avoid setup-python api limit

nf-core · Jan 25, 2024 · 541d4fb · 541d4fb
1 parent 3853929
commit 541d4fb
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Showing 6 changed files with 44 additions and 2 deletions.
diff --git a/.github/workflows/changelog.yml b/.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: |

diff --git a/.github/workflows/create-lint-wf.yml b/.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

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.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
 

diff --git a/.github/workflows/create-test-wf.yml b/.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
 

diff --git a/.github/workflows/pytest.yml b/.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 }}
@@ -165,9 +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:

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -2,6 +2,7 @@ mypy
 myst_parser
 pytest-cov
 pytest-datafiles
+pytest-xdist
 responses
 ruff
 Sphinx