Improve test coverage, fix abundance recomputing bug after biotype fi… #136
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| name: Test & lint package & deploy documentation | |
| on: | |
| schedule: | |
| # run every Monday at 15:00 UTC | |
| - cron: "0 15 * * 1" | |
| push: | |
| branches: [main, dev] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: [3.9.16] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} | |
| - name: Install dependencies | |
| run: | | |
| export FLIT_ROOT_INSTALL=1 | |
| python -m pip install --upgrade pip | |
| python -m pip install flit | |
| python -m flit install --deps production | |
| python -m pip install biocframe dolomite dolomite-se summarizedexperiment | |
| python -m pip install black flake8 flake8-docstrings isort flake8-comprehensions mypy | |
| python -m pip install coverage pytest bandit sphinx sphinx-autoapi \ | |
| myst-parser pybiomart pygments sphinx-autodoc-typehints sphinx-rtd-theme furo sphinx_design \ | |
| sphinx-copybutton sphinxcontrib-bibtex sphinxcontrib-mermaid nbsphinx pandoc | |
| sudo apt-get update | |
| sudo apt-get install -y pandoc | |
| - name: Format with black | |
| run: | | |
| python -m black . | |
| - name: Lint with flake8 | |
| run: | | |
| python -m flake8 pytximport | |
| - name: Check imports with isort | |
| run: | | |
| python -m isort --check-only --diff --recursive pytximport | |
| - name: Type check with mypy | |
| run: | | |
| python -m mypy -p pytximport | |
| - name: Check security with bandit | |
| run: | | |
| python -m bandit --verbose --ini .bandit.ini -ll --recursive pytximport | |
| - name: Test with pytest | |
| run: | | |
| coverage run -m pytest --maxfail=10 | |
| coverage xml | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/[email protected] | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |