feat: automatically retrieve references/annotations and cache them #1597
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| 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: Install Python via conda | |
| uses: s-weigand/setup-conda@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| conda-channels: defaults,bioconda,conda-forge | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| fetch-depth: 2 | |
| - name: Install mamba | |
| run: conda install -y mamba>=1.0.0 | |
| - name: Prepare environment.yml file | |
| run: > | |
| cp environment.yml /tmp/environment.yml && sed -i -e | |
| 's/- python=.*/- python=${{ matrix.python-version }}/' | |
| /tmp/environment.yml | |
| - name: Update environment using mamba | |
| run: mamba env update --name root --file /tmp/environment.yml | |
| - name: Fail early on htslib etc. problems | |
| run: | | |
| set -euo pipefail | |
| bgzip -c /dev/null >/dev/null | |
| samtools version | |
| bcftools version | |
| - name: Install some more dependencies via pip | |
| # Workaround - see https://github.com/pytest-dev/pytest/issues/10420#issuecomment-1290697849 | |
| run: pip install ".[test]"; pip install --ignore-installed py | |
| - 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 |