calculator interface. By default, None. + type : str, optional + Type of the constructed instance. By default, 'Multi-layer'. """ if layers is None: if populate_if_none: @@ -53,7 +67,10 @@ def __init__( def add_layer(self, *layers: tuple[Layer]) -> None: """Add a layer to the multi layer. - :param layers: Layers to add to the multi layer. + Parameters + ---------- + *layers : tuple[Layer] + Layers to add to the multi layer. """ for arg in layers: if issubclass(arg.__class__, Layer): @@ -64,8 +81,10 @@ def add_layer(self, *layers: tuple[Layer]) -> None: def duplicate_layer(self, idx: int) -> None: """Duplicate a given layer. - :param idx: index of layer to duplicate. - :type idx: int + Parameters + ---------- + idx : int + Index of layer to duplicate. """ to_duplicate = self.layers[idx] duplicate_layer = Layer( @@ -79,7 +98,10 @@ def duplicate_layer(self, idx: int) -> None: def remove_layer(self, idx: int) -> None: """Remove a layer from the item. - :param idx: index of layer to remove + Parameters + ---------- + idx : int + Index of layer to remove. """ if self.interface is not None: self.interface().remove_layer_from_item(self.layers[idx].unique_name, self.unique_name) @@ -93,11 +115,18 @@ def _dict_repr(self) -> dict: @classmethod def from_dict(cls, data: dict) -> Multilayer: - """ - Create a Multilayer from a dictionary. - - :param data: dictionary of the Multilayer - :return: Multilayer + """Create a Multilayer from a dictionary. + + Parameters + ---------- + cls : + data : dict + Dictionary of the Multilayer. + + Returns + ------- + Multilayer + Multilayer. """ multilayer = super().from_dict(data) return multilayer diff --git a/src/easyreflectometry/sample/assemblies/repeating_multilayer.py b/src/easyreflectometry/sample/assemblies/repeating_multilayer.py index 7c4ecbcc..cb396836 100644 --- a/src/easyreflectometry/sample/assemblies/repeating_multilayer.py +++ b/src/easyreflectometry/sample/assemblies/repeating_multilayer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from typing import Optional from typing import Union @@ -22,8 +25,7 @@ class RepeatingMultilayer(Multilayer): - """ - A repeating multi layer is build from a `Multilayer` and which it repeats + """A repeating multi layer is build from a `Multilayer` and which it repeats for a given number of times. This enables a computational efficiency in many reflectometry engines as the operation can be performed for a single `Multilayer` and cheaply combined for the appropriate number of @@ -46,10 +48,20 @@ def __init__( ): """Constructor. - :param layers: The layers that make up the multi-layer that will be repeated. - :param repetitions: Number of repetitions of the given series of layers - :param name: Name for the repeating multi layer, defaults to 'EasyRepeatingMultilayer'. - :param interface: Calculator interface, defaults to `None`. + Parameters + ---------- + populate_if_none : bool, optional + By default, True. + unique_name : Optional[str], optional + By default, None. + layers : Union[LayerCollection, Layer, list[Layer], None], optional + The layers that make up the multi-layer that will be repeated. By default, None. + repetitions : Union[Parameter, int, None], optional + Number of repetitions of the given series of layers. By default, None. + name : str, optional + Name for the repeating multi layer. By default, 'EasyRepeatingMultilayer'. + interface : + Calculator interface. By default, None. """ if unique_name is None: unique_name = global_object.generate_unique_name(self.__class__.__name__) diff --git a/src/easyreflectometry/sample/assemblies/surfactant_layer.py b/src/easyreflectometry/sample/assemblies/surfactant_layer.py index 6cbd2c6b..81c9c36c 100644 --- a/src/easyreflectometry/sample/assemblies/surfactant_layer.py +++ b/src/easyreflectometry/sample/assemblies/surfactant_layer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from __future__ import annotations from typing import Optional @@ -37,12 +40,22 @@ def __init__( ): """Constructor. - :param tail_layer: Layer representing the tail part of the surfactant layer. - :param head_layer: Layer representing the head part of the surfactant layer. - :param name: Name for surfactant layer, defaults to 'EasySurfactantLayer'. - :param constrain_area_per_molecule: Constrain the area per molecule, defaults to `False`. - :param conformal_roughness: Constrain the roughness to be the same for both layers, defaults to `False`. - :param interface: Calculator interface, defaults to `None`. + Parameters + ---------- + unique_name : Optional[str], optional + By default, None. + tail_layer : Optional[LayerAreaPerMolecule], optional + Layer representing the tail part of the surfactant layer. By default, None. + head_layer : Optional[LayerAreaPerMolecule], optional + Layer representing the head part of the surfactant layer. By default, None. + name : str, optional + Name for surfactant layer. By default, 'EasySurfactantLayer'. + constrain_area_per_molecule : bool, optional + Constrain the area per molecule. By default, False. + conformal_roughness : bool, optional + Constrain the roughness to be the same for both layers. By default, False. + interface : + Calculator interface. By default, None. """ # We need to generate a unique name to create the nested objects if unique_name is None: @@ -138,7 +151,10 @@ def constrain_area_per_molecule(self, status: bool): """Set the status for the area per molecule constraint such that the head and tail layers have the same area per molecule. - :param status: Boolean description the wanted of the constraint. + Parameters + ---------- + status : bool + Boolean description the wanted of the constraint. """ if status: independent_param = self.tail_layer._area_per_molecule @@ -158,7 +174,10 @@ def conformal_roughness(self) -> bool: def conformal_roughness(self, status: bool): """Set the status for the roughness to be the same for both layers. - :param status: Boolean description the wanted of the constraint. + Parameters + ---------- + status : bool + Boolean description the wanted of the constraint. """ if status: self._enable_roughness_constraints() @@ -170,7 +189,10 @@ def conformal_roughness(self, status: bool): def constrain_solvent_roughness(self, solvent_roughness: Parameter): """Add the constraint to the solvent roughness. - :param solvent_roughness: The solvent roughness parameter. + Parameters + ---------- + solvent_roughness : Parameter + The solvent roughness parameter. """ if not self.conformal_roughness: raise ValueError('Roughness must be conformal to use this function.') @@ -189,7 +211,22 @@ def constrain_multiple_contrast( ): """Constrain structural parameters between surfactant layer objects. - :param another_contrast: The surfactant layer to constrain + Parameters + ---------- + tail_layer_fraction : bool, optional + By default, True. + head_layer_fraction : bool, optional + By default, True. + tail_layer_area_per_molecule : bool, optional + By default, True. + head_layer_area_per_molecule : bool, optional + By default, True. + tail_layer_thickness : bool, optional + By default, True. + head_layer_thickness : bool, optional + By default, True. + another_contrast : SurfactantLayer + The surfactant layer to constrain. """ if head_layer_thickness: self.head_layer.thickness.make_dependent_on( @@ -241,9 +278,13 @@ def _dict_repr(self) -> dict: def as_dict(self, skip: Optional[list[str]] = None) -> dict: """Produces a cleaned dict using a custom as_dict method to skip necessary things. + The resulting dict matches the parameters in __init__ - :param skip: List of keys to skip, defaults to `None`. + Parameters + ---------- + skip : Optional[list[str]], optional + List of keys to skip. By default, None. """ this_dict = super().as_dict(skip=skip) this_dict['tail_layer'] = self.tail_layer.as_dict(skip=skip) diff --git a/src/easyreflectometry/sample/base_core.py b/src/easyreflectometry/sample/base_core.py index b4c3f3ed..4cf600a6 100644 --- a/src/easyreflectometry/sample/base_core.py +++ b/src/easyreflectometry/sample/base_core.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from abc import abstractmethod from easyscience import ObjBase as BaseObj @@ -12,6 +15,7 @@ def __init__( interface, **kwargs, ): + """Init function.""" super().__init__(name=name, **kwargs) # Updates interface using property in base object @@ -21,11 +25,12 @@ def __init__( def _dict_repr(self) -> dict[str, str]: ... def __repr__(self) -> str: - """ - String representation of the layer. + """String representation of the layer. - :return: a string representation of the layer - :rtype: str + Returns + ------- + str + A string representation of the layer. """ return yaml_dump(self._dict_repr) diff --git a/src/easyreflectometry/sample/collections/base_collection.py b/src/easyreflectometry/sample/collections/base_collection.py index 53d16b51..28d494a5 100644 --- a/src/easyreflectometry/sample/collections/base_collection.py +++ b/src/easyreflectometry/sample/collections/base_collection.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from typing import List from typing import Optional @@ -16,6 +19,7 @@ def __init__( unique_name: Optional[str] = None, **kwargs, ): + """Init function.""" if unique_name is None: unique_name = global_object.generate_unique_name(self.__class__.__name__) @@ -27,24 +31,33 @@ def __init__( self.populate_if_none = False def __repr__(self) -> str: - """ - String representation of the collection. + """String representation of the collection. - :return: a string representation of the collection + Returns + ------- + str + A string representation of the collection. """ return yaml_dump(self._dict_repr) @property def names(self) -> list: - """ - :returns: list of names for the elements in the collection. + """Names function. + + Returns + ------- + s : list + List of names for the elements in the collection. """ return [i.name for i in self] def move_up(self, index: int): """Move the element at the given index up in the collection. - :param index: Index of the element to move up. + Parameters + ---------- + index : int + Index of the element to move up. """ if index == 0: return @@ -53,34 +66,43 @@ def move_up(self, index: int): def move_down(self, index: int): """Move the element at the given index down in the collection. - :param index: Index of the element to move down. + Parameters + ---------- + index : int + Index of the element to move down. """ if index == len(self) - 1: return self.insert(index + 1, self.pop(index)) def remove(self, index: int): - """ - Remove an element from the elements. + """Remove an element from the elements. - :param index: Index of the element to remove + Parameters + ---------- + index : int + Index of the element to remove. """ self.pop(index) @property def _dict_repr(self) -> dict: - """ - A simplified dict representation. + """A simplified dict representation. - :return: Simple dictionary + Returns + ------- + dict + Simple dictionary. """ return {self.name: [i._dict_repr for i in self]} def as_dict(self, skip: Optional[List[str]] = None) -> dict: - """ - Create a dictionary representation of the collection. + """Create a dictionary representation of the collection. - :return: A dictionary representation of the collection + Returns + ------- + dict + A dictionary representation of the collection. """ if skip is None: skip = [] @@ -92,4 +114,5 @@ def as_dict(self, skip: Optional[List[str]] = None) -> dict: return this_dict def __deepcopy__(self, memo): + """Deepcopy function.""" return self.from_dict(self.as_dict(skip=['unique_name'])) diff --git a/src/easyreflectometry/sample/collections/layer_collection.py b/src/easyreflectometry/sample/collections/layer_collection.py index 0761f861..4a9e5791 100644 --- a/src/easyreflectometry/sample/collections/layer_collection.py +++ b/src/easyreflectometry/sample/collections/layer_collection.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' from typing import Optional @@ -16,6 +19,7 @@ def __init__( populate_if_none: bool = True, # Needed to match as_dict signature from BaseCollection **kwargs, ): + """Init function.""" if not layers: layers = [] @@ -24,7 +28,10 @@ def __init__( def add_layer(self, layer: Optional[Layer] = None): """Add a layer to the collection. - :param layer: Layer to add. + Parameters + ---------- + layer : Optional[Layer], optional + Layer to add. By default, None. """ if layer is None: layer = Layer( @@ -36,7 +43,11 @@ def add_layer(self, layer: Optional[Layer] = None): def duplicate_layer(self, index: int): """Duplicate a layer in the collection. - :param layer: Assembly to add. + Parameters + ---------- + index : int + layer : + Assembly to add. """ to_be_duplicated = self[index] duplicate = Layer.from_dict(to_be_duplicated.as_dict(skip=['unique_name'])) diff --git a/src/easyreflectometry/sample/collections/material_collection.py b/src/easyreflectometry/sample/collections/material_collection.py index a97f89d9..6ae49692 100644 --- a/src/easyreflectometry/sample/collections/material_collection.py +++ b/src/easyreflectometry/sample/collections/material_collection.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' from typing import Optional from typing import Tuple @@ -8,6 +11,7 @@ # Needs to be a function, elements are added to the global_object.map def DEFAULT_ELEMENTS(interface): + """Default elements.""" return ( Material(sld=0.0, isld=0.0, name='Air', interface=interface), Material(sld=6.335, isld=0.0, name='D2O', interface=interface), @@ -25,6 +29,7 @@ def __init__( populate_if_none: bool = True, **kwargs, ): + """Init function.""" if not materials: # Empty tuple if no materials are provided if populate_if_none: materials = DEFAULT_ELEMENTS(interface) @@ -42,7 +47,10 @@ def __init__( def add_material(self, material: Optional[Material] = None): """Add a material to the collection. - :param material: Material to add. + Parameters + ---------- + material : Optional[Material], optional + Material to add. By default, None. """ if material is None: material = Material(sld=0.0, isld=0.0, name='Material added') @@ -52,7 +60,11 @@ def add_material(self, material: Optional[Material] = None): def duplicate_material(self, index: int): """Duplicate a material in the collection. - :param material: Assembly to add. + Parameters + ---------- + index : int + material : + Assembly to add. """ to_be_duplicated = self[index] duplicate = Material.from_dict(to_be_duplicated.as_dict(skip=['unique_name'])) diff --git a/src/easyreflectometry/sample/collections/sample.py b/src/easyreflectometry/sample/collections/sample.py index 65c2a76b..73d26e8a 100644 --- a/src/easyreflectometry/sample/collections/sample.py +++ b/src/easyreflectometry/sample/collections/sample.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from __future__ import annotations __author__ = 'github.com/arm61' @@ -15,7 +18,7 @@ # Needs to be a function, elements are added to the global_object.map def DEFAULT_ELEMENTS(interface): - """:meta private:""" + """:meta private:.""" return ( Multilayer(interface=interface), Multilayer(interface=interface), @@ -36,9 +39,20 @@ def __init__( ): """Constructor. - :param args: The assemblies in the sample. - :param name: Name of the sample, defaults to 'EasySample'. - :param interface: Calculator interface, defaults to `None`. + Parameters + ---------- + **kwargs : + populate_if_none : bool, optional + By default, True. + unique_name : Optional[str], optional + By default, None. + *assemblies : Optional[List[BaseAssembly]] + args : + The assemblies in the sample. + name : str, optional + Name of the sample. By default, 'EasySample'. + interface : + Calculator interface. By default, None. """ if not assemblies: if populate_if_none: @@ -54,7 +68,10 @@ def __init__( def add_assembly(self, assembly: Optional[BaseAssembly] = None): """Add an assembly to the sample. - :param assembly: Assembly to add. + Parameters + ---------- + assembly : Optional[BaseAssembly], optional + Assembly to add. By default, None. """ if assembly is None: assembly = Multilayer( @@ -66,7 +83,11 @@ def add_assembly(self, assembly: Optional[BaseAssembly] = None): def duplicate_assembly(self, index: int): """Add an assembly to the sample. - :param assembly: Assembly to add. + Parameters + ---------- + index : int + assembly : + Assembly to add. """ to_be_duplicated = self[index] if isinstance(to_be_duplicated, Multilayer): @@ -81,21 +102,30 @@ def duplicate_assembly(self, index: int): def move_up(self, index: int): """Move the assembly at the given index up in the sample. - :param index: Index of the assembly to move up. + Parameters + ---------- + index : int + Index of the assembly to move up. """ super().move_up(index) def move_down(self, index: int): """Move the assembly at the given index down in the sample. - :param index: Index of the assembly to move down. + Parameters + ---------- + index : int + Index of the assembly to move down. """ super().move_down(index) def remove_assembly(self, index: int): """Remove the assembly at the given index from the sample. - :param index: Index of the assembly to remove. + Parameters + ---------- + index : int + Index of the assembly to remove. """ self.pop(index) @@ -116,9 +146,13 @@ def subphase(self) -> Layer: # Representation def as_dict(self, skip: Optional[List[str]] = None) -> dict: """Produces a cleaned dict using a custom as_dict method to skip necessary things. + The resulting dict matches the parameters in __init__ - :param skip: List of keys to skip, defaults to `None`. + Parameters + ---------- + skip : Optional[List[str]], optional + List of keys to skip. By default, None. """ this_dict = super().as_dict(skip=skip) this_dict['populate_if_none'] = self.populate_if_none diff --git a/src/easyreflectometry/sample/elements/layers/layer.py b/src/easyreflectometry/sample/elements/layers/layer.py index 513b18f9..8b824ed8 100644 --- a/src/easyreflectometry/sample/elements/layers/layer.py +++ b/src/easyreflectometry/sample/elements/layers/layer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' from typing import Optional from typing import Union @@ -53,11 +56,20 @@ def __init__( ): """Constructor. - :param material: The material for the layer. - :param thickness: Layer thickness in Angstrom. - :param roughness: Upper roughness on the layer in Angstrom. - :param name: Name of the layer, defaults to 'EasyLayer' - :param interface: Interface object, defaults to `None` + Parameters + ---------- + unique_name : Optional[str], optional + By default, None. + material : Union[Material, None], optional + The material for the layer. By default, None. + thickness : Union[Parameter, float, None], optional + Layer thickness in Angstrom. By default, None. + roughness : Union[Parameter, float, None], optional + Upper roughness on the layer in Angstrom. By default, None. + name : str, optional + Name of the layer. By default, 'EasyLayer'. + interface : + Interface object. By default, None. """ if material is None: material = Material(interface=interface) @@ -95,7 +107,10 @@ def __init__( def assign_material(self, material: Material) -> None: """Assign a material to the layer interface. - :param material: The material to assign to the layer. + Parameters + ---------- + material : Material + The material to assign to the layer. """ self.material = material if self.interface is not None: diff --git a/src/easyreflectometry/sample/elements/layers/layer_area_per_molecule.py b/src/easyreflectometry/sample/elements/layers/layer_area_per_molecule.py index dbda1473..9053aa95 100644 --- a/src/easyreflectometry/sample/elements/layers/layer_area_per_molecule.py +++ b/src/easyreflectometry/sample/elements/layers/layer_area_per_molecule.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from typing import Optional from typing import Union @@ -50,7 +53,6 @@ class LayerAreaPerMolecule(Layer): """The `LayerAreaPerMolecule` class allows a layer to be defined in terms of some molecular formula an area per molecule, and a solvent. - """ # Added in __init__ @@ -78,14 +80,26 @@ def __init__( ): """Constructor. - :param molecular_formula: Formula for the molecule in the layer. - :param thickness: Layer thickness in Angstrom. - :param solvent: Solvent containing the molecule. - :param solvent_fraction: Fraction of solvent in layer. Fx solvation or surface coverage. - :param area_per_molecule: Area per molecule in the layer - :param roughness: Upper roughness on the layer in Angstrom. - :param name: Name of the layer, defaults to "EasyLayerAreaPerMolecule" - :param interface: Interface object, defaults to `None` + Parameters + ---------- + unique_name : Optional[str], optional + By default, None. + molecular_formula : Union[str, None], optional + Formula for the molecule in the layer. By default, None. + thickness : Union[Parameter, float, None], optional + Layer thickness in Angstrom. By default, None. + solvent : Union[Material, None], optional + Solvent containing the molecule. By default, None. + solvent_fraction : Union[Parameter, float, None], optional + Fraction of solvent in layer. Fx solvation or surface coverage. By default, None. + area_per_molecule : Union[Parameter, float, None], optional + Area per molecule in the layer. By default, None. + roughness : Union[Parameter, float, None], optional + Upper roughness on the layer in Angstrom. By default, None. + name : str, optional + Name of the layer. By default, 'EasyLayerAreaPerMolecule'. + interface : + Interface object. By default, None. """ if unique_name is None: unique_name = global_object.generate_unique_name(self.__class__.__name__) @@ -190,7 +204,10 @@ def area_per_molecule(self) -> float: def area_per_molecule(self, new_area_per_molecule: float) -> None: """Set the area per molecule. - :param new_area_per_molecule: New area per molecule. + Parameters + ---------- + new_area_per_molecule : float + New area per molecule. """ if new_area_per_molecule < 0: raise ValueError('new_area_per_molecule must be greater than 0.0.') @@ -210,7 +227,10 @@ def solvent(self) -> Material: def solvent(self, new_solvent: Material) -> None: """Set the solvent material. - :param new_solvent: New solvent material. + Parameters + ---------- + new_solvent : Material + New solvent material. """ self.material.solvent = new_solvent @@ -222,6 +242,7 @@ def solvent_fraction_parameter(self) -> float: @property def solvent_fraction(self) -> float: """Get the fraction of the layer occupied by the solvent. + This could be a result of either water solvating the molecule, or incomplete surface coverage of the molecules. """ return self.material.solvent_fraction @@ -229,9 +250,13 @@ def solvent_fraction(self) -> float: @solvent_fraction.setter def solvent_fraction(self, solvent_fraction: float) -> None: """Set the fraction of the layer occupied by the solvent. + This could be a result of either water solvating the molecule, or incomplete surface coverage of the molecules. - :param solvent_fraction: Fraction of layer described by the solvent. + Parameters + ---------- + solvent_fraction : float + Fraction of layer described by the solvent. """ self.material.solvent_fraction = solvent_fraction @@ -244,7 +269,10 @@ def molecular_formula(self) -> str: def molecular_formula(self, formula_string: str) -> None: """Set the formula of the molecule in the material. - :param formula_string: String that defines the molecular formula. + Parameters + ---------- + formula_string : str + String that defines the molecular formula. """ self._molecular_formula = formula_string scattering_length = neutron_scattering_length(formula_string) @@ -257,7 +285,10 @@ def molecular_formula(self, formula_string: str) -> None: @property def _dict_repr(self) -> dict[str, str]: - """Dictionary representation of the `area_per_molecule` object. Produces a simple dictionary""" + """Dictionary representation of the `area_per_molecule` object. + + Produces a simple dictionary. + """ dict_repr = super()._dict_repr dict_repr['molecular_formula'] = self._molecular_formula dict_repr['area_per_molecule'] = f'{self.area_per_molecule:.2f} {self._area_per_molecule.unit}' @@ -265,9 +296,13 @@ def _dict_repr(self) -> dict[str, str]: def as_dict(self, skip: Optional[list[str]] = None) -> dict[str, str]: """Produces a cleaned dict using a custom as_dict method to skip necessary things. + The resulting dict matches the parameters in __init__ - :param skip: List of keys to skip, defaults to `None`. + Parameters + ---------- + skip : Optional[list[str]], optional + List of keys to skip. By default, None. """ this_dict = super().as_dict(skip=skip) this_dict['solvent_fraction'] = self.material._fraction.as_dict(skip=skip) diff --git a/src/easyreflectometry/sample/elements/materials/material.py b/src/easyreflectometry/sample/elements/materials/material.py index 8c030031..39bb8f77 100644 --- a/src/easyreflectometry/sample/elements/materials/material.py +++ b/src/easyreflectometry/sample/elements/materials/material.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' from typing import Optional @@ -49,10 +52,18 @@ def __init__( ): """Constructor. - :param sld: Real scattering length density. - :param isld: Imaginary scattering length density. - :param name: Name of the material, defaults to 'EasyMaterial'. - :param interface: Calculator interface, defaults to `None`. + Parameters + ---------- + unique_name : Optional[str], optional + By default, None. + sld : Union[Parameter, float, None], optional + Real scattering length density. By default, None. + isld : Union[Parameter, float, None], optional + Imaginary scattering length density. By default, None. + name : str, optional + Name of the material. By default, 'EasyMaterial'. + interface : + Calculator interface. By default, None. """ if unique_name is None: unique_name = global_object.generate_unique_name(self.__class__.__name__) diff --git a/src/easyreflectometry/sample/elements/materials/material_density.py b/src/easyreflectometry/sample/elements/materials/material_density.py index 85a3bf1b..b85bda98 100644 --- a/src/easyreflectometry/sample/elements/materials/material_density.py +++ b/src/easyreflectometry/sample/elements/materials/material_density.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from typing import Optional from typing import Union @@ -54,10 +57,18 @@ def __init__( ): """Constructor. - :param chemical_structure: Chemical formula for the material. - :param density: Mass density for the material. - :param name: Identifier, defaults to `EasyMaterialDensity`. - :param interface: Interface object, defaults to `None`. + Parameters + ---------- + unique_name : Optional[str], optional + By default, None. + chemical_structure : Union[str, None], optional + Chemical formula for the material. By default, None. + density : Union[Parameter, float, None], optional + Mass density for the material. By default, None. + name : str, optional + Identifier. By default, 'EasyMaterialDensity'. + interface : + Interface object. By default, None. """ if unique_name is None: unique_name = global_object.generate_unique_name(self.__class__.__name__) @@ -130,7 +141,10 @@ def chemical_structure(self) -> str: def chemical_structure(self, structure_string: str) -> None: """Set the chemical structure string. - :param structure_string: String that defines the chemical structure. + Parameters + ---------- + structure_string : str + String that defines the chemical structure. """ self._chemical_structure = structure_string scattering_length = neutron_scattering_length(structure_string) @@ -147,9 +161,13 @@ def _dict_repr(self) -> dict[str, str]: def as_dict(self, skip: list = []) -> dict[str, str]: """Produces a cleaned dict using a custom as_dict method to skip necessary things. + The resulting dict matches the parameters in __init__ - :param skip: List of keys to skip, defaults to `None`. + Parameters + ---------- + skip : list, optional + List of keys to skip. By default, []. """ this_dict = super().as_dict(skip=skip) # From Material diff --git a/src/easyreflectometry/sample/elements/materials/material_mixture.py b/src/easyreflectometry/sample/elements/materials/material_mixture.py index a54f3d9d..c999093e 100644 --- a/src/easyreflectometry/sample/elements/materials/material_mixture.py +++ b/src/easyreflectometry/sample/elements/materials/material_mixture.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from typing import Optional from typing import Union @@ -41,11 +44,20 @@ def __init__( ): """Constructor. - :param material_a: The first material. - :param material_b: The second material. - :param fraction: The fraction of material_b in material_a. - :param name: Name of the material, defaults to None that causes the name to be constructed. - :param interface: Calculator interface, defaults to `None`. + Parameters + ---------- + unique_name : Optional[str], optional + By default, None. + material_a : Union[Material, None], optional + The first material. By default, None. + material_b : Union[Material, None], optional + The second material. By default, None. + fraction : Union[Parameter, float, None], optional + The fraction of material_b in material_a. By default, None. + name : Union[str, None], optional + Name of the material. By default, None. + interface : + Calculator interface. By default, None. """ if unique_name is None: unique_name = global_object.generate_unique_name(self.__class__.__name__) @@ -102,22 +114,34 @@ def __init__( self.interface = interface def _get_linkable_attributes(self): + """Get linkable attributes.""" return [self._sld, self._isld] @property def sld(self) -> float: + """Sld function.""" return self._sld.value @property def isld(self) -> float: + """Isld function.""" return self._isld.value def _materials_constraints(self): + """Materials constraints.""" dependency_expression = 'a * (1 - p) + b * p' - dependency_map = {'a': self._material_a.sld, 'b': self._material_b.sld, 'p': self._fraction} + dependency_map = { + 'a': self._material_a.sld, + 'b': self._material_b.sld, + 'p': self._fraction, + } self._sld.make_dependent_on(dependency_expression=dependency_expression, dependency_map=dependency_map) - dependency_map = {'a': self._material_a.isld, 'b': self._material_b.isld, 'p': self._fraction} + dependency_map = { + 'a': self._material_a.isld, + 'b': self._material_b.isld, + 'p': self._fraction, + } self._isld.make_dependent_on(dependency_expression=dependency_expression, dependency_map=dependency_map) @property @@ -129,7 +153,10 @@ def fraction(self) -> float: def fraction(self, fraction: float) -> None: """Setter for fraction of material_b. - :param fraction: The fraction of material_b in material_a. + Parameters + ---------- + fraction : float + The fraction of material_b in material_a. """ if not isinstance(fraction, float): raise ValueError('fraction must be a float') @@ -142,9 +169,12 @@ def material_a(self) -> Material: @material_a.setter def material_a(self, new_material_a: Material) -> None: - """Setter for material_a + """Setter for material_a. - :param new_material_a: New Material for material_a + Parameters + ---------- + new_material_a : Material + New Material for material_a. """ self._material_a = new_material_a self._materials_constraints() @@ -159,9 +189,12 @@ def material_b(self) -> Material: @material_b.setter def material_b(self, new_material_b: Material) -> None: - """Setter for material_b + """Setter for material_b. - :param new_material_b: New Materialfor material_b + Parameters + ---------- + new_material_b : Material + New Materialfor material_b. """ self._material_b = new_material_b self._materials_constraints() @@ -170,6 +203,7 @@ def material_b(self, new_material_b: Material) -> None: self._update_name() def _update_name(self) -> None: + """Update name.""" self.name = self._material_a.name + '/' + self._material_b.name # Representation @@ -188,9 +222,13 @@ def _dict_repr(self) -> dict[str, str]: def as_dict(self, skip: Optional[list[str]] = None) -> dict[str, str]: """Produces a cleaned dict using a custom as_dict method to skip necessary things. + The resulting dict matches the parameters in __init__ - :param skip: List of keys to skip, defaults to `None`. + Parameters + ---------- + skip : Optional[list[str]], optional + List of keys to skip. By default, None. """ this_dict = super().as_dict(skip=skip) this_dict['material_a'] = self._material_a.as_dict(skip=skip) diff --git a/src/easyreflectometry/sample/elements/materials/material_solvated.py b/src/easyreflectometry/sample/elements/materials/material_solvated.py index 563e3550..454904ba 100644 --- a/src/easyreflectometry/sample/elements/materials/material_solvated.py +++ b/src/easyreflectometry/sample/elements/materials/material_solvated.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from typing import Optional from typing import Union @@ -33,11 +36,20 @@ def __init__( ): """Constructor. - :param material: The material being solvated. - :param solvent: The solvent material. - :param solvent_fraction: Fraction of solvent in layer. E.g. solvation or surface coverage. - :param name: Name of the material, defaults to None that causes the name to be constructed. - :param interface: Calculator interface, defaults to `None`. + Parameters + ---------- + unique_name : Optional[str], optional + By default, None. + material : Union[Material, None], optional + The material being solvated. By default, None. + solvent : Union[Material, None], optional + The solvent material. By default, None. + solvent_fraction : Union[Parameter, float, None], optional + Fraction of solvent in layer. E.g. solvation or surface coverage. By default, None. + name : + Name of the material. By default, None. + interface : + Calculator interface. By default, None. """ if unique_name is None: unique_name = global_object.generate_unique_name(self.__class__.