Merge pull request #79 from lycosystem/release-1.0.0

Release 1.0.0

Author: rmnldwg

CHANGELOG.md

@@ -2,6 +2,44 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.0.0] - 2025-09-04
+
+### Bug Fixes
+
+- Change `info` to `core` for mid-level lydata columns
+- Use bug-fixed lydata `.ly.enhance()` method.
+
+### Documentation
+
+- Update documentation for `integrate` and `evidence` commands.
+- Improve `data collect` description.
+
+### Features
+
+- Add `integrate` command for thermodynamic integration. Thanks [@noemibuehrer]!
+- Add command spawning websever for interactive data collection.
+
+### Miscellaneous Tasks
+
+- Add missing links to changelog.
+- Add CITATION.cff.
+
+### Testing
+
+- Update tests for new lydata.
+
+### Build
+
+- Add uvicorn, fastapi to deps.
+- Require at least lydata 0.4.0.
+
+### Change
+
+- Make compatible with new lyDATA version.
+- Centralize inverse temperature schedule generation.
+- Store selected log-level globally.
+- Disable properties in collector.
+
 ## [1.0.0rc3] - 2025-07-22
 
 ### Documentation
@@ -356,7 +394,7 @@ over diagnosis times cannot be converted to a `DistributionConfig`.
   BREAKING CHANGES: `generate` command is better configurable
 - (**config**) Merge sample/sampling configs.
 - Use lydata's `ModalityConfig`.\
-  Since the [lydata](https://github.com/rmnldwg/lydata) package is
+  Since the [lydata](https://github.com/lycosystem/lydata) package is
   evolving quickly, I added it as a dependency and moved the first bit of
   code over there.
 - Enable use of lydata to load patient data.
@@ -871,6 +909,8 @@ returns `None` instead. Fixes [#11]
 ## [0.5.3] - 2022-08-22
 
 <!-- markdownlint-disable-file MD024 -->
+[1.0.0]: https://github.com/lycosystem/lyscripts/compare/1.0.0rc3...1.0.0
+[1.0.0rc3]: https://github.com/lycosystem/lyscripts/compare/1.0.0rc2...1.0.0rc3
 [1.0.0rc2]: https://github.com/lycosystem/lyscripts/compare/1.0.0rc1...1.0.0rc2
 [1.0.0rc1]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a7...1.0.0rc1
 [1.0.0.a7]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a6...1.0.0.a7
@@ -931,8 +971,10 @@ returns `None` instead. Fixes [#11]
 [#70]: https://github.com/lycosystem/lyscripts/issues/70
 [#72]: https://github.com/lycosystem/lyscripts/issues/72
 [#74]: https://github.com/lycosystem/lyscripts/issues/74
+[#75]: https://github.com/lycosystem/lyscripts/issues/75
 
 [`emcee`]: https://emcee.readthedocs.io/en/stable/
 [`rich`]: https://rich.readthedocs.io/en/latest/
 [`rich_argparse`]: https://github.com/hamdanal/rich_argparse
 [LyProX]: https://lyprox.org
+[@noemibuehrer]: https://github.com/noemibuehrer

CITATION.cff

@@ -0,0 +1,25 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: lyscripts
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Roman
+    family-names: Ludwig
+    orcid: 'https://orcid.org/0000-0001-9434-328X'
+    affiliation: University Hospital Zurich
+repository-code: 'https://github.com/lycosystem/lyscripts'
+url: 'https://lyscripts.readthedocs.io'
+abstract: >-
+  Scripts for reproducible research on lymphatic tumor
+  progression in head and neck cancer.
+keywords:
+  - cancer
+  - metastasis
+  - lymphatic system
+  - head and neck
+license: MIT

README.md

@@ -9,7 +9,7 @@
 
 ## What are these `lyscripts`?
 
-This package provides convenient scripts for performing inference and learning regarding the lymphatic spread of head & neck cancer. Essentially, it provides a *command line interface* (CLI) to the [lymph](https://github.com/lycosystem/lymph) library and the [lydata](https://github.com/rmnldwg/lydata) repository that stores lymphatic progression data.
+This package provides convenient scripts for performing inference and learning regarding the lymphatic spread of head & neck cancer. Essentially, it provides a *command line interface* (CLI) to the [lymph](https://github.com/lycosystem/lymph) library and the [lydata](https://github.com/lycosystem/lydata) repository that stores lymphatic progression data.
 
 We are making these "convenience" scripts public, because doing so is one necessary requirement to making our research easily and fully reproducible. There exists another repository, [lynference](https://github.com/lycosystem/lynference), where we stored the pipelines that produced our published results in a persistent way.
 
