update CI matrix (#70)

* update CI matrix

- fix #69
- only test Python 3.10 - 3.12
- manually specify versions of MDAnalysis in the test matrix that do not
  support some of the python versions (see MDAnalysis/cookiecutter-mdakit#110
  for background)

* bumped Python and MDAnalysis versions in pyproject.toml

- Python 3.10+
- MDAnalysis 2.1.0+

.github/workflows/gh-ci.yaml

@@ -20,30 +20,23 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  environment-config:
-    runs-on: ubuntu-latest
-    outputs:
-      stable-python-version: ${{ steps.get_python_version.outputs.python-version }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - id: get-python-version
-        uses: MDAnalysis/get-latest-python-version@main
-        with:
-          last-n-minor-release: 1
-
   main-tests:
     if: "github.repository == 'Becksteinlab/propkatraj'"
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         mdanalysis-version: ["latest", "develop"]
-
+        # Manually exclude any combinations of the test matrix that can't be run 
+        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"
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -54,15 +47,17 @@ jobs:
         ulimit -a
 
     - name: Install conda dependencies
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/environment.yml
         add-pip-as-python-dependency: true
         architecture: x64
+
         miniforge-variant: Mambaforge
         use-mamba: true
         channels: conda-forge, defaults
+
         activate-environment: propkatraj-test
         auto-update-conda: true
         auto-activate-base: false
@@ -95,12 +90,12 @@ jobs:
 
     - name: Run tests
       run: |
-        pytest -n 2 --cov=propkatraj --cov-report=xml -v --color=yes propkatraj/tests/
+        pytest -n auto --cov=propkatraj --cov-report=xml -v --color=yes propkatraj/tests/
 
     - name: codecov
       if: ${{ github.repository == 'Becksteinlab/propkatraj'
               && github.event_name != 'schedule' }}
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.xml
@@ -109,7 +104,6 @@ jobs:
 
   pylint_check:
     if: "github.repository == 'Becksteinlab/propkatraj'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
@@ -118,7 +112,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+        python-version: "3.11"
 
     - name: Install Pylint
       run: |
@@ -133,16 +127,15 @@ jobs:
 
   pypi_check:
     if: "github.repository == 'Becksteinlab/propkatraj'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }}
+    - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+        python-version: "3.11"
 
     - name: Install dependencies
       run: |

pyproject.toml

@@ -25,16 +25,16 @@ classifiers = [
     "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
     "Programming Language :: C",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",    
     "Topic :: Scientific/Engineering",
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
-    "MDAnalysis>=2.0.0",
+     "MDAnalysis>=2.1.0",
     "numpy",
     "pandas",
     "propka==3.1",