__name__) @@ -74,7 +86,10 @@ def material(self) -> Material: def material(self, new_material: Material) -> None: """Set the material. - :param new_material: Matrerial to be useed. + Parameters + ---------- + new_material : Material + Matrerial to be useed. """ self.material_a = new_material @@ -87,7 +102,10 @@ def solvent(self) -> Material: def solvent(self, new_solvent: Material) -> None: """Set the solvent. - :param new_solvent: Solvent to be used. + Parameters + ---------- + new_solvent : Material + Solvent to be used. """ self.material_b = new_solvent @@ -99,6 +117,7 @@ def solvent_fraction_parameter(self) -> Parameter: @property def solvent_fraction(self) -> float: """Get the fraction of layer described by the solvent. + This might be fraction of: Solvation where solvent is within the layer Patches of solvent in the layer where no material is present. @@ -108,11 +127,15 @@ def solvent_fraction(self) -> float: @solvent_fraction.setter def solvent_fraction(self, solvent_fraction: float) -> None: """Set the fraction of layer covered by the material. + This might be fraction of: Solvation where solvent is within the layer Patches of solvent in the layer where no material is present. - :param solvent_fraction : Fraction of layer described by the solvent. + Parameters + ---------- + solvent_fraction : float + Fraction of layer described by the solvent. """ try: self.fraction = solvent_fraction @@ -122,6 +145,7 @@ def solvent_fraction(self, solvent_fraction: float) -> None: raise ValueError('solvent_fraction must be a float between 0 and 1') def _update_name(self) -> None: + """Update name.""" self.name = self._material_a.name + ' in ' + self._material_b.name # Representation @@ -140,9 +164,13 @@ def _dict_repr(self) -> dict[str, str]: def as_dict(self, skip: Optional[list[str]] = None) -> dict[str, str]: """Produces a cleaned dict using a custom as_dict method to skip necessary things. + The resulting dict matches the parameters in __init__ - :param skip: List of keys to skip, defaults to `None`. + Parameters + ---------- + skip : Optional[list[str]], optional + List of keys to skip. By default, None. """ this_dict = super().as_dict(skip=skip) this_dict['material'] = self.material.as_dict(skip=skip) diff --git a/src/easyreflectometry/special/calculations.py b/src/easyreflectometry/special/calculations.py index f7ea9068..62a4006b 100644 --- a/src/easyreflectometry/special/calculations.py +++ b/src/easyreflectometry/special/calculations.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' import periodictable as pt @@ -6,23 +9,37 @@ def weighted_average(a: float, b: float, p: float) -> float: - """ - Determine the weighted average for a and b, where p is the weight. - - :param a: First value - :param b: Second value - :param p: Weight - :return: Weighted average + """Determine the weighted average for a and b, where p is the weight. + + Parameters + ---------- + a : float + First value. + b : float + Second value. + p : float + Weight. + + Returns + ------- + float + Weighted average. """ return a * (1 - p) + b * p def neutron_scattering_length(formula: str) -> complex: - """ - Determine the neutron scattering length for a chemical formula. + """Determine the neutron scattering length for a chemical formula. + + Parameters + ---------- + formula : str + Chemical formula. - :param formula: Chemical formula. - :return: Real and imaginary descriptors for the scattering length in angstrom. + Returns + ------- + complex + Real and imaginary descriptors for the scattering length in angstrom. """ formula_as_dict = parse_formula(formula) scattering_length = 0 + 0j @@ -37,11 +54,17 @@ def neutron_scattering_length(formula: str) -> complex: def molecular_weight(formula: str) -> float: - """ - Determine the molecular weight for a chemical formula. + """Determine the molecular weight for a chemical formula. - :param formula: Chemical formula - :return: Molecular weight of the material in kilograms. + Parameters + ---------- + formula : str + Chemical formula. + + Returns + ------- + float + Molecular weight of the material in kilograms. """ formula_as_dict = parse_formula(formula) mw = 0 @@ -55,25 +78,41 @@ def area_per_molecule_to_scattering_length_density( thickness: float, area_per_molecule: float, ) -> float: - """ - Find the scattering length density for a given area per molecule. - - :param scattering_length: Scattering length of component, in angstrom. - :param thickness: Thickness of component, in angstrom. - :param area_per_molecule: Area per molecule, in angstrom^2. - :return: Scattering length density of layer in e-6 1/angstrom^2. + """Find the scattering length density for a given area per molecule. + + Parameters + ---------- + scattering_length : float + Scattering length of component, in angstrom. + thickness : float + Thickness of component, in angstrom. + area_per_molecule : float + Area per molecule, in angstrom^2. + + Returns + ------- + float + Scattering length density of layer in e-6 1/angstrom^2. """ return scattering_length / (thickness * area_per_molecule) * 1e6 def density_to_sld(scattering_length: float, molecular_weight: float, density: float) -> float: - """ - Find the scattering length density from the mass density of a material. - - :param scattering_length: Scattering length of component, in angstrom. - :param molecular_weight: Molecular weight of component, in u. - :param density: Mass density of the component, in gram centimeter^-3. - :return: Scattering length density of layer in e-6 1/angstrom^2. + """Find the scattering length density from the mass density of a material. + + Parameters + ---------- + scattering_length : float + Scattering length of component, in angstrom. + molecular_weight : float + Molecular weight of component, in u. + density : float + Mass density of the component, in gram centimeter^-3. + + Returns + ------- + float + Scattering length density of layer in e-6 1/angstrom^2. """ # 0.602214076 is avogadros constant times 1e-24 return 0.602214076e6 * density * scattering_length / molecular_weight diff --git a/src/easyreflectometry/special/parsing.py b/src/easyreflectometry/special/parsing.py index 0d52195e..48e9b463 100644 --- a/src/easyreflectometry/special/parsing.py +++ b/src/easyreflectometry/special/parsing.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' import re @@ -9,9 +12,17 @@ def _dictify(tuples: Tuple[Tuple[str, str]]) -> dict: - """ - :param tuples: tuples of tuples with atom and occurance. - :return: Dict of atoms and occurance. + """Dictify function. + + Parameters + ---------- + tuples : Tuple[Tuple[str, str]] + Tuples of tuples with atom and occurance. + + Returns + ------- + dict + Dict of atoms and occurance. """ res = dict() for atom, n in tuples: @@ -23,19 +34,37 @@ def _dictify(tuples: Tuple[Tuple[str, str]]) -> dict: def _fuse(mol1: dict, mol2: dict, w: int = 1) -> dict: - """ - :param mol1: First dict to fuse - :param mol2: Second dict to fuse - :param w: Weight for dicts - :return: Fused dictionaries + """Fuse function. + + Parameters + ---------- + mol1 : dict + First dict to fuse. + mol2 : dict + Second dict to fuse. + w : int, optional + Weight for dicts. By default, 1. + + Returns + ------- + dict + Fused dictionaries. """ return {atom: (mol1.get(atom, 0) + mol2.get(atom, 0)) * w for atom in set(mol1) | set(mol2)} def _parse(formula: str) -> Tuple[dict, int]: - """ - :param formula: Chemical formula as a string - :return: Tuple containing; formula as a dictwith occurences + """Parse function. + + Parameters + ---------- + formula : str + Chemical formula as a string. + + Returns + ------- + + Tuple containing; formula as a dictwith occurences of each atom and an iterator. """ token_list = [] @@ -73,8 +102,16 @@ def _parse(formula: str) -> Tuple[dict, int]: def parse_formula(formula: str) -> dict: - """ - :param formula: Chemical formula as a string - :return: Formula as a dict with occurences of each atom. + """Parse formula. + + Parameters + ---------- + formula : str + Chemical formula as a string. + + Returns + ------- + dict + Formula as a dict with occurences of each atom. """ return _parse(formula)[0] diff --git a/src/easyreflectometry/summary/__init__.py b/src/easyreflectometry/summary/__init__.py index af9d5fa4..f4afd83c 100644 --- a/src/easyreflectometry/summary/__init__.py +++ b/src/easyreflectometry/summary/__init__.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from .summary import Summary __all__ = [Summary] diff --git a/src/easyreflectometry/summary/html_templates.py b/src/easyreflectometry/summary/html_templates.py index dc8afc0e..9b770c01 100644 --- a/src/easyreflectometry/summary/html_templates.py +++ b/src/easyreflectometry/summary/html_templates.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + HTML_TEMPLATE = """ @@ -39,7 +42,7 @@ experiments_section - +

Refinement

@@ -49,7 +52,7 @@ figures_section - + """ @@ -75,18 +78,18 @@ HTML_PARAMETER_HEADER_TEMPLATE = """ - parameter_name + parameter_name parameter_value - parameter_unit + parameter_unit parameter_error """ HTML_PARAMETER_TEMPLATE = """ - parameter_name + parameter_name parameter_value - parameter_unit + parameter_unit parameter_error """ diff --git a/src/easyreflectometry/summary/summary.py b/src/easyreflectometry/summary/summary.py index 34da2974..394c9d78 100644 --- a/src/easyreflectometry/summary/summary.py +++ b/src/easyreflectometry/summary/summary.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import matplotlib.pyplot as plt import numpy as np from easyscience import global_object @@ -16,9 +19,11 @@ class Summary: def __init__(self, project: Project): + """Init function.""" self._project = project def compile_html_summary(self, figures: bool = False) -> str: + """Compile html summary.""" html = HTML_TEMPLATE html = html.replace('project_information_section', self._project_information_section()) @@ -40,11 +45,13 @@ def compile_html_summary(self, figures: bool = False) -> str: return html def save_html_summary(self, filename: str) -> None: + """Save html summary.""" html = self.compile_html_summary(figures=True) with open(filename, 'w') as f: f.write(html) def save_pdf_summary(self, filename: str) -> None: + """Save pdf summary.""" html = self.compile_html_summary(figures=True) with open(filename, 'w+b') as result_file: @@ -57,6 +64,7 @@ def save_pdf_summary(self, filename: str) -> None: print('An error occured when generating PDF summary!') def save_sld_plot(self, filename: str) -> None: + """Save sld plot.""" fig = plt.figure() ax = fig.add_subplot(1, 1, 1) @@ -70,6 +78,7 @@ def save_sld_plot(self, filename: str) -> None: plt.close() def save_fit_experiment_plot(self, filename: str) -> None: + """Save fit experiment plot.""" fig = plt.figure() ax = fig.add_subplot(1, 1, 1) legends = [] @@ -92,6 +101,7 @@ def save_fit_experiment_plot(self, filename: str) -> None: plt.close() def _project_information_section(self) -> str: + """Project information section.""" html_project = HTML_PROJECT_INFORMATION_TEMPLATE name = self._project._info['name'] @@ -102,6 +112,7 @@ def _project_information_section(self) -> str: return html_project def _sample_section(self) -> str: + """Sample section.""" html_parameters = [] html_parameter = HTML_PARAMETER_HEADER_TEMPLATE @@ -137,6 +148,7 @@ def _sample_section(self) -> str: return html_parameters_str def _experiments_section(self) -> str: + """Experiments section.""" html_experiments = [] for idx, experiment in self._project.experiments.items(): @@ -163,6 +175,7 @@ def _experiments_section(self) -> str: return html_experiments_str def _refinement_section(self) -> str: + """Refinement section.""" html_refinement = HTML_REFINEMENT_TEMPLATE # Get parameters directly from the model @@ -186,6 +199,7 @@ def _refinement_section(self) -> str: return html_refinement def _figures_section(self) -> None: + """Figures section.""" html_figures = HTML_FIGURES_TEMPLATE path_sld = self._project.path / 'sld_plot.jpg' path_fit_experiment = self._project.path / 'fit_experiment_plot.jpg' diff --git a/src/easyreflectometry/utils.py b/src/easyreflectometry/utils.py index 43be7821..43ac58d8 100644 --- a/src/easyreflectometry/utils.py +++ b/src/easyreflectometry/utils.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from copy import deepcopy from numbers import Number from typing import Optional @@ -14,15 +17,16 @@ def get_as_parameter( default_dict: dict, unique_name_prefix: Optional[str] = None, ) -> Parameter: - """ - This function creates a parameter for the variable `name`. A parameter has a value and metadata. + """This function creates a parameter for the variable `name`. + + A parameter has a value and metadata. If the value already is a parameter, it is returned. - If the value is a number, a parameter is created with this value and metadata from the dictionary. - If the value is None, a parameter is created with the default value and metadata from the dictionary. + If the value is a number, a parameter is created with this value and metadata from the dictionary. + If the value is None, a parameter is created with the default value and metadata from the dictionary. - param value: The value to use for the parameter. If None, the default value in the dictionary is used. - param name: The name of the parameter - param default_dict: Dictionary with entry for `name` containing the default value and metadata for the parameter + param value: The value to use for the parameter. If None, the default value in the dictionary is used. + param name: The name of the parameter + param default_dict: Dictionary with entry for `name` containing the default value and metadata for the parameter """ # This is a parameter, return it if isinstance(value, Parameter): @@ -51,17 +55,17 @@ def get_as_parameter( def yaml_dump(dict_repr: dict) -> str: + """Yaml dump.""" return yaml.dump(dict_repr, sort_keys=False, allow_unicode=True) def collect_unique_names_from_dict(structure_dict: dict, unique_names: Optional[list[str]] = None) -> list[str]: - """ - This function returns a list with the 'unique_name' found the input dictionary. - """ + """This function returns a list with the 'unique_name' found the input dictionary.""" if unique_names is None: unique_names = [] def _collect(item): + """Collect function.""" if isinstance(item, dict): if 'unique_name' in item: unique_names.append(item['unique_name']) @@ -76,12 +80,15 @@ def _collect(item): def count_free_parameters(project) -> int: + """Count free parameters.""" return sum(1 for parameter in project.parameters if parameter.free) def count_fixed_parameters(project) -> int: + """Count fixed parameters.""" return sum(1 for parameter in project.parameters if not parameter.free) def count_parameter_user_constraints(project) -> int: + """Count parameter user constraints.""" return sum(1 for parameter in project.parameters if not parameter.independent) diff --git a/tests/calculators/bornagain/test_bornagain_calculator.py b/tests/calculators/bornagain/test_bornagain_calculator.py index e16cdc70..7497445d 100644 --- a/tests/calculators/bornagain/test_bornagain_calculator.py +++ b/tests/calculators/bornagain/test_bornagain_calculator.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for BornAgain calculator. """ diff --git a/tests/calculators/bornagain/test_bornagain_wrapper.py b/tests/calculators/bornagain/test_bornagain_wrapper.py index 84b2a2d7..ce4646ed 100644 --- a/tests/calculators/bornagain/test_bornagain_wrapper.py +++ b/tests/calculators/bornagain/test_bornagain_wrapper.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for the BornAgain wrapper. """ diff --git a/tests/calculators/refl1d/test_refl1d_calculator.py b/tests/calculators/refl1d/test_refl1d_calculator.py index ba8c8d35..f2c4d2b1 100644 --- a/tests/calculators/refl1d/test_refl1d_calculator.py +++ b/tests/calculators/refl1d/test_refl1d_calculator.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for Refnx calculator. """ diff --git a/tests/calculators/refl1d/test_refl1d_wrapper.py b/tests/calculators/refl1d/test_refl1d_wrapper.py index e19dfe42..9546205b 100644 --- a/tests/calculators/refl1d/test_refl1d_wrapper.py +++ b/tests/calculators/refl1d/test_refl1d_wrapper.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for Refl1d wrapper. """ diff --git a/tests/calculators/refnx/test_refnx_calculator.py b/tests/calculators/refnx/test_refnx_calculator.py index 27283c10..b29899c5 100644 --- a/tests/calculators/refnx/test_refnx_calculator.py +++ b/tests/calculators/refnx/test_refnx_calculator.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for Refnx calculator. """ diff --git a/tests/calculators/refnx/test_refnx_wrapper.py b/tests/calculators/refnx/test_refnx_wrapper.py index 74b50ec9..0cf13628 100644 --- a/tests/calculators/refnx/test_refnx_wrapper.py +++ b/tests/calculators/refnx/test_refnx_wrapper.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for Refnx wrapper. """ @@ -290,7 +293,7 @@ def test_sld_profile(self): assert_almost_equal(p.sld_profile('MyModel')[1][0], 0) assert_almost_equal(p.sld_profile('MyModel')[1][-1], 4) - ### Tests from https://github.com/reflectivity/analysis/tree/master/validation/test/unpolarised + # Tests from https://github.com/reflectivity/analysis/tree/master/validation/test/unpolarised def test_calculate_github_test0(self): p = RefnxWrapper() p.create_material('Material1') @@ -327,15 +330,13 @@ def test_calculate_github_test0(self): p.add_item('Item4', 'MyModel') p.set_resolution_function(PercentageFwhm(0)) p.update_model('MyModel', bkg=0) - q = np.array( - [ - 5.000000000000000104e-03, - 3.717499999999999971e-02, - 5.449999999999999983e-02, - 1.005349999999999994e-01, - 2.955650000000000222e-01, - ] - ) + q = np.array([ + 5.000000000000000104e-03, + 3.717499999999999971e-02, + 5.449999999999999983e-02, + 1.005349999999999994e-01, + 2.955650000000000222e-01, + ]) expected = [ 9.665000503913141472e-01, 3.486325360684768590e-04, @@ -365,15 +366,13 @@ def test_calculate_github_test2(self): p.add_item('Item2', 'MyModel') p.set_resolution_function(PercentageFwhm(0)) p.update_model('MyModel', bkg=0) - q = np.array( - [ - 5.000000000000000104e-03, - 7.564500000000000390e-02, - 1.433050000000000157e-01, - 2.368350000000000177e-01, - 5.920499999999999652e-01, - ] - ) + q = np.array([ + 5.000000000000000104e-03, + 7.564500000000000390e-02, + 1.433050000000000157e-01, + 2.368350000000000177e-01, + 5.920499999999999652e-01, + ]) expected = [ 1.000000000000000222e00, 1.964576414578978456e-04, diff --git a/tests/data/test_data_store.py b/tests/data/test_data_store.py index ea66f8ff..66ba9b04 100644 --- a/tests/data/test_data_store.py +++ b/tests/data/test_data_store.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from unittest.mock import Mock import numpy as np @@ -29,7 +32,13 @@ def test_constructor_default_values(self): def test_constructor_with_values(self): # When data = DataSet1D( - x=[1, 2, 3], y=[4, 5, 6], ye=[7, 8, 9], xe=[10, 11, 12], x_label='label_x', y_label='label_y', name='MyDataSet1D' + x=[1, 2, 3], + y=[4, 5, 6], + ye=[7, 8, 9], + xe=[10, 11, 12], + x_label='label_x', + y_label='label_y', + name='MyDataSet1D', ) # Then diff --git a/tests/functional/test_dummy.py b/tests/functional/test_dummy.py new file mode 100644 index 00000000..230dfead --- /dev/null +++ b/tests/functional/test_dummy.py @@ -0,0 +1,8 @@ +# SPDX-FileCopyrightText: 2021-2026 EasyReflectometry contributors +# SPDX-License-Identifier: BSD-3-Clause + + +def test_dummy(): + calculated = 2 + 2 + expected = 4 + assert calculated == expected diff --git a/tests/integration/fitting/test_dummy.py b/tests/integration/fitting/test_dummy.py new file mode 100644 index 00000000..78d1220d --- /dev/null +++ b/tests/integration/fitting/test_dummy.py @@ -0,0 +1,17 @@ +# SPDX-FileCopyrightText: 2021-2026 EasyReflectometry contributors +# SPDX-License-Identifier: BSD-3-Clause + +import pytest + + +@pytest.mark.fast +def test_dummy_fast(): + calculated = 2 + 2 + expected = 4 + assert calculated == expected + + +def test_dummy_slow(): + calculated = sum(i * j for i in range(10000) for j in range(10000)) + expected = 2499500025000000 + assert calculated == expected diff --git a/tests/integration/scipp-analysis/test_dummy.py b/tests/integration/scipp-analysis/test_dummy.py new file mode 100644 index 00000000..78d1220d --- /dev/null +++ b/tests/integration/scipp-analysis/test_dummy.py @@ -0,0 +1,17 @@ +# SPDX-FileCopyrightText: 2021-2026 EasyReflectometry contributors +# SPDX-License-Identifier: BSD-3-Clause + +import pytest + + +@pytest.mark.fast +def test_dummy_fast(): + calculated = 2 + 2 + expected = 4 + assert calculated == expected + + +def test_dummy_slow(): + calculated = sum(i * j for i in range(10000) for j in range(10000)) + expected = 2499500025000000 + assert calculated == expected diff --git a/tests/model/test_model.py b/tests/model/test_model.py index 49ce60fc..594ebaf7 100644 --- a/tests/model/test_model.py +++ b/tests/model/test_model.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for Model class. """ diff --git a/tests/model/test_model_collection.py b/tests/model/test_model_collection.py index cc98534d..4a6fd521 100644 --- a/tests/model/test_model_collection.py +++ b/tests/model/test_model_collection.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from easyscience import global_object from easyreflectometry.model.model import COLORS @@ -113,7 +116,10 @@ def test_as_dict(self): dict_repr = collection.as_dict() # Expect - assert dict_repr['data'][0]['resolution_function'] == {'smearing': 'PercentageFwhm', 'constant': 5.0} + assert dict_repr['data'][0]['resolution_function'] == { + 'smearing': 'PercentageFwhm', + 'constant': 5.0, + } def test_dict_round_trip(self): # When diff --git a/tests/model/test_resolution_functions.py b/tests/model/test_resolution_functions.py index 6ff8afd1..e28a99f2 100644 --- a/tests/model/test_resolution_functions.py +++ b/tests/model/test_resolution_functions.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import unittest import numpy as np @@ -64,7 +67,11 @@ def test_as_dict(self): resolution_function = LinearSpline(q_data_points=[0, 10], fwhm_values=[5, 10]) # Then Expect - resolution_function.as_dict() == {'smearing': 'LinearSpline', 'q_data_points': [0, 10], 'fwhm_values': [5, 10]} + resolution_function.as_dict() == { + 'smearing': 'LinearSpline', + 'q_data_points': [0, 10], + 'fwhm_values': [5, 10], + } def test_dict_round_trip(self): # When @@ -90,7 +97,8 @@ def test_constructor(self): # Then Expect assert np.allclose( - np.array(resolution_function.smearing()), np.array([2.51664683, 2.84038734, 3.2460762, 3.6796519, 4.07869271]) + np.array(resolution_function.smearing()), + np.array([2.51664683, 2.84038734, 3.2460762, 3.6796519, 4.07869271]), ) def test_as_dict(self): diff --git a/tests/sample/assemblies/test_base_assembly.py b/tests/sample/assemblies/test_base_assembly.py index 178f6382..482cf669 100644 --- a/tests/sample/assemblies/test_base_assembly.py +++ b/tests/sample/assemblies/test_base_assembly.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for BaseAssembly class module """ diff --git a/tests/sample/assemblies/test_bilayer.py b/tests/sample/assemblies/test_bilayer.py index b96e6a78..e10659be 100644 --- a/tests/sample/assemblies/test_bilayer.py +++ b/tests/sample/assemblies/test_bilayer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for Bilayer class module """ diff --git a/tests/sample/assemblies/test_gradient_layer.py b/tests/sample/assemblies/test_gradient_layer.py index 3b88df47..7efda4a9 100644 --- a/tests/sample/assemblies/test_gradient_layer.py +++ b/tests/sample/assemblies/test_gradient_layer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for GradientLayer class module """ @@ -168,7 +171,11 @@ def test_prepare_gradient_layers(monkeypatch): mock_LayerCollection = MagicMock() mock_Material = MagicMock(return_value='Material_from_mock') mock_linear_gradient = MagicMock(return_value=[1.0, 2.0, 3.0]) - monkeypatch.setattr(easyreflectometry.sample.assemblies.gradient_layer, '_linear_gradient', mock_linear_gradient) + monkeypatch.setattr( + easyreflectometry.sample.assemblies.gradient_layer, + '_linear_gradient', + mock_linear_gradient, + ) monkeypatch.setattr(easyreflectometry.sample.assemblies.gradient_layer, 'Layer', mock_Layer) monkeypatch.setattr(easyreflectometry.sample.assemblies.gradient_layer, 'Material', mock_Material) monkeypatch.setattr(easyreflectometry.sample.assemblies.gradient_layer, 'LayerCollection', mock_LayerCollection) diff --git a/tests/sample/assemblies/test_multilayer.py b/tests/sample/assemblies/test_multilayer.py index 82f807a4..42be8584 100644 --- a/tests/sample/assemblies/test_multilayer.py +++ b/tests/sample/assemblies/test_multilayer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for MultiLayer class module """ diff --git a/tests/sample/assemblies/test_repeating_multilayer.py b/tests/sample/assemblies/test_repeating_multilayer.py index 6eb17d0a..6e00ea71 100644 --- a/tests/sample/assemblies/test_repeating_multilayer.py +++ b/tests/sample/assemblies/test_repeating_multilayer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for RepeatingMultiLayer module """ diff --git a/tests/sample/assemblies/test_surfactant_layer.py b/tests/sample/assemblies/test_surfactant_layer.py index 3a0549cd..8205201f 100644 --- a/tests/sample/assemblies/test_surfactant_layer.py +++ b/tests/sample/assemblies/test_surfactant_layer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for SurfactantLayer class module """ @@ -111,7 +114,12 @@ def test_dict_repr(self): 'solvent_fraction': '0.200 dimensionless', 'sld': '2.269e-6 1/Å^2', 'isld': '0.000e-6 1/Å^2', - 'material': {'C10H18NO8P': {'sld': '1.246e-6 1/Å^2', 'isld': '0.000e-6 1/Å^2'}}, + 'material': { + 'C10H18NO8P': { + 'sld': '1.246e-6 1/Å^2', + 'isld': '0.000e-6 1/Å^2', + } + }, 'solvent': {'D2O': {'sld': '6.360e-6 1/Å^2', 'isld': '0.000e-6 1/Å^2'}}, } }, diff --git a/tests/sample/collections/test_base_collection.py b/tests/sample/collections/test_base_collection.py index b9ad429e..44b8e208 100644 --- a/tests/sample/collections/test_base_collection.py +++ b/tests/sample/collections/test_base_collection.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from unittest.mock import MagicMock from easyreflectometry.sample.collections.base_collection import BaseCollection diff --git a/tests/sample/collections/test_layer_collection.py b/tests/sample/collections/test_layer_collection.py index 543e9235..d8f475d5 100644 --- a/tests/sample/collections/test_layer_collection.py +++ b/tests/sample/collections/test_layer_collection.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for LayerCollection class. """ diff --git a/tests/sample/collections/test_material_collection.py b/tests/sample/collections/test_material_collection.py index 25f30b59..3ca9f22b 100644 --- a/tests/sample/collections/test_material_collection.py +++ b/tests/sample/collections/test_material_collection.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for LayerCollection class. """ diff --git a/tests/sample/collections/test_sample.py b/tests/sample/collections/test_sample.py index 3cb1d0c1..1f00614e 100644 --- a/tests/sample/collections/test_sample.py +++ b/tests/sample/collections/test_sample.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for Sample class. """ diff --git a/tests/sample/elements/layers/test_layer.py b/tests/sample/elements/layers/test_layer.py index 1cbecb17..818abe21 100644 --- a/tests/sample/elements/layers/test_layer.py +++ b/tests/sample/elements/layers/test_layer.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for Layer class. """ diff --git a/tests/sample/elements/layers/test_layer_area_per_molecule.py b/tests/sample/elements/layers/test_layer_area_per_molecule.py index 505eec5d..4d0abf7d 100644 --- a/tests/sample/elements/layers/test_layer_area_per_molecule.py +++ b/tests/sample/elements/layers/test_layer_area_per_molecule.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for LayerAreaPerMolecule class. """ diff --git a/tests/sample/elements/materials/test_material.py b/tests/sample/elements/materials/test_material.py index c07a2217..584d942f 100644 --- a/tests/sample/elements/materials/test_material.py +++ b/tests/sample/elements/materials/test_material.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Tests for Material class. """ diff --git a/tests/sample/elements/materials/test_material_density.py b/tests/sample/elements/materials/test_material_density.py index d1945e1e..99c6615a 100644 --- a/tests/sample/elements/materials/test_material_density.py +++ b/tests/sample/elements/materials/test_material_density.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import unittest import numpy as np diff --git a/tests/sample/elements/materials/test_material_mixture.py b/tests/sample/elements/materials/test_material_mixture.py index 423bfb2d..0e70a2b7 100644 --- a/tests/sample/elements/materials/test_material_mixture.py +++ b/tests/sample/elements/materials/test_material_mixture.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from unittest.mock import MagicMock from easyscience import global_object diff --git a/tests/sample/elements/materials/test_material_solvated.py b/tests/sample/elements/materials/test_material_solvated.py index a50211d5..3d4a9917 100644 --- a/tests/sample/elements/materials/test_material_solvated.py +++ b/tests/sample/elements/materials/test_material_solvated.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from unittest.mock import MagicMock import pytest diff --git a/tests/special/test_calculations.py b/tests/special/test_calculations.py index e7f1f89f..1c963ce3 100644 --- a/tests/special/test_calculations.py +++ b/tests/special/test_calculations.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2022 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' import unittest diff --git a/tests/summary/test_summary.py b/tests/summary/test_summary.py index 3bbb186e..8a8f581f 100644 --- a/tests/summary/test_summary.py +++ b/tests/summary/test_summary.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import os from unittest.mock import MagicMock diff --git a/tests/test_data.py b/tests/test_data.py index 0ee95d94..c9cb7899 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2022 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' __version__ = '0.0.1' @@ -224,7 +227,10 @@ def test_load_txt_three_columns(self): assert coords_name in er_data['coords'] # xe should be zeros for 3-column file - assert_almost_equal(er_data['coords'][coords_name].variances, np.zeros_like(er_data['coords'][coords_name].values)) + assert_almost_equal( + er_data['coords'][coords_name].variances, + np.zeros_like(er_data['coords'][coords_name].values), + ) def test_load_txt_with_zero_errors(self): fpath = os.path.join(PATH_STATIC, 'ref_zero_var.txt') diff --git a/tests/test_fitting.py b/tests/test_fitting.py index 2a03a98c..94056544 100644 --- a/tests/test_fitting.py +++ b/tests/test_fitting.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + __author__ = 'github.com/arm61' import os @@ -175,12 +178,10 @@ def test_fitting_with_manual_zero_variance(): variances[30:32] = 0.0 # 2 more zero variance points # Create scipp DataGroup manually - data = sc.DataGroup( - { - 'coords': {'Qz_0': sc.array(dims=['Qz_0'], values=qz_values)}, - 'data': {'R_0': sc.array(dims=['Qz_0'], values=r_values, variances=variances)}, - } - ) + data = sc.DataGroup({ + 'coords': {'Qz_0': sc.array(dims=['Qz_0'], values=qz_values)}, + 'data': {'R_0': sc.array(dims=['Qz_0'], values=r_values, variances=variances)}, + }) # Create a simple model for fitting si = Material(2.07, 0, 'Si') @@ -428,7 +429,12 @@ def test_prepare_fit_arrays_legacy_mask_drops_zero_variance(): assert np.allclose(x_out, [0.01, 0.03]) assert np.allclose(y_eff, [1.0, 0.6]) assert np.allclose(weights, [1.0 / np.sqrt(0.01), 1.0 / np.sqrt(0.04)]) - assert stats == {'valid': 2, 'mighell_substituted': 0, 'masked': 1, 'transformed_all_points': False} + assert stats == { + 'valid': 2, + 'mighell_substituted': 0, + 'masked': 1, + 'transformed_all_points': False, + } def test_prepare_fit_arrays_hybrid_transforms_zero_variance(): @@ -449,7 +455,12 @@ def test_prepare_fit_arrays_hybrid_transforms_zero_variance(): assert y_eff[1] == pytest.approx(0.8 + 0.8) # sigma = sqrt(y + 1) = sqrt(1.8) assert weights[1] == pytest.approx(1.0 / np.sqrt(1.8)) - assert stats == {'valid': 2, 'mighell_substituted': 1, 'masked': 0, 'transformed_all_points': False} + assert stats == { + 'valid': 2, + 'mighell_substituted': 1, + 'masked': 0, + 'transformed_all_points': False, + } def test_prepare_fit_arrays_mighell_transforms_all(): @@ -466,7 +477,12 @@ def test_prepare_fit_arrays_mighell_transforms_all(): # sigma = sqrt(y + 1) assert weights[0] == pytest.approx(1.0 / np.sqrt(1.5)) assert weights[1] == pytest.approx(1.0 / np.sqrt(1.3)) - assert stats == {'valid': 0, 'mighell_substituted': 2, 'masked': 0, 'transformed_all_points': True} + assert stats == { + 'valid': 0, + 'mighell_substituted': 2, + 'masked': 0, + 'transformed_all_points': True, + } def test_fit_single_data_set_1d_hybrid_keeps_zero_variance_points(): @@ -553,13 +569,17 @@ def test_classical_and_objective_chi_are_split_for_fit_results(): fitter._models = [MagicMock(unique_name='model_0', as_dict=MagicMock(return_value={'name': 'model_0'}))] fitter._fit_func = [lambda x: np.array([0.8, 0.75, 0.7])] - data = sc.DataGroup( - { - 'coords': {'Qz_0': sc.array(dims=['Qz_0'], values=np.array([0.01, 0.02, 0.03]), unit=sc.Unit('1/angstrom'))}, - 'data': {'R_0': sc.array(dims=['Qz_0'], values=np.array([1.0, 0.9, 0.7]), variances=np.array([0.01, 0.0, 0.04]))}, - 'attrs': {}, - } - ) + data = sc.DataGroup({ + 'coords': {'Qz_0': sc.array(dims=['Qz_0'], values=np.array([0.01, 0.02, 0.03]), unit=sc.Unit('1/angstrom'))}, + 'data': { + 'R_0': sc.array( + dims=['Qz_0'], + values=np.array([1.0, 0.9, 0.7]), + variances=np.array([0.01, 0.0, 0.04]), + ) + }, + 'attrs': {}, + }) analysed = fitter.fit(data) @@ -654,12 +674,10 @@ def test_fit_multi_dataset_hybrid_uses_transformed_y_and_weights(): variances = np.ones_like(r_values) * 0.01 variances[3:5] = 0.0 # 2 zero-variance points - data = sc.DataGroup( - { - 'coords': {'Qz_0': sc.array(dims=['Qz_0'], values=qz_values)}, - 'data': {'R_0': sc.array(dims=['Qz_0'], values=r_values, variances=variances)}, - } - ) + data = sc.DataGroup({ + 'coords': {'Qz_0': sc.array(dims=['Qz_0'], values=qz_values)}, + 'data': {'R_0': sc.array(dims=['Qz_0'], values=r_values, variances=variances)}, + }) model = Model() model.interface = CalculatorFactory() diff --git a/tests/test_limits.py b/tests/test_limits.py index e8320eb7..2fd1cc74 100644 --- a/tests/test_limits.py +++ b/tests/test_limits.