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Avoid silent preequilibration failure in JAX #11481

Avoid silent preequilibration failure in JAX

Avoid silent preequilibration failure in JAX #11481

name: C++/Python Tests
on:
push:
merge_group:
workflow_dispatch:
pull_request:
branches:
- master
- develop
jobs:
ubuntu-cpp-python-tests:
name: C++/Python tests Ubuntu
runs-on: ubuntu-22.04
strategy:
matrix:
python-version: [ "3.11" ]
steps:
- name: Cache
uses: actions/cache@v4
with:
path: |
~/.cache/pooch
key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow
- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
- name: Set up AMICI C++ libraries
uses: ./.github/actions/setup-amici-cpp
- name: Install libsuitesparse-dev
# We don't need libsuitesparse-dev, but let's have it installed,
# to ensure that its presence does not break the build
run: sudo apt-get install -y libsuitesparse-dev
- name: C++ tests
run: scripts/run-cpp-tests.sh
- name: Install python package
run: scripts/installAmiciSource.sh
- name: Check OpenMP support
run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
- name: Python tests (part 1)
run: |
source venv/bin/activate \
&& pytest \
--ignore-glob=*petab* \
--ignore-glob=*test_splines.py \
--ignore-glob=*test_splines_short.py \
--ignore-glob=*test_pysb.py \
--cov=amici \
--cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
--cov-append \
--durations=10 \
${AMICI_DIR}/python/tests
- name: Python tests splines
if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}}
run: |
source venv/bin/activate \
&& pytest \
--cov=amici \
--cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
--cov-append \
--durations=10 \
${AMICI_DIR}/python/tests/test_splines.py
- name: Codecov Python
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/codecov-action@v5
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: build/coverage_py.xml
flags: python
fail_ci_if_error: true
verbose: true
- name: Capture coverage info (lcov)
run: |
lcov --compat-libtool --no-external \
-d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \
-b ${AMICI_DIR} -c -o coverage_cpp.info \
&& lcov --compat-libtool --no-external \
-d ${AMICI_DIR}/python/sdist/build/temp_amici/CMakeFiles/amici.dir/src \
-b ${AMICI_DIR}/python/sdist -c -o coverage_py.info \
&& lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
- name: Codecov CPP
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/codecov-action@v5
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage.info
flags: cpp
fail_ci_if_error: true
- name: Run sonar-scanner
if: ${{ env.SONAR_TOKEN != '' }}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
run: |
sonar-scanner \
-Dsonar.cfamily.build-wrapper-output=bw-output \
-Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')"
ubuntu-python-tests:
name: Python tests Ubuntu
runs-on: ubuntu-22.04
strategy:
matrix:
python-version: [ "3.10" ]
steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache
uses: actions/cache@v4
with:
path: |
~/.cache/pooch
key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow
- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
- name: Set up AMICI C++ libraries
uses: ./.github/actions/setup-amici-cpp
- name: Install python package
run: scripts/installAmiciSource.sh
- name: Python tests
run: |
source venv/bin/activate \
&& pytest \
--cov=amici \
--cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
--cov-append \
--durations=10 \
${AMICI_DIR}/python/tests/test_pysb.py \
${AMICI_DIR}/python/tests/test_splines_short.py
- name: Codecov Python
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/codecov-action@v5
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: build/coverage_py.xml
flags: python
fail_ci_if_error: true
verbose: true
- name: Capture coverage info (lcov)
run: |
lcov --compat-libtool --no-external \
-d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \
-b ${AMICI_DIR} -c -o coverage_cpp.info \
&& lcov --compat-libtool --no-external \
-d ${AMICI_DIR}/python/sdist/build/temp_amici/CMakeFiles/amici.dir/src \
-b ${AMICI_DIR}/python/sdist -c -o coverage_py.info \
&& lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
- name: Codecov CPP
if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
uses: codecov/codecov-action@v5
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage.info
flags: cpp_python
fail_ci_if_error: true
- name: Run sonar-scanner
if: ${{ env.SONAR_TOKEN != '' }}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
run: |
sonar-scanner \
-Dsonar.cfamily.build-wrapper-output=bw-output \
-Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')"
ubuntu-notebook-tests:
name: Notebook tests Ubuntu
runs-on: ubuntu-22.04
strategy:
matrix:
python-version: [ "3.11" ]
steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache
uses: actions/cache@v4
with:
path: |
~/.cache/pooch
key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow
- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
- name: Set up AMICI C++ libraries
uses: ./.github/actions/setup-amici-cpp
- name: Install python package
run: scripts/installAmiciSource.sh
- name: example notebooks
run: scripts/runNotebook.sh python/examples/example_*/
- name: doc notebooks
run: scripts/runNotebook.sh documentation/GettingStarted.ipynb
# TODO: Include notebooks in coverage report
macos_cpp_py:
name: Tests MacOS C++/Python
runs-on: macos-latest
env:
PYTHONFAULTHANDLER: "1"
steps:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow
- name: Install dependencies
uses: ./.github/actions/install-macos-dependencies
- name: homebrew
run: brew install cppcheck
- name: Build AMICI
run: scripts/buildAll.sh
- name: Install python package
run: scripts/installAmiciSource.sh
- name: Check OpenMP support
run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
- name: cppcheck
run: scripts/run-cppcheck.sh
- name: C++ tests
run: scripts/run-cpp-tests.sh
- name: Get Pooch Cache Directory
id: get-pooch-cache
run: |
echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
- name: Cache Pooch Directory
uses: actions/cache@v4
with:
path: ${{ env.pooch-cache }}
key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
- name: Python tests
run: |
# ignore warnings until https://github.com/swig/swig/issues/3061 is resolved
scripts/run-python-tests.sh -W ignore:: \
test_pregenerated_models.py \
test_splines_short.py \
test_misc.py
macos_python:
name: Tests MacOS Python
runs-on: macos-latest
env:
PYTHONFAULTHANDLER: "1"
steps:
- name: Cache
uses: actions/cache@v4
with:
path: |
~/Library/Caches/pooch
key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow
- name: Install dependencies
uses: ./.github/actions/install-macos-dependencies
- name: Install python package
run: |
pip show numpy > /dev/null || python3 -m pip install numpy
scripts/installAmiciSource.sh
- name: Check OpenMP support
run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
- name: Get BioNetGen
run: scripts/buildBNGL.sh
- name: Get Pooch Cache Directory
id: get-pooch-cache
run: |
echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
- name: Cache Pooch Directory
uses: actions/cache@v4
with:
path: ${{ env.pooch-cache }}
key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
- name: Install PEtab benchmark collection
run: |
git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
&& export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
&& source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python
- name: Python tests
run: |
# ignore warnings until https://github.com/swig/swig/issues/3061 is resolved
scripts/run-python-tests.sh -W ignore:: \
--ignore=test_pregenerated_models.py \
--ignore=test_splines_short.py \
--ignore=test_misc.py