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pythonpackage.yml
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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