Update tutorial #56
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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: | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ['ubuntu-latest', 'macos-13'] | |
| 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@v4 | |
| # Install requirements | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| 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 | |