fix import #91
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| name: Python package | |
| on: | |
| push: | |
| branches: [ "main", "master" ] | |
| pull_request: | |
| branches: [ "main", "master" ] | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os-version }} | |
| name: ${{ matrix.os-version }} (${{ matrix.python-version }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os-version: ["ubuntu-latest"] | |
| python-version: ["3.9"] # ["3.8", "3.9", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: "Set up Python ${{ matrix.python-version }}" | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: "Install flake8" | |
| run: | | |
| pip install flake8 | |
| - name: "Lint with flake8" | |
| run: | | |
| # 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: "Install miniconda" | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| mamba-version: "*" | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,bioconda | |
| environment-file: environment.yml | |
| - name: "Install pytest" | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install setuptools wheel build pytest | |
| - name: "Test with pytest" | |
| shell: bash -l {0} | |
| run: | | |
| pytest -s |