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.. #9470

Workflow file for this run

.github/workflows/test_python_cplusplus.yml at f97e038
name: C++/Python Tests
on:
push:
merge_group:
workflow_dispatch:
pull_request:
branches:
- master
jobs:
build:
name: Tests Ubuntu
# TODO: prepare image with more deps preinstalled
runs-on: ubuntu-22.04
env:
AMICI_PARALLEL_COMPILE: ""
ENABLE_GCOV_COVERAGE: "TRUE"
CI_SONARCLOUD: "TRUE"
strategy:
matrix:
python-version: [ 3.9 ]
steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- uses: actions/checkout@v3
- run: git fetch --prune --unshallow
- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
- run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
# sonar cloud
- run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
- run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
- run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
- run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
- run: echo "${HOME}/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
# TODO: add to ci image
- name: Install sonarcloud tools
run: |
sudo apt-get install nodejs curl unzip \
&& curl --create-dirs -sSLo $HOME/.sonar/sonar-scanner.zip \
https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-$SONAR_SCANNER_VERSION-linux.zip \
&& unzip -o $HOME/.sonar/sonar-scanner.zip -d $HOME/.sonar/ \
&& curl --create-dirs -sSLo $HOME/.sonar/build-wrapper-linux-x86.zip \
https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
&& unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
- name: Install apt dependencies
uses: ./.github/actions/install-apt-dependencies
# install amici dependencies
- name: apt
run: |
sudo apt-get update \
&& sudo apt-get install -y \
cmake \
g++ \
python3-venv \
lcov \
libboost-math-dev
- name: Build AMICI dependencies
run: |
scripts/buildDependencies.sh
- name: Build AMICI
run: |
CI_SONARCLOUD=TRUE scripts/buildAmici.sh
- name: C++ tests
run: |
scripts/run-cpp-tests.sh
- name: Install python package
run: |
scripts/installAmiciSource.sh
- name: Python tests
run: |
source build/venv/bin/activate \
&& pytest \
--ignore-glob=*petab* \
--ignore-glob=*test_splines.py \
--cov=amici \
--cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
--cov-append \
--durations=10 \
${AMICI_DIR}/python/tests
- name: Python tests splines
if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}}
run: |
source build/venv/bin/activate \
&& pytest \
--cov=amici \
--cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
--cov-append \
--durations=10 \
${AMICI_DIR}/python/tests/test_splines.py
- name: Install notebook dependencies
run: |
source build/venv/bin/activate \
&& pip install jax[cpu]
- name: example notebooks
run: |
scripts/runNotebook.sh python/examples/example_*/
- name: doc notebooks
run: |
scripts/runNotebook.sh documentation/GettingStarted.ipynb
- name: Codecov Python
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: build/coverage_py.xml
flags: python
fail_ci_if_error: true
verbose: true
- name: 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
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage.info
flags: cpp
fail_ci_if_error: true
- name: Run sonar-scanner
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')"
osx:
name: Tests OSX
runs-on: macos-latest
steps:
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: 3.9
- uses: actions/checkout@v3
- run: git fetch --prune --unshallow
- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
- run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
# Ensure CMake is using the python version that we will use for the python tests later on
- run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
# install amici dependencies
- name: homebrew
run: |
brew install hdf5 swig gcc cppcheck libomp boost \
&& brew ls -v boost \
&& brew ls -v libomp \
&& echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.81.0_1/lib/" >> $GITHUB_ENV \
&& echo CPPFLAGS="-I /usr/local/Cellar/boost/1.81.0_1/include/" >> $GITHUB_ENV
- name: Build AMICI
run: |
scripts/buildAll.sh
- name: Install python package
run: |
scripts/installAmiciSource.sh
- name: cppcheck
run: |
scripts/run-cppcheck.sh
- name: Python tests
run: |
scripts/run-python-tests.sh
- name: C++ tests
run: |
scripts/run-cpp-tests.sh