docker: update CNVkit package installed to 0.9.11 #137
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| paths-ignore: | |
| - 'docs/**' | |
| - '*.md' | |
| - '*.rst' | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| - '*.md' | |
| - '*.rst' | |
| jobs: | |
| tests: | |
| name: ${{ matrix.name }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - {name: '3.12', python: '3.12', os: ubuntu-latest, tox: py312} | |
| - {name: '3.12-MacOS', python: '3.12', os: macos-latest, tox: py312} | |
| - {name: '3.11', python: '3.11', os: ubuntu-latest, tox: py311} | |
| - {name: '3.11-min', python: '3.11', os: ubuntu-latest, tox: "py311-min"} | |
| - {name: '3.10', python: '3.10', os: ubuntu-latest, tox: py310} | |
| - {name: '3.9', python: '3.9', os: ubuntu-latest, tox: py39} | |
| - {name: '3.9-min', python: '3.9', os: ubuntu-latest, tox: "py39-min"} | |
| - {name: '3.8', python: '3.8', os: ubuntu-latest, tox: py38} | |
| - {name: '3.8-MacOS', python: '3.8', os: macos-latest, tox: py38} | |
| - {name: Typing, python: '3.12', os: ubuntu-latest, tox: typing} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: 'pip' | |
| cache-dependency-path: 'requirements/*.txt' | |
| - name: Update pip | |
| run: | | |
| pip install -U setuptools wheel | |
| python -m pip install -U pip | |
| - name: Install Linux dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y liblzma-dev python3-dev r-bioc-dnacopy zlib1g-dev | |
| - name: Install Mac OS dependencies | |
| if: runner.os == 'macOS' | |
| run: | | |
| Rscript --no-environ -e "install.packages('BiocManager', repos='https://cloud.r-project.org'); BiocManager::install('DNAcopy')" | |
| - name: Install test runner tools | |
| run: pip install flake8 pytest tox | |
| - name: Lint with flake8 | |
| run: | | |
| # Stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| - name: Cache mypy | |
| if: matrix.tox == 'typing' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ./.mypy_cache | |
| key: mypy|${{ matrix.python }}|${{ hashFiles('pyproject.toml') }} | |
| - name: Run the unit test suite | |
| run: tox -e ${{ matrix.tox }} | |