test using xdist for faster tests [skip changelog]

.github/workflows/changelog.yml

@@ -34,9 +34,18 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@v5
+      # Check if python is installed
+      - name: Check python version
+        id: python-version
+        run: python --version
+
+      # Set up nf-core/tools
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        if: steps.python-version.outcome == 'failure'
         with:
           python-version: "3.11"
+          cache: "pip"
 
       - name: Install packages
         run: |

.github/workflows/create-lint-wf.yml

@@ -36,9 +36,15 @@ jobs:
       - uses: actions/checkout@v4
         name: Check out source-code repository
 
+      # Check if python is installed
+      - name: Check python version
+        id: python-version
+        run: python --version
+
       # Set up nf-core/tools
       - name: Set up Python 3.11
         uses: actions/setup-python@v5
+        if: steps.python-version.outcome == 'failure'
         with:
           python-version: 3.11
           cache: pip

.github/workflows/create-test-lint-wf-template.yml

@@ -49,8 +49,14 @@ jobs:
       - uses: actions/checkout@v4
         name: Check out source-code repository
 
+      # Check if python is installed
+      - name: Check python version
+        id: python-version
+        run: python --version
+
       - name: Set up Python 3.11
         uses: actions/setup-python@v5
+        if: steps.python-version.outcome == 'failure'
         with:
           python-version: 3.11
 

.github/workflows/create-test-wf.yml

@@ -35,8 +35,15 @@ jobs:
       - uses: actions/checkout@v4
         name: Check out source-code repository
 
+      # Check if python is installed
+      - name: Check python version
+        id: python-version
+        run: python --version
+
+      # Set up nf-core/tools
       - name: Set up Python 3.11
         uses: actions/setup-python@v5
+        if: steps.python-version.outcome == 'failure'
         with:
           python-version: 3.11
 

.github/workflows/pytest.yml

@@ -78,7 +78,13 @@ jobs:
       - uses: actions/checkout@v4
         name: Check out source-code repository
 
+        # Check if python is installed, by outputing major and minor version, but not patch version
+      - name: Check python version
+        id: python-version
+        run: echo "python-version=$(python --version)" | sed 's/Python \([0-9]\+\.[0-9]\+\)\.[0-9]\+/\1/' >> $GITHUB_OUTPUT
+
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
+        if: steps.python-version.outputs.python-version == ${{ needs.setup.outputs.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
@@ -136,7 +142,11 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
+          # run in parallel with xdist if not test_modules.py or test_subworkflows.py
+          if [ "${{ matrix.test }}" != "test_modules.py" ] && [ "${{ matrix.test }}" != "test_subworkflows.py" ]; then
+            python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 -n 2 && exit_code=0|| exit_code=$?
+          else
+            python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"
@@ -161,9 +171,16 @@ jobs:
           mkdir -p pytest
           cd pytest
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4 #
+
+      - name: Check python version
+        id: python-version
+        run: python --version
+
+      # Set up nf-core/tools
       - name: Set up Python 3.11
         uses: actions/setup-python@v5
+        if: steps.python-version.outcome == 'failure'
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:

requirements-dev.txt

@@ -2,6 +2,7 @@ mypy
 myst_parser
 pytest-cov
 pytest-datafiles
+pytest-xdist
 responses
 ruff
 Sphinx