Fix Nextflow config syntax #1266
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| # Modified from GitHub Actions template | |
| name: QA | |
| # Improves reproducibility and speed | |
| env: | |
| OPENBLAS_NUM_THREADS: 1 | |
| OMP_NUM_THREADS: 1 | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| jobs: | |
| Pytest: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip wheel | |
| pip install numpy==1.26.4 | |
| pip install -r requirements.txt | |
| - name: Compile Cython components | |
| run: | | |
| make clean compile | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest --cov-report xml:cov.xml --cov=ecoli --cov=reconstruction --cov=wholecell --cov=runscripts --durations=0 | |
| - name: Code Coverage Report | |
| uses: irongut/[email protected] | |
| with: | |
| filename: cov.xml | |
| format: markdown | |
| indicators: true | |
| output: both | |
| - name: Add Coverage PR Comment | |
| uses: marocchino/sticky-pull-request-comment@v2 | |
| if: github.event_name == 'pull_request' | |
| with: | |
| recreate: true | |
| path: code-coverage-results.md | |
| Mypy: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip wheel | |
| pip install numpy==1.26.4 mypy | |
| pip install -r requirements.txt | |
| - name: Compile Cython components | |
| run: | | |
| make clean compile | |
| - name: Mypy | |
| run: | | |
| mypy | |
| Lint: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip wheel | |
| pip install numpy==1.26.4 ruff | |
| pip install -r requirements.txt | |
| - name: Compile Cython components | |
| run: | | |
| make clean compile | |
| - name: Ruff | |
| run: | | |
| ruff check doc ecoli migration wholecell runscripts validation reconstruction |