small changes in blast -> USI accessions #310
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python application | |
| on: | |
| push: | |
| branches: [ spectrumAI ] | |
| pull_request: | |
| branches: [ spectrumAI ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7, 3.8] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Setup Miniconda | |
| uses: conda-incubator/[email protected] | |
| with: | |
| use-mamba: true | |
| auto-activate-base: true | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda install --channel conda-forge --channel bioconda bedtools htslib | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| 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: Test with pytest | |
| shell: bash -l {0} | |
| run: | | |
| python setup.py install | |
| cd pypgatk | |
| python tests/pypgatk_tests.py | |
| - name: Update changelog | |
| uses: heinrichreimer/[email protected] | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Update repo with new version info | |
| uses: EndBug/add-and-commit@v7 | |
| with: | |
| add: CHANGELOG.md | |
| author_name: Release Auto-Commit | |
| author_email: [email protected] | |
| branch: dev | |
| message: Updates version info for ${{github.event.release.name}} | |
| - name: Generate coverage report | |
| shell: bash -l {0} | |
| run: | | |
| pip install pytest | |
| pip install pytest-cov | |
| python setup.py install | |
| cd pypgatk | |
| pytest -s --cov=./ --cov-report=xml tests/* | |