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test_petab_test_suite.yml
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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