chore(CI): Run workflow on PRs #225
Workflow file for this run
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| name: CapCruncher CI | |
| on: | |
| push: | |
| pull_request: | |
| branches: [master, develop] | |
| env: | |
| CACHE_NUMBER: 1 | |
| jobs: | |
| install-and-test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Linux dependencies | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libcurl4-openssl-dev | |
| # - name: Install Mac dependencies | |
| # if: matrix.os == 'macos-latest' | |
| # run: | | |
| # brew install curl-openssl coreutils | |
| - name: Restore bowtie2 cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: tests/data/data_for_pipeline_run/chr14_bowtie2_indicies/*.bt2 | |
| key: ${{ env.CACHE_NUMBER }} | |
| id: bowtie2_cache | |
| - name: Get Date | |
| id: get-date | |
| run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: test | |
| use-mamba: true | |
| - name: Cache Conda env | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: conda-${{ runner.os }}--${{ runner.arch }}--${{ | |
| steps.get-date.outputs.today }}-${{ | |
| hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER}} | |
| env: | |
| # Increase this value to reset cache if etc/example-environment.yml has not changed | |
| CACHE_NUMBER: 0 | |
| id: cache-conda-env | |
| - name: Update environment | |
| run: mamba env update -n test -f environment.yml | |
| if: steps.cache-conda-env.outputs.cache-hit != 'true' | |
| - name: Check installed packages | |
| shell: bash -el {0} | |
| run: | | |
| mamba info | |
| - name: Install the package | |
| shell: bash -el {0} | |
| run: | | |
| pip install .[full] | |
| - name: Test with pytest and generate report | |
| shell: bash -el {0} | |
| run: | | |
| pip install pytest-cov pytest-lazy-fixture pytest-order pytest-xdist | |
| pytest -vv -s --log-cli-level info --cov=./ --cov-report=xml --cores 2 | |
| - name: Upload Coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| env_vars: OS,PYTHON | |
| token: ${{secrets.CODECOV_TOKEN}} | |
| fail_ci_if_error: true | |
| files: ./coverage.xml | |
| verbose: true |