Merge pull request #74 from Becksteinlab/auto-deploy

- new GHA workflow deploy.yaml using MDAnalysis/pypi-deployment action
- add Trusted Publisher Management for PyPi and TestPyPi (externally done)
- Additional fixes
   - make RTD work again by mamba-installing dependencies
   - update sphinx conf.py

.github/workflows/deploy.yaml

@@ -0,0 +1,57 @@
+name: Build and upload to PyPi
+
+on:
+  push:
+    tags:
+      - "*"
+  release:
+    types:
+      - published
+
+jobs:
+  test_pypi_push:
+    environment:
+      name: TestPyPi
+      url: https://test.pypi.org/p/propkatraj
+    permissions:
+      id-token: write
+    if: |
+      github.repository == 'Becksteinlab/propkatraj' &&
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
+    name: "TestPyPi: Build and upload pure Python wheels"
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: testpypi_deploy
+        uses: MDAnalysis/pypi-deployment@main
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+        with:
+          test_submission: true
+          package_name: 'propkatraj'
+          module_name: 'propkatraj'
+          tests: true
+
+  pypi_push:
+    environment:
+      name: PyPi
+      url: https://pypi.org/p/propkatraj
+    permissions:
+      id-token: write
+    if: |
+      github.repository == 'Becksteinlab/propkatraj' &&
+      (github.event_name == 'release' && github.event.action == 'published')
+    name: "PyPi: Build and upload pure Python wheels"
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: pypi_deploy
+        uses: MDAnalysis/pypi-deployment@main
+        if: github.event_name == 'release' && github.event.action == 'published'
+        with:        
+          package_name: 'propkatraj'
+          module_name: 'propkatraj'
+          tests: true

devtools/environment.yml

@@ -1,7 +1,6 @@
 name: propkatraj
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - MDAnalysis>=2.0.0
   - MDAnalysisTests>=2.0.0
@@ -10,6 +9,5 @@ dependencies:
   - pytest-cov
   - pytest-xdist
   - codecov
-  - pip
-  - pip:
-    - propka==3.1
+  - propka==3.1.0
+

docs/requirements.yaml

@@ -2,8 +2,13 @@ name: propkatrajdocs
 channels:
   - conda-forge
 dependencies:
-  - python
+  - python >=3.10
   - pip
+  # propkatraj dependencies
+  - MDAnalysis >=2.0.0
+  - pandas
+  - propka==3.1.0  
+  # sphinx on RTD
   - sphinx
   - sphinx_rtd_theme
   - sphinx-sitemap

docs/sphinx/conf.py

@@ -47,8 +47,8 @@
 # Configuration for intersphinx: refer to the Python standard library
 # and other packages used by MDAnalysis
 intersphinx_mapping = {
-                       'https://docs.python.org/3/': None,
-                       'https://docs.mdanalysis.org/stable/index.html': None,
-                       'https://numpy.org/doc/stable/': None,
-                       'https://pandas.pydata.org/pandas-docs/stable/': None,
+                       'python': ('https://docs.python.org/3/', None),
+                       'mdanalysis': ('https://docs.mdanalysis.org/stable/', None),
+                       'numpy': ('https://numpy.org/doc/stable/', None),
+                       'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
                        }

readthedocs.yaml

@@ -5,7 +5,15 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "mambaforge-4.10"
+    python: "mambaforge-22.9"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/sphinx/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
 
 python:
   install: