Add Aviti FCs to bioinfo tab #177
Workflow file for this run
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| name: Lint code | |
| on: [push, pull_request] | |
| jobs: | |
| # Use ruff to check for code style violations | |
| ruff-check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11.5" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ruff | |
| - name: ruff --> Check for style violations | |
| # Configured in pyproject.toml | |
| run: ruff check . | |
| # Use ruff to check code formatting | |
| ruff-format: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11.5" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ruff | |
| - name: ruff --> Check code formatting | |
| run: ruff format --check . | |
| # Use mypy for static type checking | |
| mypy-check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11.5" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install mypy | |
| # Start by installing type stubs | |
| - name: mypy --> Install stubs | |
| run: echo -e "y" | mypy --install-types . || exit 0 | |
| - name: mypy --> Static type checking | |
| # Configured in pyprojet.toml | |
| run: mypy . | |
| # Use pipreqs to check for missing dependencies | |
| pipreqs-check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11.5" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| - name: Run pipreqs | |
| run: | | |
| pipreqs --savepath pipreqs.txt taca 2>&1 | tee pipreqs_output.log | |
| if grep -q 'WARNING: Package .* does not exist or network problems' pipreqs_output.log; then | |
| missing_packages=$(grep 'WARNING: Package .* does not exist or network problems' pipreqs_output.log | sed -E 's/.*Package "(.*)" does not exist.*/\1/') | |
| echo "ERROR: Add unresolved packages to requirements. Missing package(s): $missing_packages. Example: '<pkg> @ git+https://github.com/<author>/<repo>.git'" | |
| exit 1 | |
| fi | |
| - name: Compare requirements | |
| run: | | |
| # Extract and sort package names | |
| awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' requirements.txt | tr '[:upper:]' '[:lower:]' | sort -u > requirements.compare | |
| awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' pipreqs.txt | tr '[:upper:]' '[:lower:]' | sort -u > pipreqs.compare | |
| # Compare package lists | |
| if cmp -s requirements.compare pipreqs.compare | |
| then | |
| echo "Requirements are the same" | |
| exit 0 | |
| else | |
| echo "Requirements are different" | |
| echo "" | |
| echo "=== current requirements.txt ===" | |
| echo "" | |
| cat requirements.compare | |
| echo "" | |
| echo "=== pipreqs requirements ===" | |
| echo "" | |
| cat pipreqs.compare | |
| exit 1 | |
| fi | |
| # Use Prettier to check various file formats | |
| prettier: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup node | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g prettier | |
| - name: Run Prettier --check | |
| run: prettier --check . |