Merge pull request #263 from CovertLab/tweaks #1262
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |