Use a shortcut for globals to reduce time #7822
Workflow file for this run
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name: NEURON Code Coverage | |
concurrency: | |
# Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow | |
group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }} | |
cancel-in-progress: true | |
on: | |
merge_group: | |
push: | |
branches: | |
- master | |
- release/** | |
pull_request: | |
branches: | |
- master | |
- release/** | |
# TODO : https://github.com/neuronsimulator/nrn/issues/1063 | |
# paths-ignore: | |
# - '**.md' | |
# - '**.rst' | |
# - 'docs/**' | |
env: | |
PY_MIN_VERSION: '3.8' | |
PY_MID_VERSION: '3.10' | |
PY_MAX_VERSION: '3.12' | |
jobs: | |
coverage: | |
runs-on: ubuntu-22.04 | |
name: Code Coverage | |
timeout-minutes: 60 | |
env: | |
DISPLAY: ${{ ':0' }} | |
MUSIC_INSTALL_DIR: /opt/MUSIC | |
MUSIC_VERSION: 1.2.0 | |
steps: | |
- name: Install apt packages | |
run: | | |
sudo apt-get install xfonts-100dpi build-essential doxygen lcov libboost-all-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin gpg ninja-build flex bison libfl-dev | |
shell: bash | |
- name: Setup Caliper profiler | |
run: | | |
git clone https://github.com/LLNL/Caliper.git | |
cd Caliper | |
mkdir build && cd build | |
cmake .. | |
make && sudo make install | |
- name: Setup MUSIC@${{ env.MUSIC_VERSION }} | |
run: | | |
python3 -m venv music-venv | |
source music-venv/bin/activate | |
python3 -m pip install mpi4py "cython<3" 'numpy<2' setuptools | |
sudo mkdir -p $MUSIC_INSTALL_DIR | |
sudo chown -R $USER $MUSIC_INSTALL_DIR | |
curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip | |
unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC | |
./autogen.sh | |
./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource | |
make -j install | |
deactivate | |
working-directory: ${{runner.temp}} | |
- name: Setup Xvfb | |
run: | | |
sudo apt-get install xvfb | |
sudo /usr/bin/Xvfb $DISPLAY -screen 0 1600x1200x24 -noreset -nolock -shmem & # run in bg | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 2 | |
- name: Clone nmodl | |
working-directory: ${{runner.workspace}}/nrn | |
run: | | |
git submodule update --init --recursive --force --depth 1 -- external/nmodl | |
- name: Set up Python@${{ env.PY_MIN_VERSION }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ env.PY_MIN_VERSION }} | |
- name: Install Python@${{ env.PY_MIN_VERSION }} dependencies | |
working-directory: ${{runner.workspace}}/nrn | |
run: | | |
python -m pip install --upgrade -r external/nmodl/requirements.txt | |
python -m pip install --upgrade -r ci_requirements.txt | |
python -m pip install --upgrade pip -r nrn_requirements.txt | |
- name: Set up Python@${{ env.PY_MID_VERSION }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ env.PY_MID_VERSION }} | |
- name: Set up Python@${{ env.PY_MAX_VERSION }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ env.PY_MAX_VERSION }} | |
- name: Install Python@${{ env.PY_MAX_VERSION }} dependencies | |
working-directory: ${{runner.workspace}}/nrn | |
run: | | |
python -m pip install --upgrade -r external/nmodl/requirements.txt | |
python -m pip install --upgrade -r ci_requirements.txt | |
python -m pip install --upgrade pip -r nrn_requirements.txt | |
- name: Build & Test | |
id: build-test | |
shell: bash | |
working-directory: ${{runner.workspace}}/nrn | |
run: | | |
export SHELL="/bin/bash" | |
# Compiler setup | |
export CC=gcc | |
export CXX=g++ | |
# Python setup | |
export PYTHON_MIN=$(which $PYTHON_MIN_NAME); | |
export PYTHON_MID=$(which $PYTHON_MID_NAME); | |
export PYTHON_MAX=$(which $PYTHON_MAX_NAME); | |
mkdir build && cd build; | |
# CMake options & flags | |
cmake_args=(-G Ninja \ | |
-DCMAKE_BUILD_TYPE=Debug \ | |
-DCMAKE_C_COMPILER="$CC" \ | |
-DCMAKE_CXX_COMPILER="$CXX" \ | |
-DNRN_ENABLE_BACKTRACE=ON \ | |
-DNRN_ENABLE_CORENEURON=ON \ | |
-DNRN_ENABLE_COVERAGE=ON \ | |
-DNRN_ENABLE_INTERVIEWS=ON \ | |
-DNRN_ENABLE_MPI=ON \ | |
-DNRN_ENABLE_PERFORMANCE_TESTS=OFF \ | |
-DNRN_ENABLE_PROFILING=ON \ | |
-DNRN_ENABLE_PYTHON=ON \ | |
-DNRN_ENABLE_PYTHON_DYNAMIC=ON \ | |
-DNRN_PYTHON_DYNAMIC="${PYTHON_MIN};${PYTHON_MAX}" \ | |
-DNRN_PYTHON_EXTRA_FOR_TESTS=${PYTHON_MID} \ | |
-DNRN_ENABLE_TESTS=ON \ | |
-DNRN_ENABLE_MUSIC=ON \ | |
-DCMAKE_PREFIX_PATH="${MUSIC_INSTALL_DIR}" \ | |
-DMUSIC_ROOT="${MUSIC_INSTALL_DIR}") | |
cmake .. "${cmake_args[@]}" | |
# Coverage | |
# The Linux runners apparently have 2 cores, but jobs were being killed when we did not specify this explicitly. | |
# https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources | |
# By default we get a modern version of CMake that understands --parallel. | |
cmake --build . --parallel 2 | |
cmake --build . --target cover_baseline | |
xvfb-run ctest --rerun-failed --output-on-failure; | |
for python in "${PYTHON_MIN}" "${PYTHON_MAX}" | |
do | |
echo "Using ${python}" | |
NEURONHOME="${PWD}/share/nrn" \ | |
PYTHONPATH="${PWD}/lib/python:${PYTHONPATH}" \ | |
PATH="${PWD}/bin:${PATH}" \ | |
LD_LIBRARY_PATH="${PWD}/lib:${LD_LIBRARY_PATH}" \ | |
DYLD_LIBRARY_PATH="${PWD}/lib:${DYLD_LIBRARY_PATH}" \ | |
"${python}" -c "from neuron import h; import neuron; neuron.test();neuron.test_rxd();" | |
done | |
cmake --build . --target cover_collect | |
cmake --build . --target cover_combine | |
env: | |
MATRIX_EVAL: "CC=gcc CXX=g++" | |
PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}" | |
PYTHON_MID_NAME: "python${{ env.PY_MID_VERSION }}" | |
PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}" | |
# This step will set up an SSH connection on tmate.io for live debugging. | |
# To enable it, you have to: | |
# * add 'live-debug-coverage' to your PR title | |
# * push something to your PR branch (note that just re-running the pipeline disregards the title update) | |
- name: live debug session on failure (manual steps required, check `.github/coverage.yml`) | |
if: failure() && contains(github.event.pull_request.title, 'live-debug-coverage') | |
uses: mxschmitt/action-tmate@v3 | |
- uses: codecov/codecov-action@v4 | |
with: | |
directory: ./build | |
fail_ci_if_error: true | |
verbose: true | |
token: ${{ secrets.CODECOV_TOKEN }} |