Adding shell script for generating stats and running checkm2 #24
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| # This file configures the continuous integration (CI) system on GitHub. | |
| # Introductory materials can be found here: https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions. | |
| # Documentation for editing this file can be found here: https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions | |
| name: Tests | |
| on: | |
| pull_request: | |
| push: | |
| jobs: | |
| # lint: | |
| # name: Code Quality | |
| # runs-on: ubuntu-latest | |
| # strategy: | |
| # matrix: | |
| # python-version: [ "3.12", "3.10" ] | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # - name: "Install python" | |
| # uses: "astral-sh/setup-uv@v3" | |
| # with: | |
| # enable-cache: true | |
| # cache-dependency-glob: "pyproject.toml" | |
| # - name: "Run command" | |
| # run: | | |
| # uvx -p ${{ matrix.python-version }} --with tox-uv tox -e ${{ matrix.tox-command }} | |
| generate_suppl_files: | |
| name: Generate extra files | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@main | |
| with: | |
| fetch-depth: 0 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: 3.8 | |
| activate-environment: genome_loader_env | |
| environment-file: env.yml | |
| auto-activate-base: false | |
| - name: Run tests | |
| shell: bash -l {0} | |
| continue-on-error: true | |
| run: | | |
| bash scripts/run_tools.sh tests/data/genome_paths.json test_results | |
| - name: upload artefacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| path: test_results/ | |
| tests: | |
| name: Run tests (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # os: ["ubuntu-22.02", "ubuntu-24.04"] | |
| # python-version: ["3.10", "3.11", "3.12"] | |
| os: ["ubuntu-24.04"] | |
| python-version: ["3.8"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@main | |
| with: | |
| fetch-depth: 0 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: genome_loader_env | |
| environment-file: env.yml | |
| auto-activate-base: false | |
| - name: install prerequisites | |
| shell: bash -l {0} | |
| run: pip install -r requirements.txt | |
| - name: Run tests | |
| shell: bash -l {0} | |
| continue-on-error: true | |
| run: pytest --cov=genome_loader_scripts --cov-report=xml tests/ | |
| - name: Send to Codecov | |
| id: send_to_codecov | |
| continue-on-error: true | |
| uses: codecov/codecov-action@main | |
| with: | |
| files: coverage.xml | |
| # fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Run tests | |
| shell: bash -l {0} | |
| continue-on-error: true | |
| run: | | |
| stats.sh --format=8 in=tests/data/FW305-C-112.1/FW305-C-112.1_scaffolds.fna,tests/data/FW305-3-2-15-C-TSA1/FW305-3-2-15-C-TSA1_scaffolds.fna > tests/data/fna-stats.json | |
| checkm2 database --download | |
| mkdir tests/data/checkm2 | |
| checkm2 predict --threads 10 --input tests/data/FW305-3-2-15-C-TSA1/FW305-3-2-15-C-TSA1_scaffolds.fna tests/data/FW305-C-112.1/FW305-C-112.1_scaffolds.fna -o tests/data/checkm2 | |
| - name: upload artefacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| path: tests/ |