CI #45
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | ||
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | ||
| name: CI | ||
| on: | ||
| pull_request: | ||
| branches: | ||
| - '*' | ||
| # Allows you to run this workflow manually from the Actions tab | ||
| workflow_dispatch: | ||
| jobs: | ||
| build: | ||
| os: ['ubuntu-latest', 'macos-13'] | ||
|
Check failure on line 16 in .github/workflows/binette_ci.yml
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||
| defaults: | ||
| run: | ||
| shell: bash -el {0} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| python-version: [3.8] #["3.8", "3.9", "3.10"] | ||
| steps: | ||
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | ||
| - uses: actions/checkout@v3 | ||
| # Install requirements | ||
| - uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| mamba-version: "*" | ||
| python-version: ${{ matrix.python-version }} | ||
| channels: conda-forge,bioconda,defaults | ||
| environment-file: binette.yaml | ||
| activate-environment: binette | ||
| - name: Install binette | ||
| run: | | ||
| pip install . | ||
| binette -h | ||
| - name: Lint with flake8 | ||
| run: | | ||
| mamba install flake8 | ||
| # stop the build if there are Python syntax errors or undefined names | ||
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | ||
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | ||
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | ||
| - name: Test with pytest | ||
| run: | | ||
| mamba install pytest pytest-cov | ||
| pytest --cov=binette --cov-report=html --cov-report=xml | ||
| - name: Generate coverage badge | ||
| run: | | ||
| pip install genbadge[coverage] | ||
| genbadge coverage -i coverage.xml -o htmlcov/coverage-badge.svg | ||
| rm htmlcov/.gitignore | ||
| - name: Publish coverage report to GitHub Pages | ||
| if: github.ref == format('refs/heads/{0}', github.event.repository.default_branch) | ||
| uses: JamesIves/github-pages-deploy-action@v4 | ||
| with: | ||
| folder: htmlcov | ||
| branch: gh-pages | ||
| - name: Download test data | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| repository: genotoul-bioinfo/Binette_TestData | ||
| path: test_data | ||
| - name: Run simple test case from bin2table | ||
| run: | | ||
| cd test_data | ||
| binette -b binning_results/*binning --contigs all_contigs.fna --checkm2_db checkm2_tiny_db/checkm2_tiny_db.dmnd -v -o test_results | ||
| - name: Compare results from bin2table with expectation | ||
| run: | | ||
| cd test_data | ||
| head expected_results/final_bins_quality_reports.tsv test_results/final_bins_quality_reports.tsv | ||
| python scripts/compare_results.py expected_results/final_bins_quality_reports.tsv test_results/final_bins_quality_reports.tsv | ||
| - name: Run simple test case from bin dirs | ||
| run: | | ||
| cd test_data | ||
| binette -d binning_results/A/ binning_results/B/ binning_results/C/ --contigs all_contigs.fna --checkm2_db checkm2_tiny_db/checkm2_tiny_db.dmnd -v -o test_results_from_dirs | ||
| - name: Compare results from bin dirs with expectation | ||
| run: | | ||
| cd test_data | ||
| head expected_results/final_bins_quality_reports.tsv test_results_from_dirs/final_bins_quality_reports.tsv | ||
| python scripts/compare_results.py expected_results/final_bins_quality_reports.tsv test_results_from_dirs/final_bins_quality_reports.tsv | ||
