ENM Base class

.github/workflows/deploy.yml

@@ -2,62 +2,54 @@ name: Building and deploying Springcraft
 
 on:
   release:
-    types: 
-    - published
+    types:
+      - published
   workflow_dispatch: {}
 
 jobs:
-  build-distribution:
-    name: Building distribution
-
+  build-dist:
+    name: Build distribution
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-
     steps:
-      - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
         with:
-          activate-environment: springcraft-dev
-          auto-update-conda: true
-          python-version:"3.12"
-      - name: Installing dependencies
-        run: conda install -c conda-forge poetry
-      - name: Building distributions
-        run: poetry build
-      - uses: actions/upload-artifact@v4
+          python-version: "3.12"
+          cache: "pip"
+          cache-dependency-path: "pyproject.toml"
+      - name: Install hatch
+        run: pip install hatch
+      - name: Build dist
+        run: hatch build
+      - uses: actions/upload-artifact@v7
         with:
-          name: Springcraft distribution
+          name: release-dist
           path: dist/*
           if-no-files-found: error
-
-
-  build-doc:
+
+  build-docs:
     name: Building documentation
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
-
     steps:
-      - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/checkout@v6
+      - uses: conda-incubator/setup-miniconda@v4
         with:
-          activate-environment: springcraft-dev
-          auto-update-conda: true
-          python-version:"3.12"
+          miniforge-version: latest
           environment-file: environment.yml
+          activate-environment: springcraft-docs
           mamba-version: "*"
       - name: Installing Springcraft
-        run: pip install .
+        run: pip install .[docs]
       - name: Building documentation
-        run: sphinx-build ./doc ./build/doc
+        run: sphinx-build doc build/doc
       - name: Zipping documentation
-        run: cd ./build; zip -r doc.zip doc; cd ..
-      - uses: actions/upload-artifact@v4
+        run: cd build; zip -r doc.zip doc; cd ..
+      - uses: actions/upload-artifact@v7
         with:
-          name: Springcraft documentation
+          name: release-doc
           path: build/doc.zip
           if-no-files-found: error
 
@@ -67,25 +59,27 @@ jobs:
       contents: write
       id-token: write
     needs:
-    - lint
-    - test
+      - build-dist
+      - build-docs
     runs-on: ubuntu-latest
     environment:
       name: publish
       url: https://pypi.org/project/springcraft/
     steps:
-    - uses: actions/download-artifact@v4
-      with:
-        pattern: release-*
-        merge-multiple: true
-        path: dist
-    - name: List distributions to be uploaded
-      run: ls dist
-    - name: Upload to GitHub Releases
-      uses: softprops/action-gh-release@v2.0.5
-      if: github.event_name == 'release' && github.event.action == 'published'
-      with:
-        files: dist/*
-    - name: Upload to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-      if: github.event_name == 'release' && github.event.action == 'published'
+      - uses: actions/checkout@v6
+      - uses: actions/download-artifact@v8
+        with:
+          pattern: release-*
+          merge-multiple: true
+          path: dist
+      - name: List distributions to be uploaded
+        run: ls dist
+      - name: Upload to GitHub Releases
+        if: github.event_name == 'release' && github.event.action == 'published'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh release upload ${{ github.event.release.tag_name }} dist/* --clobber
+      - name: Upload to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        if: github.event_name == 'release' && github.event.action == 'published'

.github/workflows/test.yml

@@ -1,42 +1,38 @@
 name: Testing Springcraft
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
 
 jobs:
   lint:
     name: Check code style
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: "3.12"
-    - name: Install ruff
-      run: pip install ruff==0.5.2
-    - name: Check code formatting
-      run: ruff format --diff
-    - name: Lint code base
-      run: ruff check
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+          cache: "pip"
+          cache-dependency-path: "pyproject.toml"
+      - name: Install Hatch
+        run: pip install hatch
+      - name: Run linting
+        run: hatch run lint:run
+
   test:
     name: Testing
-
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-
     steps:
-      - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
         with:
-          activate-environment: springcraft-dev
-          auto-update-conda: true
           python-version: "3.12"
-      - name: Installing dependencies
-        run: conda install -c conda-forge poetry pytest
-      - name: Building distribution
-        run: poetry build -f wheel
-      - name: Installing distribution
-        run: pip install ./dist/*.whl
+          cache: "pip"
+          cache-dependency-path: "pyproject.toml"
+      - name: Install Hatch
+        run: pip install hatch
       - name: Testing code
-        run: pytest
+        run: hatch run test:run

.gitignore

@@ -4,6 +4,8 @@ __pycache__/
 *$py.class
 
 # C extensions
+*.c
+*.cpp
 *.so
 
 # Autogenerated example gallery
@@ -139,6 +141,9 @@ dmypy.json
 .vscode/*
 profile.json
 
+# Zed
+.zed/*
+
 # Temporarily disable freezing of dependency versions
 poetry.lock
 

