feature added, ##289, 1-3. Now a cls file will write when call gsea f… #321
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: GSEApy | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # see supported version syntax in actions/setup-python. e.g. ">=3.10", "3.x"(latest) | |
| python-version: ["3.7", "3.10", "3.x"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade setuptools | |
| python -m pip install wheel | |
| python -m pip install tqdm | |
| pip install -r requirements.txt | |
| - name: Lint with flake8 | |
| run: | | |
| pip install flake8 flake8-black flake8-isort | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82,BLK100,I001,I002,I003,I004,I005 --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 covarege | |
| # run: | | |
| # cd ${GITHUB_WORKSPACE} | |
| # pip install coverage | |
| # pip install coveralls | |
| # python setup.py install | |
| # # coverage run setup.py test | |
| - name: Test with pytest | |
| run: | | |
| cd ${GITHUB_WORKSPACE} | |
| pip install pytest | |
| pip install pytest-cov | |
| pip install -e . | |
| pytest | |
| build_wheels: | |
| name: Build wheels on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| name: Install Python | |
| with: | |
| python-version: '3.x' | |
| - uses: dtolnay/rust-toolchain@stable | |
| with: | |
| toolchain: stable | |
| - name: Install cibuildwheel | |
| run: | | |
| python -m pip install cibuildwheel twine wheel | |
| - name: Build wheels | |
| run: | | |
| python -m cibuildwheel --output-dir wheelhouse | |
| env: | |
| CIBW_BEFORE_ALL_LINUX: "curl https://sh.rustup.rs -sSf | sh -s -- -y" | |
| CIBW_ENVIRONMENT_LINUX: 'PATH="$PATH:$HOME/.cargo/bin"' | |
| # CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=10.9 | |
| CIBW_MANYLINUX_X86_64_IMAGE: quay.io/pypa/manylinux2014_x86_64:latest | |
| CIBW_MANYLINUX_I686_IMAGE: quay.io/pypa/manylinux2014_i686:latest | |
| CIBW_SKIP: cp36-* pp* *win32 *musl* | |
| CIBW_PRERELEASE_PYTHONS: True | |
| CIBW_BEFORE_BUILD: pip install -U setuptools-rust | |
| # CIBW_TEST_REQUIRES: numpy scipy pandas requests | |