feat: irods download refactoring and new generic sodar downloader with preset for dragen data (#226 ) #222
Workflow file for this run
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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/pull-request-workflow-cancel@1.0.0 | |
| 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_black.txt | |
| pip freeze | |
| - name: Run linting tools | |
| run: | | |
| make lint | |
| - name: Comment PR | |
| if: github.event_name == 'pull_request' && failure() | |
| uses: marocchino/sticky-pull-request-comment@v1.1.0 | |
| with: | |
| message: 'Please format your code with [black](https://black.readthedocs.io): `make black`.' | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| 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: ${{ matrix.python-version }} | |
| conda-channels: defaults,bioconda,conda-forge | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| with: | |
| lfs: true | |
| - name: Install mamba | |
| run: conda install -y mamba | |
| - name: Prepare environment.yaml file | |
| run: > | |
| cp environment.yaml /tmp/environment.yaml && sed -i -e | |
| 's/- python/- python=${{ matrix.python-version }}/' | |
| /tmp/environment.yaml | |
| - name: Update environment using mamba | |
| run: mamba env update --name root --file /tmp/environment.yaml | |
| - name: Save time by installing packages via mamba. | |
| run: mamba install -y pysam | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements/test_black.txt | |
| pip freeze | |
| - name: Run tests | |
| run: pytest | |
| - uses: codecov/codecov-action@v3 |