GHA: Fix actions for PRs from forks (#2219) #5366
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name: PEtab | |
on: | |
push: | |
branches: | |
- develop | |
- master | |
pull_request: | |
branches: | |
- master | |
- develop | |
merge_group: | |
workflow_dispatch: | |
jobs: | |
build: | |
name: PEtab Testsuite | |
runs-on: ubuntu-22.04 | |
env: | |
ENABLE_GCOV_COVERAGE: TRUE | |
strategy: | |
matrix: | |
python-version: [3.9] | |
steps: | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 20 | |
- name: Install apt dependencies | |
uses: ./.github/actions/install-apt-dependencies | |
# install dependencies | |
- name: apt | |
run: | | |
sudo apt-get update \ | |
&& sudo apt-get install -y python3-venv | |
- name: Build BNGL | |
run: scripts/buildBNGL.sh | |
- run: | | |
echo "${HOME}/.local/bin/" >> $GITHUB_PATH | |
echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH | |
echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV | |
# install AMICI | |
- name: Install python package | |
run: scripts/installAmiciSource.sh | |
- name: Install petab | |
run: | | |
source ./build/venv/bin/activate \ | |
&& pip3 install wheel pytest shyaml pytest-cov pysb | |
# retrieve test models | |
- name: Download and install PEtab test suite | |
run: | | |
git clone --depth 1 --branch main \ | |
https://github.com/PEtab-dev/petab_test_suite \ | |
&& source ./build/venv/bin/activate \ | |
&& cd petab_test_suite && pip3 install -e . | |
- name: Run PEtab-related unit tests | |
run: | | |
source ./build/venv/bin/activate \ | |
&& pytest --cov-report=xml:coverage.xml \ | |
--cov=./ python/tests/test_*petab*.py | |
# run test models | |
- name: Run PEtab test suite | |
run: | | |
source ./build/venv/bin/activate \ | |
&& AMICI_PARALLEL_COMPILE=2 pytest -v \ | |
--cov-report=xml:coverage.xml \ | |
--cov-append \ | |
--cov=amici \ | |
tests/petab_test_suite/ | |
- name: Codecov | |
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev' | |
uses: codecov/[email protected] | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: coverage.xml | |
flags: petab | |
fail_ci_if_error: true |