Workflow file for this run
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| name: Run With Test Files | |
| on: | |
| push: | |
| branches: [ "main", "dev" ] | |
| pull_request: | |
| branches: [ "main", "dev" ] | |
| jobs: | |
| test: | |
| name: Test on Python ${{ matrix.python-version }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| # 1. Check out your code (including tests/data) | |
| - uses: actions/checkout@v4 | |
| # 2. Set up Python | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| # 3. CRITICAL: Install zlib (Required for building mappy/minimap2 from source) | |
| - name: Install System Dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y zlib1g-dev | |
| # 4. Install your package and pytest | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest build | |
| # Installs your package and dependencies defined in pyproject.toml | |
| pip install . | |
| # 5. Run the tests | |
| - name: Run Basic Example Commands | |
| run: | | |
| minkemap -r tests/data/3670018.fasta -i tests/data/*fasta --outdir test1_output | |
| ls test1_output/minkemap_plot.png | |
| - name: Run Basic Example Commands With GenkBank Reference | |
| run: | | |
| minkemap -r tests/data/3670018.gbk -i tests/data/*fasta --outdir test2_output | |
| ls test2_output/minkemap_plot.png | |
| - name: Run GC-Skew and Min Coverage Example | |
| run: | | |
| minkemap -r ./tests/data/3670018.gbk -i tests/data/*fasta --min-coverage 90 --gc-skew --outdir test3_output | |
| ls test3_output/minkemap_plot.png | |
| - name: Run Clean Visualization Example | |
| run: | | |
| minkemap -r ./tests/data/3670018.gbk -i tests/data/*fasta --no-backbone --palette viridis --exclude-genes "hypothetical" --outdir test4_output | |
| ls test4_output/minkemap_plot.png | |
| - name: Run with Manifest File | |
| run: | | |
| minkemap -r ./tests/data/3670018.gbk -f tests/data/manifest.csv --highlights tests/data/highlights.csv --outdir test5_output | |
| ls test5_output/minkemap_plot.png |