Benchmark Collection #7312
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name: Benchmark Collection | |
on: | |
push: | |
branches: | |
- develop | |
- master | |
pull_request: | |
branches: | |
- master | |
- develop | |
merge_group: | |
workflow_dispatch: | |
schedule: | |
- cron: '48 4 * * *' | |
jobs: | |
build: | |
name: Benchmark Collection | |
runs-on: ubuntu-22.04 | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: [ "3.11" ] | |
extract_subexpressions: ["true", "false"] | |
env: | |
AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }} | |
steps: | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 20 | |
- name: Install apt dependencies | |
uses: ./.github/actions/install-apt-dependencies | |
- run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH | |
# install AMICI | |
- name: Create AMICI sdist | |
run: pip3 install build && cd python/sdist && python3 -m build --sdist | |
- name: Install AMICI sdist | |
run: | | |
pip3 install --user petab[vis] && \ | |
AMICI_PARALLEL_COMPILE="" pip3 install -v --user \ | |
$(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis] | |
- run: | | |
python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \ | |
&& python3 -m pip install -U sympy | |
# retrieve test models | |
- name: Download and test benchmark collection | |
run: | | |
git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \ | |
&& export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \ | |
&& AMICI_PARALLEL_COMPILE="" tests/benchmark-models/test_benchmark_collection.sh | |
# run gradient checks | |
- name: Run Gradient Checks | |
run: | | |
pip install git+https://github.com/ICB-DCM/fiddy.git \ | |
&& cd tests/benchmark-models && pytest ./test_petab_benchmark.py | |
# upload results | |
- uses: actions/upload-artifact@v4 | |
with: | |
name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }} | |
path: | | |
tests/benchmark-models/computation_times.csv | |
tests/benchmark-models/computation_times.png |