chore: pin version 0.2.1 for getphylo #922
Workflow file for this run
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| name: snakemake-actions | |
| on: [push] | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Formatting | |
| uses: github/super-linter@v5 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: main | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Linting | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: .tests | |
| snakefile: workflow/Snakefile | |
| stagein: "conda config --set channel_priority strict" | |
| args: "--lint" | |
| dry-run: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Dry-run workflow | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: .tests | |
| snakefile: workflow/Snakefile | |
| stagein: "conda config --set channel_priority strict" | |
| args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n" | |
| dry-run-report: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Dry-run workflow | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: .tests | |
| snakefile: workflow/Report | |
| stagein: "conda config --set channel_priority strict" | |
| args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n" | |
| dry-run-metabase: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Dry-run workflow | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: .tests | |
| snakefile: workflow/Metabase | |
| stagein: "conda config --set channel_priority strict" | |
| args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n" | |
| dry-run-bgc: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Dry-run workflow | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: .tests | |
| snakefile: workflow/BGC | |
| stagein: "conda config --set channel_priority strict" | |
| args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n" | |
| dry-run-ppanggolin: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Dry-run workflow | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: .tests | |
| snakefile: workflow/ppanggolin | |
| stagein: "conda config --set channel_priority strict" | |
| args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n" | |
| dry-run-lsabgc: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Dry-run workflow | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: .tests | |
| snakefile: workflow/lsabgc | |
| stagein: "conda config --set channel_priority strict" | |
| args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n" | |
| unit-test: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - dry-run | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - run: pip install bgcflow_wrapper | |
| - run: pip install pytest-cov | |
| - run: pip install alive-progress | |
| - run: pip install snakemake==8.5.2 | |
| - name: Test coverage | |
| run: pytest --cov=.tests/unit .tests/unit/ | |
| - name: Build coverage file | |
| run: pytest --cov=.tests/unit .tests/unit/ > pytest-coverage.txt | |
| - name: Comment coverage | |
| uses: coroo/pytest-coverage-commentator@v1.0.2 | |
| with: | |
| pytest-coverage: pytest-coverage.txt |