Merge pull request #83 from Becksteinlab/update-gha

updated actions in workflows

Author: orbeckst

.github/workflows/docs.yaml

@@ -21,14 +21,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 0         
 
     - name: setup_miniconda
-      uses: conda-incubator/setup-miniconda@v3
+      uses: conda-incubator/setup-miniconda@v4
       with:
-        python-version: 3.11
+        python-version: 3.14
         environment-file: docs/requirements.yaml
         add-pip-as-python-dependency: true
         architecture: x64
@@ -56,7 +56,7 @@ jobs:
 
     - name: deploy docs
       if: github.event_name != 'pull_request'    
-      uses: peaceiris/actions-gh-pages@v4
+      uses: peaceiris/actions-gh-pages@v4.1.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./docs/html

.github/workflows/gh-ci.yaml

@@ -24,17 +24,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        os: [macOS-latest, ubuntu-latest]   # ignore windows-latest for now
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
         mdanalysis-version: ["latest", "develop"]
         # Manually exclude any combinations of the test matrix that can't be run 
-        exclude:
+        #exclude:
           # The latest release of MDAnalysis only supports up to Python 3.11
           # so we exclude 3.12 from the test matrix (issue #69)
-          - python-version: "3.12"
-            mdanalysis-version: "latest"
+          #- python-version: "3.12"
+          #  mdanalysis-version: "latest"
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 0
 
@@ -45,7 +45,7 @@ jobs:
         ulimit -a
 
     - name: Install conda dependencies
-      uses: conda-incubator/setup-miniconda@v3
+      uses: conda-incubator/setup-miniconda@v4
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/environment.yml
@@ -93,10 +93,10 @@ jobs:
     - name: codecov
       if: ${{ github.repository == 'Becksteinlab/propkatraj'
               && github.event_name != 'schedule' }}
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v7
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: coverage.xml
+        files: coverage.xml
         fail_ci_if_error: True
         verbose: True
 
@@ -105,10 +105,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v7
 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: "3.11"
 
@@ -128,10 +128,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v7
 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: "3.11"
 

docs/requirements.yaml

@@ -2,7 +2,8 @@ name: propkatrajdocs
 channels:
   - conda-forge
 dependencies:
-  - python >=3.10
+  - python >=3.11
+  - setuptools>=61.2,<81
   - pip
   # propkatraj dependencies
   - MDAnalysis >=2.0.0

pyproject.toml

@@ -25,15 +25,17 @@ classifiers = [
     "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
     "Programming Language :: C",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",    
+    "Programming Language :: Python :: 3.12",   
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering",
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
+    "setuptools >= 61.2,<81",  # pkg_resources are currently required and were removed in 81.0.0, see gh-80
     "MDAnalysis>=2.1.0",
     "numpy",
     "pandas",

readthedocs.yaml

@@ -3,22 +3,21 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
+    # Miniforge provides mamba; Python version comes from docs/requirements.yaml
+    python: miniforge3-latest
 
-# Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/sphinx/conf.py
+  configuration: docs/sphinx/conf.py
 
-# Optionally build your docs in additional formats such as PDF
 formats:
-   - pdf
+  - pdf
+
+conda:
+  environment: docs/requirements.yaml
 
 python:
   install:
     - method: pip
       path: .
-
-conda:
-  environment: docs/requirements.yaml