Merge pull request #34 from Clinical-Genomics/fix-cli-pip-install #30
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: Crunchy CI | |
| on: [push, pull_request] | |
| jobs: | |
| test-coverage: | |
| name: Test Crunchy | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10"] | |
| steps: | |
| - name: Git checkout | |
| uses: actions/checkout@v2.5.0 | |
| - name: Install and configure Poetry | |
| uses: snok/install-poetry@v1 | |
| - name: Install Dependencies | |
| run: poetry install | |
| - name: Get Conda | |
| uses: conda-incubator/setup-miniconda@v2.2.0 | |
| with: | |
| auto-update-conda: true | |
| # Need to add shell to make conda environments work | |
| - name: Install spring | |
| shell: bash -l {0} | |
| run: | | |
| conda install -c bioconda spring | |
| - name: Install samtools | |
| shell: bash -l {0} | |
| run: | | |
| conda install -c bioconda samtools | |
| - name: Unit tests and coverage | |
| run: | | |
| poetry run pytest --cov=./ --cov-report xml --cov-report term | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3.1.1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests |