Backport numpy pinning to 8.2 #8243
Workflow file for this run
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name: NEURON CI | |
concurrency: | |
group: ${{ github.workflow }}#${{ github.ref }} | |
cancel-in-progress: true | |
on: | |
push: | |
branches: | |
- master | |
- release/** | |
pull_request: | |
branches: | |
- master | |
- release/** | |
# TODO : https://github.com/neuronsimulator/nrn/issues/1063 | |
# paths-ignore: | |
# - '**.md' | |
# - '**.rst' | |
# - 'docs/**' | |
env: | |
BUILD_TYPE: Release | |
DESIRED_CMAKE_VERSION: 3.15.0 | |
PY_MIN_VERSION: '3.7' | |
PY_MAX_VERSION: '3.11' | |
jobs: | |
ci: | |
runs-on: ${{ matrix.os }} | |
name: ${{ matrix.os }} - ${{ matrix.config.build_mode }} (${{ matrix.config.cmake_option }}${{ matrix.config.config_options }}${{ matrix.config.matrix_eval }}) | |
timeout-minutes: 45 | |
env: | |
INSTALL_DIR: install | |
SDK_ROOT: $(xcrun --sdk macosx --show-sdk-path) | |
SKIP_WHEELHOUSE_REPAIR: true | |
BUILD_TYPE: Release | |
DESIRED_CMAKE_VERSION: 3.15.0 | |
PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.8' }} | |
PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.11' }} | |
MUSIC_INSTALL_DIR: /opt/MUSIC | |
strategy: | |
matrix: | |
os: [ macOS-12, ubuntu-20.04] | |
config: | |
- { matrix_eval : "CC=gcc-9 CXX=g++-9", build_mode: "setuptools"} | |
- { matrix_eval : "CC=gcc-8 CXX=g++-8", build_mode: "cmake", music: ON} | |
- { matrix_eval : "CC=gcc-9 CXX=g++-9", build_mode: "cmake", python_dynamic: ON} | |
- { matrix_eval : "CC=gcc-7 CXX=g++-7" , build_mode: "cmake", cmake_option: "-DNRN_ENABLE_CORENEURON=ON"} | |
- { matrix_eval : "CC=gcc-7 CXX=g++-7", build_mode: "cmake", cmake_option: "-DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_CORENEURON=ON"} | |
- { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", cmake_option: "-DNRN_ENABLE_PYTHON=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_CORENEURON=ON"} | |
include: | |
- os: ubuntu-22.04 | |
config: | |
build_mode: cmake | |
# TODO: -DCORENRN_ENABLE_NMODL=ON -DNMODL_SANITIZERS=undefined | |
cmake_option: -DNRN_ENABLE_CORENEURON=ON | |
-DNRN_ENABLE_INTERVIEWS=OFF -DCORENRN_SANITIZERS=undefined | |
flag_warnings: ON | |
sanitizer: undefined | |
- os: ubuntu-22.04 | |
config: | |
build_mode: cmake | |
# TODO: -DCORENRN_ENABLE_NMODL=ON -DNMODL_SANITIZERS=address,leak | |
# TODO: CoreNEURON is only LeakSanitizer-clean if we disable MPI | |
cmake_option: -DNRN_ENABLE_CORENEURON=ON | |
-DNRN_ENABLE_INTERVIEWS=OFF -DCORENRN_SANITIZERS=address | |
# TODO: address-leak is the dream, but there are many problems, | |
# including external ones from the MPI implementations | |
sanitizer: address | |
fail-fast: false | |
steps: | |
- name: Setup cmake | |
uses: jwlawson/actions-setup-cmake@v2 | |
with: | |
cmake-version: ${{ env.DESIRED_CMAKE_VERSION }} | |
- name: Fix kernel mmap rnd bits | |
if: ${{matrix.os == 'ubuntu-22.04'}} | |
# Asan in llvm 14 provided in ubuntu 22.04 is incompatible with | |
# high-entropy ASLR in much newer kernels that GitHub runners are | |
# using leading to random crashes: https://reviews.llvm.org/D148280 | |
run: sudo sysctl vm.mmap_rnd_bits=28 | |
- name: Install homebrew packages | |
if: startsWith(matrix.os, 'macOS') | |
run: | | |
brew install ccache coreutils doxygen flex mpich ninja xz autoconf autoconf automake libtool | |
brew unlink mpich | |
brew install openmpi | |
brew install --cask xquartz | |
echo /usr/local/opt/flex/bin >> $GITHUB_PATH | |
# Core https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources | |
echo CMAKE_BUILD_PARALLEL_LEVEL=3 >> $GITHUB_ENV | |
echo CTEST_PARALLEL_LEVEL=3 >> $GITHUB_ENV | |
echo CI_OS_NAME=osx >> $GITHUB_ENV | |
shell: bash | |
- name: Install apt packages | |
if: startsWith(matrix.os, 'ubuntu') | |
run: | | |
sudo apt-get install build-essential ccache libopenmpi-dev \ | |
libmpich-dev libx11-dev libxcomposite-dev mpich ninja-build \ | |
openmpi-bin patchelf | |
# The sanitizer builds use ubuntu 22.04 | |
if [[ "${{matrix.os}}" == "ubuntu-20.04" ]]; then | |
sudo apt-get install g++-7 g++-8 | |
fi | |
# Core https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources | |
echo CMAKE_BUILD_PARALLEL_LEVEL=2 >> $GITHUB_ENV | |
echo CTEST_PARALLEL_LEVEL=2 >> $GITHUB_ENV | |
echo CI_OS_NAME=linux >> $GITHUB_ENV | |
shell: bash | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 2 | |
- name: Set up Python@${{ env.PY_MIN_VERSION }} | |
if: ${{matrix.config.python_dynamic == 'ON'}} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ env.PY_MIN_VERSION }} | |
- name: Install Python@${{ env.PY_MIN_VERSION }} dependencies | |
if: ${{ matrix.config.python_dynamic == 'ON' }} | |
working-directory: ${{runner.workspace}}/nrn | |
run: | | |
python -m pip install --upgrade pip -r nrn_requirements.txt | |
- name: Set up Python@${{ 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 pip -r nrn_requirements.txt | |
- name: Setup MUSIC | |
if: matrix.config.music == 'ON' | |
run: | | |
python3 -m venv music-venv | |
source music-venv/bin/activate | |
python3 -m pip install mpi4py "cython<3" "numpy<2" | |
sudo mkdir -p $MUSIC_INSTALL_DIR | |
sudo chown -R $USER $MUSIC_INSTALL_DIR | |
# Stable build: https://github.com/INCF/MUSIC/archive/refs/heads/switch-to-MPI-C-interface.zip @ f33b66ea9348888eed1761738ab48c23ffc8a0d0 | |
curl -L -o MUSIC.zip https://codeload.github.com/INCF/MUSIC/zip/f33b66ea9348888eed1761738ab48c23ffc8a0d0 | |
unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC | |
./autogen.sh | |
# workaround for MUSIC on MacOS 12 | |
if [[ "${{matrix.os}}" == "macOS-12" ]]; then | |
MPI_CXXFLAGS="-g" MPI_CFLAGS="-g" MPI_LDFLAGS="-g" CC=mpicc CXX=mpicxx ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource | |
else | |
./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource | |
fi | |
make -j install | |
deactivate | |
working-directory: ${{runner.temp}} | |
- name: Register gcc problem matcher | |
if: ${{matrix.config.flag_warnings == 'ON'}} | |
run: echo "::add-matcher::.github/problem-matchers/gcc.json" | |
- name: Register sanitizer problem matcher | |
if: ${{matrix.config.sanitizer}} | |
run: echo "::add-matcher::.github/problem-matchers/${{matrix.config.sanitizer}}.json" | |
- name: Hash config dictionary | |
run: | | |
cat << EOF > matrix.json | |
${{toJSON(matrix.config)}} | |
EOF | |
echo matrix.config JSON: | |
cat matrix.json | |
echo ----- | |
- name: Restore compiler cache | |
uses: actions/cache@v4 | |
with: | |
path: ${{runner.workspace}}/ccache | |
save-always: true | |
key: ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-${{github.sha}} | |
restore-keys: | | |
${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}- | |
${{matrix.os}}-${{hashfiles('matrix.json')}}- | |
- name: Build and Test | |
id: build-test | |
shell: bash | |
working-directory: ${{runner.workspace}}/nrn | |
run: | | |
# OS related | |
if [ "$RUNNER_OS" == "Linux" ]; then | |
export ${MATRIX_EVAL}; | |
export SHELL="/bin/bash" | |
else | |
export CXX=${CXX:-g++}; | |
export CC=${CC:-gcc}; | |
fi | |
if [ "$RUNNER_OS" == "macOS" ]; then | |
# TODO - this is a workaround that was implemented for Azure being reported as getting stuck. | |
# However it does not get stuck: neuron module not found and script goes to interpreter, seeming stuck. | |
# This needs to be addressed and SKIP_EMBEDED_PYTHON_TEST logic removed everywhere. | |
export SKIP_EMBEDED_PYTHON_TEST="true" | |
fi | |
# Python setup | |
export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python/ | |
# Python setup | |
export PYTHON_MIN=$(command -v $PYTHON_MIN_NAME); | |
export PYTHON_MAX=$(command -v $PYTHON_MAX_NAME); | |
export PYTHON=$PYTHON_MAX | |
if [ "$RUNNER_OS" == "macOS" ]; then | |
# Python is not installed as a framework, so we need to writ 'backend: TkAgg' to `matplotlibrc`. | |
# Since we are in a virtual environment, we cannot use `$HOME/matplotlibrc` | |
# The following solution is generic and relies on `matplotlib.__file__` to know where to append backend setup. | |
$PYTHON -c "import os,matplotlib; f =open(os.path.join(os.path.dirname(matplotlib.__file__), 'mpl-data/matplotlibrc'),'a'); f.write('backend: TkAgg');f.close();" | |
fi; | |
# Some logging | |
echo $LANG | |
echo $LC_ALL | |
python3 -c 'import os,sys; os.set_blocking(sys.stdout.fileno(), True)' | |
cmake --version | |
# different builds with CMake | |
if [[ "$BUILD_MODE" == "cmake" ]]; then | |
cmake_args=(-G Ninja) | |
# Sanitizer-specific setup | |
if [[ -n "${{matrix.config.sanitizer}}" ]]; then | |
CC=$(command -v clang-14) | |
CXX=$(command -v clang++-14) | |
symbolizer_path=$(realpath $(command -v llvm-symbolizer-14)) | |
echo symbolizer_path=${symbolizer_path} | |
cmake_args+=(-DCMAKE_BUILD_TYPE=Custom \ | |
-DCMAKE_C_FLAGS="-O1 -g -Wno-writable-strings" \ | |
-DCMAKE_CXX_FLAGS="-O1 -g -Wno-writable-strings" \ | |
-DLLVM_SYMBOLIZER_PATH="${symbolizer_path}" \ | |
-DNRN_SANITIZERS=$(echo ${{matrix.config.sanitizer}} | sed -e 's/-/,/g')) | |
fi | |
cmake_args+=(-DCMAKE_C_COMPILER="${CC}" \ | |
-DCMAKE_C_COMPILER_LAUNCHER=ccache \ | |
-DCMAKE_CXX_COMPILER="${CXX}" \ | |
-DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ | |
-DCMAKE_INSTALL_PREFIX="${INSTALL_DIR}" \ | |
-DNRN_ENABLE_TESTS=ON \ | |
${{matrix.config.cmake_option}}) | |
if [[ "$NRN_ENABLE_PYTHON_DYNAMIC" == "ON" ]]; then | |
cmake_args+=(-DNRN_ENABLE_PYTHON=ON \ | |
-DNRN_ENABLE_PYTHON_DYNAMIC=ON \ | |
-DNRN_PYTHON_DYNAMIC="${PYTHON_MIN};${PYTHON_MAX}" \ | |
-DNRN_ENABLE_CORENEURON=ON) | |
else | |
cmake_args+=(-DPYTHON_EXECUTABLE="${PYTHON}") | |
fi | |
if [[ "$NRN_ENABLE_MUSIC" == "ON" ]]; then | |
cmake_args+=(-DNRN_ENABLE_MUSIC=ON \ | |
-DCMAKE_PREFIX_PATH=${MUSIC_INSTALL_DIR} \ | |
-DMUSIC_ROOT=${MUSIC_INSTALL_DIR}) | |
fi | |
# Enable more warnings in the builds whose compiler warnings we | |
# highlight in the GitHub UI | |
if [[ "${{matrix.config.flag_warnings}}" == "ON" ]]; then | |
cmake_args+=(-DNRN_EXTRA_CXX_FLAGS="-Wall \ | |
-Wno-char-subscripts \ | |
-Wno-unknown-pragmas \ | |
-Wno-unused-variable \ | |
-Wno-unused-function \ | |
-Wno-unused-but-set-variable \ | |
-Wno-reorder \ | |
-Wno-sign-compare \ | |
-Wno-strict-aliasing \ | |
-Wno-missing-braces \ | |
-Wno-mismatched-tags" \ | |
-DNRN_EXTRA_MECH_CXX_FLAGS="") | |
fi | |
mkdir build && cd build | |
echo "Building with: ${cmake_args[@]}" | |
cmake .. "${cmake_args[@]}" | |
if ccache --version | grep -E '^ccache version 4\.(4|4\.1)$' | |
then | |
echo "------- Disable ccache direct mode -------" | |
# https://github.com/ccache/ccache/issues/935 | |
export CCACHE_NODIRECT=1 | |
fi | |
ccache -z | |
# Older versions don't support -v (verbose) | |
ccache -vs 2>/dev/null || ccache -s | |
cmake --build . --parallel | |
ccache -vs 2>/dev/null || ccache -s | |
if [ "$RUNNER_OS" == "macOS" ] | |
then | |
echo $'[install]\nprefix='>src/nrnpython/setup.cfg; | |
fi | |
if [[ "$NRN_ENABLE_PYTHON_DYNAMIC" == "ON" ]]; then | |
echo "--RUNNING BASIC TESTS FROM BUILD DIR--" | |
for python in "${PYTHON_MIN}" "${PYTHON_MAX}" | |
do | |
echo "Using ${python}" | |
NEURONHOME="${PWD}/share/nrn" \ | |
PYTHONPATH="${PWD}/lib/python" \ | |
PATH="${PWD}/bin" \ | |
LD_LIBRARY_PATH="${PWD}/lib:${LD_LIBRARY_PATH}" \ | |
DYLD_LIBRARY_PATH="${PWD}/lib:${DYLD_LIBRARY_PATH}" \ | |
"${python}" -c "from neuron import h; import neuron; neuron.test()" | |
done | |
fi | |
ctest --output-on-failure | |
cmake --build . --target install | |
export PATH="${INSTALL_DIR}/bin:${PATH}" | |
if [[ -f "${INSTALL_DIR}/bin/nrn-enable-sanitizer" ]]; then | |
echo --- bin/nrn-enable-sanitizer --- | |
cat bin/nrn-enable-sanitizer | |
echo --- | |
nrn_enable_sanitizer=${INSTALL_DIR}/bin/nrn-enable-sanitizer | |
