Fix error handling with class representation not found. (#1093) #2003
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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] | |
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 | |
test: | |
needs: [build-sdist] | |
runs-on: ${{ matrix.os }} | |
continue-on-error: ${{ matrix.experimental }} | |
strategy: | |
max-parallel: 4 | |
matrix: | |
python-version: [3.8, 3.9, "3.10", "3.11"] | |
r-version: ['release'] | |
os: [ubuntu-latest, ubuntu-20.04, macOS-latest] | |
experimental: [false] | |
venv_activate: ["source pyenv_base/bin/activate"] | |
ld_libpath: ["export LD_LIBRARY_PATH=$(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: Install package (Windows) | |
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 |