Merge branch 'master' into mingw #2022
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| name: Python package | |
| on: [push, pull_request] | |
| jobs: | |
| code-qc: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Lint with flake8 | |
| run: | | |
| python -m pip install flake8 | |
| ./scripts/run_linting.sh | |
| - name: Check type hints. | |
| run: | | |
| python -m pip install mypy | |
| pip install -r requirements.types.txt | |
| ./scripts/run_mypy.sh | |
| build-sdist: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Set up R ${{ matrix.r-version }} | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: release | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install setuptools build | |
| - name: Build sdist | |
| run: | | |
| python -m build -o dist/ --sdist . | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: rpy2-sdist | |
| path: dist/rpy2-*.tar.gz | |
| build-wheel-posix: | |
| runs-on: ${{ matrix.os }} | |
| continue-on-error: false | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", "3.11"] | |
| r-version: [release] | |
| os: [ubuntu-latest, macOS-latest, macos-14] | |
| exclude: | |
| - os: macos-14 | |
| python-version: 3.8 | |
| - os: macos-14 | |
| python-version: 3.9 | |
| - os: macos-14 | |
| python-version: "3.10" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Set up R ${{ matrix.r-version }} | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install setuptools build | |
| - name: Build wheel | |
| run: | | |
| python -m build -o dist/ --wheel . | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: rpy2-${{ matrix.os }}-py${{ matrix.python-version }}-r${{ matrix.r-version }} | |
| path: dist/rpy2-*.whl | |
| build-wheel-windows: | |
| runs-on: ${{ matrix.os }} | |
| continue-on-error: true | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", "3.11"] | |
| r-version: [release] | |
| os: [windows-latest] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Set up R ${{ matrix.r-version }} | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install setuptools build | |
| - name: Build wheel (no options) | |
| run: | | |
| python -m build -o dist/ --wheel . | |
| - name: Build wheel - windows | |
| run: | | |
| python -m build -o dist/ --wheel -C--global-option=--verbose -C--build-option="build --compiler=mingw32" . | |
| test: | |
| needs: [build-sdist] | |
| runs-on: ${{ matrix.os }} | |
| continue-on-error: ${{ matrix.experimental }} | |
| strategy: | |
| max-parallel: 4 | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", "3.11"] | |
| r-version: ['release'] | |
| os: [ubuntu-latest, ubuntu-20.04, macOS-latest] | |
| experimental: [false] | |
| venv_activate: ["source pyenv_base/bin/activate"] | |
| ld_libpath: ["export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}"] | |
| include: | |
| - os: windows-latest | |
| experimental: true | |
| r-version: 'release' | |
| python-version: 3.8 | |
| venv_activate: "" | |
| ld_libpath: "" | |
| exclude: | |
| - os: macOS-latest | |
| r-version: 'release' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Set up R ${{ matrix.r-version }} | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r-version }} | |
| - name: Create base virtualenv (non-windows) | |
| if: matrix.os != 'windows-latest' | |
| run: | | |
| python -m venv pyenv_base | |
| ${{ matrix.venv_activate }} | |
| python -m pip install -U pip wheel | |
| - name: Create base virtualenv (windows) | |
| if: matrix.os == 'windows-latest' | |
| shell: cmd | |
| run: | | |
| python -m pip install -U pip wheel | |
| - name: Install extra dependencies | |
| if: matrix.os == 'windows-latest' && matrix.python-version == '3.8' | |
| run: | | |
| echo "Bug in setuptools requires update" | |
| ${{ matrix.venv_activate }} | |
| python -m pip install --upgrade setuptools pycparser | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: rpy2-sdist | |
| path: dist/ | |
| - name: Source package path. | |
| shell: bash | |
| run: echo "RPY2_SRC_DIST=$(ls -1 dist/rpy2-*.tar.gz | tail -n 1)" >> $GITHUB_ENV | |
| - name: Install package (non-Windows) | |
| if: matrix.os != 'windows-latest' | |
| run: | | |
| ${{ matrix.venv_activate }} | |
| pip install $RPY2_SRC_DIST | |
| - name: Get the situation (windows) | |
| if: matrix.os == 'windows-latest' | |
| shell: cmd | |
| run: | | |
| python -m pip install packaging | |
| python rpy2/situation.py | |
| python -m pip uninstall --yes packaging | |
| - name: Install package | |
| # if: matrix.os == 'windows-latest' | |
| shell: bash | |
| run: | | |
| ${{ matrix.venv_activate }} | |
| RPY2_API_FORCE=True pip install $RPY2_SRC_DIST | |
| - name: Test with minimal dependencies | |
| run: | | |
| ${{ matrix.ld_libpath }} | |
| ${{ matrix.venv_activate }} | |
| python -m pip install $RPY2_SRC_DIST'[test_minimal]' | |
| bash -e ./scripts/run_test_min_deps.sh | |
| - name: Test with numpy | |
| run: | | |
| ${{ matrix.ld_libpath }} | |
| ${{ matrix.venv_activate }} | |
| python -m pip install $RPY2_SRC_DIST'[numpy]' | |
| bash -e ./scripts/run_test_numpy.sh | |
| - name: Test with pandas | |
| run: | | |
| ${{ matrix.ld_libpath }} | |
| ${{matrix.venv_activate }} | |
| python -m pip install $RPY2_SRC_DIST'[pandas]' | |
| bash -e ./scripts/run_test_pandas.sh | |
| - name: Test with ipython | |
| run: | | |
| ${{ matrix.ld_libpath }} | |
| ${{matrix.venv_activate }} | |
| python -m pip install ipython | |
| bash -e ./scripts/run_test_pandas.sh | |
| - name: Set RSPM | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| echo "RSPM=\"https://packagemanager.rstudio.com/cran/__linux__/$(lsb_release -sc)/latest\"" >> $GITHUB_ENV | |
| - name: Install R dependencies | |
| run: | | |
| install.packages(c("ggplot2", "dplyr", "tidyr", "dbplyr", "lazyeval", "rlang")) | |
| shell: Rscript {0} | |
| - name: Test with R deps | |
| if: matrix.os != 'windows-latest' | |
| run: | | |
| ${{ matrix.ld_libpath }} | |
| ${{ matrix.venv_activate }} | |
| bash -e ./scripts/run_test_rdeps.sh | |
| - name: Test with R deps (windows) | |
| continue-on-error: true | |
| if: matrix.os == 'windows-latest' | |
| run: | | |
| ${{ matrix.ld_libpath }} | |
| ${{ matrix.venv_activate }} | |
| pytest --cache-clear --cov-append --cov-report=xml --cov-report=term --cov=rpy2.rinterface_lib --cov=rpy2.rinterface --cov=rpy2.rlike --cov=rpy2.robjects rpy2/tests/robjects/lib | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| if: matrix.os == 'ubuntu-20.04' && matrix.python-version == '3.8' && matrix.r-version == 'release' | |
| env: | |
| OS: ${{ runner.os }} | |
| PYTHON: ${{ matrix.python-version }} | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| env_vars: OS,PYTHON |