Extention to CI capabilities with comparisions between CodeEntropy and MDAnalysis

.github/workflows/mdanalysis-compatibility-failure.md

@@ -0,0 +1,10 @@
+---
+title: CI Failure: MDAnalysis v{{ env.MDA_VERSION }} / Python {{ env.PYTHON_VERSION }}
+labels: CI Failure, MDAnalysis Compatibility
+---
+
+### Automated MDAnalysis Compatibility Test Failure
+
+**MDAnalysis version**: `{{ env.MDA_VERSION }}`  
+**Python version**: `{{ env.PYTHON_VERSION }}`  
+**Workflow Run**: [Run #{{ env.RUN_NUMBER }}]({{ env.RUN_URL }})

.github/workflows/project-ci.yaml

@@ -0,0 +1,115 @@
+name: CodeEntropy CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  schedule:
+    - cron: '0 8 * * 1'
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    name: Run tests
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install CodeEntropy and its testing dependencies
+        run: pip install -e .[testing]
+
+      - name: Run test suite
+        run: pytest --cov CodeEntropy --cov-report term-missing --cov-append .
+
+      - name: Coveralls GitHub Action
+        uses: coverallsapp/github-action@v2.3.6
+        with:
+          github-token: ${{ secrets.COVERALLS_REPO_TOKEN }}
+
+  docs:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[docs]
+      - name: Build docs
+        run: cd docs && make
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[pre-commit,docs,testing]
+      - name: Run pre-commit
+        run: |
+          pre-commit install
+          pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+
+  mdanalysis-compatibility:
+    if: github.event_name == 'schedule'
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+        mdanalysis-version: ["2.7.0", "2.8.0", "2.9.0", "latest"]
+    name: MDAnalysis Compatibility Tests
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies with MDAnalysis ${{ matrix.mdanalysis-version }}
+        run: |
+          pip install --upgrade pip
+          pip install -e .[testing]
+          if [ "${{ matrix.mdanalysis-version }}" = "latest" ]; then
+            pip install MDAnalysis
+          else
+            pip install "MDAnalysis==${{ matrix.mdanalysis-version }}"
+          fi
+
+      - name: Run compatibility tests
+        run: pytest --cov CodeEntropy --cov-report=term-missing --cov-append
+
+      - name: Create Issue on Failure
+        if: failure()
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PYTHON_VERSION: ${{ matrix.python-version }}
+          MDA_VERSION: ${{ matrix.mdanalysis-version }}
+          RUN_NUMBER: ${{ github.run_number }}
+          RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+        with:
+          filename: .github/mdanalysis-compatibility-failure.md
+          update_existing: true
+          search_existing: open

pyproject.toml

@@ -30,10 +30,10 @@ classifiers = [
     "Development Status :: 4 - Beta"
 ]
 keywords = ["entropy", "macromolecular systems", "MD simulation"]
-requires-python = ">=3.8"
+requires-python = ">=3.11"
 dependencies = [
     "numpy==2.2.3",
-    "mdanalysis==2.8.0",
+    "mdanalysis>=2.7.0",
     "pandas==2.2.3",
     "psutil==5.9.5",
     "PyYAML==6.0.2",

tests/test_CodeEntropy/test_run.py

@@ -136,9 +136,12 @@ def test_run_entropy_workflow(self):
         run_manager._config_manager.merge_configs.return_value = mock_args
 
         mock_entropy_manager = MagicMock()
-        with unittest.mock.patch(
-            "CodeEntropy.run.EntropyManager", return_value=mock_entropy_manager
-        ), unittest.mock.patch("CodeEntropy.run.mda.Universe") as mock_universe:
+        with (
+            unittest.mock.patch(
+                "CodeEntropy.run.EntropyManager", return_value=mock_entropy_manager
+            ),
+            unittest.mock.patch("CodeEntropy.run.mda.Universe") as mock_universe,
+        ):
 
             run_manager.run_entropy_workflow()