Fix rdkit tests #5874
Workflow file for this run
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name: GH Actions CI | |
on: | |
push: | |
branches: | |
- develop | |
pull_request: | |
branches: | |
- develop | |
workflow_dispatch: | |
concurrency: | |
# Probably overly cautious group naming. | |
# Commits to develop will cancel each other, but PRs will only cancel | |
# commits within the same PR | |
group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}" | |
cancel-in-progress: true | |
defaults: | |
run: | |
shell: bash -l {0} | |
jobs: | |
main_tests: | |
if: "github.repository == 'MDAnalysis/mdanalysis'" | |
runs-on: ${{ matrix.os }} | |
timeout-minutes: 60 | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest, ] | |
python-version: ["3.10", "3.11", "3.12"] | |
full-deps: [true, ] | |
codecov: [true, ] | |
include: | |
- name: macOS_monterey_py311 | |
os: macOS-12 | |
python-version: "3.12" | |
full-deps: true | |
codecov: true | |
- name: macOS_14_arm64_py312 | |
os: macOS-14 | |
python-version: "3.12" | |
full-deps: false | |
codecov: true | |
- name: numpy_min | |
os: ubuntu-latest | |
python-version: "3.10" | |
full-deps: false | |
codecov: true | |
numpy: numpy=1.23.2 | |
- name: asv_check | |
os: ubuntu-latest | |
python-version: "3.10" | |
full-deps: true | |
codecov: false | |
extra-pip-deps: asv | |
env: | |
CYTHON_TRACE_NOGIL: 1 | |
MPLBACKEND: agg | |
steps: | |
- uses: actions/checkout@v4 | |
- name: setup_os | |
uses: ./.github/actions/setup-os | |
with: | |
os-type: ${{ matrix.os }} | |
- name: setup_micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-name: mda | |
create-args: >- | |
python=${{ matrix.python-version }} | |
pip | |
# using jaime's shim to avoid pulling down the cudatoolkit | |
condarc: | | |
channels: | |
- jaimergp/label/unsupported-cudatoolkit-shim | |
- conda-forge | |
- bioconda | |
- name: install_deps | |
uses: ./.github/actions/setup-deps | |
with: | |
micromamba: true | |
full-deps: ${{ matrix.full-deps }} | |
# in most cases will just default to empty, i.e. pick up max version from other deps | |
numpy: ${{ matrix.numpy }} | |
extra-pip-deps: ${{ matrix.extra-pip-deps }} | |
- name: build_srcs | |
uses: ./.github/actions/build-src | |
with: | |
build-tests: true | |
build-docs: false | |
# The standard mdanalysis deployment is to build with the | |
# oldest supported numpy version and then use whatever new | |
# numpy version we want at runtime. To do this we ensure | |
# that we use build isolation | |
isolation: true | |
- name: check_deps | |
run: | | |
micromamba list | |
pip list | |
- name: run_tests | |
if: contains(matrix.name, 'asv_check') != true | |
run: | | |
PYTEST_FLAGS="--disable-pytest-warnings --durations=50" | |
if [ ${{ matrix.codecov }} = "true" ]; then | |
PYTEST_FLAGS="${PYTEST_FLAGS} --cov-config=.coveragerc --cov=MDAnalysis --cov-report=xml" | |
fi | |
echo $PYTEST_FLAGS | |
pytest -n auto --timeout=200 testsuite/MDAnalysisTests $PYTEST_FLAGS | |
- name: run_asv | |
if: contains(matrix.name, 'asv_check') | |
run: | | |
cd benchmarks | |
time python -m asv check -E existing | |
- name: codecov | |
if: matrix.codecov | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: coverage.xml | |
fail_ci_if_error: False | |
verbose: True | |
build_docs: | |
if: "github.repository == 'MDAnalysis/mdanalysis'" | |
runs-on: ubuntu-latest | |
timeout-minutes: 15 | |
env: | |
CYTHON_TRACE_NOGIL: 1 | |
MPLBACKEND: agg | |
steps: | |
- uses: actions/checkout@v4 | |
- name: setup_micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-name: mda | |
create-args: >- | |
python=3.10 | |
pip | |
# using jaime's shim to avoid pulling down the cudatoolkit | |
condarc: | | |
channels: | |
- jaimergp/label/unsupported-cudatoolkit-shim | |
- conda-forge | |
- bioconda | |
- name: install_deps | |
uses: ./.github/actions/setup-deps | |
with: | |
micromamba: true | |
full-deps: true | |