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import numpy as np import pytest from easyscience import global_object diff --git a/tests/test_measurement_comprehensive.py b/tests/test_measurement_comprehensive.py index d6bb0c46..baffb2b8 100644 --- a/tests/test_measurement_comprehensive.py +++ b/tests/test_measurement_comprehensive.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2025 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ Comprehensive tests for measurement and data store functionality. Tests for all functions in measurement.py and data_store.py modules. @@ -113,7 +116,10 @@ def test_load_txt_handles_three_columns(self): coords_key = list(result['coords'].keys())[0] # xe should be zeros - assert_array_equal(result['coords'][coords_key].variances, np.zeros_like(result['coords'][coords_key].values)) + assert_array_equal( + result['coords'][coords_key].variances, + np.zeros_like(result['coords'][coords_key].values), + ) def test_load_txt_with_insufficient_columns(self): """Test that _load_txt raises error for files with too few columns.""" @@ -159,7 +165,16 @@ def test_constructor_all_parameters(self): xe = [0.1, 0.1, 0.1, 0.1] ye = [1, 2, 3, 4] - dataset = DataSet1D(name='TestData', x=x, y=y, xe=xe, ye=ye, x_label='Q (Å⁻¹)', y_label='Reflectivity', model=None) + dataset = DataSet1D( + name='TestData', + x=x, + y=y, + xe=xe, + ye=ye, + x_label='Q (Å⁻¹)', + y_label='Reflectivity', + model=None, + ) assert dataset.name == 'TestData' assert_array_equal(dataset.x, np.array(x)) @@ -233,7 +248,8 @@ def test_datastore_as_sequence(self): assert store[0].name == 'item2' def test_datastore_experiments_and_simulations_filtering(self): - """Test experiments and simulations properties filter correctly.""" + """Test experiments and simulations properties + filter correctly.""" exp1 = DataSet1D(name='exp1', x=[1], y=[2], model=Mock()) exp2 = DataSet1D(name='exp2', x=[3], y=[4], model=Mock()) sim1 = DataSet1D(name='sim1', x=[5], y=[6]) @@ -264,7 +280,8 @@ class TestProjectDataComprehensive: """Comprehensive tests for ProjectData class.""" def test_project_data_initialization(self): - """Test ProjectData initializes with correct default values.""" + """Test ProjectData initializes with correct + default values.""" project = ProjectData() assert project.name == 'DataStore' @@ -274,7 +291,8 @@ def test_project_data_initialization(self): assert project.sim_data.name == 'Sim Datastore' def test_project_data_with_custom_stores(self): - """Test ProjectData with custom experiment and simulation stores.""" + """Test ProjectData with custom experiment and + simulation stores.""" custom_exp = DataStore(name='CustomExp') custom_sim = DataStore(name='CustomSim') @@ -303,7 +321,8 @@ class TestIntegrationScenarios: """Integration tests for common usage scenarios.""" def test_complete_workflow_orso_file(self): - """Test complete workflow: load ORSO file -> create dataset -> store in project.""" + """Test complete workflow: load ORSO file + -> create dataset -> store in project.""" # Load file fpath = os.path.join(PATH_STATIC, 'test_example1.ort') dataset = load_as_dataset(fpath) @@ -318,7 +337,8 @@ def test_complete_workflow_orso_file(self): assert isinstance(project.exp_data[0], DataSet1D) def test_complete_workflow_txt_file(self): - """Test complete workflow: load txt file -> create dataset -> store in project.""" + """Test complete workflow: load txt file -> + create dataset -> store in project.""" # Load file fpath = os.path.join(PATH_STATIC, 'ref_concat_1.txt') dataset = load_as_dataset(fpath) diff --git a/tests/test_orso_utils.py b/tests/test_orso_utils.py index ebb662a1..df931b33 100644 --- a/tests/test_orso_utils.py +++ b/tests/test_orso_utils.py @@ -91,10 +91,12 @@ def test_load_data_from_orso_file(): def test_orso_sld_unit_conversion(orso_data): - """Test that SLD values from ORSO are correctly converted from A^-2 to 10^-6 A^-2. + """Test that SLD values from ORSO are correctly converted + from A^-2 to 10^-6 A^-2. ORSO stores SLD in absolute units (A^-2), e.g., 3.47e-06. - The internal representation uses 10^-6 A^-2, so the value should be 3.47. + The internal representation uses 10^-6 A^-2, + so the value should be 3.47. """ sample = load_orso_model(orso_data) @@ -114,9 +116,7 @@ def test_orso_sld_unit_conversion(orso_data): subphase = sample[2] si_layer = subphase.layers[0] assert si_layer.material.name == 'Si' - assert abs(si_layer.material.sld.value - 2.07) < 1e-6, ( - f'Expected SLD ~2.07 (10^-6 A^-2), got {si_layer.material.sld.value}' - ) + assert abs(si_layer.material.sld.value - 2.07) < 1e-6, f'Expected SLD ~2.07 (10^-6 A^-2), got {si_layer.material.sld.value}' # Check air superphase layer # ORSO file has: sld: {real: 0.0, imag: 0.0} @@ -152,7 +152,8 @@ def test_LoadOrso_with_nonexistent_file(): def test_get_sld_values_defaults_to_zero_when_sld_and_density_missing(): - """_get_sld_values should return (0.0, 0.0) when both sld and mass_density are None.""" + """_get_sld_values should return (0.0, 0.0) when both + sld and mass_density are None.""" material = SimpleNamespace(sld=None, mass_density=None) m_sld, m_isld = _get_sld_values(material, 'Unknown') assert m_sld == 0.0 @@ -160,7 +161,8 @@ def test_get_sld_values_defaults_to_zero_when_sld_and_density_missing(): def test_load_orso_model_returns_none_and_warns_when_no_sample_model(): - """load_orso_model should return None and emit a warning when the ORSO file has no sample model.""" + """load_orso_model should return None and emit a warning + when the ORSO file has no sample model.""" orso_data = orso.load_orso(os.path.join(PATH_STATIC, 'test_example1.ort')) # Verify the file indeed has no model assert orso_data[0].info.data_source.sample.model is None diff --git a/tests/test_ort_file.py b/tests/test_ort_file.py index 8ef1de16..245ec566 100644 --- a/tests/test_ort_file.py +++ b/tests/test_ort_file.py @@ -154,7 +154,8 @@ def test_validate_physical_data__r_values_ureal_positive(load_data): for val_a, val_b in zip(a, b): if val_a > val_b: pytest.warns( - UserWarning, reason=f'Reflectivity value {val_a} is unphysically large compared to its uncertainty {val_b}' + UserWarning, + reason=f'Reflectivity value {val_a} is unphysically large compared to its uncertainty {val_b}', ) assert all(load_data['data']['R_0'].values <= 1 + 2 * np.sqrt(load_data['data']['R_0'].variances)) diff --git a/tests/test_parameter_utils.py b/tests/test_parameter_utils.py index d8d2ce97..72e3bbc0 100644 --- a/tests/test_parameter_utils.py +++ b/tests/test_parameter_utils.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import numpy as np import pytest from numpy.testing import assert_equal diff --git a/tests/test_project.py b/tests/test_project.py index 3c390960..73aeca85 100644 --- a/tests/test_project.py +++ b/tests/test_project.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + import datetime import os from pathlib import Path @@ -133,7 +136,8 @@ def remove_interface(d): models_dict['unique_name'] = 'project_models' remove_interface(project_models_dict) remove_interface(models_dict) - # Since as_dict may not include unique_name, remove it for comparison + # Since as_dict may not include unique_name, + # remove it for comparison for d in [project_models_dict, models_dict]: if 'unique_name' in d: del d['unique_name'] @@ -171,7 +175,12 @@ def test_sld_data_for_model_at_index(self): assert len(sample_data.x) == 500 assert_allclose( np.array([4.6119497e-08, 6.3189932e00, 6.3350000e00, 2.0740000e00]), - np.array([sample_data.y[0], sample_data.y[100], sample_data.y[300], sample_data.y[499]]), + np.array([ + sample_data.y[0], + sample_data.y[100], + sample_data.y[300], + sample_data.y[499], + ]), ) def test_sample_data_for_model_at_index(self): @@ -200,7 +209,12 @@ def test_model_data_for_model_at_index(self): # Expect assert len(model_data.y) == 4 assert_allclose( - np.array([0.9738701849233727, 0.0017678986451491123, 0.00016581714423990004, 3.3290653551465554e-08]), + np.array([ + 0.9738701849233727, + 0.0017678986451491123, + 0.00016581714423990004, + 3.3290653551465554e-08, + ]), model_data.y, ) @@ -558,7 +572,8 @@ def test_load_from_json(self, tmp_path): # Then new_project.load_from_json(tmp_path / 'name' / 'project.json') - # Do it twice to ensure that potential global objects don't collide + # Do it twice to ensure that potential + # global objects don't collide new_project.load_from_json(tmp_path / 'name' / 'project.json') # Expect @@ -904,11 +919,13 @@ def test_add_sample_from_orso_with_shared_materials(self): # Expect - shared material should not be duplicated assert len(project._models) == 2 - # The shared material instance is already in the collection, so count should stay the same + # The shared material instance is already in the collection, + # so count should stay the same assert len(project._materials) == initial_material_count def test_replace_models_from_orso(self): - """Test that replace_models_from_orso replaces all existing models with a single new model.""" + """Test that replace_models_from_orso replaces all existing + models with a single new model.""" # When global_object.map._clear() project = Project() @@ -1077,7 +1094,12 @@ def test_remove_model_at_index_removes_experiment_at_same_index(self): project._models.append(model) # Add experiment linked to model 0 experiment = DataSet1D( - name='exp0', x=[0.01, 0.02], y=[1.0, 0.5], ye=[0.1, 0.1], xe=[0.001, 0.001], model=project._models[0] + name='exp0', + x=[0.01, 0.02], + y=[1.0, 0.5], + ye=[0.1, 0.1], + xe=[0.001, 0.001], + model=project._models[0], ) project._experiments[0] = experiment diff --git a/tests/test_topmost_nesting.py b/tests/test_topmost_nesting.py index 5c38ec0b..622991b2 100644 --- a/tests/test_topmost_nesting.py +++ b/tests/test_topmost_nesting.py @@ -1,5 +1,8 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + """ -Tests exercising the methods of the topmost classes for nested structure. +Testing the methods of the topmost classes for nested structure. To ensure that the parameters are relayed. """ diff --git a/tests/test_utils.py b/tests/test_utils.py index 64bd7791..4d9c4828 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + from easyreflectometry import Project from easyreflectometry.utils import count_fixed_parameters from easyreflectometry.utils import count_free_parameters @@ -27,16 +30,3 @@ def test_count_fixed_parameters(): # Expect assert count == 13 - - -def test_count_parameter_user_constraints(): - # When - project = Project() - project.default_model() - # project.parameters[0].user_constraints['name_other_parameter'] = 'constraint' - - # # Then - # count = count_parameter_user_constraints(project) - - # # Expect - # assert count == 1 diff --git a/tests/unit/test_dummy.py b/tests/unit/test_dummy.py new file mode 100644 index 00000000..230dfead --- /dev/null +++ b/tests/unit/test_dummy.py @@ -0,0 +1,8 @@ +# SPDX-FileCopyrightText: 2021-2026 EasyReflectometry contributors +# SPDX-License-Identifier: BSD-3-Clause + + +def test_dummy(): + calculated = 2 + 2 + expected = 4 + assert calculated == expected diff --git a/tools/license_headers.py b/tools/license_headers.py new file mode 100644 index 00000000..f276ca1b --- /dev/null +++ b/tools/license_headers.py @@ -0,0 +1,321 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Add, remove, or check SPDX headers in Python files.""" + +from __future__ import annotations + +import argparse +import fnmatch +import tomllib +from datetime import datetime +from pathlib import Path +from typing import Any +from typing import Optional +from typing import Union + +from git import Repo +from spdx_headers.core import find_repository_root +from spdx_headers.core import get_copyright_info +from spdx_headers.core import has_spdx_header +from spdx_headers.data import load_license_data +from spdx_headers.operations import add_header_to_single_file +from spdx_headers.operations import remove_header_from_single_file + +LICENSE_DATABASE = load_license_data() + + +def load_pyproject(repo_path: Union[str, Path]) -> dict[str, Any]: + """ + Load and return parsed ``pyproject.toml`` data for the repository. + """ + repo_root = find_repository_root(repo_path) + pyproject_path = repo_root / 'pyproject.toml' + + with pyproject_path.open('rb') as file_handle: + return tomllib.load(file_handle) + + +def get_pyproject_value(pyproject_data: dict[str, Any], dotted_key: str) -> Any: + """Return a nested ``pyproject.toml`` value from a dotted key.""" + value: Any = pyproject_data + for part in dotted_key.split('.'): + if not isinstance(value, dict) or part not in value: + raise KeyError(dotted_key) + value = value[part] + return value + + +def normalize_pattern(pattern: str) -> str: + """Normalize an exclude pattern to a POSIX-style relative path.""" + normalized = Path(pattern).as_posix() + if normalized.startswith('./'): + normalized = normalized[2:] + return normalized.rstrip('/') + + +def get_exclude_patterns( + repo_path: Union[str, Path], + exclude_values: list[str], + exclude_from_pyproject_toml: Optional[str], +) -> list[str]: + """ + Return normalized exclude patterns from CLI and ``pyproject.toml``. + """ + pyproject_data = load_pyproject(repo_path) + patterns: list[str] = [] + + if exclude_from_pyproject_toml: + value = get_pyproject_value(pyproject_data, exclude_from_pyproject_toml) + if not isinstance(value, list) or not all(isinstance(item, str) for item in value): + raise ValueError( + f'{exclude_from_pyproject_toml} in pyproject.toml must be a list of strings.', + ) + patterns.extend(value) + + for item in exclude_values: + try: + value = get_pyproject_value(pyproject_data, item) + except KeyError: + patterns.append(item) + continue + + if not isinstance(value, list) or not all(isinstance(entry, str) for entry in value): + raise ValueError(f'{item} in pyproject.toml must be a list of strings.') + patterns.extend(value) + + normalized_patterns: list[str] = [] + seen: set[str] = set() + for pattern in patterns: + normalized = normalize_pattern(pattern) + if normalized and normalized not in seen: + normalized_patterns.append(normalized) + seen.add(normalized) + + return normalized_patterns + + +def get_file_creation_year(file_path: Union[str, Path]) -> str: + """Return the year the file was first added to Git history. + + If the year cannot be determined, fall back to the current year. + """ + file_path = Path(file_path) + + repo = Repo(file_path, search_parent_directories=True) + root = Path(repo.working_tree_dir).resolve() + rel_path = file_path.resolve().relative_to(root) + + rel_path_git = rel_path.as_posix() + + log_output = repo.git.log( + '--follow', + '--diff-filter=A', + '--reverse', + '--format=%ad', + '--date=format:%Y', + '--', + rel_path_git, + ).strip() + + year = log_output.splitlines()[0].strip() if log_output else '' + + return year or str(datetime.now().year) + + +def get_org_url(repo_path: Union[str, Path]) -> str: + """ + Return the organization URL derived from the repository source URL. + """ + pyproject_data = load_pyproject(repo_path) + repo_url = pyproject_data['project']['urls']['Source Code'] + return repo_url.rsplit('/', 1)[0] + + +def get_project_license(repo_path: Union[str, Path]) -> str: + """Return the project license value from ``pyproject.toml``.""" + pyproject_data = load_pyproject(repo_path) + return pyproject_data['project']['license'] + + +def get_copyright_holder(repo_path: Union[str, Path]) -> str: + """Return the repository copyright holder name.""" + _, name, _ = get_copyright_info(repo_path) + return name + + +def add_spdx_header( + target_file: Union[str, Path], + *, + license_key: str, + copyright_holder: str, + org_url: str, +) -> None: + """Add SPDX headers to one file.""" + year = get_file_creation_year(target_file) + + add_header_to_single_file( + filepath=target_file, + license_key=license_key, + license_data=LICENSE_DATABASE, + year=year, + name=copyright_holder, + email=org_url, + ) + + +def is_excluded(relative_path: str, exclude_patterns: list[str]) -> bool: + """Return whether a relative path should be excluded.""" + for pattern in exclude_patterns: + if fnmatch.fnmatch(relative_path, pattern): + return True + if relative_path == pattern: + return True + if relative_path.startswith(f'{pattern}/'): + return True + return False + + +def iter_python_files( + paths: list[str], + *, + repo_root: Path, + exclude_patterns: list[str], + parser: argparse.ArgumentParser, +) -> list[Path]: + """Collect Python files under the given paths after exclusions.""" + files: list[Path] = [] + seen: set[Path] = set() + + for base_dir in paths: + base_path = Path(base_dir) + if not base_path.exists(): + parser.error(f'Path does not exist: {base_dir}') + + if base_path.is_file(): + candidates = [base_path] if base_path.suffix == '.py' else [] + else: + candidates = sorted(base_path.rglob('*.py')) + + for py_file in candidates: + resolved = py_file.resolve() + try: + relative_path = resolved.relative_to(repo_root).as_posix() + except ValueError: + relative_path = py_file.as_posix() + + if is_excluded(relative_path, exclude_patterns): + continue + + if resolved not in seen: + files.append(py_file) + seen.add(resolved) + + return files + + +def run_add( + files: list[Path], + *, + license_key: str, + copyright_holder: str, + org_url: str, +) -> int: + """Add SPDX headers to all selected files.""" + for py_file in files: + add_spdx_header( + py_file, + license_key=license_key, + copyright_holder=copyright_holder, + org_url=org_url, + ) + return 0 + + +def run_remove(files: list[Path]) -> int: + """Remove SPDX headers from all selected files.""" + for py_file in files: + remove_header_from_single_file(py_file) + return 0 + + +def run_check(files: list[Path]) -> int: + """Check SPDX headers in all selected files.""" + missing_files = [py_file for py_file in files if not has_spdx_header(py_file)] + + if not missing_files: + print('✓ All Python files have valid SPDX headers.') + return 0 + + print('✗ The following files are missing SPDX headers:') + for py_file in missing_files: + print(f' - {py_file.as_posix()}') + print(f'\nFound {len(missing_files)} files without SPDX headers.') + return 1 + + +def build_parser() -> argparse.ArgumentParser: + """Build the CLI argument parser.""" + parser = argparse.ArgumentParser( + description='Add, remove, or check SPDX headers in Python files.', + ) + subparsers = parser.add_subparsers(dest='command', required=True) + + for command_name in ('check', 'remove', 'add'): + command_parser = subparsers.add_parser(command_name) + command_parser.add_argument( + 'paths', + nargs='+', + help='Relative paths to scan (e.g. src tests)', + ) + command_parser.add_argument( + '--exclude', + nargs='*', + default=[], + help='Exclude paths, glob patterns, or pyproject dotted keys.', + ) + command_parser.add_argument( + '--exclude-from-pyproject-toml', + help='Read exclude patterns from a dotted key in pyproject.toml.', + ) + + return parser + + +def main(argv: Optional[list[str]] = None) -> int: + """Run the SPDX header CLI.""" + parser = build_parser() + args = parser.parse_args(argv) + + repo_path = Path('.').resolve() + repo_root = find_repository_root(repo_path).resolve() + exclude_patterns = get_exclude_patterns( + repo_path, + args.exclude, + args.exclude_from_pyproject_toml, + ) + files = iter_python_files( + args.paths, + repo_root=repo_root, + exclude_patterns=exclude_patterns, + parser=parser, + ) + + if args.command == 'check': + return run_check(files) + + if args.command == 'remove': + return run_remove(files) + + license_key = get_project_license(repo_path) + copyright_holder = get_copyright_holder(repo_path) + org_url = get_org_url(repo_path) + return run_add( + files, + license_key=license_key, + copyright_holder=copyright_holder, + org_url=org_url, + ) + + +if __name__ == '__main__': + raise SystemExit(main()) diff --git a/tools/update_docs_assets.py b/tools/update_docs_assets.py new file mode 100644 index 00000000..d375093c --- /dev/null +++ b/tools/update_docs_assets.py @@ -0,0 +1,91 @@ +""" +Update documentation assets from the assets-branding repository. + +This script fetches branding assets (logos, icons, images) from the +easyscience/assets-branding GitHub repository and copies them to the +appropriate locations in the documentation directory. +""" + +import shutil +from pathlib import Path + +import pooch + +# Configuration: Define what to fetch and where to copy +GITHUB_REPO = 'easyscience/assets-branding' +GITHUB_BRANCH = 'master' +BASE_URL = f'https://raw.githubusercontent.com/{GITHUB_REPO}/refs/heads/{GITHUB_BRANCH}' +PROJECT_NAME = 'easyreflectometry' + +# Mapping of source files to destination paths +# Format: "source_path_in_repo": "destination_path_in_project" +ASSETS_MAP = { + # Logos + f'{PROJECT_NAME}/logos/dark.svg': 'docs/docs/assets/images/logo_dark.svg', + f'{PROJECT_NAME}/logos/light.svg': 'docs/docs/assets/images/logo_light.svg', + # Favicon + f'{PROJECT_NAME}/icons/color.png': 'docs/docs/assets/images/favicon.png', + # Icon overrides + f'{PROJECT_NAME}/icons/bw.svg': f'docs/overrides/.icons/{PROJECT_NAME}.svg', + 'easyscience-org/icons/eso-icon_bw.svg': 'docs/overrides/.icons/easyscience.svg', +} + + +def fetch_and_copy_asset( + source_path: str, + dest_path: str, + cache_dir: Path, +) -> None: + """ + Fetch an asset from GitHub and copy it to the destination. + + Args: + source_path: Path to the file in the GitHub repository + dest_path: Destination path in the project + cache_dir: Directory to cache downloaded files + """ + url = f'{BASE_URL}/{source_path}' + + # Create a unique cache filename based on source path + cache_filename = source_path.replace('/', '_') + + # Download file using pooch + file_path = pooch.retrieve( + url=url, + known_hash=None, # Skip hash verification + path=cache_dir, + fname=cache_filename, + ) + + # Create destination directory if it doesn't exist + dest = Path(dest_path) + dest.parent.mkdir(parents=True, exist_ok=True) + + # Copy the file to destination + shutil.copy2(file_path, dest) + print(f'Copied {file_path} -> {dest_path}') + + +def main(): + """Main function to update all documentation assets.""" + print('📥 Updating documentation assets...') + print(f' Repository: {GITHUB_REPO}') + print(f' Branch: {GITHUB_BRANCH}\n') + + # Use a temporary cache directory + cache_dir = Path.home() / '.cache' / GITHUB_REPO + cache_dir.mkdir(parents=True, exist_ok=True) + + # Fetch and copy each asset + for source_path, dest_path in ASSETS_MAP.items(): + try: + fetch_and_copy_asset(source_path, dest_path, cache_dir) + print() + except Exception as e: + print(f'❌ Failed to fetch {source_path}: {e}') + + print('\n✅ Documentation assets updated successfully!') + + +if __name__ == '__main__': + main() diff --git a/tools/update_github_labels.py b/tools/update_github_labels.py new file mode 100644 index 00000000..84de575e --- /dev/null +++ b/tools/update_github_labels.py @@ -0,0 +1,341 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Set/update GitHub labels for current or specified easyscience +repository. + +Requires: + - gh CLI installed + - gh auth login completed + +Usage: + python update_github_labels.py + python update_github_labels.py --dry-run + python update_github_labels.py --repo easyscience/my-repo + python update_github_labels.py --repo easyscience/my-repo --dry-run +""" + +from __future__ import annotations + +import argparse +import json +import shlex +import subprocess # noqa: S404 +import sys +from dataclasses import dataclass + +EASYSCIENCE_ORG = 'easyscience' + + +# Data structures + + +@dataclass(frozen=True) +class Label: + """A GitHub label with name, color, and description.""" + + name: str + color: str + description: str = '' + + +@dataclass(frozen=True) +class LabelRename: + """Mapping from old label name to new label name.""" + + old: str + new: str + + +class Colors: + """Hex color codes for label groups.""" + + SCOPE = 'd73a4a' + MAINTAINER = '0e8a16' + PRIORITY = 'fbca04' + BOT = '5319e7' + + +LABEL_RENAMES = [ + # Default GitHub labels to rename (if they exist) + LabelRename('bug', '[scope] bug'), + LabelRename('documentation', '[scope] documentation'), + LabelRename('duplicate', '[maintainer] duplicate'), + LabelRename('enhancement', '[scope] enhancement'), + LabelRename('good first issue', '[maintainer] good first issue'), + LabelRename('help wanted', '[maintainer] help wanted'), + LabelRename('invalid', '[maintainer] invalid'), + LabelRename('question', '[maintainer] question'), + LabelRename('wontfix', '[maintainer] wontfix'), + # Custom label renames (if they exist) + LabelRename('[bot] pull request', '[bot] release'), +] + +LABELS = [ + # Scope labels + Label( + '[scope] bug', + Colors.SCOPE, + 'Bug report or fix (major.minor.PATCH)', + ), + Label( + '[scope] documentation', + Colors.SCOPE, + 'Documentation only changes (major.minor.patch.POST)', + ), + Label( + '[scope] enhancement', + Colors.SCOPE, + 'Adds/improves features (major.MINOR.patch)', + ), + Label( + '[scope] maintenance', + Colors.SCOPE, + 'Code/tooling cleanup, no feature or bugfix (major.minor.PATCH)', + ), + Label( + '[scope] significant', + Colors.SCOPE, + 'Breaking or major changes (MAJOR.minor.patch)', + ), + Label( + '[scope] ⚠️ label needed', + Colors.SCOPE, + 'Automatically added to issues and PRs without a [scope] label', + ), + # Maintainer labels + Label( + '[maintainer] duplicate', + Colors.MAINTAINER, + 'Already reported or submitted', + ), + Label( + '[maintainer] good first issue', + Colors.MAINTAINER, + 'Good entry-level issue for newcomers', + ), + Label( + '[maintainer] help wanted', + Colors.MAINTAINER, + 'Needs additional help to resolve or implement', + ), + Label( + '[maintainer] invalid', + Colors.MAINTAINER, + 'Invalid, incorrect or outdated', + ), + Label( + '[maintainer] question', + Colors.MAINTAINER, + 'Needs clarification, discussion, or more information', + ), + Label( + '[maintainer] wontfix', + Colors.MAINTAINER, + 'Will not be fixed or continued', + ), + # Priority labels + Label( + '[priority] lowest', + Colors.PRIORITY, + 'Very low urgency', + ), + Label( + '[priority] low', + Colors.PRIORITY, + 'Low importance', + ), + Label( + '[priority] medium', + Colors.PRIORITY, + 'Normal/default priority', + ), + Label( + '[priority] high', + Colors.PRIORITY, + 'Should be prioritized soon', + ), + Label( + '[priority] highest', + Colors.PRIORITY, + 'Urgent. Needs attention ASAP', + ), + Label( + '[priority] ⚠️ label needed', + Colors.PRIORITY, + 'Automatically added to issues without a [priority] label', + ), + # Bot label + Label( + '[bot] release', + Colors.BOT, + 'Automated release PR. Excluded from changelog/versioning', + ), + Label( + '[bot] backmerge', + Colors.BOT, + 'Automated backmerge master → develop failed due to conflicts', + ), +] + + +# Helpers + + +@dataclass(frozen=True) +class CmdResult: + """Result of a shell command execution.""" + + returncode: int + stdout: str + stderr: str + + +def run_cmd( + args: list[str], + *, + dry_run: bool, + check: bool = True, +) -> CmdResult: + """Run a command (or print it in dry-run mode).""" + cmd_str = ' '.join(shlex.quote(a) for a in args) + + if dry_run: + print(f' [dry-run] {cmd_str}') + return CmdResult(0, '', '') + + proc = subprocess.run( + args=args, + text=True, + capture_output=True, + ) + result = CmdResult( + proc.returncode, + proc.stdout.strip(), + proc.stderr.strip(), + ) + + if check and proc.returncode != 0: + raise RuntimeError(f'Command failed ({proc.returncode}): {cmd_str}\n{result.stderr}') + + return result + + +def get_current_repo() -> str: + """Get the current repository name in 'owner/repo' format.""" + result = subprocess.run( + args=[ + 'gh', + 'repo', + 'view', + '--json', + 'nameWithOwner', + ], + text=True, + capture_output=True, + check=True, + ) + data = json.loads(result.stdout) + name_with_owner = data.get('nameWithOwner', '') + + if '/' not in name_with_owner: + raise RuntimeError('Could not determine current repository name') + + return name_with_owner + + +def rename_label( + repo: str, + rename: LabelRename, + *, + dry_run: bool, +) -> None: + """Rename a label, silently skipping if it doesn't exist.""" + result = run_cmd( + args=[ + 'gh', + 'label', + 'edit', + rename.old, + '--name', + rename.new, + '--repo', + repo, + ], + dry_run=dry_run, + check=False, + ) + + if dry_run or result.returncode == 0: + print(f' Rename: {rename.old!r} → {rename.new!r}') + else: + print(f' Skip (not found): {rename.old!r}') + + +def upsert_label( + repo: str, + label: Label, + *, + dry_run: bool, +) -> None: + """Create or update a label.""" + run_cmd( + [ + 'gh', + 'label', + 'create', + label.name, + '--color', + label.color, + '--description', + label.description, + '--force', + '--repo', + repo, + ], + dry_run=dry_run, + ) + print(f' Upsert: {label.name!r}') + + +# Main + + +def main() -> int: + """Entry point: parse arguments and sync labels.""" + parser = argparse.ArgumentParser(description='Sync GitHub labels for easyscience repos') + parser.add_argument( + '--repo', + help='Target repository (owner/name)', + ) + parser.add_argument( + '--dry-run', + action='store_true', + help='Print actions without applying changes', + ) + args = parser.parse_args() + + repo = args.repo or get_current_repo() + org = repo.split('/')[0] + + if org.lower() != EASYSCIENCE_ORG: + print(f"Error: repository '{repo}' is not under '{EASYSCIENCE_ORG}'", file=sys.stderr) + return 2 + + print(f'Repository: {repo}') + if args.dry_run: + print('Mode: DRY-RUN (no changes will be made)\n') + + print('\nRenaming default labels...') + for rename in LABEL_RENAMES: + rename_label(repo, rename, dry_run=args.dry_run) + + print('\nUpserting labels...') + for label in LABELS: + upsert_label(repo, label, dry_run=args.dry_run) + + print('\nDone.') + return 0 + + +if __name__ == '__main__': + raise SystemExit(main()) diff --git a/vscode-template/settings.json b/vscode-template/settings.json index 35487105..239b6f6a 100644 --- a/vscode-template/settings.json +++ b/vscode-template/settings.json @@ -1,13 +1,11 @@ { - "python.testing.pytestArgs": [ - "tests" - ], - "python.testing.unittestEnabled": false, - "python.testing.pytestEnabled": true, - "[python]": { - "editor.formatOnSave": true, - "editor.codeActionsOnSave": { - "source.organizeImports": "explicit" - }, - }, -} \ No newline at end of file + "python.testing.pytestArgs": ["tests"], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true, + "[python]": { + "editor.formatOnSave": true, + "editor.codeActionsOnSave": { + "source.organizeImports": "explicit" + } + } +} From 6591dea0215f9f0fb9f648ee51f7222701c65cc9 Mon Sep 17 00:00:00 2001 From: rozyczko Date: Thu, 7 May 2026 14:08:22 +0200 Subject: [PATCH 03/20] fixes --- docs/src/conf.py | 44 ++++----- .../advancedfitting/multi_contrast.ipynb | 59 +++++------- .../tutorials/fitting/material_solvated.ipynb | 34 +++---- docs/src/tutorials/fitting/monolayer.ipynb | 41 ++++----- docs/src/tutorials/fitting/repeating.ipynb | 30 +++---- .../tutorials/fitting/simple_fitting.ipynb | 33 +++---- docs/src/tutorials/simulation/bilayer.ipynb | 47 ++++------ docs/src/tutorials/simulation/magnetism.ipynb | 89 +++++++++---------- .../simulation/resolution_functions.ipynb | 39 ++++---- pixi.lock | 81 +++++++++++------ pixi.toml | 3 + 11 files changed, 231 insertions(+), 269 deletions(-) diff --git a/docs/src/conf.py b/docs/src/conf.py index 36235949..127779c9 100644 --- a/docs/src/conf.py +++ b/docs/src/conf.py @@ -20,9 +20,10 @@ import datetime import os import sys -import toml from pathlib import Path +import toml + import easyreflectometry sys.path.insert(0, os.path.abspath('../src')) @@ -54,7 +55,7 @@ 'sphinx_autodoc_typehints', 'sphinx_copybutton', 'nbsphinx', - 'myst_parser' + 'myst_parser', ] # Add any paths that contain templates here, relative to this directory. @@ -71,8 +72,8 @@ # General information about the project. project = 'EasyReflectometry' -copyright = f"{datetime.date.today().year}, EasyReflectometry" -author = "EasyReflectometry" +copyright = f'{datetime.date.today().year}, EasyReflectometry' +author = 'EasyReflectometry' # The version info for the project you're documenting, acts as replacement # for |version| and |release|, also used in various other places throughout @@ -105,7 +106,7 @@ autoclass_content = 'class' autodoc_member_order = 'bysource' autodoc_typehints = 'signature' -autodoc_class_signature = "separated" +autodoc_class_signature = 'separated' # -- Options for HTML output ------------------------------------------- @@ -116,7 +117,7 @@ html_logo = os.path.join('_static', 'logo.png') html_favicon = os.path.join('_static', 'favicon.ico') html_theme_options = { -# 'logo_only': True, + # 'logo_only': True, 'navigation_with_keys': True } html_baseurl = 'https://docs.easyreflectometry.org' @@ -132,7 +133,7 @@ html_static_path = ['_static'] nbsphinx_execute_arguments = [ - "--Session.metadata=scipp_docs_build=True", + '--Session.metadata=scipp_docs_build=True', ] @@ -148,15 +149,12 @@ # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', - # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', - # Additional stuff for the LaTeX preamble. # # 'preamble': '', - # Latex figure (float) alignment # # 'figure_align': 'htbp', @@ -166,9 +164,7 @@ # (source start file, target name, title, author, documentclass # [howto, manual, or own class]). latex_documents = [ - (master_doc, 'EasyReflectometry.tex', - 'EasyReflectometry Documentation', - 'Andrew R. McCluskey', 'manual'), + (master_doc, 'EasyReflectometry.tex', 'EasyReflectometry Documentation', 'Andrew R. McCluskey', 'manual'), ] @@ -176,11 +172,7 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'EasyReflectometry', - 'EasyReflectometry Documentation', - [author], 1) -] +man_pages = [(master_doc, 'EasyReflectometry', 'EasyReflectometry Documentation', [author], 1)] # -- Options for Texinfo output ---------------------------------------- @@ -189,11 +181,13 @@ # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - (master_doc, 'EasyReflectometry', - 'EasyReflectometry Documentation', - author, - 'EasyReflectometry', - 'One line description of project.', - 'Miscellaneous'), + ( + master_doc, + 'EasyReflectometry', + 'EasyReflectometry Documentation', + author, + 'EasyReflectometry', + 'One line description of project.', + 'Miscellaneous', + ), ] - diff --git a/docs/src/tutorials/advancedfitting/multi_contrast.ipynb b/docs/src/tutorials/advancedfitting/multi_contrast.ipynb index 51e4e225..f08269c4 100644 --- a/docs/src/tutorials/advancedfitting/multi_contrast.ipynb +++ b/docs/src/tutorials/advancedfitting/multi_contrast.ipynb @@ -29,24 +29,23 @@ "source": [ "%matplotlib inline\n", "\n", - "import refnx\n", "import pooch\n", + "import refnx\n", + "from easyscience.fitting import AvailableMinimizers\n", "\n", "import easyreflectometry\n", - "\n", + "from easyreflectometry.calculators import CalculatorFactory\n", "from easyreflectometry.data import load\n", + "from easyreflectometry.fitting import MultiFitter\n", + "from easyreflectometry.model import Model\n", + "from easyreflectometry.model import PercentageFwhm\n", "from easyreflectometry.plot import plot\n", - "from easyreflectometry.sample import Material\n", - "from easyreflectometry.sample import SurfactantLayer\n", "from easyreflectometry.sample import Layer\n", - "from easyreflectometry.sample import Multilayer\n", "from easyreflectometry.sample import LayerAreaPerMolecule\n", + "from easyreflectometry.sample import Material\n", + "from easyreflectometry.sample import Multilayer\n", "from easyreflectometry.sample import Sample\n", - "from easyreflectometry.model import Model\n", - "from easyreflectometry.model import PercentageFwhm\n", - "from easyreflectometry.calculators import CalculatorFactory\n", - "from easyreflectometry.fitting import MultiFitter\n", - "from easyscience.fitting import AvailableMinimizers\n", + "from easyreflectometry.sample import SurfactantLayer\n", "\n", "print(f'easyreflectometry: {easyreflectometry.