Update CI (MDAnalysis#66)

* fix MDAnalysis#65 
* Update CI: manually set the test matrix for MDAnalysis
* Update pyproject.toml
* Update CHANGELOG.md
* Update CHANGELOG.md

Author: IAlibay

.github/workflows/gh-ci.yaml

@@ -23,35 +23,25 @@ defaults:
     shell: bash  -l {0} 
 
 jobs:
-  environment-config:
-    runs-on: ubuntu-latest
-    outputs:
-      stable-python-version: ${{ steps.get-compatible-python.outputs.stable-python }}
-      latest-python-version: ${{ steps.get-compatible-python.outputs.latest-python }}
-      python-matrix: ${{ steps.get-compatible-python.outputs.python-versions }}
-    steps:
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-
-      - id: get-compatible-python
-        uses: MDAnalysis/mdanalysis-compatible-python@main
-        with:
-          release: "latest"
-
   main-tests:
     if: "github.repository == 'MDAnalysis/mdaencore'"
-    needs: environment-config
     runs-on: ${{ matrix.os }}
     strategy:
         fail-fast: false
         matrix:
-          os: [macOS-latest, ubuntu-latest, windows-latest, macos-14]
-          python-version: ${{ fromJSON(needs.environment-config.outputs.python-matrix) }}
+          # macos-13 is x86_64 and macos-14 is arm64
+          os: [ubuntu-latest, windows-latest, macos-14, macos-13]
+          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 #68)
+            - python-version: "3.12"
+              mdanalysis-version: "latest"
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -63,7 +53,7 @@ jobs:
 
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - 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/conda-envs/test_env.yaml
@@ -108,29 +98,30 @@ jobs:
 
     - name: Run tests
       run: |
-        pytest -n 2 -v --cov=mdaencore --cov-report=xml --color=yes --pyargs mdaencore
+        pytest -n auto -v --cov=mdaencore --cov-report=xml --color=yes --pyargs mdaencore
 
     - name: codecov
       if: github.repository == 'MDAnalysis/mdaencore' && github.event_name != 'schedule'
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         file: coverage.xml
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+        token: ${{ secrets.CODECOV_TOKEN }}
         verbose: True
+        fail_ci_if_error: True
 
 
   pylint_check:
     if: "github.repository == 'MDAnalysis/mdaencore'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - 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: |
@@ -147,16 +138,15 @@ jobs:
 
   pypi_check:
     if: "github.repository == 'MDAnalysis/mdaencore'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - 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: |

CHANGELOG.md

@@ -32,6 +32,8 @@ The rules for this file:
 
 ### Changed
 - Update CI and wheel deployment to include macos-arm64 and py3.12 (PR #63)
+- Minimum Python version has been raised to 3.10 (PR #66)
+- Minimum MDAnalysis version has been raised to 2.1.0 (PR #66)
 
 ### Deprecated
 <!-- Soon-to-be removed features -->

pyproject.toml

@@ -35,16 +35,16 @@ classifiers = [
     "Operating System :: POSIX",
     "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",
     "joblib",
     "numpy",
     "scipy",