README.rst

@@ -24,7 +24,7 @@ Installation
 
    $ pip install springcraft
 
-or 
+or
 
 .. code-block:: console
 
@@ -41,12 +41,63 @@ via *pip*:
    $ git clone https://github.com/biotite-dev/springcraft.git
    $ pip install ./springcraft
 
-A development conda environment with all required dependencies for testing
-can be installed from `environment.yml`
+Development
+-----------
 
-Scripts to generate reference files for tests are stored in tests/data; 
-a separate environment to rerun these locally can be found in `test_create_data_env.yml`.
-BioPhysConnectoR has to be installed separately. 
+Conda Environment
+~~~~~~~~~~~~~~~~~
+
+You can use conda's optimized libraries for development by creating the provided
+conda enviroment in `environment.yml` and than installing the project in editable
+mode. This creates symlinks from conda environment to your project files so that
+changes are synced directly.
+
+.. code-block:: console
+
+   $ mamba env create -f environment.yml
+   $ mamba activate springcraft-dev
+   $ pip install -e .
+
+Linting is done by `ruff` and tests are resolved by `pytest`. After installing the
+dependencies into the conda env you can run them by
+
+.. code-block:: console
+
+   $ pip install -e .[lint,test]
+   $ ruff check .  # run linter
+   $ pytest  # run test
+   $ pytest --cov=springcraft --cov-report=html --cov-branch  # run test with coverage
+
+You can lint the numpy docstrings using `numpydoc` and built the documentation with
+`sphinx-build` like this
+
+.. code-block:: console
+
+   $ pip install -e .[docs]
+   $ python -m numpydoc lint src/springcraft/*.py
+   $ sphinx-build doc build/doc
+
+Hatch Virtual Environment
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You can also Hatch's virtual environment system. After installing `hatch` all further
+dependency management will be done by `hatch` itself. Dependencies will be installed
+into a virtual environment. Just run the following:
+
+.. code-block:: console
+
+   $ hatch run lint:run  # run linter
+   $ hatch run test:run  # run tests
+   $ hatch run docs:lint  # run linter on docstrings
+
+Building the documentation does not work using hatch. Use the conda env instead.
+
+Generate test files
+~~~~~~~~~~~~~~~~~~~
+
+Scripts to generate reference files for tests are stored in tests/data;
+a separate environment to rerun these locally can be found in `environment-test-data.yml`.
+BioPhysConnectoR has to be installed separately.
 
 Example
 =======
@@ -91,4 +142,4 @@ Output:
     [ 0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1.  0.  0.  0. -1.  4. -1. -1.  0.]
     [ 0.  0.  0.  0.  0. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  5. -1. -1.]
     [ 0. -1. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  5. -1.]
-    [ 0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  2.]]
+    [ 0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  2.]]

doc/advanced.rst

@@ -6,9 +6,11 @@ Advanced usage
 Adding or removing contacts between atoms
 -----------------------------------------
 Altering the contacts between two atom can be achieved using the
-:class:`PatchedForceField`.
-It wraps another :class:`ForceField` and applied custom changes to it.
-As example the contact between the first and second residue should be removed.
+:class:`PatchedForceField` or by modifying the model directly.
+
+The :class:`PatchedForceField` wraps another :class:`ForceField` and applied
+custom changes to it. As example the contact between the first and second
+residue should be removed.
 
 .. code-block:: python
 
@@ -62,10 +64,10 @@ For the purpose of an example a chimeric force field is created
                 self._type_ff(atom_i, atom_j, sq_distance) *
                 self._dist_ff(atom_i, atom_j, sq_distance)
             )
-        
+
         @property
         def natoms(self):
             return self._type_ff.natoms
 
 
-    ff = ChimericForceField(atoms)
+    ff = ChimericForceField(atoms)

doc/apidoc.rst

@@ -8,19 +8,47 @@ API Reference
    :depth: 3
 
 
-Network models
+Network Models
 --------------
 
 .. autoclass:: GNM
-   :members:
+
+   Normal Mode Analysis
+   ~~~~~~~~~~~~~~~~~~~~
+   .. automethod:: frequencies
+   .. automethod:: mean_square_fluctuation
+   .. automethod:: bfactor
+   .. automethod:: dcc
 
 |
 
 .. autoclass:: ANM
-   :members:
-
+
+   Normal Mode Analysis
+   ~~~~~~~~~~~~~~~~~~~~
+   .. automethod:: frequencies
+   .. automethod:: mean_square_fluctuation
+   .. automethod:: bfactor
+   .. automethod:: dcc
+
 |
 
+.. autoclass:: springcraft.enm.ENM
+
+   .. automethod:: eigen
+
+
+Normal Mode Analysis
+--------------------
+
+.. autofunction:: springcraft.nma.frequencies
+
+.. autofunction:: springcraft.nma.mean_square_fluctuation
+
+.. autofunction:: springcraft.nma.bfactor
+
+.. autofunction:: springcraft.nma.dcc
+
 
 Force Fields
 ------------
@@ -56,4 +84,4 @@ Miscellaneous
 
 .. autofunction:: compute_kirchhoff
 
-.. autofunction:: compute_hessian
+.. autofunction:: compute_hessian