nrn_enable_sanitizer_preload="${nrn_enable_sanitizer} --preload" | |
else | |
echo nrn-enable-sanitizer not found, not using it | |
fi | |
elif [[ "$BUILD_MODE" == "setuptools" ]]; then | |
./packaging/python/build_wheels.bash CI; | |
fi; | |
# basic test for cmake when python is not disabled | |
if [[ "$BUILD_MODE" == "cmake" && ! "${cmake_args[*]}" =~ "NRN_ENABLE_PYTHON=OFF" ]]; then | |
$PYTHON --version && ${nrn_enable_sanitizer_preload} $PYTHON -c 'import neuron; neuron.test()' | |
fi; | |
# test neurondemo with cmake | |
if [[ "$BUILD_MODE" != "setuptools" ]]; then | |
${nrn_enable_sanitizer} neurondemo -nogui -c 'demo(4)' -c 'run()' -c 'quit()' | |
fi; | |
# with cmake dynamic check python_min and python_max together | |
if [[ "$BUILD_MODE" == "cmake" && "$NRN_ENABLE_PYTHON_DYNAMIC" == "ON" ]]; then | |
${nrn_enable_sanitizer_preload} $PYTHON_MAX -c 'import neuron; neuron.test()' | |
${nrn_enable_sanitizer_preload} $PYTHON_MIN -c 'import neuron; neuron.test()' | |
fi; | |
# run rxd tests manually if rxd is enabled *and CoreNEURON is | |
# disabled -- otherwise hh-related tests fail | |
if [[ "$BUILD_MODE" == "cmake" \ | |
&& ! "${cmake_args[*]}" =~ "NRN_ENABLE_RX3D=OFF" \ | |
&& ! "${cmake_args[*]}" =~ "NRN_ENABLE_CORENEURON=ON" ]]; then | |
${nrn_enable_sanitizer_preload} $PYTHON ../share/lib/python/neuron/rxdtests/run_all.py | |
fi; | |
if [ "$BUILD_MODE" == "setuptools" ]; then | |
neuron_wheel=wheelhouse/NEURON*.whl; | |
# test with virtual environment | |
${nrn_enable_sanitizer_preload} ./packaging/python/test_wheels.sh $PYTHON $neuron_wheel | |
# test with global installation | |
${nrn_enable_sanitizer_preload} ./packaging/python/test_wheels.sh $PYTHON $neuron_wheel false | |
fi; | |
env: | |
BUILD_MODE: ${{ matrix.config.build_mode }} | |
CCACHE_BASEDIR: ${{runner.workspace}}/nrn | |
CCACHE_DIR: ${{runner.workspace}}/ccache | |
NRN_ENABLE_PYTHON_DYNAMIC : ${{ matrix.config.python_dynamic }} | |
NRN_ENABLE_MUSIC: ${{ matrix.config.music }} | |
PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}" | |
PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}" | |
INSTALL_DIR : ${{ runner.workspace }}/install | |
MATRIX_EVAL: ${{ matrix.config.matrix_eval }} | |
# This step will set up an SSH connection on tmate.io for live debugging. | |
# To enable it, you have to: | |
# * add 'live-debug-ci' 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/neuron-ci.yml`) | |
if: failure() && contains(github.event.pull_request.title, 'live-debug-ci') | |
uses: mxschmitt/action-tmate@v3 | |
# see https://github.com/orgs/community/discussions/26822 | |
final: | |
name: Final CI | |
needs: [ci] | |
if: ${{ always() }} | |
runs-on: ubuntu-latest | |
steps: | |
- name: Check ci matrix all done | |
if: >- | |
${{ | |
contains(needs.*.result, 'failure') | |
|| contains(needs.*.result, 'cancelled') | |
|| contains(needs.*.result, 'skipped') | |
}} | |
run: exit 1 |