@@ -41,7 +41,11 @@ Simply run
 lyscripts --help
 ```
 
-in your terminal and let the output guide you through the functions of the program.
+in your terminal to display the help text for the main command. It will list all subcommands that are avialable, which you can then also call with `lyscripts <subcommand> --help` to get more information on its use and the available arguments.
+
+For example, one subcommand is `lyscripts data collect`, which will launch a small web server that allows a user to enter patient records on lymphatic involvement in head and neck cancer one row at a time and construct a standardized CSV file from it.
+
+<!--- ### --->
 
 You can also refer to the [documentation] for a written-down version of all these help texts and even more context on how and why to use the provided commands.
 

docs/source/data/collect.rst

@@ -0,0 +1,13 @@
+.. currentmodule:: lyscripts.data.collect
+
+Collect lyDATA Tables Interactively
+===================================
+
+.. automodule:: lyscripts.data.collect
+    :members:
+    :show-inheritance:
+
+Command Help
+------------
+
+.. program-output:: lyscripts data collect --help

docs/source/data/init.rst

@@ -19,6 +19,7 @@ Submodules
 .. toctree::
     :maxdepth: 1
 
+    collect
     lyproxify
     join
     split

docs/source/index.rst

@@ -8,7 +8,7 @@ Introduction
 
 
 .. include:: ../../README.md
-    :end-line: 30
+    :end-before: <!--- ### --->
     :parser: myst_parser.sphinx_
 
 

pyproject.toml

@@ -50,8 +50,10 @@ dependencies = [
     "pydantic",
     "pydantic-settings >= 2.7.0, != 2.9.1, != 2.9.0",
     "numpydantic",
-    "lydata >= 0.3.3",
     "loguru",
+    "fastapi",
+    "uvicorn",
+    "lydata >= 0.4.0",
 ]
 dynamic = ["version"]
 
@@ -81,9 +83,18 @@ dev = [
 [project.scripts]
 lyscripts = "lyscripts:main"
 
+[tool.setuptools]
+include-package-data = true
+
 [tool.setuptools.packages.find]
 where = ["src"]
 
+[tool.setuptools.package-data]
+"lyscripts" = [
+    "src/lyscripts/data/collect/collector.js",
+    "src/lyscripts/data/collect/index.html",
+]
+
 [tool.setuptools_scm]
 write_to = "src/lyscripts/_version.py"
 local_scheme = "no-local-version"
@@ -191,10 +202,7 @@ skip_tags = "v0.1.0-beta.1"
 ignore_tags = ""
 # sort the tags topologically
 topo_order = false
-# sort the commits inside sections by oldest/newest order
-sort_commits = "oldest"
-
-[tool.uv.sources]
-lydata = { path = "../lydata-package", editable = true }
 # limit the number of commits included in the changelog.
 # limit_commits = 42
+# sort the commits inside sections by oldest/newest order
+sort_commits = "oldest"

schemas/ly.json

@@ -308,18 +308,46 @@
           "type": "string"
         },
         "repo_name": {
-          "default": "rmnldwg/lydata",
+          "anyOf": [
+            {
+              "minLength": 1,
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": "lycosystem/lydata",
           "description": "GitHub `repository/owner`.",
-          "minLength": 1,
-          "title": "Repo Name",
-          "type": "string"
+          "title": "Repo Name"
         },
         "ref": {
+          "anyOf": [
+            {
+              "minLength": 1,
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
           "default": "main",
           "description": "Branch/tag/commit of the repo.",
-          "minLength": 1,
-          "title": "Ref",
-          "type": "string"
+          "title": "Ref"
+        },
+        "local_dataset_dir": {
+          "anyOf": [
+            {
+              "format": "directory-path",
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "description": "Path to directory containing all the dataset subdirectories. So, e.g. if `path_on_disk` is `~/datasets` and the dataset is `2023-clb-multisite`, then the CSV file is expected to be at `~/datasets/2023-clb-multisite/data.csv`.",
+          "title": "Local Dataset Dir"
         }
       },
       "required": [
@@ -501,6 +529,19 @@
           "title": "Relative Thresh",
           "type": "number"
         },
+        "burnin_steps": {
+          "anyOf": [
+            {
+              "type": "integer"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "description": "Number of burn-in steps to take. If None, burn-in runs until convergence.",
+          "title": "Burnin Steps"
+        },
         "num_steps": {
           "anyOf": [
             {
@@ -623,6 +664,52 @@
       ],
       "title": "ScenarioConfig",
       "type": "object"
+    },
+    "ScheduleConfig": {
+      "description": "Configuration for generating a schedule of inverse temperatures.",
+      "properties": {
+        "method": {
+          "default": "power",
+          "description": "Method to generate the inverse temperature schedule.",
+          "enum": [
+            "geometric",
+            "linear",
+            "power"
+          ],
+          "title": "Method",
+          "type": "string"
+        },
+        "num": {
+          "default": 32,
+          "description": "Number of inverse temperatures in the schedule.",
+          "title": "Num",
+          "type": "integer"
+        },
+        "power": {
+          "default": 4.0,
+          "description": "If a power schedule is chosen, use this as power.",
+          "title": "Power",
+          "type": "number"
+        },
+        "values": {
+          "anyOf": [
+            {
+              "items": {
+                "type": "number"
+              },
+              "type": "array"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "description": "List of inverse temperatures to use instead of generating a schedule. If a list is provided, the other parameters are ignored.",
+          "title": "Values"
+        }
+      },
+      "title": "ScheduleConfig",
+      "type": "object"
     }
   },
   "description": "Settings for generating a JSON schema for lyscripts configuration files.",
@@ -685,6 +772,10 @@
       },
       "title": "Scenarios",
       "type": "array"
+    },
+    "schedule": {
+      "$ref": "#/$defs/ScheduleConfig",
+      "default": null
     }
   },
   "required": [

src/lyscripts/__init__.py

@@ -17,7 +17,7 @@
     CliSubCommand,
 )
 
-from lyscripts import compute, data, sample, schedule  # noqa: F401
+from lyscripts import compute, data, integrate, sample, schedule  # noqa: F401
 from lyscripts._version import version
 from lyscripts.cli import assemble_main, configure_logging
 from lyscripts.utils import console
@@ -51,6 +51,7 @@ class LyscriptsCLI(BaseSettings):
     sample: CliSubCommand[sample.SampleCLI]
     compute: CliSubCommand[compute.ComputeCLI]
     schedule: CliSubCommand[schedule.ScheduleCLI]
+    integrate: CliSubCommand[integrate.IntegrateCLI]
 
     def __init__(self, **kwargs):
         """Add logging configuration to the lyscripts CLI."""