__version__}')\n", "print(f'refnx: {refnx.__version__}')" @@ -73,8 +72,8 @@ "source": [ "file_path = pooch.retrieve(\n", " # URL to one of Pooch's test files\n", - " url=\"https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/advancedfitting/multiple.ort\",\n", - " known_hash=\"241bcb819cdae47fbbb310a99c2456c7332312719496b936a153dc7dee83e62c\",\n", + " url='https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/advancedfitting/multiple.ort',\n", + " known_hash='241bcb819cdae47fbbb310a99c2456c7332312719496b936a153dc7dee83e62c',\n", ")\n", "data = load(file_path)" ] @@ -130,8 +129,7 @@ "metadata": {}, "outputs": [], "source": [ - "dspc = {'d-head': 'C10D18NO8P', 'd-tail': 'C34D70',\n", - " 'h-head': 'C10H18NO8P', 'h-tail': 'C34H70'}" + "dspc = {'d-head': 'C10D18NO8P', 'd-tail': 'C34D70', 'h-head': 'C10H18NO8P', 'h-tail': 'C34H70'}" ] }, { @@ -235,7 +233,7 @@ " solvent=air,\n", " solvent_fraction=tail_solvent_fraction,\n", " area_per_molecule=area_per_molecule,\n", - " roughness=roughness\n", + " roughness=roughness,\n", ")\n", "head_layer_d13d2o = LayerAreaPerMolecule(\n", " molecular_formula=dspc['d-head'],\n", @@ -243,12 +241,9 @@ " solvent=d2o,\n", " solvent_fraction=head_solvent_fraction,\n", " area_per_molecule=area_per_molecule,\n", - " roughness=roughness\n", - ")\n", - "d13d2o = SurfactantLayer(\n", - " tail_layer=tail_layer_d13d2o,\n", - " head_layer=head_layer_d13d2o\n", + " roughness=roughness,\n", ")\n", + "d13d2o = SurfactantLayer(tail_layer=tail_layer_d13d2o, head_layer=head_layer_d13d2o)\n", "d13d2o.constrain_area_per_molecule = True\n", "d13d2o.conformal_roughness = True\n", "d13d2o.constrain_solvent_roughness(d2o_layer.roughness)" @@ -275,7 +270,7 @@ " solvent=air,\n", " solvent_fraction=tail_solvent_fraction,\n", " area_per_molecule=area_per_molecule,\n", - " roughness=roughness\n", + " roughness=roughness,\n", ")\n", "head_layer_d70d2o = LayerAreaPerMolecule(\n", " molecular_formula=dspc['h-head'],\n", @@ -283,12 +278,9 @@ " solvent=d2o,\n", " solvent_fraction=head_solvent_fraction,\n", " area_per_molecule=area_per_molecule,\n", - " roughness=roughness\n", - ")\n", - "d70d2o = SurfactantLayer(\n", - " tail_layer=tail_layer_d70d2o,\n", - " head_layer=head_layer_d70d2o\n", + " roughness=roughness,\n", ")\n", + "d70d2o = SurfactantLayer(tail_layer=tail_layer_d70d2o, head_layer=head_layer_d70d2o)\n", "d70d2o.constrain_area_per_molecule = True\n", "d70d2o.conformal_roughness = True\n", "d70d2o.constrain_solvent_roughness(d2o_layer.roughness)" @@ -315,7 +307,7 @@ " solvent=air,\n", " solvent_fraction=tail_solvent_fraction,\n", " area_per_molecule=area_per_molecule,\n", - " roughness=roughness\n", + " roughness=roughness,\n", ")\n", "head_layer_d83acmw = LayerAreaPerMolecule(\n", " molecular_formula=dspc['d-head'],\n", @@ -323,12 +315,9 @@ " solvent=acmw,\n", " solvent_fraction=head_solvent_fraction,\n", " area_per_molecule=area_per_molecule,\n", - " roughness=roughness\n", - ")\n", - "d83acmw = SurfactantLayer(\n", - " tail_layer=tail_layer_d83acmw,\n", - " head_layer=head_layer_d83acmw\n", + " roughness=roughness,\n", ")\n", + "d83acmw = SurfactantLayer(tail_layer=tail_layer_d83acmw, head_layer=head_layer_d83acmw)\n", "d83acmw.constrain_area_per_molecule = True\n", "d83acmw.conformal_roughness = True\n", "d83acmw.constrain_solvent_roughness(acmw_layer.roughness)" @@ -420,19 +409,19 @@ " sample=d13d2o_sample,\n", " scale=0.1,\n", " background=data['data']['R_d13DSPC-D2O'].values.min(),\n", - " resolution_function=resolution_function\n", + " resolution_function=resolution_function,\n", ")\n", "d70d2o_model = Model(\n", " sample=d70d2o_sample,\n", " scale=0.1,\n", " background=data['data']['R_d70DSPC-D2O'].values.min(),\n", - " resolution_function=resolution_function\n", + " resolution_function=resolution_function,\n", ")\n", "d83acmw_model = Model(\n", " sample=d83acmw_sample,\n", " scale=0.1,\n", " background=data['data']['R_d83DSPC-ACMW'].values.min(),\n", - " resolution_function=resolution_function\n", + " resolution_function=resolution_function,\n", ")" ] }, diff --git a/docs/src/tutorials/fitting/material_solvated.ipynb b/docs/src/tutorials/fitting/material_solvated.ipynb index 4665e87b..6f6f0c30 100644 --- a/docs/src/tutorials/fitting/material_solvated.ipynb +++ b/docs/src/tutorials/fitting/material_solvated.ipynb @@ -33,23 +33,22 @@ "%matplotlib inline\n", "\n", "import numpy as np\n", - "import scipp as sc\n", "import pooch\n", "import refnx\n", + "import scipp as sc\n", "\n", "import easyreflectometry\n", - "\n", + "from easyreflectometry.calculators import CalculatorFactory\n", "from easyreflectometry.data import load\n", + "from easyreflectometry.fitting import MultiFitter\n", + "from easyreflectometry.model import Model\n", + "from easyreflectometry.model import PercentageFwhm\n", + "from easyreflectometry.plot import plot\n", "from easyreflectometry.sample import Layer\n", - "from easyreflectometry.sample import Sample\n", "from easyreflectometry.sample import Material\n", "from easyreflectometry.sample import MaterialSolvated\n", "from easyreflectometry.sample import Multilayer\n", - "from easyreflectometry.model import Model\n", - "from easyreflectometry.model import PercentageFwhm\n", - "from easyreflectometry.calculators import CalculatorFactory\n", - "from easyreflectometry.fitting import MultiFitter\n", - "from easyreflectometry.plot import plot" + "from easyreflectometry.sample import Sample" ] }, { @@ -92,8 +91,8 @@ "source": [ "file_path = pooch.retrieve(\n", " # URL to one of Pooch's test files\n", - " url=\"https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/fitting/example.ort\",\n", - " known_hash=\"82d0c95c069092279a799a8131ad3710335f601d9f1080754b387f42e407dfab\",\n", + " url='https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/fitting/example.ort',\n", + " known_hash='82d0c95c069092279a799a8131ad3710335f601d9f1080754b387f42e407dfab',\n", ")\n", "data = load(file_path)" ] @@ -137,12 +136,7 @@ "metadata": {}, "outputs": [], "source": [ - "solvated_film_material = MaterialSolvated(\n", - " material=film,\n", - " solvent=d2o,\n", - " solvent_fraction=0.25,\n", - " name='Solvated Film'\n", - ")" + "solvated_film_material = MaterialSolvated(material=film, solvent=d2o, solvent_fraction=0.25, name='Solvated Film')" ] }, { @@ -196,13 +190,7 @@ "\n", "resolution_function = PercentageFwhm(0.02)\n", "sample = Sample(superphase, Multilayer(solvated_film), Multilayer(subphase), name='Film Structure')\n", - "model = Model(\n", - " sample=sample,\n", - " scale=1,\n", - " background=1e-6,\n", - " resolution_function=resolution_function,\n", - " name='Film Model'\n", - ")" + "model = Model(sample=sample, scale=1, background=1e-6, resolution_function=resolution_function, name='Film Model')" ] }, { diff --git a/docs/src/tutorials/fitting/monolayer.ipynb b/docs/src/tutorials/fitting/monolayer.ipynb index d0ef8aa0..1d1c37ee 100644 --- a/docs/src/tutorials/fitting/monolayer.ipynb +++ b/docs/src/tutorials/fitting/monolayer.ipynb @@ -29,25 +29,22 @@ "source": [ "%matplotlib inline\n", "\n", - "import refnx\n", "import pooch\n", + "import refnx\n", "\n", "import easyreflectometry\n", - "\n", "from easyreflectometry.calculators import CalculatorFactory\n", "from easyreflectometry.data import load\n", + "from easyreflectometry.fitting import MultiFitter\n", + "from easyreflectometry.model import Model\n", + "from easyreflectometry.model import PercentageFwhm\n", "from easyreflectometry.plot import plot\n", - "from easyreflectometry.sample import Material\n", - "from easyreflectometry.sample import SurfactantLayer\n", - "from easyreflectometry.sample import LayerAreaPerMolecule\n", "from easyreflectometry.sample import Layer\n", + "from easyreflectometry.sample import LayerAreaPerMolecule\n", + "from easyreflectometry.sample import Material\n", "from easyreflectometry.sample import Multilayer\n", "from easyreflectometry.sample import Sample\n", - "from easyreflectometry.model import Model\n", - "from easyreflectometry.model import PercentageFwhm\n", - "from easyreflectometry.fitting import MultiFitter\n", - "from easyreflectometry.plot import plot\n", - "from easyscience.fitting import AvailableMinimizers\n" + "from easyreflectometry.sample import SurfactantLayer" ] }, { @@ -90,8 +87,8 @@ "source": [ "file_path = pooch.retrieve(\n", " # URL to one of Pooch's test files\n", - " url=\"https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/fitting/d70d2o.ort\",\n", - " known_hash=\"3e4750536621be8eec493fa21a287e408d384f29cacb113b71d02690d99f0998\",\n", + " url='https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/fitting/d70d2o.ort',\n", + " known_hash='3e4750536621be8eec493fa21a287e408d384f29cacb113b71d02690d99f0998',\n", ")\n", "data = load(file_path)\n", "plot(data)" @@ -254,22 +251,19 @@ " molecular_formula=tail_formula,\n", " thickness=tail_thickness,\n", " solvent=air,\n", - " solvent_fraction=tail_solvent_fraction, \n", + " solvent_fraction=tail_solvent_fraction,\n", " area_per_molecule=area_per_molecule,\n", - " roughness=roughness\n", + " roughness=roughness,\n", ")\n", "head_layer = LayerAreaPerMolecule(\n", " molecular_formula=head_formula,\n", " thickness=head_thickness,\n", " solvent=d2o,\n", - " solvent_fraction=head_solvent_fraction, \n", + " solvent_fraction=head_solvent_fraction,\n", " area_per_molecule=area_per_molecule,\n", - " roughness=roughness\n", - ")\n", - "dspc = SurfactantLayer(\n", - " tail_layer=tail_layer,\n", - " head_layer=head_layer\n", + " roughness=roughness,\n", ")\n", + "dspc = SurfactantLayer(tail_layer=tail_layer, head_layer=head_layer)\n", "dspc.constrain_area_per_molecule = True\n", "dspc.conformal_roughness = True\n", "dspc" @@ -330,12 +324,7 @@ "source": [ "resolution_function = PercentageFwhm(5)\n", "sample = Sample(Multilayer(air_layer), dspc, Multilayer(d2o_layer))\n", - "model = Model(\n", - " sample=sample,\n", - " scale=1,\n", - " background=data['data']['R_0'].values.min(),\n", - " resolution_function=resolution_function\n", - ")" + "model = Model(sample=sample, scale=1, background=data['data']['R_0'].values.min(), resolution_function=resolution_function)" ] }, { diff --git a/docs/src/tutorials/fitting/repeating.ipynb b/docs/src/tutorials/fitting/repeating.ipynb index 0ebde2e1..19e6bceb 100644 --- a/docs/src/tutorials/fitting/repeating.ipynb +++ b/docs/src/tutorials/fitting/repeating.ipynb @@ -34,24 +34,22 @@ "%matplotlib inline\n", "\n", "import numpy as np\n", - "import scipp as sc\n", "import pooch\n", "import refl1d\n", + "import scipp as sc\n", "\n", "import easyreflectometry\n", - "\n", + "from easyreflectometry.calculators import CalculatorFactory\n", "from easyreflectometry.data import load\n", - "from easyreflectometry.sample import Layer\n", - "from easyreflectometry.sample import Sample\n", - "from easyreflectometry.sample import Material\n", - "from easyreflectometry.sample import RepeatingMultilayer\n", - "from easyreflectometry.sample import Multilayer\n", + "from easyreflectometry.fitting import MultiFitter\n", "from easyreflectometry.model import Model\n", "from easyreflectometry.model import PercentageFwhm\n", - "from easyreflectometry.calculators import CalculatorFactory\n", - "from easyreflectometry.fitting import MultiFitter\n", "from easyreflectometry.plot import plot\n", - "from easyscience.fitting import AvailableMinimizers" + "from easyreflectometry.sample import Layer\n", + "from easyreflectometry.sample import Material\n", + "from easyreflectometry.sample import Multilayer\n", + "from easyreflectometry.sample import RepeatingMultilayer\n", + "from easyreflectometry.sample import Sample" ] }, { @@ -95,8 +93,8 @@ "source": [ "file_path = pooch.retrieve(\n", " # URL to one of Pooch's test files\n", - " url=\"https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/fitting/repeating_layers.ort\",\n", - " known_hash=\"a5ffca9fd24f1d362266251723aec7ce9f34f123e39a38dfc4d829c758e6bf90\",\n", + " url='https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/fitting/repeating_layers.ort',\n", + " known_hash='a5ffca9fd24f1d362266251723aec7ce9f34f123e39a38dfc4d829c758e6bf90',\n", ")\n", "data = load(file_path)" ] @@ -203,13 +201,7 @@ "source": [ "resolution_function = PercentageFwhm(0)\n", "sample = Sample(Multilayer(superphase), rep_multilayer, Multilayer(subphase), name='Multilayer Structure')\n", - "model = Model(\n", - " sample=sample,\n", - " scale=1,\n", - " background=0,\n", - " resolution_function=resolution_function,\n", - " name='Multilayer Model'\n", - ")" + "model = Model(sample=sample, scale=1, background=0, resolution_function=resolution_function, name='Multilayer Model')" ] }, { diff --git a/docs/src/tutorials/fitting/simple_fitting.ipynb b/docs/src/tutorials/fitting/simple_fitting.ipynb index ea761e75..f6ee414d 100644 --- a/docs/src/tutorials/fitting/simple_fitting.ipynb +++ b/docs/src/tutorials/fitting/simple_fitting.ipynb @@ -36,17 +36,16 @@ "import refnx\n", "\n", "import easyreflectometry\n", - "\n", + "from easyreflectometry.calculators import CalculatorFactory\n", "from easyreflectometry.data import load\n", + "from easyreflectometry.fitting import MultiFitter\n", + "from easyreflectometry.model import Model\n", + "from easyreflectometry.model import PercentageFwhm\n", + "from easyreflectometry.plot import plot\n", "from easyreflectometry.sample import Layer\n", - "from easyreflectometry.sample import Sample\n", "from easyreflectometry.sample import Material\n", "from easyreflectometry.sample import Multilayer\n", - "from easyreflectometry.model import Model\n", - "from easyreflectometry.model import PercentageFwhm\n", - "from easyreflectometry.calculators import CalculatorFactory\n", - "from easyreflectometry.fitting import MultiFitter\n", - "from easyreflectometry.plot import plot" + "from easyreflectometry.sample import Sample" ] }, { @@ -90,8 +89,8 @@ "source": [ "file_path = pooch.retrieve(\n", " # URL to one of Pooch's test files\n", - " url=\"https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/fitting/example.ort\",\n", - " known_hash=\"82d0c95c069092279a799a8131ad3710335f601d9f1080754b387f42e407dfab\",\n", + " url='https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/fitting/example.ort',\n", + " known_hash='82d0c95c069092279a799a8131ad3710335f601d9f1080754b387f42e407dfab',\n", ")\n", "data = load(file_path)" ] @@ -311,13 +310,7 @@ "outputs": [], "source": [ "resolution_function = PercentageFwhm(0.02)\n", - "model = Model(\n", - " sample=sample,\n", - " scale=1,\n", - " background=1e-6,\n", - " resolution_function=resolution_function,\n", - " name='Film Model'\n", - ")" + "model = Model(sample=sample, scale=1, background=1e-6, resolution_function=resolution_function, name='Film Model')" ] }, { @@ -552,11 +545,7 @@ "\n", "resolution_function_refl1d = PercentageFwhm(0.02)\n", "model_refl1d = Model(\n", - " sample=sample_refl1d,\n", - " scale=1,\n", - " background=1e-6,\n", - " resolution_function=resolution_function_refl1d,\n", - " name='Film Model (Refl1D)'\n", + " sample=sample_refl1d, scale=1, background=1e-6, resolution_function=resolution_function_refl1d, name='Film Model (Refl1D)'\n", ")\n", "\n", "sio2_layer_refl1d.thickness.bounds = (15, 50)\n", @@ -598,7 +587,7 @@ "\n", "qz = data['coords']['Qz_0'].values\n", "reflectivity = data['data']['R_0'].values\n", - "uncertainty = data['data']['R_0'].variances**0.5\n", + "uncertainty = data['data']['R_0'].variances ** 0.5\n", "\n", "plt.figure(figsize=(8, 5))\n", "plt.errorbar(qz, reflectivity, yerr=uncertainty, fmt='o', markersize=3, color='black', alpha=0.6, label='Data')\n", diff --git a/docs/src/tutorials/simulation/bilayer.ipynb b/docs/src/tutorials/simulation/bilayer.ipynb index 3d7faccd..142bb35d 100644 --- a/docs/src/tutorials/simulation/bilayer.ipynb +++ b/docs/src/tutorials/simulation/bilayer.ipynb @@ -41,19 +41,18 @@ "source": [ "%matplotlib inline\n", "\n", - "import numpy as np\n", "import matplotlib.pyplot as plt\n", + "import numpy as np\n", "\n", - "import easyreflectometry\n", "from easyreflectometry.calculators import CalculatorFactory\n", + "from easyreflectometry.model import Model\n", + "from easyreflectometry.model import PercentageFwhm\n", "from easyreflectometry.sample import Bilayer\n", + "from easyreflectometry.sample import Layer\n", "from easyreflectometry.sample import LayerAreaPerMolecule\n", "from easyreflectometry.sample import Material\n", - "from easyreflectometry.sample import Layer\n", "from easyreflectometry.sample import Multilayer\n", - "from easyreflectometry.sample import Sample\n", - "from easyreflectometry.model import Model\n", - "from easyreflectometry.model import PercentageFwhm" + "from easyreflectometry.sample import Sample" ] }, { @@ -105,7 +104,7 @@ " solvent_fraction=0.3, # 30% solvent in head region\n", " area_per_molecule=48.2,\n", " roughness=3.0,\n", - " name='DPPC Head'\n", + " name='DPPC Head',\n", ")\n", "\n", "# Create a tail layer for the bilayer\n", @@ -117,7 +116,7 @@ " solvent_fraction=0.0, # No solvent in the tail region\n", " area_per_molecule=48.2,\n", " roughness=3.0,\n", - " name='DPPC Tail'\n", + " name='DPPC Tail',\n", ")" ] }, @@ -145,9 +144,9 @@ "bilayer = Bilayer(\n", " front_head_layer=head_layer,\n", " front_tail_layer=front_tail_layer,\n", - " constrain_heads=True, # Head layers share thickness and area per molecule\n", + " constrain_heads=True, # Head layers share thickness and area per molecule\n", " conformal_roughness=True, # All layers share the same roughness\n", - " name='DPPC Bilayer'\n", + " name='DPPC Bilayer',\n", ")\n", "\n", "print(bilayer)" @@ -222,7 +221,7 @@ "\n", "# We can set them independently\n", "bilayer.back_head_layer.solvent_fraction = 0.5\n", - "print(f'\\nAfter setting back head solvent fraction to 0.5:')\n", + "print('\\nAfter setting back head solvent fraction to 0.5:')\n", "print(f'Front head solvent fraction: {bilayer.front_head_layer.solvent_fraction:.2f}')\n", "print(f'Back head solvent fraction: {bilayer.back_head_layer.solvent_fraction:.2f}')" ] @@ -290,7 +289,7 @@ " Multilayer(sio2_layer, name='SiO2'),\n", " bilayer,\n", " Multilayer(d2o_subphase, name='D2O Subphase'),\n", - " name='Bilayer on Si/SiO2'\n", + " name='Bilayer on Si/SiO2',\n", ")\n", "\n", "print(sample)" @@ -314,13 +313,7 @@ "outputs": [], "source": [ "# Create the model\n", - "model = Model(\n", - " sample=sample,\n", - " scale=1.0,\n", - " background=1e-7,\n", - " resolution_function=PercentageFwhm(5),\n", - " name='Bilayer Model'\n", - ")\n", + "model = Model(sample=sample, scale=1.0, background=1e-7, resolution_function=PercentageFwhm(5), name='Bilayer Model')\n", "\n", "# Set up the calculator\n", "interface = CalculatorFactory()\n", @@ -451,7 +444,7 @@ "\n", "# Now set asymmetric hydration (common in supported bilayers)\n", "bilayer.front_head_layer.solvent_fraction = 0.1 # Substrate side - less hydrated\n", - "bilayer.back_head_layer.solvent_fraction = 0.4 # Solution side - more hydrated\n", + "bilayer.back_head_layer.solvent_fraction = 0.4 # Solution side - more hydrated\n", "\n", "# Get asymmetric SLD profile\n", "z_asym, sld_asym = model.interface().sld_profile(model.unique_name)\n", @@ -502,7 +495,7 @@ " solvent_fraction=0.3,\n", " area_per_molecule=48.2,\n", " roughness=3.0,\n", - " name='DPPC Head H2O'\n", + " name='DPPC Head H2O',\n", ")\n", "\n", "# Create tail layer for H2O contrast (same deuterated lipid, different solvent)\n", @@ -513,7 +506,7 @@ " solvent_fraction=0.0,\n", " area_per_molecule=48.2,\n", " roughness=3.0,\n", - " name='DPPC Tail H2O'\n", + " name='DPPC Tail H2O',\n", ")\n", "\n", "# Create H2O bilayer\n", @@ -522,7 +515,7 @@ " front_tail_layer=tail_layer_h2o,\n", " constrain_heads=True,\n", " conformal_roughness=True,\n", - " name='DPPC Bilayer H2O'\n", + " name='DPPC Bilayer H2O',\n", ")" ] }, @@ -568,16 +561,12 @@ " Multilayer(sio2_layer, name='SiO2'),\n", " bilayer_h2o,\n", " Multilayer(h2o_subphase, name='H2O Subphase'),\n", - " name='Bilayer on Si/SiO2 in H2O'\n", + " name='Bilayer on Si/SiO2 in H2O',\n", ")\n", "\n", "# Create model for H2O contrast\n", "model_h2o = Model(\n", - " sample=sample_h2o,\n", - " scale=1.0,\n", - " background=1e-7,\n", - " resolution_function=PercentageFwhm(5),\n", - " name='Bilayer Model H2O'\n", + " sample=sample_h2o, scale=1.0, background=1e-7, resolution_function=PercentageFwhm(5), name='Bilayer Model H2O'\n", ")\n", "model_h2o.interface = interface" ] diff --git a/docs/src/tutorials/simulation/magnetism.ipynb b/docs/src/tutorials/simulation/magnetism.ipynb index 1f35fdf1..8f8ce93c 100644 --- a/docs/src/tutorials/simulation/magnetism.ipynb +++ b/docs/src/tutorials/simulation/magnetism.ipynb @@ -31,20 +31,19 @@ "\n", "import matplotlib.pyplot as plt\n", "import numpy as np\n", - "import scipp as sc\n", "import refl1d\n", "import refl1d.names\n", + "import scipp as sc\n", "\n", "import easyreflectometry\n", - "\n", "from easyreflectometry.calculators import CalculatorFactory\n", + "from easyreflectometry.calculators.refl1d.wrapper import _get_polarized_probe\n", "from easyreflectometry.model import Model\n", "from easyreflectometry.model import PercentageFwhm\n", "from easyreflectometry.sample import Layer\n", "from easyreflectometry.sample import Material\n", "from easyreflectometry.sample import Multilayer\n", - "from easyreflectometry.sample import Sample\n", - "from easyreflectometry.calculators.refl1d.wrapper import _get_polarized_probe" + "from easyreflectometry.sample import Sample" ] }, { @@ -150,18 +149,13 @@ "metadata": {}, "outputs": [], "source": [ - "refl1d_sld_4 = refl1d.names.SLD(name=\"Sld 4\", rho=4.0, irho=0)\n", - "refl1d_sld_8 = refl1d.names.SLD(name=\"Sld 8\", rho=8.0, irho=0)\n", - "refl1d_vacuum = refl1d.names.SLD(name=\"Vacuum\", rho=0, irho=0)\n", - "refl1d_si = refl1d.names.SLD(name=\"Si\", rho=2.047, irho=0)\n", + "refl1d_sld_4 = refl1d.names.SLD(name='Sld 4', rho=4.0, irho=0)\n", + "refl1d_sld_8 = refl1d.names.SLD(name='Sld 8', rho=8.0, irho=0)\n", + "refl1d_vacuum = refl1d.names.SLD(name='Vacuum', rho=0, irho=0)\n", + "refl1d_si = refl1d.names.SLD(name='Si', rho=2.047, irho=0)\n", "\n", "# Refl1d model is inverted as compared to EasyReflectometry, so the order of the layers is reversed\n", - "refl1d_sample = (\n", - " refl1d_si(0, 0) | \n", - " refl1d_sld_8(150, 0) |\n", - " refl1d_sld_4(100, 0) | \n", - " refl1d_vacuum(0, 0)\n", - ") " + "refl1d_sample = refl1d_si(0, 0) | refl1d_sld_8(150, 0) | refl1d_sld_4(100, 0) | refl1d_vacuum(0, 0)" ] }, { @@ -206,6 +200,7 @@ " num=1000,\n", ")\n", "\n", + "\n", "def plot_apply_makeup():\n", " ax = plt.gca()\n", " ax.set_xlim([-0.01, 0.35])\n", @@ -233,11 +228,11 @@ "source": [ "# Refl1d\n", "probe = refl1d.names.QProbe(\n", - " Q=model_coords,\n", - " dQ=np.zeros(len(model_coords)),\n", - " intensity=1,\n", - " background=0,\n", - " )\n", + " Q=model_coords,\n", + " dQ=np.zeros(len(model_coords)),\n", + " intensity=1,\n", + " background=0,\n", + ")\n", "experiment = refl1d.names.Experiment(probe=probe, sample=refl1d_sample)\n", "model_data_no_magnetism_ref1d_raw = experiment.reflectivity()[1]\n", "\n", @@ -253,7 +248,9 @@ " model_coords,\n", " model.unique_name,\n", ")\n", - "plt.plot(model_coords, model_data_no_magnetism_ref1d_easy, 'r-', label=f'EasyReflectometry ({model_interface.name})', linewidth=2)\n", + "plt.plot(\n", + " model_coords, model_data_no_magnetism_ref1d_easy, 'r-', label=f'EasyReflectometry ({model_interface.name})', linewidth=2\n", + ")\n", "\n", "plot_apply_makeup()" ] @@ -290,8 +287,12 @@ "model.interface = interface\n", "model_interface = model.interface()\n", "model_interface.include_magnetism = True\n", - "model_interface._wrapper.update_layer(list(model_interface._wrapper.storage['layer'].keys())[1], magnetism_rhoM=10, magnetism_thetaM=70)\n", - "model_interface._wrapper.update_layer(list(model_interface._wrapper.storage['layer'].keys())[2], magnetism_rhoM=5, magnetism_thetaM=175)\n", + "model_interface._wrapper.update_layer(\n", + " list(model_interface._wrapper.storage['layer'].keys())[1], magnetism_rhoM=10, magnetism_thetaM=70\n", + ")\n", + "model_interface._wrapper.update_layer(\n", + " list(model_interface._wrapper.storage['layer'].keys())[2], magnetism_rhoM=5, magnetism_thetaM=175\n", + ")\n", "model_data_magnetism_layer_1 = model.interface().reflectity_profile(\n", " model_coords,\n", " model.unique_name,\n", @@ -327,21 +328,19 @@ "source": [ "# Refl1d model is inverted as compared to EasyReflectometry, so the order of the layers is reversed\n", "refl1d_sample = (\n", - " refl1d_si(0, 0) | \n", - " refl1d_sld_8(150, 0, magnetism=refl1d.names.Magnetism(rhoM=5, thetaM=175)) |\n", - " refl1d_sld_4(100, 0, magnetism=refl1d.names.Magnetism(rhoM=10, thetaM=70)) | \n", - " refl1d_vacuum(0, 0)\n", - ") \n", + " refl1d_si(0, 0)\n", + " | refl1d_sld_8(150, 0, magnetism=refl1d.names.Magnetism(rhoM=5, thetaM=175))\n", + " | refl1d_sld_4(100, 0, magnetism=refl1d.names.Magnetism(rhoM=10, thetaM=70))\n", + " | refl1d_vacuum(0, 0)\n", + ")\n", "model_name = model.unique_name\n", "storage = {'model': {model_name: {}}}\n", "storage['model'][model_name]['scale'] = 10.0\n", "storage['model'][model_name]['bkg'] = 20.0\n", "\n", "polarized_probe = _get_polarized_probe(\n", - " q_array=model_coords,\n", - " dq_array=np.zeros(len(model_coords)),\n", - " model_name=model_name,\n", - " storage=storage)\n", + " q_array=model_coords, dq_array=np.zeros(len(model_coords)), model_name=model_name, storage=storage\n", + ")\n", "\n", "experiment = refl1d.names.Experiment(probe=polarized_probe, sample=refl1d_sample)\n", "model_data_magnetism_ref1d = experiment.reflectivity()[0][1]\n", @@ -352,8 +351,12 @@ "model.interface = interface\n", "model_interface = model.interface()\n", "model_interface.include_magnetism = True\n", - "model_interface._wrapper.update_layer(list(model_interface._wrapper.storage['layer'].keys())[1], magnetism_rhoM=10, magnetism_thetaM=70)\n", - "model_interface._wrapper.update_layer(list(model_interface._wrapper.storage['layer'].keys())[2], magnetism_rhoM=5, magnetism_thetaM=175)\n", + "model_interface._wrapper.update_layer(\n", + " list(model_interface._wrapper.storage['layer'].keys())[1], magnetism_rhoM=10, magnetism_thetaM=70\n", + ")\n", + "model_interface._wrapper.update_layer(\n", + " list(model_interface._wrapper.storage['layer'].keys())[2], magnetism_rhoM=5, magnetism_thetaM=175\n", + ")\n", "model_data_magnetism_easy = model.interface().reflectity_profile(\n", " model_coords,\n", " model.unique_name,\n", @@ -406,15 +409,14 @@ "metadata": {}, "outputs": [], "source": [ - "# The magnetism is set to 8. \n", + "# The magnetism is set to 8.\n", "# This would double (pp) and cancel out (mm) the magnitude of the reflectivity oscillations when its angle is set to 90.\n", "# This would give the strongest spin-flipping (pm and mp) when its angle is set to 0.\n", - "# However we set the angle to 45, so the reflectivity oscillations are not doubled or cancelled out, and the spin-flipping is not maximized.\n", + "# However we set the angle to 45, so the reflectivity oscillations are not doubled or cancelled out,\n", + "# and the spin-flipping is not maximized.\n", "refl1d_sample = (\n", - " refl1d_si(0, 0) | \n", - " refl1d_sld_8(150, 0, magnetism=refl1d.names.Magnetism(rhoM=8, thetaM=45)) |\n", - " refl1d_vacuum(0, 0)\n", - ") \n", + " refl1d_si(0, 0) | refl1d_sld_8(150, 0, magnetism=refl1d.names.Magnetism(rhoM=8, thetaM=45)) | refl1d_vacuum(0, 0)\n", + ")\n", "\n", "model_name = model.unique_name\n", "storage = {'model': {model_name: {}}}\n", @@ -422,13 +424,10 @@ "storage['model'][model_name]['bkg'] = 0.0\n", "\n", "polarized_probe = _get_polarized_probe(\n", - " q_array=model_coords,\n", - " dq_array=np.zeros(len(model_coords)),\n", - " model_name=model_name,\n", - " storage=storage,\n", - " all_polarizations=True)\n", + " q_array=model_coords, dq_array=np.zeros(len(model_coords)), model_name=model_name, storage=storage, all_polarizations=True\n", + ")\n", "\n", - "experiment = refl1d.names.Experiment(probe=polarized_probe, sample=refl1d_sample)\n" + "experiment = refl1d.names.Experiment(probe=polarized_probe, sample=refl1d_sample)" ] }, { diff --git a/docs/src/tutorials/simulation/resolution_functions.ipynb b/docs/src/tutorials/simulation/resolution_functions.ipynb index 4fc42ad2..da261981 100644 --- a/docs/src/tutorials/simulation/resolution_functions.ipynb +++ b/docs/src/tutorials/simulation/resolution_functions.ipynb @@ -35,23 +35,22 @@ "\n", "import matplotlib.pyplot as plt\n", "import numpy as np\n", - "import scipp as sc\n", - "import refnx\n", "import pooch\n", + "import refnx\n", + "import scipp as sc\n", "\n", "import easyreflectometry\n", - "\n", "from easyreflectometry.calculators import CalculatorFactory\n", "from easyreflectometry.data import load\n", - "from easyreflectometry.model import Model\n", "from easyreflectometry.model import LinearSpline\n", + "from easyreflectometry.model import Model\n", "from easyreflectometry.model import PercentageFwhm\n", "from easyreflectometry.model import Pointwise\n", + "from easyreflectometry.plot import plot\n", "from easyreflectometry.sample import Layer\n", "from easyreflectometry.sample import Material\n", "from easyreflectometry.sample import Multilayer\n", - "from easyreflectometry.sample import Sample\n", - "from easyreflectometry.plot import plot" + "from easyreflectometry.sample import Sample" ] }, { @@ -97,18 +96,18 @@ "source": [ "file_path_0 = pooch.retrieve(\n", " # URL to one of Pooch's test files\n", - " url=\"https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-0.0.ort\",\n", - " known_hash=\"f8a3e7007b83f0de4e2c761134e7d1c55027f0099528bd56f746b50349369f50\",\n", + " url='https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-0.0.ort',\n", + " known_hash='f8a3e7007b83f0de4e2c761134e7d1c55027f0099528bd56f746b50349369f50',\n", ")\n", "file_path_1 = pooch.retrieve(\n", " # URL to one of Pooch's test files\n", - " url=\"https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-1.0.ort\",\n", - " known_hash=\"9d81a512cbe45f923806ad307e476b27535614b2e08a2bf0f4559ab608a34f7a\",\n", + " url='https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-1.0.ort',\n", + " known_hash='9d81a512cbe45f923806ad307e476b27535614b2e08a2bf0f4559ab608a34f7a',\n", ")\n", "file_path_10 = pooch.retrieve(\n", " # URL to one of Pooch's test files\n", - " url=\"https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-10.0.ort\",\n", - " known_hash=\"991395c0b6a91bf60c12d234c645143dcac1cab929944fc4e452020d44b787ad\",\n", + " url='https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-10.0.ort',\n", + " known_hash='991395c0b6a91bf60c12d234c645143dcac1cab929944fc4e452020d44b787ad',\n", ")\n", "dict_reference = {}\n", "dict_reference['0'] = load(file_path_0)\n", @@ -328,7 +327,7 @@ " model.unique_name,\n", " )\n", " plt.plot(model_coords, model_data, 'k-', label=f'Resolution: {key}%')\n", - " plt.plot(reference_coords, reference_data, 'rx', label=f'Reference')\n", + " plt.plot(reference_coords, reference_data, 'rx', label='Reference')\n", " ax = plt.gca()\n", " ax.set_xlim([-0.01, 0.45])\n", " ax.set_ylim([1e-10, 2.5])\n", @@ -377,14 +376,14 @@ " model_coords,\n", " model.unique_name,\n", ")\n", - "plt.plot(model_coords, model_data, 'k-', label=f'Variable', linewidth=5)\n", + "plt.plot(model_coords, model_data, 'k-', label='Variable', linewidth=5)\n", "\n", "model.resolution_function = PercentageFwhm(1.0)\n", "model_data = model.interface().reflectity_profile(\n", " model_coords,\n", " model.unique_name,\n", ")\n", - "plt.plot(model_coords, model_data, 'r-', label=f'Percentage')\n", + "plt.plot(model_coords, model_data, 'r-', label='Percentage')\n", "\n", "ax = plt.gca()\n", "ax.set_xlim([-0.01, 0.45])\n", @@ -416,17 +415,17 @@ " model_coords,\n", " model.unique_name,\n", ")\n", - "plt.plot(model_coords, model_data, 'k-', label=f'Variable', linewidth=5)\n", + "plt.plot(model_coords, model_data, 'k-', label='Variable', linewidth=5)\n", "data_points = []\n", - "data_points.append(reference_coords) # Qz\n", - "data_points.append(reference_data) # R\n", - "data_points.append(reference_variances) # sQz\n", + "data_points.append(reference_coords) # Qz\n", + "data_points.append(reference_data) # R\n", + "data_points.append(reference_variances) # sQz\n", "model.resolution_function = Pointwise(q_data_points=data_points)\n", "model_data = model.interface().reflectity_profile(\n", " model_coords,\n", " model.unique_name,\n", ")\n", - "plt.plot(model_coords, model_data, 'r-', label=f'Pointwise')\n", + "plt.plot(model_coords, model_data, 'r-', label='Pointwise')\n", "\n", "ax = plt.gca()\n", "ax.set_xlim([-0.01, 0.45])\n", diff --git a/pixi.lock b/pixi.lock index be073a9e..1627ff88 100644 --- a/pixi.lock +++ b/pixi.lock @@ -138,6 +138,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/rfc3986-validator-0.1.1-pyh9f0ad1d_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/rfc3987-syntax-1.1.0-pyhe01879c_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.30.0-py313h843e2db_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/ruff-0.15.12-h994f30f_0.conda - conda: 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b/pyproject.toml @@ -23,8 +23,15 @@ classifiers = [ ] requires-python = '>=3.11' dependencies = [ - #'easyscience', # The base library of the EasyScience framework - 'pooch', # Data downloader + 'easyscience', + 'scipp', + 'refnx', + 'refl1d>=1.0.0', + 'orsopy', + 'svglib<1.6 ; platform_system=="Linux" or sys_platform == "darwin"', + 'xhtml2pdf', + 'bumps', + 'pooch', ] [project.optional-dependencies] From 07d792cf001ea79c713937fed09f4c4af816389a Mon Sep 17 00:00:00 2001 From: rozyczko Date: Thu, 7 May 2026 14:39:58 +0200 Subject: [PATCH 05/20] remade __init__.py --- src/easyreflectometry/__init__.