Merge branch 'main' into integrate_kmer_tracking

.github/workflows/pytest.yml

@@ -0,0 +1,34 @@
+name: Python Tests
+
+on: [pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]  # Test with Python 3.10 to the latest available version
+
+    steps:
+      # Checkout the latest commit associated with the PR
+      - uses: actions/checkout@v4
+
+      - name: Debug matrix value
+        run: echo "Python version is ${{ matrix.python-version }}"
+
+      # Set up Python based on the matrix version
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Install dependencies, including test dependencies from pyproject.toml
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install '.[test]'  # Install all dependencies, including test-specific ones
+
+      # Run pytest on the specified directory
+      - name: Run tests
+        run: pytest src/python/tests

.github/workflows/ruff.yml

@@ -3,16 +3,14 @@ on: [pull_request]
 jobs:
   ruff:
     runs-on: ubuntu-latest
-    #concurrency:
-    #  group: ${{ github.ref }}
-    #  cancel-in-progress: true
     permissions:
       # Give the default GITHUB_TOKEN write permission to commit and push the changed files.
       contents: write
     steps:
       - uses: actions/checkout@v4
         with:
           ref: ${{ github.sha }}
+          token: ${{ secrets.ACTION_TOKEN }}
       - uses: chartboost/ruff-action@v1
         with:
           src: './src/python'