Merge pull request #14 from pirl-unc/dev #21
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| name: "CI" | |
| on: | |
| push: | |
| branches: [main, dev] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Run linter | |
| run: | | |
| pip install pylint==3.3.5 | |
| chmod +x lint.sh | |
| bash lint.sh | |
| test-rust: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 120 | |
| needs: lint | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Free disk space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| tool-cache: false | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| docker-images: true | |
| swap-storage: true | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: test-env | |
| python-version: "3.10" | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: strict | |
| - name: Install Rust toolchain | |
| run: | | |
| conda install -y rust=1.88.0 | |
| - name: Run Rust unit tests | |
| run: | | |
| cd exacto/ | |
| cargo test -- --nocapture | |
| test-python: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 120 | |
| needs: lint | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Free disk space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| tool-cache: false | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| docker-images: true | |
| swap-storage: true | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: test-env | |
| python-version: "3.10" | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: strict | |
| - name: Install dependencies | |
| run: | | |
| conda install -y \ | |
| pip \ | |
| rust=1.88.0 \ | |
| pandas=2.2.3 \ | |
| polars=1.26.0 \ | |
| pyarrow=19.0.1 \ | |
| coveralls=4.0.1 \ | |
| pytest=8.3.5 \ | |
| pytest-cov=6.1.1 | |
| python -m pip install pysam==0.23.0 | |
| python -m pip install . --verbose | |
| - name: Verify install | |
| run: | | |
| which python | |
| which pip | |
| python -c "import sys; print('sys.executable:', sys.executable)" | |
| python -c "import pysam; print('pysam OK:', pysam.__file__)" | |
| python -c "import exactolib; print('exactolib OK:', exactolib.__file__)" | |
| - name: Run Python unit tests | |
| run: | | |
| chmod +x unittest.sh | |
| bash unittest.sh |