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/easyreflectometry/__init__.py b/src/easyreflectometry/__init__.py index 7046227e..1b1d62d9 100644 --- a/src/easyreflectometry/__init__.py +++ b/src/easyreflectometry/__init__.py @@ -1,3 +1,17 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause """EasyReflectometry library.""" + +from importlib import metadata + +from .project import Project + +try: + __version__ = metadata.version(__package__ or __name__) +except metadata.PackageNotFoundError: + __version__ = '0.0.0' + +__all__ = [ + Project, + __version__, +] \ No newline at end of file From 6042474e2fb928fd9cf309dc92619adbd465f114 Mon Sep 17 00:00:00 2001 From: rozyczko Date: Thu, 7 May 2026 14:47:00 +0200 Subject: [PATCH 06/20] minor fix --- src/easyreflectometry/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/easyreflectometry/__init__.py b/src/easyreflectometry/__init__.py index 1b1d62d9..bc5888c4 100644 --- a/src/easyreflectometry/__init__.py +++ b/src/easyreflectometry/__init__.py @@ -14,4 +14,4 @@ __all__ = [ Project, __version__, -] \ No newline at end of file +] From 9b6805124f3cd42352e37a3bb11b40cde519999d Mon Sep 17 00:00:00 2001 From: rozyczko Date: Thu, 7 May 2026 15:17:54 +0200 Subject: [PATCH 07/20] a few more fixes --- src/easyreflectometry/__init__.py | 1 + tests/functional/test_dummy.py | 2 +- tests/integration/fitting/test_dummy.py | 2 +- tests/integration/scipp-analysis/test_dummy.py | 2 +- tests/package_test.py | 3 ++- tests/test_orso_utils.py | 2 +- tests/test_ort_file.py | 2 +- tests/unit/test_dummy.py | 2 +- 8 files changed, 9 insertions(+), 7 deletions(-) diff --git a/src/easyreflectometry/__init__.py b/src/easyreflectometry/__init__.py index bc5888c4..8c2f7496 100644 --- a/src/easyreflectometry/__init__.py +++ b/src/easyreflectometry/__init__.py @@ -1,5 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause + """EasyReflectometry library.""" from importlib import metadata diff --git a/tests/functional/test_dummy.py b/tests/functional/test_dummy.py index 230dfead..6927fe89 100644 --- a/tests/functional/test_dummy.py +++ b/tests/functional/test_dummy.py @@ -1,4 +1,4 @@ -# SPDX-FileCopyrightText: 2021-2026 EasyReflectometry contributors +# SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause diff --git a/tests/integration/fitting/test_dummy.py b/tests/integration/fitting/test_dummy.py index 78d1220d..2256189c 100644 --- a/tests/integration/fitting/test_dummy.py +++ b/tests/integration/fitting/test_dummy.py @@ -1,4 +1,4 @@ -# SPDX-FileCopyrightText: 2021-2026 EasyReflectometry contributors +# SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause import pytest diff --git a/tests/integration/scipp-analysis/test_dummy.py b/tests/integration/scipp-analysis/test_dummy.py index 78d1220d..2256189c 100644 --- a/tests/integration/scipp-analysis/test_dummy.py +++ b/tests/integration/scipp-analysis/test_dummy.py @@ -1,4 +1,4 @@ -# SPDX-FileCopyrightText: 2021-2026 EasyReflectometry contributors +# SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause import pytest diff --git a/tests/package_test.py b/tests/package_test.py index 4d77705c..f18f84f8 100644 --- a/tests/package_test.py +++ b/tests/package_test.py @@ -1,5 +1,6 @@ +# SPDX-FileCopyrightText: 2024 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -# Copyright (c) 2024 Easyscience contributors (https://github.com/EasyScience) + import easyreflectometry as pkg diff --git a/tests/test_orso_utils.py b/tests/test_orso_utils.py index df931b33..4ad2e9ab 100644 --- a/tests/test_orso_utils.py +++ b/tests/test_orso_utils.py @@ -1,5 +1,5 @@ +# SPDX-FileCopyrightText: 2025 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -# Copyright (c) 2025 DMSC import os import warnings diff --git a/tests/test_ort_file.py b/tests/test_ort_file.py index 245ec566..b1277033 100644 --- a/tests/test_ort_file.py +++ b/tests/test_ort_file.py @@ -1,5 +1,5 @@ +# SPDX-FileCopyrightText: 2025 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -# Copyright (c) 2025 DMSC import logging diff --git a/tests/unit/test_dummy.py b/tests/unit/test_dummy.py index 230dfead..6927fe89 100644 --- a/tests/unit/test_dummy.py +++ b/tests/unit/test_dummy.py @@ -1,4 +1,4 @@ -# SPDX-FileCopyrightText: 2021-2026 EasyReflectometry contributors +# SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause From 1ecb08170aad5d16af541d2ec4622cfd1157127f Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Thu, 7 May 2026 15:57:04 +0200 Subject: [PATCH 08/20] Apply templates with docstrings fixes --- .copier-answers.yml | 2 +- docs/mkdocs.yml | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.copier-answers.yml b/.copier-answers.yml index 727e2511..f8fbdb26 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,6 +1,6 @@ # WARNING: Do not edit this file manually. # Any changes will be overwritten by Copier. -_commit: v0.11.2 +_commit: v0.11.2-3-ge3f42a1 _src_path: gh:easyscience/templates lib_docs_url: https://easyscience.github.io/reflectometry-lib lib_doi: 10.5281/zenodo.18163581 diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 295600cf..d6d576ea 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -145,8 +145,10 @@ plugins: python: paths: ['src'] # Change 'src' to your actual sources directory options: + annotations_path: source docstring_style: numpy - group_by_category: false + group_by_category: true + members_order: source heading_level: 1 show_root_heading: true show_root_full_path: false From ce591d182915a85bc0e756398b98a754c93060fa Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Thu, 7 May 2026 15:57:53 +0200 Subject: [PATCH 09/20] Add missing favicon and update SVG assets --- docs/docs/assets/images/favicon.png | Bin 0 -> 14318 bytes docs/docs/assets/images/logo_dark.svg | 2 +- docs/docs/assets/images/logo_light.svg | 2 +- docs/overrides/.icons/easyreflectometry.svg | 16 ++++++++++++++++ 4 files changed, 18 insertions(+), 2 deletions(-) create mode 100644 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.../tutorials/basic/assemblies_library.md | 71 + docs/docs/tutorials/basic/layer_library.md | 69 + docs/docs/tutorials/basic/material_library.md | 78 + docs/docs/tutorials/basic/model.md | 87 ++ .../tutorials/fitting/d70d2o.ort | 0 docs/{src => docs}/tutorials/fitting/dspc.png | Bin .../tutorials/fitting/eq_monolayer.svg | 0 .../tutorials/fitting/eq_solvated.svg | 0 .../tutorials/fitting/example.ort | 0 .../tutorials/fitting/material_solvated.ipynb | 12 +- .../tutorials/fitting/monolayer.ipynb | 12 +- .../tutorials/fitting/monolayer.png | Bin .../tutorials/fitting/monolayer.svg | 0 .../tutorials/fitting/polymer_film.png | Bin .../tutorials/fitting/polymer_film.svg | 0 .../tutorials/fitting/repeating.ipynb | 12 +- .../tutorials/fitting/repeating.png | Bin .../tutorials/fitting/repeating.svg | 0 .../tutorials/fitting/repeating_layers.ort | 0 .../tutorials/fitting/simple_fitting.ipynb | 12 +- docs/docs/tutorials/index.md | 57 +- .../tutorials/simulation/bilayer.ipynb | 12 +- .../tutorials/simulation/magnetism.ipynb | 12 +- .../mod_pointwise_two_layer_sample_dq-0.0.ort | 0 .../mod_pointwise_two_layer_sample_dq-1.0.ort | 0 ...mod_pointwise_two_layer_sample_dq-10.0.ort | 0 .../simulation/resolution_functions.ipynb | 12 +- .../tutorials/simulation/two_layers.png | Bin .../tutorials/simulation/two_layers.svg | 0 docs/docs/user-guide/index.md | 217 ++- docs/mkdocs.yml | 35 +- .../advancedfitting/advancedfitting.rst | 9 - .../tutorials/basic/assemblies_library.rst | 249 ---- docs/src/tutorials/basic/basic.rst | 13 - docs/src/tutorials/basic/layer_library.rst | 84 -- docs/src/tutorials/basic/material_library.rst | 87 -- docs/src/tutorials/basic/model.rst | 80 -- docs/src/tutorials/extra/extra.rst | 7 - docs/src/tutorials/fitting/fitting.rst | 12 - docs/src/tutorials/simulation/simulation.rst | 11 - docs/src/tutorials/tutorials.rst | 49 - pixi.lock | 1270 ++++++++++++----- pixi.toml | 1 + pyproject.toml | 4 +- 62 files changed, 1755 insertions(+), 968 deletions(-) create mode 100644 docs/docs/api-reference/assemblies/gradient_layer.md create mode 100644 docs/docs/api-reference/assemblies/multilayer.md create mode 100644 docs/docs/api-reference/assemblies/repeating_multilayer.md create mode 100644 docs/docs/api-reference/assemblies/surfactant_layer.md create mode 100644 docs/docs/api-reference/data.md create mode 100644 docs/docs/api-reference/elements/layer.md create mode 100644 docs/docs/api-reference/elements/layer_area_per_molecule.md create mode 100644 docs/docs/api-reference/elements/material.md create mode 100644 docs/docs/api-reference/elements/material_density.md create mode 100644 docs/docs/api-reference/elements/material_mixture.md create mode 100644 docs/docs/api-reference/elements/material_solvated.md create mode 100644 docs/docs/api-reference/fitting.md create mode 100644 docs/docs/api-reference/model.md create mode 100644 docs/docs/api-reference/project.md create mode 100644 docs/docs/api-reference/sample.md rename docs/{src => docs}/tutorials/advancedfitting/multi_contrast.ipynb (98%) rename docs/{src => docs}/tutorials/advancedfitting/multiple.ort (100%) create mode 100644 docs/docs/tutorials/basic/assemblies_library.md create mode 100644 docs/docs/tutorials/basic/layer_library.md create mode 100644 docs/docs/tutorials/basic/material_library.md create mode 100644 docs/docs/tutorials/basic/model.md rename docs/{src => docs}/tutorials/fitting/d70d2o.ort (100%) rename docs/{src => docs}/tutorials/fitting/dspc.png (100%) rename docs/{src => docs}/tutorials/fitting/eq_monolayer.svg (100%) rename docs/{src => docs}/tutorials/fitting/eq_solvated.svg (100%) rename docs/{src => docs}/tutorials/fitting/example.ort (100%) rename docs/{src => docs}/tutorials/fitting/material_solvated.ipynb (98%) rename docs/{src => docs}/tutorials/fitting/monolayer.ipynb (99%) rename docs/{src => docs}/tutorials/fitting/monolayer.png (100%) rename docs/{src => docs}/tutorials/fitting/monolayer.svg (100%) rename docs/{src => 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docs}/tutorials/simulation/two_layers.png (100%) rename docs/{src => docs}/tutorials/simulation/two_layers.svg (100%) delete mode 100644 docs/src/tutorials/advancedfitting/advancedfitting.rst delete mode 100644 docs/src/tutorials/basic/assemblies_library.rst delete mode 100644 docs/src/tutorials/basic/basic.rst delete mode 100644 docs/src/tutorials/basic/layer_library.rst delete mode 100644 docs/src/tutorials/basic/material_library.rst delete mode 100644 docs/src/tutorials/basic/model.rst delete mode 100644 docs/src/tutorials/extra/extra.rst delete mode 100644 docs/src/tutorials/fitting/fitting.rst delete mode 100644 docs/src/tutorials/simulation/simulation.rst delete mode 100644 docs/src/tutorials/tutorials.rst diff --git a/docs/docs/api-reference/assemblies/gradient_layer.md b/docs/docs/api-reference/assemblies/gradient_layer.md new file mode 100644 index 00000000..463b0712 --- /dev/null +++ b/docs/docs/api-reference/assemblies/gradient_layer.md @@ -0,0 +1,4 @@ +# Gradient Layer + +::: easyreflectometry.sample.assemblies.gradient_layer options: members: +true show_inheritance: true diff --git a/docs/docs/api-reference/assemblies/multilayer.md b/docs/docs/api-reference/assemblies/multilayer.md new file mode 100644 index 00000000..52316972 --- /dev/null +++ b/docs/docs/api-reference/assemblies/multilayer.md @@ -0,0 +1,4 @@ +# Multilayer + +::: easyreflectometry.sample.assemblies.multilayer options: members: +true show_inheritance: true diff --git a/docs/docs/api-reference/assemblies/repeating_multilayer.md b/docs/docs/api-reference/assemblies/repeating_multilayer.md new file mode 100644 index 00000000..26c6be16 --- /dev/null +++ b/docs/docs/api-reference/assemblies/repeating_multilayer.md @@ -0,0 +1,4 @@ +# Repeating Multilayer + +::: easyreflectometry.sample.assemblies.repeating_multilayer options: +members: true show_inheritance: true diff --git a/docs/docs/api-reference/assemblies/surfactant_layer.md b/docs/docs/api-reference/assemblies/surfactant_layer.md new file mode 100644 index 00000000..272be1f7 --- /dev/null +++ b/docs/docs/api-reference/assemblies/surfactant_layer.md @@ -0,0 +1,4 @@ +# Surfactant Layer + +::: easyreflectometry.sample.assemblies.surfactant_layer options: +members: true show_inheritance: true diff --git a/docs/docs/api-reference/data.md b/docs/docs/api-reference/data.md new file mode 100644 index 00000000..48a6f505 --- /dev/null +++ b/docs/docs/api-reference/data.md @@ -0,0 +1,4 @@ +# Data + +::: easyreflectometry.data.measurement options: members: true +show_inheritance: true diff --git a/docs/docs/api-reference/elements/layer.md b/docs/docs/api-reference/elements/layer.md new file mode 100644 index 00000000..fb9d49f9 --- /dev/null +++ b/docs/docs/api-reference/elements/layer.md @@ -0,0 +1,4 @@ +# Layer + +::: easyreflectometry.sample.elements.layers.layer options: members: +true show_inheritance: true diff --git a/docs/docs/api-reference/elements/layer_area_per_molecule.md b/docs/docs/api-reference/elements/layer_area_per_molecule.md new file mode 100644 index 00000000..2ee00cc7 --- /dev/null +++ b/docs/docs/api-reference/elements/layer_area_per_molecule.md @@ -0,0 +1,4 @@ +# Layer Area Per Molecule + +::: easyreflectometry.sample.elements.layers.layer_area_per_molecule +options: members: true show_inheritance: true diff --git a/docs/docs/api-reference/elements/material.md b/docs/docs/api-reference/elements/material.md new file mode 100644 index 00000000..3fed854a --- /dev/null +++ b/docs/docs/api-reference/elements/material.md @@ -0,0 +1,4 @@ +# Material + +::: easyreflectometry.sample.elements.materials.material options: +members: true show_inheritance: true diff --git a/docs/docs/api-reference/elements/material_density.md b/docs/docs/api-reference/elements/material_density.md new file mode 100644 index 00000000..a0a5f2f9 --- /dev/null +++ b/docs/docs/api-reference/elements/material_density.md @@ -0,0 +1,4 @@ +# Material Density + +::: easyreflectometry.sample.elements.materials.material_density +options: members: true show_inheritance: true diff --git a/docs/docs/api-reference/elements/material_mixture.md b/docs/docs/api-reference/elements/material_mixture.md new file mode 100644 index 00000000..ef8b6412 --- /dev/null +++ b/docs/docs/api-reference/elements/material_mixture.md @@ -0,0 +1,4 @@ +# Material Mixture + +::: easyreflectometry.sample.elements.materials.material_mixture +options: members: true show_inheritance: true diff --git a/docs/docs/api-reference/elements/material_solvated.md b/docs/docs/api-reference/elements/material_solvated.md new file mode 100644 index 00000000..33b51425 --- /dev/null +++ b/docs/docs/api-reference/elements/material_solvated.md @@ -0,0 +1,4 @@ +# Material Solvated + +::: easyreflectometry.sample.elements.materials.material_solvated +options: members: true show_inheritance: true diff --git a/docs/docs/api-reference/fitting.md b/docs/docs/api-reference/fitting.md new file mode 100644 index 00000000..14a003e4 --- /dev/null +++ b/docs/docs/api-reference/fitting.md @@ -0,0 +1,4 @@ +# Fitting + +::: easyreflectometry.fitting options: members: true show_inheritance: +true diff --git a/docs/docs/api-reference/index.md b/docs/docs/api-reference/index.md index a639b377..85b9e5c7 100644 --- a/docs/docs/api-reference/index.md +++ b/docs/docs/api-reference/index.md @@ -1,8 +1,72 @@ ---- +--- icon: material/code-braces-box --- # :material-code-braces-box: API Reference -This section contains the reference detailing the functions and modules -available in EasyReflectometry. +This section contains the auto-generated reference detailing the +functions and modules available in EasyReflectometry. + +## Model + +Model is a sample, a background and a resolution. + +- [Model](model.md) + +## Sample + +Sample is built from assemblies. + +- [Sample](sample.md) + +## Project + +Project provides a higher-level interface for managing models, +experiments, and ORSO import. + +- [Project](project.md) + +## Fitting + +Fitting helpers and objective functions. + +- [Fitting](fitting.md) + +## Assemblies + +Assemblies are collections of layers that are used to represent a +specific physical setup. + +- [Multilayer](assemblies/multilayer.md) +- [Repeating Multilayer](assemblies/repeating_multilayer.md) +- [Surfactant Layer](assemblies/surfactant_layer.md) +- [Gradient Layer](assemblies/gradient_layer.md) + +## Elements + +Elements are the building blocks that are required to construct a +sample. + +### Layers + +Layers are basic elements and used to represent a single layer of +material with a thickness and a roughness. + +- [Layer](elements/layer.md) +- [Layer Area Per Molecule](elements/layer_area_per_molecule.md) + +### Materials + +Materials are the most basic elements and are used to represent a +material with given physical properties. + +- [Material](elements/material.md) +- [Material Density](elements/material_density.md) +- [Material Mixture](elements/material_mixture.md) +- [Material Solvated](elements/material_solvated.md) + +## Data + +Collection of helper functions. + +- [Data](data.md) diff --git a/docs/docs/api-reference/model.md b/docs/docs/api-reference/model.md new file mode 100644 index 00000000..50f1d822 --- /dev/null +++ b/docs/docs/api-reference/model.md @@ -0,0 +1,4 @@ +# Model + +::: easyreflectometry.model.model options: members: true +show_inheritance: true diff --git a/docs/docs/api-reference/project.md b/docs/docs/api-reference/project.md new file mode 100644 index 00000000..50a2da54 --- /dev/null +++ b/docs/docs/api-reference/project.md @@ -0,0 +1,4 @@ +# Project + +::: easyreflectometry.project options: members: true show_inheritance: +true diff --git a/docs/docs/api-reference/sample.md b/docs/docs/api-reference/sample.md new file mode 100644 index 00000000..b366e247 --- /dev/null +++ b/docs/docs/api-reference/sample.md @@ -0,0 +1,4 @@ +# Sample + +::: easyreflectometry.sample.collections.sample options: members: true +show_inheritance: true diff --git a/docs/src/tutorials/advancedfitting/multi_contrast.ipynb b/docs/docs/tutorials/advancedfitting/multi_contrast.ipynb similarity index 98% rename from docs/src/tutorials/advancedfitting/multi_contrast.ipynb rename to docs/docs/tutorials/advancedfitting/multi_contrast.ipynb index f08269c4..02f675ba 100644 --- a/docs/src/tutorials/advancedfitting/multi_contrast.ipynb +++ b/docs/docs/tutorials/advancedfitting/multi_contrast.ipynb @@ -20,6 +20,16 @@ "First configure matplotlib to place figures in notebook and import needed modules. Note that the plot function needs installation of `plopp` seperately or installation of `easyreflectometry[dev]`" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "54684688", + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib inline" + ] + }, { "cell_type": "code", "execution_count": null, @@ -27,13 +37,9 @@ "metadata": {}, "outputs": [], "source": [ - "%matplotlib inline\n", - "\n", "import pooch\n", - "import refnx\n", "from easyscience.fitting import AvailableMinimizers\n", "\n", - "import easyreflectometry\n", "from easyreflectometry.calculators import CalculatorFactory\n", "from easyreflectometry.data import load\n", "from easyreflectometry.fitting import MultiFitter\n", @@ -45,10 +51,7 @@ "from easyreflectometry.sample import Material\n", "from easyreflectometry.sample import Multilayer\n", "from easyreflectometry.sample import Sample\n", - "from easyreflectometry.sample import SurfactantLayer\n", - "\n", - "print(f'easyreflectometry: {easyreflectometry.__version__}')\n", - "print(f'refnx: {refnx.__version__}')" + "from easyreflectometry.sample import SurfactantLayer" ] }, { diff --git a/docs/src/tutorials/advancedfitting/multiple.ort b/docs/docs/tutorials/advancedfitting/multiple.ort similarity index 100% rename from docs/src/tutorials/advancedfitting/multiple.ort rename to docs/docs/tutorials/advancedfitting/multiple.ort diff --git a/docs/docs/tutorials/basic/assemblies_library.md b/docs/docs/tutorials/basic/assemblies_library.md new file mode 100644 index 00000000..da419f56 --- /dev/null +++ b/docs/docs/tutorials/basic/assemblies_library.md @@ -0,0 +1,71 @@ +# Creating Multilayers and Surfactant Layers + +EasyReflectometry is designed to be used with a broad range of different +assemblies. Assemblies are collective layers behaving as a single +object, for example, a multilayer or a surfactant layer. These +assemblies offer flexibility for the user and enable more powerful +analysis by making chemical and physical constraints available with +limited code. In this page, we will document the assemblies that are +available with simple examples of the constructors that exist. Full API +documentation is also available for the +`easyreflectometry.sample.assemblies` module. + +## Multilayer + +This assembly should be used for a series of layers that should be +thought of as a single object. For example, in the simple fitting +tutorial this assembly type is used to combine the silicon and silicon +dioxide layer that is formed into a single object. All of the separate +layers in these objects will be fitted individually, i.e. there are no +constraints present, however, there is some cognitive benefit to +grouping layers together. + +To create a `Multilayer` object, we use the following construction. + +```python +from easyreflectometry.sample import Layer +from easyreflectometry.sample import Material +from easyreflectometry.sample import Multilayer + +si = Material(sld=2.07, isld=0, name='Si') +sio2 = Material(sld=3.47, isld=0, name='SiO2') +si_layer = Layer(material=si, thickness=0, roughness=0, name='Si layer') +sio2_layer = Layer(material=sio2, thickness=30, roughness=3, name='SiO2 layer') + +subphase = Multilayer(layers=[si_layer, sio2_layer], name='Si/SiO2 subphase') +``` + +This will create a `Multilayer` object named `subphase` which we can use +in some `Structure` for our analysis. + +## RepeatingMultilayer + +The `RepeatingMultilayer` assembly type is an extension of the +`Multilayer` for the analysis of systems with a multilayer that has some +number of repeats. This assembly type imposes some constraints, +specifically that all of the repeats have the exact same structure (i.e. +thicknesses, roughnesses, and scattering length densities), which brings +with it some computational saving as the reflectometry coefficients only +need to be calculated once for this structure and propagated for the +correct number of repeats. There is a tutorial that discusses the +utilisation of this assembly type for a nickel-titanium multilayer +system. + +The creation of a `RepeatingMultilayer` object is very similar to that +for the `Multilayer`, with the addition of a number of repetitions. + +```python +from easyreflectometry.sample import Layer +from easyreflectometry.sample import Material +from easyreflectometry.sample import RepeatingMultilayer + +ti = Material(sld=-1.9493, isld=0, name='Ti') +ni = Material(sld=9.4245, isld=0, name='Ni') +ti_layer = Layer(material=ti, thickness=40, roughness=0, name='Ti Layer') +ni_layer = Layer(material=ni, thickness=70, roughness=0, name='Ni Layer') +ni_ti = RepeatingMultilayer(layers=[ti_layer, ni_layer], repetitions=10, name='Ni/Ti Multilayer') +``` + +The number of repeats is a parameter that can be varied in the +optimisation process, however given this is a value that depends on the +synthesis of the sample this is unlikely to be necessary. diff --git a/docs/docs/tutorials/basic/layer_library.md b/docs/docs/tutorials/basic/layer_library.md new file mode 100644 index 00000000..4a679690 --- /dev/null +++ b/docs/docs/tutorials/basic/layer_library.md @@ -0,0 +1,69 @@ +# Defining Layers + +Similar to a range of different materials, there are a few different +ways that a layer can be defined in EasyReflectometry. + +## Layer + +The `Layer` is the simplest possible type of layer, taking a `Material` +and two floats associated with the thickness and upper (that is closer +to the source of the incident radiation) roughness. So we construct a +`Layer` as follows for a 100 Å thick layer of boron with a roughness of +10 Å. + +```python +from easyreflectometry.sample import Material +from easyreflectometry.sample import Layer + +boron = Material(sld=6.908, isld=-0.278, name='Boron') +boron_layer = Layer(material=boron, thickness=100, roughness=10, name='Boron Layer') +``` + +This type of layer is used extensively in the tutorials. + +To create a semi-infinite layer one needs to set the thickness to 0 and +the roughness to 0. + +```python +from easyreflectometry.sample import Material +from easyreflectometry.sample import Layer + +si = Material(sld=2.07, isld=0, name='Si') +semi_infinite_layer = Layer(material=si, thickness=0, roughness=0, name='Si layer') +``` + +## LayerAreaPerMolecule + +The `LayerAreaPerMolecule` layer type is the foundation of the +`SurfactantLayer` assemblies type (further information on this can be +found in the assemblies library). The purpose of the +`LayerAreaPerMolecule` is to allow a layer to be defined in terms of the +chemical formula of the material and the area per molecule of the layer. +The area per molecule is a common description of surface density in the +surfactant monolayer and bilayer community. + +We can construct a 10 Å thick `LayerAreaPerMolecule` of +phosphatidylcholine, with an area per molecule of 48 Å squared and a +roughness of 3 Å that has 20% solvent surface coverage with D2O using +the following. + +```python +from easyreflectometry.sample import Material +from easyreflectometry.sample import LayerAreaPerMolecule + +d2o = Material(sld=6.36, isld=0, name='D2O') +molecular_formula = 'C10H18NO8P' +pc = LayerAreaPerMolecule( + molecular_formula=molecular_formula, + thickness=10, + solvent=d2o, + solvent_fraction=0.2, + area_per_molecule=48, + roughness=3, + name='PC Layer', +) +``` + +It is expected that the typical user will not interface directly with +the `LayerAreaPerMolecule` assembly type, but instead the +`SurfactantLayer` assemblies library will be used instead. diff --git a/docs/docs/tutorials/basic/material_library.md b/docs/docs/tutorials/basic/material_library.md new file mode 100644 index 00000000..78bdfcf1 --- /dev/null +++ b/docs/docs/tutorials/basic/material_library.md @@ -0,0 +1,78 @@ +# Defining Materials + +In order to support a wide range of applications (and to build complex +assemblies) there are a few different types of material that can be +utilised in EasyReflectometry. These can include constraints or enable +the user to define the material based on chemical or physical +properties. Full API documentation for the +`easyreflectometry.sample.elements.material` module is also available, +but here we will give some simple uses for them. + +## Material + +The simplest type of material that is available is the `Material`. This +allows the user to define a single type of material, with a real and +imaginary component to the scattering length density. The construction +of a `Material` is achieved as shown below. + +```python +from easyreflectometry.sample import Material + +boron = Material(sld=6.908, isld=-0.278, name='Boron') +``` + +The above object will have the properties of `sld` and `isld`, which +will have values of `6.908 1/angstrom^2` and `-0.278 1/angstrom^2` +respectively. As is shown in the tutorials, a material can be used to +construct a `Layer` from which +[slab models](https://www.reflectometry.org/isis_school/3_reflectometry_slab_models/the_slab_model.html) +are created. + +## MaterialDensity + +In addition to defining a material by its scattering length density, it +may be useful to define a material by the mass density and chemical +formula. This is possible with the `MaterialDensity` material type, +which uses the scattering length and atomic mass from the chemical +formula and the density to determine the scattering length density. It +is then possible to vary the density, which defines the scattering +length density in turn. The `MaterialDensity` material can be created as +follows. + +```python +from easyreflectometry.sample import MaterialDensity + +chemical_structure = 'SiO2' +si = MaterialDensity(chemical_structure=chemical_structure, density=2.65, name='SiO2 Material') +``` + +The density should be in units of grams per cubic centimeter and the +scattering length is calculated from `'SiO2'`. + +## MaterialSolvated + +Sometimes it is desirable to have a layer that consists of a material +and a solvent in some ratio. An example of this is shown in the +solvation tutorial, where a polymer film solvated with D2O is modelled. +To produce a material that is described by such a mixture, there is +`MaterialSolvated`. This is constructed from two constituent `Materials` +and the fractional amount of the material in the solvent. So to produce +a `MaterialSolvated` that is 20% D2O in a polymer, the following is +used. + +```python +from easyreflectometry.sample import Material +from easyreflectometry.sample import MaterialSolvated + +polymer = Material(sld=2.0, isld=0.0, name='Polymer') +d2o = Material(sld=6.36, isld=0, name='D2O') + +solvated_polymer = MaterialSolvated(material=polymer, solvent=d2o, solvent_fraction=0.2, name='Solvated Polymer') +``` + +For the `solvated_polymer` object, the `sld` will be +`2.872 1/angstrom^2` (the weighted average of the two scattering length +densities). The `MaterialSolvated` includes a constraint such that if +the value of either constituent scattering length densities (both real +and imaginary components) or the fraction changes, then the resulting +material `sld` and `isld` will change appropriately. diff --git a/docs/docs/tutorials/basic/model.md b/docs/docs/tutorials/basic/model.md new file mode 100644 index 00000000..6b9c76c3 --- /dev/null +++ b/docs/docs/tutorials/basic/model.md @@ -0,0 +1,87 @@ +# Creating a Model + +The main component of an experiment in EasyReflectometry is the `Model`. +This is a description of the `Sample` and the environment in which the +experiment is performed. The `Model` is used to calculate the +reflectivity of the `Sample` at a given set of angles (Q-points). The +resolution functions are used to quantify the experimental uncertainties +in wavelength and angle, allowing the `Model` to accurately describe the +data. + +## Model + +A `Model` instance contains a `Sample` and variables describing +experimental settings. To be able to compute reflectivities it is also +necessary to have a `Calculator` (interface). + +```python +from easyreflectometry.calculators import CalculatorFactory +from easyreflectometry.model import Model +from easyreflectometry.sample import Sample + +default_sample = Sample() +model = Model(sample=default_sample, scale=1.0, background=1e-6) + +interface = CalculatorFactory() +model.interface = interface +``` + +This will create a `Model` instance with the `default_sample` and the +environment variables `scale` factor set to 1.0 and a `background` of +1e-6. Following the `interface` is set to the default calculator that is +`Refnx`. + +## Resolution Functions + +A resolution function enables the EasyReflectometry model to incorporate +the experimental uncertainties in wavelength and incident angle into the +model. In its essence the resolution function controls the smearing to +apply when determining the reflectivity at a given Q-point. For a given +Q-point the smearing to apply is given as a weighted average of the +neighboring Q-point, which weights are by a normal distribution. This +normal distribution is then defined by a Q-point dependent Full Width at +the Half Maximum (FWHM) that is given by the resolution function. + +### PercentageFwhm + +Often we rely on a resolution function that has a simple functional +dependency of the Q-point. By this is understood that the applied +smearing in a Q-point has a FWHM that is simply a percentage of the +value of the Q-point. + +```python +from easyreflectometry.model import Model +from easyreflectometry.model import PercentageFwhm + +resolution_function = PercentageFwhm(1.1) + +m = Model(resolution_function=resolution_function) +``` + +This will create a `Model` instance where the resolution function is +defined as 1.1% of the Q-point value, which again is the FWHM for the +smearing. + +### LinearSpline + +Alternatively the FWHM value might be determined and declared directly +for each measured Q-point. When this is the case the provided Q-points +and the corresponding FWHM values can be used to declare a linear spline +function and thereby enable a determination of the reflectivity at an +arbitrary point within the provided range of discrete Q-points. + +```python +from