Fixed pre-commit erros #77
Workflow file for this run
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| name: BioNeuralNet CI | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: ["3.10", "3.11"] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| check-latest: true | |
| - name: Cache pip dependencies | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt', '**/requirements-dev.txt') }} | |
| restore-keys: ${{ runner.os }}-pip- | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| pip install torch | |
| pip install torch_geometric | |
| shell: bash | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "latest" | |
| - name: Install R packages | |
| run: | | |
| Rscript -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager', repos='https://cran.r-project.org')" | |
| Rscript -e "install.packages(c('dplyr', 'jsonlite'), repos='https://cran.r-project.org')" | |
| Rscript -e "BiocManager::install(c('impute', 'preprocessCore', 'GO.db', 'AnnotationDbi'), update=FALSE, ask=FALSE)" | |
| Rscript -e "install.packages('SmCCNet', repos='https://cran.r-project.org')" | |
| Rscript -e "install.packages('WGCNA', repos='https://cran.r-project.org')" | |
| shell: bash | |
| - name: Run tests with pytest | |
| run: | | |
| find . -name ".coverage*" -delete | |
| pytest --cov=bioneuralnet --cov-report=xml tests/ | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella |