Add bader_exe_path
keyword to BaderAnalysis
and run bader
tests…
#37
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# Runs the complete test suite incl. many external command line dependencies (like Openbabel) | |
# as well as the pymatgen.ext package. Coverage is computed based on this workflow. | |
name: Tests | |
on: | |
push: | |
branches: [master] | |
pull_request: | |
branches: [master] | |
release: | |
types: [published] | |
workflow_dispatch: | |
inputs: | |
task: | |
type: choice | |
options: [tests, release] | |
default: tests | |
description: Only run tests or release a new version of pymatgen to PyPI after tests pass. | |
permissions: | |
contents: read | |
jobs: | |
test: | |
# prevent this action from running on forks | |
if: github.repository == 'materialsproject/pymatgen' | |
strategy: | |
fail-fast: false | |
matrix: | |
# pytest-split automatically distributes work load so parallel jobs finish in similar time | |
os: [ubuntu-latest, windows-latest] | |
python-version: ["3.8", "3.11"] | |
split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] | |
# include/exclude is meant to maximize CI coverage of different platforms and python | |
# versions while minimizing the total number of jobs. We run all pytest splits with the | |
# oldest supported python version (currently 3.8) on windows (seems most likely to surface | |
# errors) and with newest version (currently 3.11) on ubuntu (to get complete and speedy | |
# coverage on unix). Also sample some splits on macos for all python versions | |
exclude: | |
- os: windows-latest | |
python-version: "3.11" | |
- os: ubuntu-latest | |
python-version: "3.8" | |
include: | |
- os: macos-latest | |
python-version: "3.8" | |
split: 1 | |
- os: macos-latest | |
python-version: "3.9" | |
split: 2 | |
- os: macos-latest | |
python-version: "3.10" | |
split: 3 | |
- os: macos-latest | |
python-version: "3.11" | |
split: 4 | |
runs-on: ${{ matrix.os }} | |
env: | |
PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }} | |
MPLBACKEND: Agg # https://github.com/orgs/community/discussions/26434 | |
PMG_TEST_FILES_DIR: ${{ github.workspace }}/test_files | |
GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
cache: pip | |
cache-dependency-path: setup.py | |
- name: Add CLIs to GITHUB_PATH | |
if: runner.os != 'Windows' | |
# This is the way to update env variables in a way that persist for the entire job. | |
run: | | |
for pkg in cmd_line/*; | |
do echo "$(pwd)/cmd_line/$pkg/Linux_64bit" >> "$GITHUB_PATH"; | |
done | |
- name: Install Bader | |
if: runner.os == 'Linux' | |
run: | | |
wget http://theory.cm.utexas.edu/henkelman/code/bader/download/bader_lnx_64.tar.gz | |
tar xvzf bader_lnx_64.tar.gz | |
sudo mv bader /usr/local/bin/ | |
continue-on-error: true | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip wheel | |
python -m pip install numpy cython packaging | |
python -m pip install -e '.[dev,optional]' | |
- name: pytest split ${{ matrix.split }} | |
# to update the test durations, run | |
# pytest --store-durations --durations-path test_files/.pytest-split-durations | |
# and commit the results (requires pip install pytest-split) | |
run: | | |
pytest --cov=pymatgen --splits 10 --group ${{ matrix.split }} --durations-path test_files/.pytest-split-durations | |
- name: Upload coverage | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage-${{ matrix.split }} | |
path: .coverage | |
coverage: | |
needs: test | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python 3.10 | |
uses: actions/setup-python@v4 | |
with: | |
python-version: "3.10" | |
- name: Install Coverage | |
run: python -m pip install coverage | |
- name: Download coverage artifacts | |
continue-on-error: true | |
uses: actions/download-artifact@v3 | |
- name: Run coverage | |
continue-on-error: true | |
run: | | |
coverage combine coverage*/.coverage* | |
coverage report | |
coverage xml | |
- name: Coveralls Python | |
continue-on-error: true | |
uses: AndreMiras/coveralls-python-action@v20201129 | |
build_sdist: | |
if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release') | |
needs: test | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: actions/setup-python@v4 | |
name: Install Python | |
with: | |
python-version: "3.10" | |
- run: python -m pip install build | |
- name: Build sdist | |
run: python -m build --sdist | |
- uses: actions/upload-artifact@v3 | |
with: | |
path: dist/*.tar.gz | |
build_wheels: | |
if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release') | |
needs: test | |
strategy: | |
matrix: | |
os: [ubuntu-latest, macos-latest, windows-latest] | |
python-version: ["38", "39", "310", "311"] | |
runs-on: ${{ matrix.os }} | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Build wheels | |
uses: pypa/cibuildwheel@v2.12.3 | |
env: | |
CIBW_BUILD: cp${{ matrix.python-version }}-* | |
- name: Save artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
path: ./wheelhouse/*.whl | |
release: | |
needs: [build_wheels, build_sdist] | |
if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release') | |
runs-on: ubuntu-latest | |
permissions: | |
# For pypi trusted publishing | |
id-token: write | |
steps: | |
- name: Set up Python 3.11 | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.11 | |
- name: Get build artifacts | |
uses: actions/download-artifact@v3 | |
with: | |
name: artifact | |
path: dist | |
- name: Publish to PyPi | |
uses: pypa/gh-action-pypi-publish@release/v1 | |
with: | |
skip-existing: true | |
verbose: true |