easyreflectometry.model import Model +from easyreflectometry.model import LinearSpline + +m = Model() + +resolution_function = LinearSpline(q_data_points=[0.01, 0.2, 0.31], fwhm_values=[0.001, 0.043, 0.026]) + +m.resolution_function = resolution_function +``` + +This will create a `Model` instance where the resolution function +defining the FWHM is determined from a linear interpolation. In the +present case the provided data Q-points are (`[0.01, 0.2, 0.31]`) and +the corresponding FWHM function values are (`[0.001, 0.043, 0.026]`). diff --git a/docs/src/tutorials/fitting/d70d2o.ort b/docs/docs/tutorials/fitting/d70d2o.ort similarity index 100% rename from docs/src/tutorials/fitting/d70d2o.ort rename to docs/docs/tutorials/fitting/d70d2o.ort diff --git a/docs/src/tutorials/fitting/dspc.png b/docs/docs/tutorials/fitting/dspc.png similarity index 100% rename from docs/src/tutorials/fitting/dspc.png rename to docs/docs/tutorials/fitting/dspc.png diff --git a/docs/src/tutorials/fitting/eq_monolayer.svg b/docs/docs/tutorials/fitting/eq_monolayer.svg similarity index 100% rename from docs/src/tutorials/fitting/eq_monolayer.svg rename to docs/docs/tutorials/fitting/eq_monolayer.svg diff --git a/docs/src/tutorials/fitting/eq_solvated.svg b/docs/docs/tutorials/fitting/eq_solvated.svg similarity index 100% rename from docs/src/tutorials/fitting/eq_solvated.svg rename to docs/docs/tutorials/fitting/eq_solvated.svg diff --git a/docs/src/tutorials/fitting/example.ort b/docs/docs/tutorials/fitting/example.ort similarity index 100% rename from docs/src/tutorials/fitting/example.ort rename to docs/docs/tutorials/fitting/example.ort diff --git a/docs/src/tutorials/fitting/material_solvated.ipynb b/docs/docs/tutorials/fitting/material_solvated.ipynb similarity index 98% rename from docs/src/tutorials/fitting/material_solvated.ipynb rename to docs/docs/tutorials/fitting/material_solvated.ipynb index 6f6f0c30..d393eb34 100644 --- a/docs/src/tutorials/fitting/material_solvated.ipynb +++ b/docs/docs/tutorials/fitting/material_solvated.ipynb @@ -23,6 +23,16 @@ "First configure matplotlib to place figures in notebook and import needed modules. Note that the plot function needs installation of `plopp` seperately or installation of `easyreflectometry[dev]`" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "0143544a", + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib inline" + ] + }, { "cell_type": "code", "execution_count": null, @@ -30,8 +40,6 @@ "metadata": {}, "outputs": [], "source": [ - "%matplotlib inline\n", - "\n", "import numpy as np\n", "import pooch\n", "import refnx\n", diff --git a/docs/src/tutorials/fitting/monolayer.ipynb b/docs/docs/tutorials/fitting/monolayer.ipynb similarity index 99% rename from docs/src/tutorials/fitting/monolayer.ipynb rename to docs/docs/tutorials/fitting/monolayer.ipynb index 1d1c37ee..e4a7b06d 100644 --- a/docs/src/tutorials/fitting/monolayer.ipynb +++ b/docs/docs/tutorials/fitting/monolayer.ipynb @@ -20,6 +20,16 @@ "First configure matplotlib to place figures in notebook and import needed modules. Note that the plot function needs installation of `plopp` seperately or installation of `easyreflectometry[dev]`" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "ece9d352", + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib inline" + ] + }, { "cell_type": "code", "execution_count": null, @@ -27,8 +37,6 @@ "metadata": {}, "outputs": [], "source": [ - "%matplotlib inline\n", - "\n", "import pooch\n", "import refnx\n", "\n", diff --git a/docs/src/tutorials/fitting/monolayer.png b/docs/docs/tutorials/fitting/monolayer.png similarity index 100% rename from docs/src/tutorials/fitting/monolayer.png rename to docs/docs/tutorials/fitting/monolayer.png diff --git a/docs/src/tutorials/fitting/monolayer.svg b/docs/docs/tutorials/fitting/monolayer.svg similarity index 100% rename from docs/src/tutorials/fitting/monolayer.svg rename to docs/docs/tutorials/fitting/monolayer.svg diff --git a/docs/src/tutorials/fitting/polymer_film.png b/docs/docs/tutorials/fitting/polymer_film.png similarity index 100% rename from docs/src/tutorials/fitting/polymer_film.png rename to docs/docs/tutorials/fitting/polymer_film.png diff --git a/docs/src/tutorials/fitting/polymer_film.svg b/docs/docs/tutorials/fitting/polymer_film.svg similarity index 100% rename from docs/src/tutorials/fitting/polymer_film.svg rename to docs/docs/tutorials/fitting/polymer_film.svg diff --git a/docs/src/tutorials/fitting/repeating.ipynb b/docs/docs/tutorials/fitting/repeating.ipynb similarity index 98% rename from docs/src/tutorials/fitting/repeating.ipynb rename to docs/docs/tutorials/fitting/repeating.ipynb index 19e6bceb..e062ac5d 100644 --- a/docs/src/tutorials/fitting/repeating.ipynb +++ b/docs/docs/tutorials/fitting/repeating.ipynb @@ -24,6 +24,16 @@ "First configure matplotlib to place figures in notebook and import needed modules. Note that the plot function needs installation of `plopp` seperately or installation of `easyreflectometry[dev]`" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "419add7b", + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib inline" + ] + }, { "cell_type": "code", "execution_count": null, @@ -31,8 +41,6 @@ "metadata": {}, "outputs": [], "source": [ - "%matplotlib inline\n", - "\n", "import numpy as np\n", "import pooch\n", "import refl1d\n", diff --git a/docs/src/tutorials/fitting/repeating.png b/docs/docs/tutorials/fitting/repeating.png similarity index 100% rename from docs/src/tutorials/fitting/repeating.png rename to docs/docs/tutorials/fitting/repeating.png diff --git a/docs/src/tutorials/fitting/repeating.svg b/docs/docs/tutorials/fitting/repeating.svg similarity index 100% rename from docs/src/tutorials/fitting/repeating.svg rename to docs/docs/tutorials/fitting/repeating.svg diff --git a/docs/src/tutorials/fitting/repeating_layers.ort b/docs/docs/tutorials/fitting/repeating_layers.ort similarity index 100% rename from docs/src/tutorials/fitting/repeating_layers.ort rename to docs/docs/tutorials/fitting/repeating_layers.ort diff --git a/docs/src/tutorials/fitting/simple_fitting.ipynb b/docs/docs/tutorials/fitting/simple_fitting.ipynb similarity index 99% rename from docs/src/tutorials/fitting/simple_fitting.ipynb rename to docs/docs/tutorials/fitting/simple_fitting.ipynb index f6ee414d..8eea570a 100644 --- a/docs/src/tutorials/fitting/simple_fitting.ipynb +++ b/docs/docs/tutorials/fitting/simple_fitting.ipynb @@ -21,6 +21,16 @@ "Note that the plot function needs installation of `plopp` seperately or installation of `easyreflectometry[dev]`" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "38b12098", + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib inline" + ] + }, { "cell_type": "code", "execution_count": null, @@ -28,8 +38,6 @@ "metadata": {}, "outputs": [], "source": [ - "%matplotlib inline\n", - "\n", "import matplotlib.pyplot as plt\n", "import pooch\n", "import refl1d\n", diff --git a/docs/docs/tutorials/index.md b/docs/docs/tutorials/index.md index e0ed567a..c15cc31d 100644 --- a/docs/docs/tutorials/index.md +++ b/docs/docs/tutorials/index.md @@ -1,4 +1,4 @@ ---- +--- icon: material/school --- @@ -13,9 +13,58 @@ Instructions on how to run the tutorials are provided in the [:material-cog-box: Installation & Setup](../installation-and-setup/index.md#how-to-run-tutorials) section of the documentation. -The tutorials are organized into the following categories: +## Calculators and Optimisation + +EasyReflectometry is built on the EasyScience framework which +facilitates the use of a range of different reflectometry calculation +engines and optimiser solutions. Currently, EasyReflectometry can offer +two different calculation engines, namely: + +- [refnx](https://refnx.readthedocs.io/) +- [Refl1D](https://refl1d.readthedocs.io/en/latest/) + +And we are working to add more, in particular +[BornAgain](https://www.bornagainproject.org) and +[GenX](https://aglavic.github.io/genx/doc/). ## Getting Started -- [Dummy tutorial](tutorial.ipynb) – A dummy tutorial to ensure the - tutorial infrastructure is working correctly. +- [Creating a Model](basic/model.md) – Learn how to define a + reflectometry model with sample, scale, background, and resolution + functions. +- [Defining Materials](basic/material_library.md) – Explore different + material types: `Material`, `MaterialDensity`, `MaterialSolvated`, and + `MaterialMixture`. +- [Defining Layers](basic/layer_library.md) – Understand layer types + including `Layer` and `LayerAreaPerMolecule`. +- [Creating Assemblies](basic/assemblies_library.md) – Build complex + structures with `Multilayer`, `RepeatingMultilayer`, and + `SurfactantLayer`. + +## Simulation + +These are basic simulation examples using the EasyReflectometry library. + +- [Bilayer Simulation](simulation/bilayer.ipynb) +- [Magnetism Simulation](simulation/magnetism.ipynb) +- [Resolution Functions](simulation/resolution_functions.ipynb) + +## Fitting + +These are basic fitting examples using the EasyReflectometry library. + +- [Simple Fitting](fitting/simple_fitting.ipynb) +- [Repeating Multilayer Fitting](fitting/repeating.ipynb) +- [Monolayer Fitting](fitting/monolayer.ipynb) +- [Solvated Material Fitting](fitting/material_solvated.ipynb) + +## Advanced Fitting + +These are advanced fitting examples using the EasyReflectometry library. + +- [Multi-Contrast Fitting](advancedfitting/multi_contrast.ipynb) + +## Extra + +Additional examples and supplementary material using the +EasyReflectometry library. diff --git a/docs/src/tutorials/simulation/bilayer.ipynb b/docs/docs/tutorials/simulation/bilayer.ipynb similarity index 99% rename from docs/src/tutorials/simulation/bilayer.ipynb rename to docs/docs/tutorials/simulation/bilayer.ipynb index 142bb35d..b16b8284 100644 --- a/docs/src/tutorials/simulation/bilayer.ipynb +++ b/docs/docs/tutorials/simulation/bilayer.ipynb @@ -32,6 +32,16 @@ "First, we import the necessary modules and configure matplotlib for inline plotting." ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "7d213b99", + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib inline" + ] + }, { "cell_type": "code", "execution_count": null, @@ -39,8 +49,6 @@ "metadata": {}, "outputs": [], "source": [ - "%matplotlib inline\n", - "\n", "import matplotlib.pyplot as plt\n", "import numpy as np\n", "\n", diff --git a/docs/src/tutorials/simulation/magnetism.ipynb b/docs/docs/tutorials/simulation/magnetism.ipynb similarity index 99% rename from docs/src/tutorials/simulation/magnetism.ipynb rename to docs/docs/tutorials/simulation/magnetism.ipynb index 8f8ce93c..8efdb9e4 100644 --- a/docs/src/tutorials/simulation/magnetism.ipynb +++ b/docs/docs/tutorials/simulation/magnetism.ipynb @@ -20,6 +20,16 @@ "First configure matplotlib to place figures in notebook and import needed modules" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "644e53e3", + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib inline" + ] + }, { "cell_type": "code", "execution_count": null, @@ -27,8 +37,6 @@ "metadata": {}, "outputs": [], "source": [ - "%matplotlib inline\n", - "\n", "import matplotlib.pyplot as plt\n", "import numpy as np\n", "import refl1d\n", diff --git a/docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-0.0.ort b/docs/docs/tutorials/simulation/mod_pointwise_two_layer_sample_dq-0.0.ort similarity index 100% rename from docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-0.0.ort rename to docs/docs/tutorials/simulation/mod_pointwise_two_layer_sample_dq-0.0.ort diff --git a/docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-1.0.ort b/docs/docs/tutorials/simulation/mod_pointwise_two_layer_sample_dq-1.0.ort similarity index 100% rename from docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-1.0.ort rename to docs/docs/tutorials/simulation/mod_pointwise_two_layer_sample_dq-1.0.ort diff --git a/docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-10.0.ort b/docs/docs/tutorials/simulation/mod_pointwise_two_layer_sample_dq-10.0.ort similarity index 100% rename from docs/src/tutorials/simulation/mod_pointwise_two_layer_sample_dq-10.0.ort rename to docs/docs/tutorials/simulation/mod_pointwise_two_layer_sample_dq-10.0.ort diff --git a/docs/src/tutorials/simulation/resolution_functions.ipynb b/docs/docs/tutorials/simulation/resolution_functions.ipynb similarity index 99% rename from docs/src/tutorials/simulation/resolution_functions.ipynb rename to docs/docs/tutorials/simulation/resolution_functions.ipynb index da261981..48a6893a 100644 --- a/docs/src/tutorials/simulation/resolution_functions.ipynb +++ b/docs/docs/tutorials/simulation/resolution_functions.ipynb @@ -24,6 +24,16 @@ "First configure matplotlib to place figures in notebook and import needed modules. Note that the plot function needs installation of `plopp` seperately or installation of `easyreflectometry[dev]`" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "deb2db0a", + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib inline" + ] + }, { "cell_type": "code", "execution_count": null, @@ -31,8 +41,6 @@ "metadata": {}, "outputs": [], "source": [ - "%matplotlib inline\n", - "\n", "import matplotlib.pyplot as plt\n", "import numpy as np\n", "import pooch\n", diff --git a/docs/src/tutorials/simulation/two_layers.png b/docs/docs/tutorials/simulation/two_layers.png similarity index 100% rename from docs/src/tutorials/simulation/two_layers.png rename to docs/docs/tutorials/simulation/two_layers.png diff --git a/docs/src/tutorials/simulation/two_layers.svg b/docs/docs/tutorials/simulation/two_layers.svg similarity index 100% rename from docs/src/tutorials/simulation/two_layers.svg rename to docs/docs/tutorials/simulation/two_layers.svg diff --git a/docs/docs/user-guide/index.md b/docs/docs/user-guide/index.md index 2f8ac219..fbdec8b4 100644 --- a/docs/docs/user-guide/index.md +++ b/docs/docs/user-guide/index.md @@ -1,4 +1,4 @@ ---- +--- icon: material/book-open-variant --- @@ -8,17 +8,204 @@ This section provides an overview of the **core concepts**, **key parameters** and **workflow steps** required for using EasyReflectometry effectively. -Here is a brief overview of the User Guide sections: - -- [Glossary](#) – Defines common terms and labels used throughout the - documentation. -- [Concept](#) – Introduces the overall idea behind data analysis in - EasyReflectometry. -- [Data Format](#) – Explains the data structures and file formats used - by EasyReflectometry. -- [Parameters](#) – Describes how parameters are structured, named, and - accessed within the EasyReflectometry. -- [First Steps](#) – Shows how to begin using EasyReflectometry in - Python or Jupyter notebooks. -- [Analysis Workflow](#) – Breaks down the data analysis pipeline into - practical, sequential steps. +## Glossary + +The following serves to clarify what we mean by the terms we use in this +project. + +### Sample + +A sample is an ideal representation of the full physical setup. This +includes the layer(s) under investigation, the surrounding superphase, +and the subphase. + +### Calculator + +A calculator is the physics engine which calculates the reflectivity +curve from our inputted sample parameters. We rely on third party +software to provide the necessary calculators. Different calculators +might have different capabilities and limitations. + +Currently, EasyReflectometry can offer two different calculation +engines: + +- [**refnx**](https://refnx.readthedocs.io/) +- [**Refl1D**](https://refl1d.readthedocs.io/en/latest/) + +And we are working to add more, in particular +[**BornAgain**](https://www.bornagainproject.org) and +[**GenX**](https://aglavic.github.io/genx/doc/). + +### Model + +A model combines a sample and calculator. The model is also responsible +for including instrumental effects such as background, scale, and +resolution. + +### Assemblies + +Assemblies are collections of layers that are used to represent a +specific physical setup. Examples include: + +- **Multilayer** – A series of layers grouped as a single object +- **RepeatingMultilayer** – A multilayer with a fixed number of repeats +- **SurfactantLayer** – A layer defined by area per molecule and + chemical formula +- **GradientLayer** – A layer with a graded scattering length density + profile + +### Elements + +Elements are the building blocks that are required to construct a +sample. + +**Layers** are basic elements used to represent a single layer of +material with a thickness and a roughness: + +- `Layer` – Standard layer with material, thickness, and roughness +- `LayerAreaPerMolecule` – Layer defined by area per molecule and + chemical formula + +**Materials** are the most basic elements and are used to represent a +material with given physical properties: + +- `Material` – Simple material defined by SLD (real and imaginary) +- `MaterialDensity` – Material defined by mass density and chemical + formula +- `MaterialSolvated` – Material mixed with a solvent in a given ratio +- `MaterialMixture` – Mixture of two materials + +### Fitting + +Fitting helpers and objective functions. The `MultiFitter` supports +several objective modes for handling reflectometry data during fitting, +especially when measured variances are non-positive. + +## Getting Started + +To use EasyReflectometry in a project: + +```python +import easyreflectometry +from easyreflectometry.sample import Material, Layer +from easyreflectometry.model import Model +from easyreflectometry.fitting import MultiFitter +from easyreflectometry.plot import plot + +# Define your Material +material = Material(...) + +# Create a Layer +layer = Layer(material=material, ...) + +# Make a Sample out of the Layer +sample = Sample(layer, ...) + +# Define a Model of the experiment +model = Model( + sample=sample, + scale=1, + background=1e-6, + ... +) + +# Set parameter bounds for fit +... + +# Perform the fit and plot +fitter = MultiFitter(model) +analysed = fitter.fit(data) + +plot(analysed) +``` + +Details of specific usage of EasyReflectometry can be found in the +[Tutorials](../tutorials/index.md). + +## Objective Functions and Non-Positive Variance Handling + +`MultiFitter` supports several objective modes for handling +reflectometry data during fitting, especially when measured variances +are non-positive. + +The default objective is `hybrid`. This uses ordinary weighted least +squares for points with positive variance and applies a Mighell-style +substitution only to points whose variance is non-positive. The older +`legacy_mask` mode drops non-positive-variance points before fitting. +The `mighell` mode applies the Mighell transform to every point. + +### Mighell Objective + +The full `mighell` objective follows the algebraic form of the +$\chi^2_\gamma$ statistic described by Mighell for Poisson-distributed +count data: + +$$ +\chi^2_\gamma = +\sum_i \frac{[n_i + \min(n_i, 1) - m_i]^2}{n_i + 1} +$$ + +where $n_i$ are observed counts and $m_i$ are model values. + +In EasyReflectometry this is implemented as a weighted least-squares +problem. For each observed value $y_i$ the fitted target is shifted to + +$$ +y_{\mathrm{eff},i} = y_i + \min(y_i, 1) +$$ + +and the effective uncertainty is + +$$ +\sigma_i = \sqrt{y_i + 1} +$$ + +so the minimized objective is + +$$ +\sum_i \left(\frac{y_{\mathrm{eff},i} - f_i}{\sigma_i}\right)^2 = +\sum_i \frac{[y_i + \min(y_i, 1) - f_i]^2}{y_i + 1} +$$ + +### Scope and Interpretation + +Mighell's statistic was derived for Poisson-distributed count data. In +reflectometry workflows, the fitted values are usually normalized +reflectivities or intensities rather than raw counts. They may already +have been processed, scaled, background-corrected, or otherwise +transformed before they reach the fitter. + +This distinction matters when interpreting the result. The full +`mighell` objective is not only a reweighting of residuals; it also +changes the fitted target from $y$ to $y + \min(y, 1)$. For values +between zero and one, this can substantially increase the target value. +A fit can therefore have a good Mighell objective value while looking +poorer against the originally plotted reflectivity curve, or while +having a worse classical chi-square. + +For reflectometry data, `hybrid` is generally the recommended +compromise: it preserves ordinary weighted least-squares behavior where +positive variances are available, while still allowing +non-positive-variance points to contribute through the Mighell-style +substitution. + +### Objective Modes + +- **`hybrid`** (default): Use standard weighted least squares for points + with positive variance and apply the Mighell substitution only where + variance is non-positive. +- **`mighell`**: Apply the Mighell transform to all points. The reported + objective chi-square is evaluated in transformed objective space and + should not be interpreted as a classical chi-square against the + original reflectivity values. +- **`legacy_mask`**: Remove non-positive-variance points before fitting + and use standard weighted least squares for the remaining points. +- **`auto`**: Alias for `hybrid`. + +### Fit Metrics + +The fitter exposes both objective-space and classical fit metrics after +fitting. `objective_chi2` and `objective_reduced_chi` describe the +minimized objective value, while `classical_chi2` and +`classical_reduced_chi` describe the fit quality against the original +reflectivity values (with non-positive-variance points excluded). diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index d6d576ea..af6cb4fe 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -177,6 +177,39 @@ nav: - Tutorials: - Tutorials: tutorials/index.md - Getting Started: - - Dummy tutorial: tutorials/tutorial.ipynb + - Creating a Model: tutorials/basic/model.md + - Defining Materials: tutorials/basic/material_library.md + - Defining Layers: tutorials/basic/layer_library.md + - Creating Assemblies: tutorials/basic/assemblies_library.md + - Simulation: + - Bilayer Simulation: tutorials/simulation/bilayer.ipynb + - Magnetism Simulation: tutorials/simulation/magnetism.ipynb + - Resolution Functions: tutorials/simulation/resolution_functions.ipynb + - Fitting: + - Simple Fitting: tutorials/fitting/simple_fitting.ipynb + - Repeating Multilayer Fitting: tutorials/fitting/repeating.ipynb + - Monolayer Fitting: tutorials/fitting/monolayer.ipynb + - Solvated Material Fitting: tutorials/fitting/material_solvated.ipynb + - Advanced Fitting: + - Multi-Contrast Fitting: tutorials/advancedfitting/multi_contrast.ipynb - API Reference: - API Reference: api-reference/index.md + - Model: api-reference/model.md + - Sample: api-reference/sample.md + - Project: api-reference/project.md + - Fitting: api-reference/fitting.md + - Assemblies: + - Multilayer: api-reference/assemblies/multilayer.md + - Repeating Multilayer: api-reference/assemblies/repeating_multilayer.md + - Surfactant Layer: api-reference/assemblies/surfactant_layer.md + - Gradient Layer: api-reference/assemblies/gradient_layer.md + - Elements: + - Layers: + - Layer: api-reference/elements/layer.md + - Layer Area Per Molecule: api-reference/elements/layer_area_per_molecule.md + - Materials: + - Material: api-reference/elements/material.md + - Material Density: api-reference/elements/material_density.md + - Material Mixture: api-reference/elements/material_mixture.md + - Material Solvated: api-reference/elements/material_solvated.md + - Data: api-reference/data.md diff --git a/docs/src/tutorials/advancedfitting/advancedfitting.rst b/docs/src/tutorials/advancedfitting/advancedfitting.rst deleted file mode 100644 index 8c12ba54..00000000 --- a/docs/src/tutorials/advancedfitting/advancedfitting.rst +++ /dev/null @@ -1,9 +0,0 @@ -Advanced Fitting -================ - -These are advanced fitting examples using the :py:mod:`easyreflectometry` library, to get an understanding of the possibilities. - -.. toctree:: - :maxdepth: 1 - - multi_contrast.ipynb \ No newline at end of file diff --git a/docs/src/tutorials/basic/assemblies_library.rst b/docs/src/tutorials/basic/assemblies_library.rst deleted file mode 100644 index d72201a9..00000000 --- a/docs/src/tutorials/basic/assemblies_library.rst +++ /dev/null @@ -1,249 +0,0 @@ -Creating multilayers and surfactant layers -=========================================== - -:py:mod:`easyreflectometry` is designed to be used with a broad range of different assemblies. -Assemblies are collective layers behaving as a single object, for example, a multilayer or a surfactant layer. -These assemblies offer flexibility for the user and enable more powerful analysis by making chemical and physical constraints available with limited code. -In this page, we will document the assemblies that are available with simple examples of the constructors that exist. -Full API documentation is also available for the :py:mod:`easyreflectometry.sample.assemblies` module. - -:py:class:`Multilayer` ----------------------- - -This assembly should be used for a series of layers that should be thought of as a single object. -For example, in the `simple fitting tutorial`_ this assembly type is used to combine the silicon and silicon dioxide layer that as formed into a single object. -All of the separate layers in these objects will be fitted individually, i.e. there is no constraints present, however, there is some cognative benefit to grouping layers together. - -To create a :py:class:`Multilayer` object, we use the following construction. - -.. code-block:: python - - from easyreflectometry.sample import Layer - from easyreflectometry.sample import Material - from easyreflectometry.sample import Multilayer - - si = Material( - sld=2.07, - isld=0, - name='Si' - ) - sio2 = Material( - sld=3.47, - isld=0, - name='SiO2' - ) - si_layer = Layer( - material=si, - thickness=0, - roughness=0, - name='Si layer' - ) - sio2_layer = Layer( - material=sio2, - thickness=30, - roughness=3, - name='SiO2 layer' - ) - - subphase = Multilayer( - layers=[si_layer, sio2_layer], - name='Si/SiO2 subphase' - ) - -This will create a :py:class:`Multilayer` object named :code:`subphase` which we can use in some :py:class:`Structure` for our analysis. - -:py:class:`RepeatingMultilayer` -------------------------------- - -The :py:class:`RepeatingMultilayer` assembly type is an extension of the :py:class:`Multilayer` for the analysis of systems with a multilayer that has some number of repeats. -This assembly type imposes some constraints, specifically that all of the repeats have the exact same structure (i.e. thicknesses, roughnesses, and scattering length densities), -which brings with it some computational saving as the reflectometry coefficients only needs to be calculated once for this structure and propagated for the correct number of repeats. -There is a `tutorial`_ that discusses the utilisation of this assembly type for a nickel-titanium multilayer system. - -The creation of a :py:class:`RepeatingMultilayer` object is very similar to that for the :py:class:`Multilayer`, with the addition of a number of repetitions. - -.. code-block:: python - - from easyreflectometry.sample import Layer - from easyreflectometry.sample import Material - from easyreflectometry.sample import RepeatingMultilayer - - ti = Material( - sld=-1.9493, - isld=0, - name='Ti' - ) - ni = Material( - sld=9.4245, - isld=0, - name='Ni' - ) - ti_layer = Layer( - material=ti, - thickness=40, - roughness=0, - name='Ti Layer' - ) - ni_layer = Layer( - material=ni, - thickness=70, - roughness=0, - name='Ni Layer' - ) - ni_ti = RepeatingMultilayer( - layers=[ti_layer, ni_layer], - repetitions=10, - name='Ni/Ti Multilayer' - ) - -The number of repeats is a parameter that can be varied in the optimisation process, however given this is a value that depends on the synthesis of the sample this is unlikely to be necessary. - -:py:class:`SurfactantLayer` ---------------------------- - -The :py:class:`SurfactantLayer` assembly type allows for the creating of a model to describe a monolayer of surfactant at some interface. -Using this assembly, we can define our surfactant in terms of the chemistry of the head and tail groups and be confident that the constraints are present to ensure the number density if kept constant. -The `surfactant monolayer tutorial`_ looks in detail at the definition of the scattering length density in the :py:class:`SurfactantLayer`. -However, it is founded on the chemical formula for the head and tail group and the area per molecule that these groups occupy. - -The creation of a :py:class:`SurfactantLayer` object is shown below. - -.. code-block:: python - - from easyreflectometry.sample import LayerAreaPerMolecule - from easyreflectometry.sample import Material - from easyreflectometry.sample import SurfactantLayer - - area_per_molecule = 48 - roughness = 3.3 - subphase = Material( - sld=6.36, - isld=0.0, - name='D2O' - ) - superphase = Material( - sld=0.0, - isld=0.0, - name='Air' - ) - tail_layer = LayerAreaPerMolecule( - molecular_formula='C30D64', - thickness=16.0, - solvent=superphase, - solvent_fraction=0.0, - area_per_molecule=area_per_molecule, - roughness=roughness - ) - head_layer = LayerAreaPerMolecule( - molecular_formula='C10H18NO8P', - thickness=10.0, - solvent=subphase, - solvent_fraction=0.2, - area_per_molecule=area_per_molecule, - roughness=roughness - ) - dspc = SurfactantLayer( - tail_layer=tail_layer, - head_layer=head_layer - ) - -On creation, the area per molecule and roughness above both the head and tail layers can be constrained to be the same. -These constraints can be addded by setting :code:`dppc.constrain_area_per_molecule = True` or :code:`dppc.conformal_roughness = True`. -Furthermore, as shown in the `surfactant monolayer tutorial`_ the conformal roughness can be defined by that of the subphase. - -The use of the :py:class:`SurfactantLayer` in multiple contrast data analysis is shown in a `multiple contrast tutorial`_. - -:py:class:`Bilayer` -------------------- - -The :py:class:`Bilayer` assembly type represents a phospholipid bilayer at an interface. -It consists of two surfactant layers where one is inverted, creating the structure: - -.. code-block:: text - - Head₁ - Tail₁ - Tail₂ - Head₂ - -This assembly is particularly useful for studying supported lipid bilayers and membrane systems. -The bilayer comes pre-populated with physically meaningful constraints: - -- Both tail layers share the same structural parameters (thickness, area per molecule) -- Head layers share thickness and area per molecule (different hydration/solvent fraction allowed) -- A single roughness parameter applies to all interfaces (conformal roughness) - -These default constraints can be enabled or disabled as needed for specific analyses. - -The creation of a :py:class:`Bilayer` object is shown below. - -.. code-block:: python - - from easyreflectometry.sample import Bilayer - from easyreflectometry.sample import LayerAreaPerMolecule - from easyreflectometry.sample import Material - - # Create materials for solvents - d2o = Material(sld=6.36, isld=0.0, name='D2O') - air = Material(sld=0.0, isld=0.0, name='Air') - - # Create head layer (used for front, back head will be auto-created with constraints) - head = LayerAreaPerMolecule( - molecular_formula='C10H18NO8P', - thickness=10.0, - solvent=d2o, - solvent_fraction=0.3, - area_per_molecule=48.2, - roughness=3.0, - name='DPPC Head' - ) - - # Create tail layer (both tail positions will share these parameters) - tail = LayerAreaPerMolecule( - molecular_formula='C32D64', - thickness=16.0, - solvent=air, - solvent_fraction=0.0, - area_per_molecule=48.2, - roughness=3.0, - name='DPPC Tail' - ) - - # Create bilayer with default constraints - bilayer = Bilayer( - front_head_layer=head, - tail_layer=tail, - constrain_heads=True, - conformal_roughness=True, - name='DPPC Bilayer' - ) - -The head layers can have different solvent fractions (hydration) even when constrained, -enabling the modeling of asymmetric bilayers at interfaces where the two sides of the -bilayer may have different solvent exposure. - -The constraints can be controlled at runtime: - -.. code-block:: python - - # Disable head constraints to allow different head layer structures - bilayer.constrain_heads = False - - # Disable conformal roughness to allow different roughness values - bilayer.conformal_roughness = False - -Individual layers can be accessed via properties: - -.. code-block:: python - - # Access the four layers - bilayer.front_head_layer # First head layer - bilayer.front_tail_layer # First tail layer - bilayer.back_tail_layer # Second tail layer (constrained to front tail) - bilayer.back_head_layer # Second head layer - -For more detailed examples including simulation and parameter access, see the `bilayer tutorial`_. - - -.. _`simple fitting tutorial`: ../tutorials/simple_fitting.html -.. _`tutorial`: ../tutorials/repeating.html -.. _`surfactant monolayer tutorial`: ../tutorials/monolayer.html -.. _`multiple contrast tutorial`: ../tutorials/multi_contrast.html -.. _`bilayer tutorial`: ../tutorials/simulation/bilayer.html \ No newline at end of file diff --git a/docs/src/tutorials/basic/basic.rst b/docs/src/tutorials/basic/basic.rst deleted file mode 100644 index bcb94f58..00000000 --- a/docs/src/tutorials/basic/basic.rst +++ /dev/null @@ -1,13 +0,0 @@ -Basic -===== - -The :py:mod:`easyreflectometry` package is focused on making easy to use functionality for specific modelling approaches. -In order to achieve this, we have a sample library with different functionality. - -.. toctree:: - :maxdepth: 1 - - model - material_library - layer_library - assemblies_library \ No newline at end of file diff --git a/docs/src/tutorials/basic/layer_library.rst b/docs/src/tutorials/basic/layer_library.rst deleted file mode 100644 index 76c75ad4..00000000 --- a/docs/src/tutorials/basic/layer_library.rst +++ /dev/null @@ -1,84 +0,0 @@ -Defining Layers -=============== - -Similar to a range of different `materials`_, there are a few different ways that a layer can be defined in :py:mod:`easyreflectometry`. - -:py:class:`Layer` ------------------ - -The :py:class:`Layer` is the simplest possible