Test cofactor networks generated with the CLI #4164
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name: "CI" | |
on: | |
pull_request: | |
branches: | |
- main | |
# Skip CI if changed files only affect the following folders | |
# - docs: documentation changes don't need code validation | |
# See here for more details: https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-excluding-paths | |
paths-ignore: | |
- "docs/*" | |
push: | |
branches: | |
- main | |
schedule: | |
# At 07:00 UTC on Monday and Thursday. | |
- cron: "0 7 * * *" | |
workflow_dispatch: | |
release: | |
types: | |
- published | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.ref }}" | |
cancel-in-progress: true | |
defaults: | |
run: | |
shell: bash -l {0} | |
jobs: | |
tests: | |
runs-on: ${{ matrix.os }} | |
name: "π»-${{matrix.os }} π-${{ matrix.python-version }} ποΈ${{ matrix.pydantic-version }} oechem: ${{ matrix.openeye }}" | |
strategy: | |
fail-fast: false | |
matrix: | |
os: ["ubuntu-latest"] | |
pydantic-version: [">1"] | |
python-version: | |
- "3.10" | |
- "3.11" | |
- "3.12" | |
openeye: ["no"] | |
include: | |
- os: "macos-latest" | |
python-version: "3.12" | |
pydantic-version: ">1" | |
- os: "ubuntu-latest" | |
python-version: "3.11" | |
pydantic-version: "<2" | |
- os: "ubuntu-latest" | |
python-version: "3.11" | |
pydantic-version: ">1" | |
openeye: "yes" | |
- os: "macos-latest" | |
python-version: "3.12" | |
pydantic-version: ">1" | |
omff-version: ">0.13" | |
openeye: ["no"] | |
env: | |
OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: Get current date | |
id: date | |
run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" | |
- name: "Setup Micromamba" | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
micromamba-version: '1.5.6-0' | |
micromamba-binary-path: ~/.local/bin/micromamba | |
environment-file: environment.yml | |
environment-name: openfe_env | |
cache-environment: true | |
cache-downloads: true | |
cache-environment-key: environment-${{ steps.date.outputs.date }} | |
cache-downloads-key: downloads-${{ steps.date.outputs.date }} | |
create-args: >- | |
python=${{ matrix.python-version }} | |
pydantic=${{ matrix.pydantic-version }} | |
init-shell: bash | |
- name: "Install OpenEye" | |
if: ${{ !github.event.pull_request.head.repo.fork | |
&& matrix.openeye == 'yes' }} | |
env: | |
OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }} | |
run: | | |
echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE} | |
micromamba install -c openeye openeye-toolkits | |
python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'oechem license check failed!'" | |
- name: "Install" | |
run: python -m pip install --no-deps -e . | |
- name: "Test imports" | |
run: | | |
# if we add more to this, consider changing to for + env vars | |
python -Ic "import openfe; print(openfe.__version__)" | |
- name: "Environment Information" | |
run: | | |
micromamba info | |
micromamba list | |
pip list | |
- name: "Run tests" | |
env: | |
# Set the OFE_SLOW_TESTS to True if running a Cron job | |
OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }} | |
DUECREDIT_ENABLE: 'yes' | |
run: | | |
pytest -n auto -v --cov=openfe --cov=openfecli --cov-report=xml --durations=10 | |
- name: codecov-pr | |
if: ${{ github.repository == 'OpenFreeEnergy/openfe' | |
&& github.event_name == 'pull_request' }} | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: coverage.xml | |
fail_ci_if_error: False | |
verbose: True | |
flags: fast-tests | |
- name: codecov-merge | |
# we only want to upload a slow report if | |
# 1) it isn't a schedule run | |
# 2) it wasn't from a PR (we don't run slow tests on PRs) | |
if: ${{ github.repository == 'OpenFreeEnergy/openfe' | |
&& github.event_name != 'schedule' | |
&& github.event_name != 'pull_request' }} | |
uses: codecov/codecov-action@v4 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: coverage.xml | |
fail_ci_if_error: False | |
verbose: True | |
flags: slow-tests |