fix: remove hard coded contig names from gcnv wrappers (#489 ) (#490) #1394
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements/test.txt | |
| 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 [black](https://black.readthedocs.io): `make black` | |
| - Please format your Snakemake code with [snakefmt](https://github.com/snakemake/snakefmt): `make snakefmt` | |
| - Please organize your imports [isorts](https://isort.readthedocs.io): `make isort` | |
| - Please ensure that your code passes [flake8](https://flake8.pycqa.org/en/latest/): `make flake8` | |
| 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@v1 | |
| - name: Install Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements/test.txt | |
| pip freeze | |
| - name: Build documentation | |
| run: | | |
| cd docs | |
| make html | |
| testing: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - "3.10" | |
| # - "3.11" # no compatible pysam yet | |
| # - "3.12" # no compatible pysam yet | |
| needs: linting | |
| steps: | |
| - name: Install Python via conda | |
| uses: s-weigand/setup-conda@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| conda-channels: defaults,bioconda,conda-forge | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| with: | |
| lfs: true | |
| fetch-depth: 2 | |
| - name: Install mamba | |
| run: conda install -y mamba>=1.0.0 | |
| - name: Prepare environment.yml file | |
| run: > | |
| cp environment.yml /tmp/environment.yml && sed -i -e | |
| 's/- python/- python=${{ 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 -r requirements/test.txt; 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 |