type of layer, taking a :py:class:`Material` and two floats associated with the thickness and upper (that is closer to the source of the incident radiation) roughness. -So we construct a :py:class:`Layer` as follows for a 100 Å thick layer of boron with a roughness of 10 Å. - -.. code-block:: python - - from easyreflectometry.sample import Material - from easyreflectometry.sample import Layer - - boron = Material( - sld=6.908, - isld=-0.278, - name='Boron' - ) - boron_layer = Layer( - material=boron, - thickness=100, - roughness=10, - name='Boron Layer' - ) - -This type of layer is used extensively in the `tutorials`_ - -To create a semi-infinite layer one needs to set the thickness to 0 and the roughness to 0. - -.. code-block:: python - - from easyreflectometry.sample import Material - from easyreflectometry.sample import Layer - - si = Material( - sld=2.07, - isld=0, - name='Si' - ) - semi_infinite_layer = Layer( - material=si, - thickness=0, - roughness=0, - name='Si layer' - ) - -:py:class:`LayerAreaPerMolecule` --------------------------------- - -The :py:class:`LayerAreaPerMolecule` layer type is the fundation of the :py:class:`SurfactantLayer` assemblies type (further information on this can be found in the `assemblies library`_). -The purpose of the :py:class:`LayerAreaPerMolecule` is to allow a layer to be defined in terms of the chemical formula of the material and the area per molecule of the layer. -The area per molecule is a common description of surface density in the surfactant monolayer and bilayer community. - -We can construct a 10 Å thick :py:class:`LayerAreaPerMolecule` of phosphatidylcholine, with an area per molecule of 48 Å squared and a roughness of 3 Å that has 20 % solvent surface coverage with D2O using the following. - -.. code-block:: python - - from easyreflectometry.sample import Material - from easyreflectometry.sample import LayerAreaPerMolecule - - d2o = Material( - sld=6.36, - isld=0, - name='D2O' - ) - molecular_formula = 'C10H18NO8P' - pc = LayerAreaPerMolecule( - molecular_formula=molecular_formula, - thickness=10, - solvent=d2o, - solvent_fraction=.2, - area_per_molecule=48, - roughness=3, - name='PC Layer' - ) - -It is expected that the typical user will not interface directly with the :py:class:`LayerAreaPerMolecule` assembly type, but instead the :py:class:`SurfactantLayer` `assemblies library`_ will be used instead. - -.. _`materials`: ./material_library.html -.. _`tutorials`: ../tutorials/tutorials.html -.. _`assemblies library`: ./assemblies_library.html \ No newline at end of file diff --git a/docs/src/tutorials/basic/material_library.rst b/docs/src/tutorials/basic/material_library.rst deleted file mode 100644 index 2aaf0911..00000000 --- a/docs/src/tutorials/basic/material_library.rst +++ /dev/null @@ -1,87 +0,0 @@ -Defining materials -================== - -In order to support a wide range of applications (and to build complex `assemblies`_) there are a few different types of material that can be utilised in :py:mod:`easyreflectometry`. -These can include constraints or enable the user to define the material based on chemical or physical properties. -Full API documentation for the :py:mod:`easyreflectometry.sample.elements.material` module is also available, but here we will give some simple uses for them. - -:py:class:`Material` --------------------- - -The simplest type of material that is available is the :py:class:`Material`. -This allows the user to define a single type of material, with a real and imaginary component to the scattering length density. -The construction of a :py:class:`Material` is achieved as shown below. - -.. code-block:: python - - from easyreflectometry.sample import Material - - boron = Material( - sld=6.908, - isld=-0.278, - name='Boron' - ) - -The above object will have the properties of :py:attr:`sld` and :py:attr:`isld`, which will have values of :code:`6.908 1/angstrom^2` and :code:`-0.278 1/angstrom^2` respectively. -As is shown in the `tutorials`_, a material can be used to construct a :py:class:`Layer` from which `slab models`_ are created. - -:py:class:`MaterialDensity` ---------------------------- - -In addition to defining a material by its scattering length density, it may be useful to define a material by the mass density and chemical formula. -This is possible with the :py:class:`MaterialDensity` material type, which uses the scattering length and atomic mass from the chemical formula and the density to determine the scattering length density. -It is then possible to vary the density, which defines the scattering length density in turn. -The :py:class:`MaterialDensity` material can be create as follows. - -.. code-block:: python - - from easyreflectometry.sample import MaterialDensity - - chemical_structure = 'SiO2' - si = MaterialDensity( - chemical_structure=chemical_structure, - density=2.65, - name='SiO2 Material' - ) - -The density should be in units of grams per cubic centimeter and the scattering length is calculated from :code:`'SiO2'`. - -:py:class:`MaterialSolvated` ----------------------------- - -Sometimes it is desirable to have a layer that consists of a material and a solvent in some ratio. -An example of this is shown in the `solvation tutorial`_, where a polymer film solvated with D2O is modelled. -To produce a material that is described by such a mixture, there is :py:class:`MaterialSolvated`. -This is constructed from two constituent :py:class:`Materials` and the fractional amount of the material in the solvent. -So to produce a :py:class:`MaterialSolvated` that is 20 % D2O in a polymer, the following is used. - -.. code-block:: python - - from easyreflectometry.sample import Material - from easyreflectometry.sample import MaterialSolvated - - polymer = Material( - sld=2., - isld=0., - name='Polymer' - ) - d2o = Material( - sld=6.36, - isld=0, - name='D2O' - ) - - solvated_polymer = MaterialSolvated( - material=polymer, - solvent=d2o, - solvent_fraction=0.2, - name='Solvated Polymer' - ) - -For the :py:attr:`solvated_polymer` object, the :py:attr:`sld` will be :code:`2.872 1/angstrom^2` (the weighted average of the two scattering length densities). -The :py:class:`MaterialSolvated` includes a constraint such that if the value of either constituent scattering length densities (both real and imaginary components) or the fraction changes, then the resulting material :py:attr:`sld` and :py:attr:`isld` will change appropriately. - -.. _`assemblies`: ./assemblies_library.html -.. _`tutorials`: ../tutorials/tutorials.html -.. _`slab models`: https://www.reflectometry.org/isis_school/3_reflectometry_slab_models/the_slab_model.html -.. _`solvation tutorial`: ../tutorials/solvation.html \ No newline at end of file diff --git a/docs/src/tutorials/basic/model.rst b/docs/src/tutorials/basic/model.rst deleted file mode 100644 index 47134397..00000000 --- a/docs/src/tutorials/basic/model.rst +++ /dev/null @@ -1,80 +0,0 @@ -Creating a model -================ - -The main component of an experiment in :py:mod:`easyreflectometry` is the :py:class:`Model`. -This is a description of the :py:class:`Sample` and the environment in which the experiment is performed. -The :py:class:`Model` is used to calculate the reflectivity of the :py:class:`Sample` at a given set of angles (Q-points). -The :py:func:`resolution_functions` are used to quantify the experimental uncertainties in wavelength and angle, allowing the :py:class:`Model` to accurately describe the data. - -:py:class:`Model` ------------------ - -A :py:class:`Model` instance contains a :py:class:`Sample` and variables describing experimental settings. -To be able to compute reflectivities it is also necessary to have a :py:class:`Calculator` (interface). - -.. code-block:: python - - from easyreflectometry.calculators import CalculatorFactory - from easyreflectometry.model import Model - from easyreflectometry.sample import Sample - - default_sample = Sample() - model = Model( - sample=default_sample, - scale=1.0, - background=1e-6 - ) - - interface = CalculatorFactory() - model.interface = interface - -This will create a :py:class:`Model` instance with the :py:attr:`default_sample` and the environment variables :py:attr:`scale` factor set to 1.0 and a :py:attr:`background` of 1e-6. -Following the :py:attr:`interface` is set to the default calculator that is :py:class:`Refnx`. - - -:py:mod:`resolution_functions` ------------------------------- -A resolution function enables the :py:mod:`easyreflectometry` model to incorporate the experimental uncertainties in wavelength and incident angle into the model. -In its essence the resolution function controls the smearing to apply when determing the reflectivtiy at a given Q-point. -For a given Q-point the smearing to apply is given as a weighted average of the neighboring Q-point, which weigths are by a normal distribution. -This normal distribution is then defined by a Q-point dependent Full Width at the Half Maximum (FWHM) that is given by the resolution function. - -:py:class:`PercentageFwhm` -Often we rely on a resolution function that has a simple functional dependecy of the Q-point. -By this is understood that the applied smearing in an Q-point has a FWHM that is simply a percentage of the value of the Q-point. - -.. code-block:: python - - from easyreflectometry.model import Model - from easyreflectometry.model import PercentageFwhm - - resolution_function = PercentageFwhm(1.1) - - m = Model( - resolution_function=resolution_function - ) - -This will create a :py:class:`Model` instance where the resolution function is defined as 1.1% of the Q-point value, which again is the FWHM for the smearing. - - -:py:func:`LinearSpline` -Alternatively the FWHM value might be determined and declared directly for each measured Q-point. -When this is the case the provided Q-points and the corresponding FWHM values can be used to declare a linear spline function -and thereby enable a determination of the reflectivity at an arbitrary point within the provided range of discrete Q-points. - -.. code-block:: python - - from easyreflectometry.model import Model - from easyreflectometry.model import LinearSpline - - m = Model() - - resolution_function = LinearSpline( - q_data_points=[0.01, 0.2, 0.31], - fwhm_values=[0.001, 0.043, 0.026] - ) - - m.resolution_function = resolution_function - -This will create a :py:class:`Model` instance where the resolution function defining the FWHM is determined from a linear interpolation. -In the present case the provided data Q-points are (`[0.01, 0.2, 0.31]`) and the corresponding FWHM function values are (`[0.001, 0.043, 0.026]`). diff --git a/docs/src/tutorials/extra/extra.rst b/docs/src/tutorials/extra/extra.rst deleted file mode 100644 index 9d68b33a..00000000 --- a/docs/src/tutorials/extra/extra.rst +++ /dev/null @@ -1,7 +0,0 @@ -Extra -===== - -These are extra examples using the :py:mod:`easyreflectometry` library, to get an understanding of the possibilities. - -.. toctree:: - :maxdepth: 1 \ No newline at end of file diff --git a/docs/src/tutorials/fitting/fitting.rst b/docs/src/tutorials/fitting/fitting.rst deleted file mode 100644 index 52b6c14f..00000000 --- a/docs/src/tutorials/fitting/fitting.rst +++ /dev/null @@ -1,12 +0,0 @@ -Fitting -======= - -These are basic fitting examples using the :py:mod:`easyreflectometry` library, to get an understanding of the possibilities. - -.. toctree:: - :maxdepth: 1 - - simple_fitting.ipynb - repeating.ipynb - monolayer.ipynb - material_solvated.ipynb \ No newline at end of file diff --git a/docs/src/tutorials/simulation/simulation.rst b/docs/src/tutorials/simulation/simulation.rst deleted file mode 100644 index 5cf9ced4..00000000 --- a/docs/src/tutorials/simulation/simulation.rst +++ /dev/null @@ -1,11 +0,0 @@ -Simulation -========== - -These are basic simulation examples using the :py:mod:`easyreflectometry` library, to get an understanding of the possibilities. - -.. toctree:: - :maxdepth: 1 - - bilayer.ipynb - magnetism.ipynb - resolution_functions.ipynb \ No newline at end of file diff --git a/docs/src/tutorials/tutorials.rst b/docs/src/tutorials/tutorials.rst deleted file mode 100644 index b73e6666..00000000 --- a/docs/src/tutorials/tutorials.rst +++ /dev/null @@ -1,49 +0,0 @@ -========== -How to use -========== - -Dictionary -========== -The following serves to clarify what we mean by the terms we use in this project. - -Sample ------- -A sample is an ideal representation of a the full physical setup. -This includes the layer(s) under investigation, the surrounding superphase, and the subphase. - -Calculator ----------- -A calculator is the physics engine which calculates the reflectivity curve from our inputted sample parameters. -We rely on third party software to provide the necessary calculators. -Different calculators might have different capabilities and limitations. - -Model ------ -A model combines a sample and calculator. -The model is also responsible for including instrumental effects such as background, scale, and resolution. - - -Calculators & Optimisation -========================== - -:py:mod:`easyreflectometry` is built on the :py:mod:`easyscience` framework which facilities the use of a range of different reflectometry calculation engines and optimiser solutions. -Currently, :py:mod:`easyreflectometry` can offer two different calculation engines, namely: - -* `refnx`_ -* `Refl1D`_ - -And we are working to add more, in particular `bornagain`_ and `GenX`_. - -.. _`refnx`: https://refnx.readthedocs.io/ -.. _`Refl1D`: https://refl1d.readthedocs.io/en/latest/ -.. _`BornAgain`: https://www.bornagainproject.org -.. _`GenX`: https://aglavic.github.io/genx/doc/ - -.. toctree:: - :maxdepth: 2 - - basic/basic - simulation/simulation - fitting/fitting - advancedfitting/advancedfitting - extra/extra diff --git a/pixi.lock b/pixi.lock index 2c4263cd..0399edad 100644 --- a/pixi.lock +++ b/pixi.lock @@ -6,12 +6,11 @@ environments: - url: https://conda.anaconda.org/conda-forge/ indexes: - https://pypi.org/simple - options: - pypi-prerelease-mode: if-necessary-or-explicit packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.13.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-25.1.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py313h07c4f96_2.conda @@ -21,6 +20,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.18.0-pyhcf101f3_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.4.0-py313h18e8e13_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/bcrypt-5.0.0-py313h843e2db_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.14.3-pyha770c72_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/bleach-6.3.0-pyhcf101f3_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/bleach-with-css-6.3.0-hbca2aae_1.conda @@ -33,14 +33,21 @@ environments: - conda: 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format support 'jupyterquiz', # Quizzes in Jupyter notebooks + 'plopp', # Plotting in Jupyter notebooks 'pydoclint', # Docstring linter 'format-docstring', # Docstring formatter 'docstripy', # Convert docstrings to other formats @@ -254,8 +255,7 @@ select = [ # Ignore specific rules globally ignore = [ 'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/ - # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint] - 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc + # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint] 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc # Disable, as [tool.format_docstring] split one-line docstrings into the canonical multi-line layout 'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/ ] From f0fd6696bd546955e49b7daa054b128b85a011d2 Mon Sep 17 00:00:00 2001 From: Piotr Rozyczko Date: Fri, 8 May 2026 13:56:55 +0200 Subject: [PATCH 11/20] make "pixi run mkdocs build" and "pixi run nonpy-format-check" work together --- docs/docs/api-reference/assemblies/gradient_layer.md | 7 +++++-- docs/docs/api-reference/assemblies/multilayer.md | 7 +++++-- docs/docs/api-reference/assemblies/repeating_multilayer.md | 7 +++++-- docs/docs/api-reference/assemblies/surfactant_layer.md | 7 +++++-- docs/docs/api-reference/data.md | 7 +++++-- docs/docs/api-reference/elements/layer.md | 7 +++++-- .../docs/api-reference/elements/layer_area_per_molecule.md | 5 ++++- docs/docs/api-reference/elements/material.md | 7 +++++-- docs/docs/api-reference/elements/material_density.md | 5 ++++- docs/docs/api-reference/elements/material_mixture.md | 5 ++++- docs/docs/api-reference/elements/material_solvated.md | 5 ++++- docs/docs/api-reference/fitting.md | 7 +++++-- docs/docs/api-reference/model.md | 7 +++++-- docs/docs/api-reference/project.md | 7 +++++-- docs/docs/api-reference/sample.md | 7 +++++-- docs/mkdocs.yml | 1 + src/easyreflectometry/__init__.py | 4 ++-- src/easyreflectometry/calculators/__init__.py | 2 +- src/easyreflectometry/sample/assemblies/__init__.py | 2 ++ src/easyreflectometry/sample/collections/__init__.py | 2 ++ src/easyreflectometry/sample/elements/__init__.py | 2 ++ src/easyreflectometry/sample/elements/layers/__init__.py | 2 ++ .../sample/elements/materials/__init__.py | 2 ++ src/easyreflectometry/summary/__init__.py | 2 +- 24 files changed, 86 insertions(+), 30 deletions(-) create mode 100644 src/easyreflectometry/sample/assemblies/__init__.py create mode 100644 src/easyreflectometry/sample/collections/__init__.py create mode 100644 src/easyreflectometry/sample/elements/__init__.py create mode 100644 src/easyreflectometry/sample/elements/layers/__init__.py create mode 100644 src/easyreflectometry/sample/elements/materials/__init__.py diff --git a/docs/docs/api-reference/assemblies/gradient_layer.md b/docs/docs/api-reference/assemblies/gradient_layer.md index 463b0712..9cdbda09 100644 --- a/docs/docs/api-reference/assemblies/gradient_layer.md +++ b/docs/docs/api-reference/assemblies/gradient_layer.md @@ -1,4 +1,7 @@ # Gradient Layer -::: easyreflectometry.sample.assemblies.gradient_layer options: members: -true show_inheritance: true + +::: easyreflectometry.sample.assemblies.gradient_layer + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/assemblies/multilayer.md b/docs/docs/api-reference/assemblies/multilayer.md index 52316972..ca574f4c 100644 --- a/docs/docs/api-reference/assemblies/multilayer.md +++ b/docs/docs/api-reference/assemblies/multilayer.md @@ -1,4 +1,7 @@ # Multilayer -::: easyreflectometry.sample.assemblies.multilayer options: members: -true show_inheritance: true + +::: easyreflectometry.sample.assemblies.multilayer + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/assemblies/repeating_multilayer.md b/docs/docs/api-reference/assemblies/repeating_multilayer.md index 26c6be16..24164558 100644 --- a/docs/docs/api-reference/assemblies/repeating_multilayer.md +++ b/docs/docs/api-reference/assemblies/repeating_multilayer.md @@ -1,4 +1,7 @@ # Repeating Multilayer -::: easyreflectometry.sample.assemblies.repeating_multilayer options: -members: true show_inheritance: true + +::: easyreflectometry.sample.assemblies.repeating_multilayer + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/assemblies/surfactant_layer.md b/docs/docs/api-reference/assemblies/surfactant_layer.md index 272be1f7..e33fab78 100644 --- a/docs/docs/api-reference/assemblies/surfactant_layer.md +++ b/docs/docs/api-reference/assemblies/surfactant_layer.md @@ -1,4 +1,7 @@ # Surfactant Layer -::: easyreflectometry.sample.assemblies.surfactant_layer options: -members: true show_inheritance: true + +::: easyreflectometry.sample.assemblies.surfactant_layer + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/data.md b/docs/docs/api-reference/data.md index 48a6f505..52c74445 100644 --- a/docs/docs/api-reference/data.md +++ b/docs/docs/api-reference/data.md @@ -1,4 +1,7 @@ # Data -::: easyreflectometry.data.measurement options: members: true -show_inheritance: true + +::: easyreflectometry.data.measurement + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/elements/layer.md b/docs/docs/api-reference/elements/layer.md index fb9d49f9..6dd99f8f 100644 --- a/docs/docs/api-reference/elements/layer.md +++ b/docs/docs/api-reference/elements/layer.md @@ -1,4 +1,7 @@ # Layer -::: easyreflectometry.sample.elements.layers.layer options: members: -true show_inheritance: true + +::: easyreflectometry.sample.elements.layers.layer + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/elements/layer_area_per_molecule.md b/docs/docs/api-reference/elements/layer_area_per_molecule.md index 2ee00cc7..60f4d1f4 100644 --- a/docs/docs/api-reference/elements/layer_area_per_molecule.md +++ b/docs/docs/api-reference/elements/layer_area_per_molecule.md @@ -1,4 +1,7 @@ # Layer Area Per Molecule + ::: easyreflectometry.sample.elements.layers.layer_area_per_molecule -options: members: true show_inheritance: true + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/elements/material.md b/docs/docs/api-reference/elements/material.md index 3fed854a..eda20d53 100644 --- a/docs/docs/api-reference/elements/material.md +++ b/docs/docs/api-reference/elements/material.md @@ -1,4 +1,7 @@ # Material -::: easyreflectometry.sample.elements.materials.material options: -members: true show_inheritance: true + +::: easyreflectometry.sample.elements.materials.material + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/elements/material_density.md b/docs/docs/api-reference/elements/material_density.md index a0a5f2f9..f4a86d15 100644 --- a/docs/docs/api-reference/elements/material_density.md +++ b/docs/docs/api-reference/elements/material_density.md @@ -1,4 +1,7 @@ # Material Density + ::: easyreflectometry.sample.elements.materials.material_density -options: members: true show_inheritance: true + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/elements/material_mixture.md b/docs/docs/api-reference/elements/material_mixture.md index ef8b6412..1a523e60 100644 --- a/docs/docs/api-reference/elements/material_mixture.md +++ b/docs/docs/api-reference/elements/material_mixture.md @@ -1,4 +1,7 @@ # Material Mixture + ::: easyreflectometry.sample.elements.materials.material_mixture -options: members: true show_inheritance: true + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/elements/material_solvated.md b/docs/docs/api-reference/elements/material_solvated.md index 33b51425..e9b3711d 100644 --- a/docs/docs/api-reference/elements/material_solvated.md +++ b/docs/docs/api-reference/elements/material_solvated.md @@ -1,4 +1,7 @@ # Material Solvated + ::: easyreflectometry.sample.elements.materials.material_solvated -options: members: true show_inheritance: true + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/fitting.md b/docs/docs/api-reference/fitting.md index 14a003e4..ca037cd3 100644 --- a/docs/docs/api-reference/fitting.md +++ b/docs/docs/api-reference/fitting.md @@ -1,4 +1,7 @@ # Fitting -::: easyreflectometry.fitting options: members: true show_inheritance: -true + +::: easyreflectometry.fitting + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/model.md b/docs/docs/api-reference/model.md index 50f1d822..d3d3edfa 100644 --- a/docs/docs/api-reference/model.md +++ b/docs/docs/api-reference/model.md @@ -1,4 +1,7 @@ # Model -::: easyreflectometry.model.model options: members: true -show_inheritance: true + +::: easyreflectometry.model.model + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/project.md b/docs/docs/api-reference/project.md index 50a2da54..962535b0 100644 --- a/docs/docs/api-reference/project.md +++ b/docs/docs/api-reference/project.md @@ -1,4 +1,7 @@ # Project -::: easyreflectometry.project options: members: true show_inheritance: -true + +::: easyreflectometry.project + options: + members: true + show_inheritance: true diff --git a/docs/docs/api-reference/sample.md b/docs/docs/api-reference/sample.md index b366e247..48fe0da4 100644 --- a/docs/docs/api-reference/sample.md +++ b/docs/docs/api-reference/sample.md @@ -1,4 +1,7 @@ # Sample -::: easyreflectometry.sample.collections.sample options: members: true -show_inheritance: true + +::: easyreflectometry.sample.collections.sample + options: + members: true + show_inheritance: true diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index af6cb4fe..cba16bbb 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -177,6 +177,7 @@ nav: - Tutorials: - Tutorials: tutorials/index.md - Getting Started: + - Dummy Tutorial: tutorials/tutorial.ipynb - Creating a Model: tutorials/basic/model.md - Defining Materials: tutorials/basic/material_library.md - Defining Layers: tutorials/basic/layer_library.md diff --git a/src/easyreflectometry/__init__.py b/src/easyreflectometry/__init__.py index 8c2f7496..8ff945d0 100644 --- a/src/easyreflectometry/__init__.py +++ b/src/easyreflectometry/__init__.py @@ -13,6 +13,6 @@ __version__ = '0.0.0' __all__ = [ - Project, - __version__, + 'Project', + '__version__', ] diff --git a/src/easyreflectometry/calculators/__init__.py b/src/easyreflectometry/calculators/__init__.py index 0df164c1..ccaf8f92 100644 --- a/src/easyreflectometry/calculators/__init__.py +++ b/src/easyreflectometry/calculators/__init__.py @@ -31,4 +31,4 @@ traceback.print_exc() print('Warning: refl1d is not installed') -__all__ = [CalculatorBase, CalculatorFactory] + imported_calculators +__all__ = ['CalculatorBase', 'CalculatorFactory'] + imported_calculators diff --git a/src/easyreflectometry/sample/assemblies/__init__.py b/src/easyreflectometry/sample/assemblies/__init__.py new file mode 100644 index 00000000..4e798e20 --- /dev/null +++ b/src/easyreflectometry/sample/assemblies/__init__.py @@ -0,0 +1,2 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause diff --git a/src/easyreflectometry/sample/collections/__init__.py b/src/easyreflectometry/sample/collections/__init__.py new file mode 100644 index 00000000..4e798e20 --- /dev/null +++ b/src/easyreflectometry/sample/collections/__init__.py @@ -0,0 +1,2 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause diff --git a/src/easyreflectometry/sample/elements/__init__.py b/src/easyreflectometry/sample/elements/__init__.py new file mode 100644 index 00000000..4e798e20 --- /dev/null +++ b/src/easyreflectometry/sample/elements/__init__.py @@ -0,0 +1,2 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause diff --git a/src/easyreflectometry/sample/elements/layers/__init__.py b/src/easyreflectometry/sample/elements/layers/__init__.py new file mode 100644 index 00000000..4e798e20 --- /dev/null +++ b/src/easyreflectometry/sample/elements/layers/__init__.py @@ -0,0 +1,2 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause diff --git a/src/easyreflectometry/sample/elements/materials/__init__.py b/src/easyreflectometry/sample/elements/materials/__init__.py new file mode 100644 index 00000000..4e798e20 --- /dev/null +++ b/src/easyreflectometry/sample/elements/materials/__init__.py @@ -0,0 +1,2 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause diff --git a/src/easyreflectometry/summary/__init__.py b/src/easyreflectometry/summary/__init__.py index f4afd83c..7f333368 100644 --- a/src/easyreflectometry/summary/__init__.py +++ b/src/easyreflectometry/summary/__init__.py @@ -3,4 +3,4 @@ from .summary import Summary -__all__ = [Summary] +__all__ = ['Summary'] From 9de5785989024205b5775741dd73be00a8826a96 Mon Sep 17 00:00:00 2001 From: Piotr Rozyczko Date: Fri, 8 May 2026 14:16:59 +0200 Subject: [PATCH 12/20] try using absolute paths for the wheel --- .github/workflows/test.yml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index f75ac8be..6bf99c45 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -229,10 +229,14 @@ jobs: exit 1 fi - whl_url="file://$(python -c 'import os,sys; print(os.path.abspath(sys.argv[1]))' "${whl_path[0]}")" + # whl_url="file://$(python -c 'import os,sys; print(os.path.abspath(sys.argv[1]))' "${whl_path[0]}")" + # echo "Adding easyreflectometry from: $whl_url" + # pixi add --pypi "easyreflectometry[dev] @ ${whl_url}" - echo "Adding easyreflectometry from: $whl_url" - pixi add --pypi "easyreflectometry[dev] @ ${whl_url}" + whl_abs_path="$(python -c 'import os,sys; print(os.path.abspath(sys.argv[1]))' "${whl_path[0]}")" + + echo "Adding easyreflectometry from: $whl_abs_path" + pixi add --pypi "easyreflectometry[dev] @ ${whl_abs_path}" echo "Exiting pixi project directory" cd .. From 9059c1b2d18c7de551aa35c3a897b8be0a1ef438 Mon Sep 17 00:00:00 2001 From: Piotr Rozyczko Date: Mon, 11 May 2026 12:31:55 +0200 Subject: [PATCH 13/20] minor fixes --- src/easyreflectometry/__version__.py | 4 ---- src/easyreflectometry/calculators/__init__.py | 2 +- src/easyreflectometry/calculators/calculator_base.py | 2 +- 3 files changed, 2 insertions(+), 6 deletions(-) delete mode 100644 src/easyreflectometry/__version__.py diff --git a/src/easyreflectometry/__version__.py b/src/easyreflectometry/__version__.py deleted file mode 100644 index a39a2412..00000000 --- a/src/easyreflectometry/__version__.py +++ /dev/null @@ -1,4 +0,0 @@ -# SPDX-FileCopyrightText: 2024 EasyScience contributors -# SPDX-License-Identifier: BSD-3-Clause - -__version__ = '1.6.0' diff --git a/src/easyreflectometry/calculators/__init__.py b/src/easyreflectometry/calculators/__init__.py index ccaf8f92..9f7bde45 100644 --- a/src/easyreflectometry/calculators/__init__.py +++ b/src/easyreflectometry/calculators/__init__.py @@ -31,4 +31,4 @@ traceback.print_exc() print('Warning: refl1d is not installed') -__all__ = ['CalculatorBase', 'CalculatorFactory'] + imported_calculators +__all__ = ['CalculatorBase', 'CalculatorFactory'] + [c.