fix: update nbitk dependency version to >=0.5.3 in pyproject.toml #351
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| name: Python package | |
| on: | |
| push: | |
| branches: [ "main", "refactor" ] | |
| tags: | |
| - 'v*' # Trigger on any tag that starts with 'v' | |
| pull_request: | |
| branches: [ "main" ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Important for setuptools_scm to determine the version | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: barcode_validator | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| - name: Install additional test dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda activate barcode_validator | |
| pip install pytest pytest-cov flake8 | |
| pip install -e . | |
| - name: Test environment | |
| shell: bash -l {0} | |
| run: | | |
| conda activate barcode_validator | |
| conda list | |
| which python | |
| which blastn | |
| which hmmalign | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| run: | | |
| conda activate barcode_validator | |
| # 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 | |
| shell: bash -l {0} | |
| run: | | |
| conda activate barcode_validator | |
| pytest --cov=barcode_validator --cov-report=xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| fail_ci_if_error: false | |
| publish: | |
| needs: build # Only run if the build job passes | |
| if: startsWith(github.ref, 'refs/tags/v') # Only run on tag pushes starting with 'v' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Important for setuptools_scm to determine the version | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: barcode_validator | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| - name: Install build dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda activate barcode_validator | |
| pip install build twine | |
| - name: Build package | |
| shell: bash -l {0} | |
| run: | | |
| conda activate barcode_validator | |
| python -m build | |
| - name: Publish package | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |