feat: revamp somatic sv calling purityploidy estimation #1745
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| jobs: | |
| cancel-previous: | |
| runs-on: ubuntu-latest | |
| if: github.ref != 'refs/heads/main' | |
| steps: | |
| - uses: khan/[email protected] | |
| with: | |
| workflows: "main.yml" | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Install Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.12" | |
| - name: Install dependencies | |
| run: | | |
| pip install -e ".[dev]" | |
| pip freeze | |
| - name: Run linting tools | |
| run: | | |
| make lint | |
| - name: Comment PR | |
| if: github.event_name == 'pull_request' && failure() | |
| uses: marocchino/[email protected] | |
| with: | |
| message: | | |
| - Please format your Python code with [ruff](https://docs.astral.sh/ruff/): `make fmt` | |
| - Please check your Python code with [ruff](https://docs.astral.sh/ruff/): `make check` | |
| - Please format your Snakemake code with [snakefmt](https://github.com/snakemake/snakefmt): `make snakefmt` | |
| You can trigger all lints locally by running `make lint` | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # sphinx-docs: | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # | |
| # - name: Install Python | |
| # uses: actions/setup-python@v5 | |
| # with: | |
| # python-version: "3.12" | |
| # | |
| # - name: Install dependencies | |
| # run: | | |
| # pip install -e ".[docs]" | |
| # pip freeze | |
| # | |
| # - name: Build documentation | |
| # run: | | |
| # cd docs | |
| # make html | |
| testing: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - "3.12" | |
| needs: linting | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| fetch-depth: 2 | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: environment.yml | |
| channels: conda-forge,bioconda,nodefaults | |
| channel-priority: strict | |
| activate-environment: test | |
| - run: which pip | |
| - name: Install some more dependencies via pip | |
| run: pip install '.[test]' # 'pyproject.toml[test]' | |
| - name: Run tests | |
| run: pytest | |
| env: | |
| DIFF_MAIN: ${{ github.event_name == 'pull_request' }} | |
| DIFF_LAST_COMMIT: ${{ github.ref == 'refs/heads/main' }} | |
| - name: Create text report | |
| run: coverage report | |
| - name: Coveralls | |
| uses: AndreMiras/coveralls-python-action@develop |