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/
coverage.yml
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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: '3.11'
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
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: ${{runner.workspace}}/nrn
run: |
python -m pip install --upgrade pip -r nrn_requirements.txt
python -m pip install --upgrade -r external/nmodl/requirements.txt
python -m pip install --upgrade -r ci_requirements.txt
- name: Set up Python@${{ 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 pip -r nrn_requirements.txt
python -m pip install --upgrade -r external/nmodl/requirements.txt
python -m pip install --upgrade -r ci_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 }}