extra-pip-deps: "docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils" | |
extra-conda-deps: "mdanalysis-sphinx-theme>=1.3.0" | |
- name: build_srcs | |
uses: ./.github/actions/build-src | |
with: | |
build-tests: true | |
build-docs: true | |
isolation: true | |
- name: doctests | |
if: github.event_name == 'pull_request' | |
continue-on-error: true | |
run: | | |
cd package && sphinx-build -b doctest --keep-going ./doc/sphinx/source ./doc/html | |
- name: deploy_docs | |
if: github.event_name != 'pull_request' | |
env: | |
GH_USER: github-actions | |
GH_EMAIL: "github-action@users.noreply.github.com" | |
GH_REPOSITORY: "github.com/${{ github.repository }}.git" | |
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
URL: https://docs.mdanalysis.org | |
run: | | |
# set up environment variables | |
# cannot execute bash to make variables in env section | |
# export URL for the Python script $UPDATE_JSON | |
export URL | |
export VERSION=$(cd package/MDAnalysis; python -c 'import version; print(version.__version__)') | |
UPDATE_JSON=$(pwd)/maintainer/update_json_stubs_sitemap.py | |
BRANCH="${GITHUB_REF#refs/heads/}" | |
# the below turns off non-blocking as it causes large writes to stdout to fail | |
# (see https://github.com/travis-ci/travis-ci/issues/4704) | |
# commented out as this is not a problem with gh-actions | |
# python -c 'import os,sys,fcntl; flags = fcntl.fcntl(sys.stdout, fcntl.F_GETFL); fcntl.fcntl(sys.stdout, fcntl.F_SETFL, flags&~os.O_NONBLOCK);' | |
cd package/doc/html/ | |
# move docs into version subfolder | |
mkdir ../${VERSION} && mv * ../${VERSION} && mv ../${VERSION} $VERSION | |
# set up git | |
REV=$(git rev-parse --short HEAD) | |
git init | |
git config user.name $GH_USER | |
git config user.email $GH_EMAIL | |
git remote add upstream "https://${GH_USER}:${GH_TOKEN}@${GH_REPOSITORY}" | |
git fetch --depth 50 upstream $BRANCH gh-pages | |
git reset upstream/gh-pages | |
# redirects and copies | |
mkdir latest | |
python $UPDATE_JSON | |
touch . | |
touch .nojekyll | |
git add -A ${VERSION}/ | |
git add .nojekyll versions.json *.xml *.html index.html latest | |
for dirname in dev stable documentation_pages ; do | |
if [ -d $dirname ]; then git add $dirname; fi | |
done | |
# check for anything to commit | |
# https://stackoverflow.com/questions/3878624/how-do-i-programmatically-determine-if-there-are-uncommited-changes | |
git diff-index --quiet HEAD -- || git commit -m "rebuilt html docs for version ${VERSION} from branch ${BRANCH} with sphinx at ${REV}" | |
git push -q upstream HEAD:gh-pages | |
sdist_check_and_build: | |
if: "github.repository == 'MDAnalysis/mdanalysis'" | |
runs-on: ubuntu-latest | |
timeout-minutes: 30 | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: 3.11 | |
- name: install_deps | |
run: | | |
python -m pip install -U pip pipx wheel build | |
python -m pip install twine "readme-renderer>=34.0" pytest-xdist pytest-timeout | |
- name: build_package_sdist | |
run: | | |
pipx run build --sdist --outdir dist package | |
- name: build_testsuite_sdist | |
run: | | |
pipx run build --sdist --outdir dist testsuite | |
- name: check_package_build | |
run: | | |
DISTRIBUTION=$(ls -t1 dist/mdanalysis-*.tar.gz | head -n1) | |
test -n "${DISTRIBUTION}" || { echo "no distribution dist/MDAnalysis-*.tar.gz found"; exit 1; } | |
twine check $DISTRIBUTION | |
- name: check_testsuite_build | |
run: | | |
DISTRIBUTION=$(ls -t1 dist/mdanalysistests-*.tar.gz | head -n1) | |
test -n "${DISTRIBUTION}" || { echo "no distribution dist/MDAnalysisTests-*.tar.gz found"; exit 1; } | |
twine check $DISTRIBUTION | |
- name: install sdist | |
working-directory: ./dist | |
run: | | |
ls -a . | |
python -m pip install mdanalysis-*.tar.gz | |
python -m pip install mdanalysistests-*.tar.gz | |
- name: run tests | |
working-directory: ./dist | |
run: python -m pytest --timeout=200 -n auto --pyargs MDAnalysisTests |