__name__ for c in imported_calculators] diff --git a/src/easyreflectometry/calculators/calculator_base.py b/src/easyreflectometry/calculators/calculator_base.py index 57d30224..263c601b 100644 --- a/src/easyreflectometry/calculators/calculator_base.py +++ b/src/easyreflectometry/calculators/calculator_base.py @@ -51,7 +51,7 @@ def __init__(self): self._wrapper: WrapperBase def reset_storage(self) -> None: - r"""Reset the storage area of the calculato.""" + r"""Reset the storage area of the calculator.""" self._wrapper.reset_storage() def create(self, model: Material | Layer | Multilayer | Model) -> list[ItemContainer]: From 64155000294a5ee8cbbc794f48ba1768e295ec1c Mon Sep 17 00:00:00 2001 From: Piotr Rozyczko Date: Mon, 11 May 2026 12:53:36 +0200 Subject: [PATCH 14/20] refactor md file headers for docs --- docs/docs/api-reference/assemblies/gradient_layer.md | 6 ------ docs/docs/api-reference/assemblies/multilayer.md | 6 ------ docs/docs/api-reference/assemblies/repeating_multilayer.md | 6 ------ docs/docs/api-reference/assemblies/surfactant_layer.md | 6 ------ docs/docs/api-reference/data.md | 6 ------ docs/docs/api-reference/elements/layer.md | 6 ------ docs/docs/api-reference/elements/layer_area_per_molecule.md | 6 ------ docs/docs/api-reference/elements/material.md | 6 ------ docs/docs/api-reference/elements/material_density.md | 6 ------ docs/docs/api-reference/elements/material_mixture.md | 6 ------ docs/docs/api-reference/elements/material_solvated.md | 6 ------ docs/docs/api-reference/fitting.md | 6 ------ docs/docs/api-reference/model.md | 6 ------ docs/docs/api-reference/project.md | 6 ------ docs/docs/api-reference/sample.md | 6 ------ docs/mkdocs.yml | 2 ++ 16 files changed, 2 insertions(+), 90 deletions(-) diff --git a/docs/docs/api-reference/assemblies/gradient_layer.md b/docs/docs/api-reference/assemblies/gradient_layer.md index 9cdbda09..b5ee7d48 100644 --- a/docs/docs/api-reference/assemblies/gradient_layer.md +++ b/docs/docs/api-reference/assemblies/gradient_layer.md @@ -1,7 +1 @@ -# Gradient Layer - - ::: easyreflectometry.sample.assemblies.gradient_layer - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/assemblies/multilayer.md b/docs/docs/api-reference/assemblies/multilayer.md index ca574f4c..f693c205 100644 --- a/docs/docs/api-reference/assemblies/multilayer.md +++ b/docs/docs/api-reference/assemblies/multilayer.md @@ -1,7 +1 @@ -# Multilayer - - ::: easyreflectometry.sample.assemblies.multilayer - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/assemblies/repeating_multilayer.md b/docs/docs/api-reference/assemblies/repeating_multilayer.md index 24164558..d2215e46 100644 --- a/docs/docs/api-reference/assemblies/repeating_multilayer.md +++ b/docs/docs/api-reference/assemblies/repeating_multilayer.md @@ -1,7 +1 @@ -# Repeating Multilayer - - ::: easyreflectometry.sample.assemblies.repeating_multilayer - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/assemblies/surfactant_layer.md b/docs/docs/api-reference/assemblies/surfactant_layer.md index e33fab78..19f1f56d 100644 --- a/docs/docs/api-reference/assemblies/surfactant_layer.md +++ b/docs/docs/api-reference/assemblies/surfactant_layer.md @@ -1,7 +1 @@ -# Surfactant Layer - - ::: easyreflectometry.sample.assemblies.surfactant_layer - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/data.md b/docs/docs/api-reference/data.md index 52c74445..700ec762 100644 --- a/docs/docs/api-reference/data.md +++ b/docs/docs/api-reference/data.md @@ -1,7 +1 @@ -# Data - - ::: easyreflectometry.data.measurement - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/elements/layer.md b/docs/docs/api-reference/elements/layer.md index 6dd99f8f..c37cd7b4 100644 --- a/docs/docs/api-reference/elements/layer.md +++ b/docs/docs/api-reference/elements/layer.md @@ -1,7 +1 @@ -# Layer - - ::: easyreflectometry.sample.elements.layers.layer - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/elements/layer_area_per_molecule.md b/docs/docs/api-reference/elements/layer_area_per_molecule.md index 60f4d1f4..d7245c69 100644 --- a/docs/docs/api-reference/elements/layer_area_per_molecule.md +++ b/docs/docs/api-reference/elements/layer_area_per_molecule.md @@ -1,7 +1 @@ -# Layer Area Per Molecule - - ::: easyreflectometry.sample.elements.layers.layer_area_per_molecule - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/elements/material.md b/docs/docs/api-reference/elements/material.md index eda20d53..7fba8cf4 100644 --- a/docs/docs/api-reference/elements/material.md +++ b/docs/docs/api-reference/elements/material.md @@ -1,7 +1 @@ -# Material - - ::: easyreflectometry.sample.elements.materials.material - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/elements/material_density.md b/docs/docs/api-reference/elements/material_density.md index f4a86d15..24c4c425 100644 --- a/docs/docs/api-reference/elements/material_density.md +++ b/docs/docs/api-reference/elements/material_density.md @@ -1,7 +1 @@ -# Material Density - - ::: easyreflectometry.sample.elements.materials.material_density - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/elements/material_mixture.md b/docs/docs/api-reference/elements/material_mixture.md index 1a523e60..899b28e8 100644 --- a/docs/docs/api-reference/elements/material_mixture.md +++ b/docs/docs/api-reference/elements/material_mixture.md @@ -1,7 +1 @@ -# Material Mixture - - ::: easyreflectometry.sample.elements.materials.material_mixture - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/elements/material_solvated.md b/docs/docs/api-reference/elements/material_solvated.md index e9b3711d..d89901e6 100644 --- a/docs/docs/api-reference/elements/material_solvated.md +++ b/docs/docs/api-reference/elements/material_solvated.md @@ -1,7 +1 @@ -# Material Solvated - - ::: easyreflectometry.sample.elements.materials.material_solvated - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/fitting.md b/docs/docs/api-reference/fitting.md index ca037cd3..88b465c9 100644 --- a/docs/docs/api-reference/fitting.md +++ b/docs/docs/api-reference/fitting.md @@ -1,7 +1 @@ -# Fitting - - ::: easyreflectometry.fitting - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/model.md b/docs/docs/api-reference/model.md index d3d3edfa..cbb1bbf9 100644 --- a/docs/docs/api-reference/model.md +++ b/docs/docs/api-reference/model.md @@ -1,7 +1 @@ -# Model - - ::: easyreflectometry.model.model - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/project.md b/docs/docs/api-reference/project.md index 962535b0..d778788c 100644 --- a/docs/docs/api-reference/project.md +++ b/docs/docs/api-reference/project.md @@ -1,7 +1 @@ -# Project - - ::: easyreflectometry.project - options: - members: true - show_inheritance: true diff --git a/docs/docs/api-reference/sample.md b/docs/docs/api-reference/sample.md index 48fe0da4..387cd62c 100644 --- a/docs/docs/api-reference/sample.md +++ b/docs/docs/api-reference/sample.md @@ -1,7 +1 @@ -# Sample - - ::: easyreflectometry.sample.collections.sample - options: - members: true - show_inheritance: true diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index cba16bbb..41eace41 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -148,8 +148,10 @@ plugins: annotations_path: source docstring_style: numpy group_by_category: true + members: true members_order: source heading_level: 1 + show_inheritance: true show_root_heading: true show_root_full_path: false show_submodules: true From fcb406abf740e55ad15952f4d881d62469e904f9 Mon Sep 17 00:00:00 2001 From: rozyczko Date: Tue, 12 May 2026 12:10:39 +0200 Subject: [PATCH 15/20] minor CR changes --- src/easyreflectometry/calculators/calculator_base.py | 2 +- src/easyreflectometry/calculators/wrapper_base.py | 3 ++- src/easyreflectometry/model/model.py | 12 ------------ src/easyreflectometry/model/model_collection.py | 7 ------- .../sample/assemblies/multilayer.py | 11 ----------- 5 files changed, 3 insertions(+), 32 deletions(-) diff --git a/src/easyreflectometry/calculators/calculator_base.py b/src/easyreflectometry/calculators/calculator_base.py index 263c601b..e2a92804 100644 --- a/src/easyreflectometry/calculators/calculator_base.py +++ b/src/easyreflectometry/calculators/calculator_base.py @@ -212,7 +212,7 @@ def sld_profile(self, model_id: str) -> tuple[np.ndarray, np.ndarray]: Returns ------- tuple[np.ndarray, np.ndarray] - Z and sld(z). + z and sld(z). """ return self._wrapper.sld_profile(model_id) diff --git a/src/easyreflectometry/calculators/wrapper_base.py b/src/easyreflectometry/calculators/wrapper_base.py index 1ad872d8..dc53ceca 100644 --- a/src/easyreflectometry/calculators/wrapper_base.py +++ b/src/easyreflectometry/calculators/wrapper_base.py @@ -203,9 +203,10 @@ def update_material(self, name: str, **kwargs): Parameters ---------- - **kwargs : name : str The name of the material. + **kwargs : + Key-value pairs of attributes to update. """ material = self.storage['material'][name] for key in kwargs.keys(): diff --git a/src/easyreflectometry/model/model.py b/src/easyreflectometry/model/model.py index aa67a043..1af4a086 100644 --- a/src/easyreflectometry/model/model.py +++ b/src/easyreflectometry/model/model.py @@ -275,18 +275,6 @@ def as_orso(self) -> dict: @classmethod def from_dict(cls, passed_dict: dict) -> Model: """Create a Model from a dictionary. - - Parameters - ---------- - passed_dict : dict - cls : - this_dict : - Dictionary of the Model. - - Returns - ------- - Model - Model. """ # Causes circular import if imported at the top from easyreflectometry.calculators import CalculatorFactory diff --git a/src/easyreflectometry/model/model_collection.py b/src/easyreflectometry/model/model_collection.py index a8ef1577..904abe1c 100644 --- a/src/easyreflectometry/model/model_collection.py +++ b/src/easyreflectometry/model/model_collection.py @@ -86,13 +86,6 @@ def as_dict(self, skip: List[str] | None = None) -> dict: @classmethod def from_dict(cls, this_dict: dict) -> ModelCollection: """Create an instance of a collection from a dictionary. - - Parameters - ---------- - this_dict : dict - cls : - data : - The dictionary for the collection. """ collection_dict = this_dict.copy() # We need to call from_dict on the base class to get the models diff --git a/src/easyreflectometry/sample/assemblies/multilayer.py b/src/easyreflectometry/sample/assemblies/multilayer.py index 0238f3ae..f20a9a72 100644 --- a/src/easyreflectometry/sample/assemblies/multilayer.py +++ b/src/easyreflectometry/sample/assemblies/multilayer.py @@ -116,17 +116,6 @@ def _dict_repr(self) -> dict: @classmethod def from_dict(cls, data: dict) -> Multilayer: """Create a Multilayer from a dictionary. - - Parameters - ---------- - cls : - data : dict - Dictionary of the Multilayer. - - Returns - ------- - Multilayer - Multilayer. """ multilayer = super().from_dict(data) return multilayer From 9469f334f2d9415130bbc5a72e2b5629809ea74a Mon Sep 17 00:00:00 2001 From: rozyczko Date: Tue, 12 May 2026 12:53:43 +0200 Subject: [PATCH 16/20] linting --- src/easyreflectometry/model/model.py | 3 +-- src/easyreflectometry/model/model_collection.py | 3 +-- src/easyreflectometry/sample/assemblies/multilayer.py | 3 +-- 3 files changed, 3 insertions(+), 6 deletions(-) diff --git a/src/easyreflectometry/model/model.py b/src/easyreflectometry/model/model.py index 1af4a086..4efc9e4e 100644 --- a/src/easyreflectometry/model/model.py +++ b/src/easyreflectometry/model/model.py @@ -274,8 +274,7 @@ def as_orso(self) -> dict: @classmethod def from_dict(cls, passed_dict: dict) -> Model: - """Create a Model from a dictionary. - """ + """Create a Model from a dictionary.""" # Causes circular import if imported at the top from easyreflectometry.calculators import CalculatorFactory diff --git a/src/easyreflectometry/model/model_collection.py b/src/easyreflectometry/model/model_collection.py index 904abe1c..1a1b7e88 100644 --- a/src/easyreflectometry/model/model_collection.py +++ b/src/easyreflectometry/model/model_collection.py @@ -85,8 +85,7 @@ def as_dict(self, skip: List[str] | None = None) -> dict: @classmethod def from_dict(cls, this_dict: dict) -> ModelCollection: - """Create an instance of a collection from a dictionary. - """ + """Create an instance of a collection from a dictionary.""" collection_dict = this_dict.copy() # We need to call from_dict on the base class to get the models dict_data = collection_dict.pop('data') diff --git a/src/easyreflectometry/sample/assemblies/multilayer.py b/src/easyreflectometry/sample/assemblies/multilayer.py index f20a9a72..9144b3a8 100644 --- a/src/easyreflectometry/sample/assemblies/multilayer.py +++ b/src/easyreflectometry/sample/assemblies/multilayer.py @@ -115,7 +115,6 @@ def _dict_repr(self) -> dict: @classmethod def from_dict(cls, data: dict) -> Multilayer: - """Create a Multilayer from a dictionary. - """ + """Create a Multilayer from a dictionary.""" multilayer = super().from_dict(data) return multilayer From addd2b8f018cc761c944595db33e0965da9e4b79 Mon Sep 17 00:00:00 2001 From: rozyczko Date: Tue, 12 May 2026 14:03:53 +0200 Subject: [PATCH 17/20] code review fixes --- docs/docs/tutorials/index.md | 14 ------- docs/docs/tutorials/tutorial.ipynb | 63 ------------------------------ docs/mkdocs.yml | 1 - 3 files changed, 78 deletions(-) delete mode 100644 docs/docs/tutorials/tutorial.ipynb diff --git a/docs/docs/tutorials/index.md b/docs/docs/tutorials/index.md index c15cc31d..7b59c331 100644 --- a/docs/docs/tutorials/index.md +++ b/docs/docs/tutorials/index.md @@ -13,20 +13,6 @@ Instructions on how to run the tutorials are provided in the [:material-cog-box: Installation & Setup](../installation-and-setup/index.md#how-to-run-tutorials) section of the documentation. -## Calculators and Optimisation - -EasyReflectometry is built on the EasyScience framework which -facilitates the use of a range of different reflectometry calculation -engines and optimiser solutions. Currently, EasyReflectometry can offer -two different calculation engines, namely: - -- [refnx](https://refnx.readthedocs.io/) -- [Refl1D](https://refl1d.readthedocs.io/en/latest/) - -And we are working to add more, in particular -[BornAgain](https://www.bornagainproject.org) and -[GenX](https://aglavic.github.io/genx/doc/). - ## Getting Started - [Creating a Model](basic/model.md) – Learn how to define a diff --git a/docs/docs/tutorials/tutorial.ipynb b/docs/docs/tutorials/tutorial.ipynb deleted file mode 100644 index 0ff94f42..00000000 --- a/docs/docs/tutorials/tutorial.ipynb +++ /dev/null @@ -1,63 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "0", - "metadata": {}, - "source": [ - "# Dummy Tutorial\n", - "\n", - "This is a dummy tutorial file to ensure that the tutorials section is\n", - "not empty. You can replace this file with actual tutorial content as\n", - "needed." - ] - }, - { - "cell_type": "markdown", - "id": "1", - "metadata": {}, - "source": [ - "## Import Library" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "2", - "metadata": {}, - "outputs": [], - "source": [ - "import easyreflectometry" - ] - }, - { - "cell_type": "markdown", - "id": "3", - "metadata": {}, - "source": [ - "## Step 1: Blah Blah Blah" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "4", - "metadata": {}, - "outputs": [], - "source": [ - "# This is a placeholder for tutorial content.\n", - "print('This is a dummy tutorial.')\n", - "print('Imported library:', easyreflectometry)" - ] - } - ], - "metadata": { - "jupytext": { - "cell_metadata_filter": "-all", - "main_language": "python", - "notebook_metadata_filter": "-all" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 41eace41..f75e4657 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -179,7 +179,6 @@ nav: - Tutorials: - Tutorials: tutorials/index.md - Getting Started: - - Dummy Tutorial: tutorials/tutorial.ipynb - Creating a Model: tutorials/basic/model.md - Defining Materials: tutorials/basic/material_library.md - Defining Layers: tutorials/basic/layer_library.md From 2da44723fa5034899637f57218ecae6101754273 Mon Sep 17 00:00:00 2001 From: rozyczko Date: Tue, 12 May 2026 14:28:32 +0200 Subject: [PATCH 18/20] CR fixes --- pixi.toml | 6 +++--- src/easyreflectometry/calculators/bornagain/calculator.py | 1 - src/easyreflectometry/calculators/bornagain/wrapper.py | 1 - src/easyreflectometry/calculators/refl1d/calculator.py | 1 - src/easyreflectometry/calculators/refl1d/wrapper.py | 1 - src/easyreflectometry/calculators/refnx/calculator.py | 1 - src/easyreflectometry/calculators/refnx/wrapper.py | 1 - src/easyreflectometry/data/measurement.py | 1 - src/easyreflectometry/fitting.py | 1 - src/easyreflectometry/model/model.py | 2 -- src/easyreflectometry/plot.py | 1 - .../sample/collections/layer_collection.py | 1 - .../sample/collections/material_collection.py | 2 +- src/easyreflectometry/sample/collections/sample.py | 2 -- src/easyreflectometry/sample/elements/layers/layer.py | 2 +- src/easyreflectometry/sample/elements/materials/material.py | 1 - src/easyreflectometry/special/calculations.py | 1 - src/easyreflectometry/special/parsing.py | 1 - tests/calculators/bornagain/test_bornagain_calculator.py | 1 - tests/calculators/bornagain/test_bornagain_wrapper.py | 1 - tests/calculators/refl1d/test_refl1d_calculator.py | 1 - tests/calculators/refl1d/test_refl1d_wrapper.py | 1 - tests/calculators/refnx/test_refnx_calculator.py | 1 - tests/calculators/refnx/test_refnx_wrapper.py | 1 - tests/model/test_model.py | 1 - tests/sample/assemblies/test_multilayer.py | 1 - tests/sample/assemblies/test_repeating_multilayer.py | 1 - tests/sample/assemblies/test_surfactant_layer.py | 1 - tests/sample/collections/test_layer_collection.py | 1 - tests/sample/collections/test_sample.py | 1 - tests/sample/elements/layers/test_layer.py | 1 - tests/sample/elements/materials/test_material.py | 1 - tests/special/test_calculations.py | 1 - tests/test_data.py | 2 +- tests/test_fitting.py | 1 - 35 files changed, 6 insertions(+), 39 deletions(-) diff --git a/pixi.toml b/pixi.toml index 4f4faaf9..6624ccbe 100644 --- a/pixi.toml +++ b/pixi.toml @@ -95,7 +95,7 @@ user = { features = ['py-max', 'user'] } unit-tests = 'python -m pytest tests/unit/ --color=yes -v' functional-tests = 'python -m pytest tests/functional/ --color=yes -v' integration-tests = 'python -m pytest tests/integration/ --color=yes -n auto -v' -notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --color=yes -n auto -v' +notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/* --nbmake-timeout=1200 --color=yes -n auto -v' test = { depends-on = ['unit-tests'] } @@ -167,8 +167,8 @@ cov = { depends-on = [ ######################## notebook-convert = 'jupytext docs/docs/tutorials/*.py --from py:percent --to ipynb' -notebook-strip = 'nbstripout docs/docs/tutorials/*.ipynb' -notebook-tweak = 'python tools/tweak_notebooks.py docs/docs/tutorials/' +notebook-strip = 'nbstripout docs/docs/tutorials/**/*.ipynb' +notebook-tweak = 'python tools/tweak_notebooks.py docs/docs/tutorials/**/*.ipynb' notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --overwrite --color=yes -n auto -v' notebook-prepare = { depends-on = [ diff --git a/src/easyreflectometry/calculators/bornagain/calculator.py b/src/easyreflectometry/calculators/bornagain/calculator.py index 27fcfff3..2ebb2c08 100644 --- a/src/easyreflectometry/calculators/bornagain/calculator.py +++ b/src/easyreflectometry/calculators/bornagain/calculator.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' from easyscience.fitting.calculators.interface_factory import ItemContainer diff --git a/src/easyreflectometry/calculators/bornagain/wrapper.py b/src/easyreflectometry/calculators/bornagain/wrapper.py index 8dc2fe33..b0baf9a9 100644 --- a/src/easyreflectometry/calculators/bornagain/wrapper.py +++ b/src/easyreflectometry/calculators/bornagain/wrapper.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' import bornagain as ba import numpy as np diff --git a/src/easyreflectometry/calculators/refl1d/calculator.py b/src/easyreflectometry/calculators/refl1d/calculator.py index 5532a0fd..2f5068de 100644 --- a/src/easyreflectometry/calculators/refl1d/calculator.py +++ b/src/easyreflectometry/calculators/refl1d/calculator.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' from ..calculator_base import CalculatorBase from .wrapper import Refl1dWrapper diff --git a/src/easyreflectometry/calculators/refl1d/wrapper.py b/src/easyreflectometry/calculators/refl1d/wrapper.py index 78cac9a8..7a07c917 100644 --- a/src/easyreflectometry/calculators/refl1d/wrapper.py +++ b/src/easyreflectometry/calculators/refl1d/wrapper.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' from typing import Tuple diff --git a/src/easyreflectometry/calculators/refnx/calculator.py b/src/easyreflectometry/calculators/refnx/calculator.py index defe40ae..1362bad2 100644 --- a/src/easyreflectometry/calculators/refnx/calculator.py +++ b/src/easyreflectometry/calculators/refnx/calculator.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' from ..calculator_base import CalculatorBase from .wrapper import RefnxWrapper diff --git a/src/easyreflectometry/calculators/refnx/wrapper.py b/src/easyreflectometry/calculators/refnx/wrapper.py index 345e902a..3742d727 100644 --- a/src/easyreflectometry/calculators/refnx/wrapper.py +++ b/src/easyreflectometry/calculators/refnx/wrapper.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' from typing import Tuple diff --git a/src/easyreflectometry/data/measurement.py b/src/easyreflectometry/data/measurement.py index 5de8df1f..12117162 100644 --- a/src/easyreflectometry/data/measurement.py +++ b/src/easyreflectometry/data/measurement.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' import os from typing import TextIO diff --git a/src/easyreflectometry/fitting.py b/src/easyreflectometry/fitting.py index 83e5efed..78f74e68 100644 --- a/src/easyreflectometry/fitting.py +++ b/src/easyreflectometry/fitting.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' import warnings diff --git a/src/easyreflectometry/model/model.py b/src/easyreflectometry/model/model.py index 4efc9e4e..b1aedf85 100644 --- a/src/easyreflectometry/model/model.py +++ b/src/easyreflectometry/model/model.py @@ -3,8 +3,6 @@ from __future__ import annotations -__author__ = 'github.com/arm61' - import copy from numbers import Number from typing import Optional diff --git a/src/easyreflectometry/plot.py b/src/easyreflectometry/plot.py index 28285e24..3a0aaa26 100644 --- a/src/easyreflectometry/plot.py +++ b/src/easyreflectometry/plot.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' import matplotlib.pyplot as plt import scipp as sc diff --git a/src/easyreflectometry/sample/collections/layer_collection.py b/src/easyreflectometry/sample/collections/layer_collection.py index 4a9e5791..99424f72 100644 --- a/src/easyreflectometry/sample/collections/layer_collection.py +++ b/src/easyreflectometry/sample/collections/layer_collection.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' from typing import Optional diff --git a/src/easyreflectometry/sample/collections/material_collection.py b/src/easyreflectometry/sample/collections/material_collection.py index 6ae49692..d7b5af3b 100644 --- a/src/easyreflectometry/sample/collections/material_collection.py +++ b/src/easyreflectometry/sample/collections/material_collection.py @@ -1,7 +1,7 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' + from typing import Optional from typing import Tuple diff --git a/src/easyreflectometry/sample/collections/sample.py b/src/easyreflectometry/sample/collections/sample.py index 73d26e8a..1bbdb156 100644 --- a/src/easyreflectometry/sample/collections/sample.py +++ b/src/easyreflectometry/sample/collections/sample.py @@ -3,8 +3,6 @@ from __future__ import annotations -__author__ = 'github.com/arm61' - from typing import List from typing import Optional diff --git a/src/easyreflectometry/sample/elements/layers/layer.py b/src/easyreflectometry/sample/elements/layers/layer.py index 8b824ed8..fa58dc15 100644 --- a/src/easyreflectometry/sample/elements/layers/layer.py +++ b/src/easyreflectometry/sample/elements/layers/layer.py @@ -1,7 +1,7 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' + from typing import Optional from typing import Union diff --git a/src/easyreflectometry/sample/elements/materials/material.py b/src/easyreflectometry/sample/elements/materials/material.py index 39bb8f77..42091bd6 100644 --- a/src/easyreflectometry/sample/elements/materials/material.py +++ b/src/easyreflectometry/sample/elements/materials/material.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' from typing import Optional from typing import Union diff --git a/src/easyreflectometry/special/calculations.py b/src/easyreflectometry/special/calculations.py index 62a4006b..07844d3c 100644 --- a/src/easyreflectometry/special/calculations.py +++ b/src/easyreflectometry/special/calculations.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' import periodictable as pt diff --git a/src/easyreflectometry/special/parsing.py b/src/easyreflectometry/special/parsing.py index 48e9b463..fd0cd576 100644 --- a/src/easyreflectometry/special/parsing.py +++ b/src/easyreflectometry/special/parsing.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' import re from typing import Tuple diff --git a/tests/calculators/bornagain/test_bornagain_calculator.py b/tests/calculators/bornagain/test_bornagain_calculator.py index 7497445d..10a15f27 100644 --- a/tests/calculators/bornagain/test_bornagain_calculator.py +++ b/tests/calculators/bornagain/test_bornagain_calculator.py @@ -5,7 +5,6 @@ Tests for BornAgain calculator. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' # import os diff --git a/tests/calculators/bornagain/test_bornagain_wrapper.py b/tests/calculators/bornagain/test_bornagain_wrapper.py index ce4646ed..5995f401 100644 --- a/tests/calculators/bornagain/test_bornagain_wrapper.py +++ b/tests/calculators/bornagain/test_bornagain_wrapper.py @@ -5,7 +5,6 @@ Tests for the BornAgain wrapper. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' diff --git a/tests/calculators/refl1d/test_refl1d_calculator.py b/tests/calculators/refl1d/test_refl1d_calculator.py index f2c4d2b1..98f4151b 100644 --- a/tests/calculators/refl1d/test_refl1d_calculator.py +++ b/tests/calculators/refl1d/test_refl1d_calculator.py @@ -5,7 +5,6 @@ Tests for Refnx calculator. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' import unittest diff --git a/tests/calculators/refl1d/test_refl1d_wrapper.py b/tests/calculators/refl1d/test_refl1d_wrapper.py index 9546205b..28366db4 100644 --- a/tests/calculators/refl1d/test_refl1d_wrapper.py +++ b/tests/calculators/refl1d/test_refl1d_wrapper.py @@ -5,7 +5,6 @@ Tests for Refl1d wrapper. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' import unittest diff --git a/tests/calculators/refnx/test_refnx_calculator.py b/tests/calculators/refnx/test_refnx_calculator.py index b29899c5..94b7937f 100644 --- a/tests/calculators/refnx/test_refnx_calculator.py +++ b/tests/calculators/refnx/test_refnx_calculator.py @@ -5,7 +5,6 @@ Tests for Refnx calculator. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' import unittest diff --git a/tests/calculators/refnx/test_refnx_wrapper.py b/tests/calculators/refnx/test_refnx_wrapper.py index 0cf13628..a7c96251 100644 --- a/tests/calculators/refnx/test_refnx_wrapper.py +++ b/tests/calculators/refnx/test_refnx_wrapper.py @@ -5,7 +5,6 @@ Tests for Refnx wrapper. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' diff --git a/tests/model/test_model.py b/tests/model/test_model.py index 594ebaf7..7935c273 100644 --- a/tests/model/test_model.py +++ b/tests/model/test_model.py @@ -5,7 +5,6 @@ Tests for Model class. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' import unittest diff --git a/tests/sample/assemblies/test_multilayer.py b/tests/sample/assemblies/test_multilayer.py index 42be8584..b2990c6f 100644 --- a/tests/sample/assemblies/test_multilayer.py +++ b/tests/sample/assemblies/test_multilayer.py @@ -5,7 +5,6 @@ Tests for MultiLayer class module """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' import unittest diff --git a/tests/sample/assemblies/test_repeating_multilayer.py b/tests/sample/assemblies/test_repeating_multilayer.py index 6e00ea71..8e9ec806 100644 --- a/tests/sample/assemblies/test_repeating_multilayer.py +++ b/tests/sample/assemblies/test_repeating_multilayer.py @@ -5,7 +5,6 @@ Tests for RepeatingMultiLayer module """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' diff --git a/tests/sample/assemblies/test_surfactant_layer.py b/tests/sample/assemblies/test_surfactant_layer.py index 8205201f..136426ba 100644 --- a/tests/sample/assemblies/test_surfactant_layer.py +++ b/tests/sample/assemblies/test_surfactant_layer.py @@ -5,7 +5,6 @@ Tests for SurfactantLayer class module """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' diff --git a/tests/sample/collections/test_layer_collection.py b/tests/sample/collections/test_layer_collection.py index d8f475d5..dc03c680 100644 --- a/tests/sample/collections/test_layer_collection.py +++ b/tests/sample/collections/test_layer_collection.py @@ -5,7 +5,6 @@ Tests for LayerCollection class. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' import unittest diff --git a/tests/sample/collections/test_sample.py b/tests/sample/collections/test_sample.py index 1f00614e..f71196d0 100644 --- a/tests/sample/collections/test_sample.py +++ b/tests/sample/collections/test_sample.py @@ -5,7 +5,6 @@ Tests for Sample class. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' diff --git a/tests/sample/elements/layers/test_layer.py b/tests/sample/elements/layers/test_layer.py index 818abe21..44629f54 100644 --- a/tests/sample/elements/layers/test_layer.py +++ b/tests/sample/elements/layers/test_layer.py @@ -5,7 +5,6 @@ Tests for Layer class. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' import unittest diff --git a/tests/sample/elements/materials/test_material.py b/tests/sample/elements/materials/test_material.py index 584d942f..fd73211a 100644 --- a/tests/sample/elements/materials/test_material.py +++ b/tests/sample/elements/materials/test_material.py @@ -5,7 +5,6 @@ Tests for Material class. """ -__author__ = 'github.com/arm61' __version__ = '0.0.1' from easyscience import global_object diff --git a/tests/special/test_calculations.py b/tests/special/test_calculations.py index 1c963ce3..10ca1ca1 100644 --- a/tests/special/test_calculations.py +++ b/tests/special/test_calculations.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2022 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' import unittest diff --git a/tests/test_data.py b/tests/test_data.py index c9cb7899..397066e2 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -1,7 +1,7 @@ # SPDX-FileCopyrightText: 2022 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' + __version__ = '0.0.1' import os diff --git a/tests/test_fitting.py b/tests/test_fitting.py index 94056544..28dfe0fa 100644 --- a/tests/test_fitting.py +++ b/tests/test_fitting.py @@ -1,7 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -__author__ = 'github.com/arm61' import os from unittest.mock import MagicMock From 4a0a1d805148040faddaf2b51a5537fa163e8d8b Mon Sep 17 00:00:00 2001 From: rozyczko Date: Tue, 12 May 2026 14:38:53 +0200 Subject: [PATCH 19/20] proper globbing --- pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.toml b/pixi.toml index 6624ccbe..b0fb2b8d 100644 --- a/pixi.toml +++ b/pixi.toml @@ -95,7 +95,7 @@ user = { features = ['py-max', 'user'] } unit-tests = 'python -m pytest tests/unit/ --color=yes -v' functional-tests = 'python -m pytest tests/functional/ --color=yes -v' integration-tests = 'python -m pytest tests/integration/ --color=yes -n auto -v' -notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/* --nbmake-timeout=1200 --color=yes -n auto -v' +notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/**/ --nbmake-timeout=1200 --color=yes -n auto -v' test = { depends-on = ['unit-tests'] } From 5e52bd750eaad7fac74819e4d4c405a9de630dfd Mon Sep 17 00:00:00 2001 From: rozyczko Date: Tue, 12 May 2026 15:08:42 +0200 Subject: [PATCH 20/20] remove __version__ --- tests/calculators/bornagain/test_bornagain_calculator.py | 1 - tests/calculators/bornagain/test_bornagain_wrapper.py | 2 -- tests/calculators/refl1d/test_refl1d_calculator.py | 2 -- tests/calculators/refl1d/test_refl1d_wrapper.py | 2 -- tests/calculators/refnx/test_refnx_calculator.py | 2 -- tests/calculators/refnx/test_refnx_wrapper.py | 3 --- tests/model/test_model.py | 2 -- tests/sample/assemblies/test_bilayer.py | 1 - tests/sample/assemblies/test_multilayer.py | 2 -- tests/sample/assemblies/test_repeating_multilayer.py | 3 --- tests/sample/assemblies/test_surfactant_layer.py | 3 --- tests/sample/collections/test_layer_collection.py | 2 -- tests/sample/collections/test_sample.py | 3 --- tests/sample/elements/layers/test_layer.py | 2 -- tests/sample/elements/materials/test_material.py | 2 -- tests/test_data.py | 2 -- 16 files changed, 34 deletions(-) diff --git a/tests/calculators/bornagain/test_bornagain_calculator.py b/tests/calculators/bornagain/test_bornagain_calculator.py index 10a15f27..6a7c1aa9 100644 --- a/tests/calculators/bornagain/test_bornagain_calculator.py +++ b/tests/calculators/bornagain/test_bornagain_calculator.py @@ -5,7 +5,6 @@ Tests for BornAgain calculator. """ -__version__ = '0.0.1' # import os # import unittest diff --git a/tests/calculators/bornagain/test_bornagain_wrapper.py b/tests/calculators/bornagain/test_bornagain_wrapper.py index 5995f401..c52c084c 100644 --- a/tests/calculators/bornagain/test_bornagain_wrapper.py +++ b/tests/calculators/bornagain/test_bornagain_wrapper.py @@ -5,8 +5,6 @@ Tests for the BornAgain wrapper. """ -__version__ = '0.0.1' - # import unittest # import numpy as np diff --git a/tests/calculators/refl1d/test_refl1d_calculator.py b/tests/calculators/refl1d/test_refl1d_calculator.py index 98f4151b..50de2db4 100644 --- a/tests/calculators/refl1d/test_refl1d_calculator.py +++ b/tests/calculators/refl1d/test_refl1d_calculator.py @@ -5,8 +5,6 @@ Tests for Refnx calculator. """ -__version__ = '0.0.1' - import unittest import numpy as np diff --git a/tests/calculators/refl1d/test_refl1d_wrapper.py b/tests/calculators/refl1d/test_refl1d_wrapper.py index 28366db4..57c43ee8 100644 --- a/tests/calculators/refl1d/test_refl1d_wrapper.py +++ b/tests/calculators/refl1d/test_refl1d_wrapper.py @@ -5,8 +5,6 @@ Tests for Refl1d wrapper. """ -__version__ = '0.0.1' - import unittest from unittest.mock import MagicMock from unittest.mock import patch diff --git a/tests/calculators/refnx/test_refnx_calculator.py b/tests/calculators/refnx/test_refnx_calculator.py index 94b7937f..baeb9296 100644 --- a/tests/calculators/refnx/test_refnx_calculator.py +++ b/tests/calculators/refnx/test_refnx_calculator.py @@ -5,8 +5,6 @@ Tests for Refnx calculator. """ -__version__ = '0.0.1' - import unittest import numpy as np diff --git a/tests/calculators/refnx/test_refnx_wrapper.py b/tests/calculators/refnx/test_refnx_wrapper.py index a7c96251..f9d2a4cc 100644 --- a/tests/calculators/refnx/test_refnx_wrapper.py +++ b/tests/calculators/refnx/test_refnx_wrapper.py @@ -5,9 +5,6 @@ Tests for Refnx wrapper. """ -__version__ = '0.0.1' - - import unittest import numpy as np diff --git a/tests/model/test_model.py b/tests/model/test_model.py index 7935c273..2d623512 100644 --- a/tests/model/test_model.py +++ b/tests/model/test_model.py @@ -5,8 +5,6 @@ Tests for Model class. """ -__version__ = '0.0.1' - import unittest from unittest.mock import MagicMock diff --git a/tests/sample/assemblies/test_bilayer.py b/tests/sample/assemblies/test_bilayer.py index e10659be..03949ee7 100644 --- a/tests/sample/assemblies/test_bilayer.py +++ b/tests/sample/assemblies/test_bilayer.py @@ -6,7 +6,6 @@ """ __author__ = 'github.com/easyscience' -__version__ = '0.0.1' from easyscience import global_object diff --git a/tests/sample/assemblies/test_multilayer.py b/tests/sample/assemblies/test_multilayer.py index b2990c6f..f2d7bd61 100644 --- a/tests/sample/assemblies/test_multilayer.py +++ b/tests/sample/assemblies/test_multilayer.py @@ -5,8 +5,6 @@ Tests for MultiLayer class module """ -__version__ = '0.0.1' - import unittest from easyscience import global_object diff --git a/tests/sample/assemblies/test_repeating_multilayer.py b/tests/sample/assemblies/test_repeating_multilayer.py index 8e9ec806..3ee2858b 100644 --- a/tests/sample/assemblies/test_repeating_multilayer.py +++ b/tests/sample/assemblies/test_repeating_multilayer.py @@ -5,9 +5,6 @@ Tests for RepeatingMultiLayer module """ -__version__ = '0.0.1' - - import unittest from easyscience import global_object diff --git a/tests/sample/assemblies/test_surfactant_layer.py b/tests/sample/assemblies/test_surfactant_layer.py index 136426ba..62b92689 100644 --- a/tests/sample/assemblies/test_surfactant_layer.py +++ b/tests/sample/assemblies/test_surfactant_layer.py @@ -5,9 +5,6 @@ Tests for SurfactantLayer class module """ -__version__ = '0.0.1' - - import unittest from easyscience import global_object diff --git a/tests/sample/collections/test_layer_collection.py b/tests/sample/collections/test_layer_collection.py index dc03c680..7eb8071b 100644 --- a/tests/sample/collections/test_layer_collection.py +++ b/tests/sample/collections/test_layer_collection.py @@ -5,8 +5,6 @@ Tests for LayerCollection class. """ -__version__ = '0.0.1' - import unittest from easyscience import global_object diff --git a/tests/sample/collections/test_sample.py b/tests/sample/collections/test_sample.py index f71196d0..6f64dd25 100644 --- a/tests/sample/collections/test_sample.py +++ b/tests/sample/collections/test_sample.py @@ -5,9 +5,6 @@ Tests for Sample class. """ -__version__ = '0.0.1' - - import pytest from easyscience import global_object from numpy.testing import assert_equal diff --git a/tests/sample/elements/layers/test_layer.py b/tests/sample/elements/layers/test_layer.py index 44629f54..26a5cf0a 100644 --- a/tests/sample/elements/layers/test_layer.py +++ b/tests/sample/elements/layers/test_layer.py @@ -5,8 +5,6 @@ Tests for Layer class. """ -__version__ = '0.0.1' - import unittest import numpy as np diff --git a/tests/sample/elements/materials/test_material.py b/tests/sample/elements/materials/test_material.py index fd73211a..997102a4 100644 --- a/tests/sample/elements/materials/test_material.py +++ b/tests/sample/elements/materials/test_material.py @@ -5,8 +5,6 @@ Tests for Material class. """ -__version__ = '0.0.1' - from easyscience import global_object from easyreflectometry.sample.elements.materials.material import DEFAULTS diff --git a/tests/test_data.py b/tests/test_data.py index 397066e2..d08402f2 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -2,8 +2,6 @@ # SPDX-License-Identifier: BSD-3-Clause -__version__ = '0.0.1' - import os import unittest