Merge branch 'main' of github.com:cribbslab/TallyTriN #84
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Python package | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| jobs: | |
| build: | |
| name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.7", "3.8"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Cache conda | |
| uses: actions/cache@v3 | |
| env: | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | |
| ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ | |
| hashFiles('conda/environment.yml') }} | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge, bioconda, defaults | |
| channel-priority: true | |
| activate-environment: tallytrin | |
| environment-file: conda/environment.yml | |
| miniforge-variant: Mambaforge | |
| - name: Show conda | |
| run: | | |
| conda info | |
| conda list | |
| mamba list | |
| - name: Install tallytrin | |
| run: pip install -e . | |
| - name: Lint with flake8 | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest pep8 nose | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| pytest -v tests/test_import.py | |
| pytest -v tests/test_style.py | |
| pytest -v tests/test_pipeline_control.py |