[REP-91] Avoid raising exception when point process is missing in a section #1284
Workflow file for this run
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| name: neurodamus build and test | |
| on: | |
| schedule: | |
| # every evening at 20:00 UTC | |
| - cron: '0 20 * * *' | |
| pull_request: | |
| branches: | |
| - main | |
| push: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| inputs: | |
| NEURON_BRANCH: | |
| description: 'NEURON branch to use' | |
| required: false | |
| LIBSONATA_REPORT_BRANCH: | |
| description: 'libsonatareport branch to use' | |
| required: false | |
| LIBSONATA_BRANCH: | |
| description: 'libsonata branch to use' | |
| required: false | |
| NEURODAMUS_MODELS_BRANCH: | |
| description: 'neurodamus-models branch to use' | |
| required: false | |
| env: | |
| NEURON_COMMIT_ID: 'c48d7d5' | |
| RDMAV_FORK_SAFE: '1' | |
| jobs: | |
| simulation: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-22.04] | |
| python-version: ['3.9.20', '3.10.15', '3.11.10', '3.12.6'] | |
| steps: | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Checkout neurodamus repository | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| fetch-depth: 0 | |
| - name: Cache pip | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ matrix.os }}-pip-${{ matrix.python-version }}-v1 | |
| restore-keys: | | |
| ${{ matrix.os }}-pip- | |
| - name: Get latest tags | |
| run: | | |
| echo "NEURON_BRANCH=${{ inputs.NEURON_BRANCH || github.event.inputs.NEURON_BRANCH || 'master' }}" >> $GITHUB_ENV | |
| LIBSONATA_LATEST=$(curl -s https://api.github.com/repos/BlueBrain/libsonata/releases/latest | grep -oP '"tag_name": "\K(.*)(?=")') | |
| echo "LIBSONATA_BRANCH=${{ inputs.LIBSONATA_BRANCH || github.event.inputs.LIBSONATA_BRANCH || '$LIBSONATA_LATEST' }}" >> $GITHUB_ENV | |
| LIBSONATA_REPORT_LATEST=$(curl -s https://api.github.com/repos/BlueBrain/libsonatareport/releases/latest | grep -oP '"tag_name": "\K(.*)(?=")') | |
| echo "LIBSONATA_REPORT_BRANCH=${{ inputs.LIBSONATA_REPORT_BRANCH || github.event.inputs.LIBSONATA_REPORT_BRANCH || '$LIBSONATA_REPORT_LATEST' }}" >> $GITHUB_ENV | |
| NEURODAMUS_MODELS_LATEST=$(curl -s https://api.github.com/repos/BlueBrain/neurodamus-models/releases/latest | grep -oP '"tag_name": "\K(.*)(?=")') | |
| echo "NEURODAMUS_MODELS_BRANCH=${{ inputs.NEURODAMUS_MODELS_BRANCH || github.event.inputs.NEURODAMUS_MODELS_BRANCH || '$NEURODAMUS_MODELS_LATEST' }}" >> $GITHUB_ENV | |
| - name: Get HEAD commit message and look for branches | |
| run: | | |
| COMMIT_MESSAGE=$(git log -1 --pretty=%B) | |
| echo $COMMIT_MESSAGE | |
| NEURON_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'NEURON_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true) | |
| if [[ ! -z $NEURON_BRANCH ]]; then echo "NEURON_BRANCH=$NEURON_BRANCH" >> $GITHUB_ENV; fi | |
| LIBSONATA_REPORT_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'LIBSONATA_REPORT_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true) | |
| if [[ ! -z $LIBSONATA_REPORT_BRANCH ]]; then echo "LIBSONATA_REPORT_BRANCH=$LIBSONATA_REPORT_BRANCH" >> $GITHUB_ENV; fi | |
| LIBSONATA_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'LIBSONATA_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true) | |
| if [[ ! -z $LIBSONATA_BRANCH ]]; then echo "LIBSONATA_BRANCH=$LIBSONATA_BRANCH" >> $GITHUB_ENV; fi | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y mpich libmpich-dev libhdf5-mpich-dev hdf5-tools flex libfl-dev bison ninja-build | |
| - name: Cache python virtual env | |
| id: cache-venv | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: cache-venv | |
| with: | |
| path: venv | |
| key: ${{ matrix.os }}-libsonata-${{ env.LIBSONATA_BRANCH }}-py${{ matrix.python-version }} | |
| - name: Upgrade pip and install base Python packages | |
| if: steps.cache-venv.outputs.cache-hit != 'true' | |
| run: | | |
| python -m venv venv | |
| . ./venv/bin/activate | |
| python -m pip install --upgrade pip setuptools | |
| pip install cython numpy wheel pkgconfig | |
| - name: Add virtual environment to PATH | |
| run: echo "${{ github.workspace }}/venv/bin" >> $GITHUB_PATH | |
| - name: Install libsonata | |
| if: steps.cache-venv.outputs.cache-hit != 'true' | |
| run: | | |
| CC=mpicc CXX=mpic++ pip install git+https://github.com/BlueBrain/libsonata@${{ env.LIBSONATA_BRANCH }} | |
| - name: Cache libsonatareport | |
| id: cache-libsonatareport | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: cache-libsonatareport | |
| with: | |
| path: libsonatareport | |
| key: ${{ matrix.os }}-libsonatareport-${{ env.LIBSONATA_REPORT_BRANCH }}-py${{ matrix.python-version }} | |
| - name: Install libsonatareport | |
| if: steps.cache-libsonatareport.outputs.cache-hit != 'true' | |
| run: | | |
| git clone --branch="${{ env.LIBSONATA_REPORT_BRANCH}}" https://github.com/BlueBrain/libsonatareport.git --recursive --depth=1 | |
| cd libsonatareport | |
| mkdir build && cd build | |
| cmake -DCMAKE_INSTALL_PREFIX=$(pwd)/install -DCMAKE_BUILD_TYPE=Release -DSONATA_REPORT_ENABLE_SUBMODULES=ON -DSONATA_REPORT_ENABLE_MPI=ON .. | |
| cmake --build . --parallel | |
| cmake --build . --target install | |
| - name: Cache NEURON | |
| id: cache-neuron | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: cache-neuron | |
| with: | |
| path: nrn | |
| key: ${{ matrix.os }}-neuron-${{ env.NEURON_BRANCH }}-${{ env.NEURON_COMMIT_ID }}-py${{ matrix.python-version }} | |
| - name: Install NEURON | |
| if: steps.cache-neuron.outputs.cache-hit != 'true' | |
| run: | | |
| export SONATAREPORT_DIR=$(pwd)/libsonatareport/build/install | |
| if [[ ${{ env.NEURON_BRANCH }} == 'master' ]]; then | |
| git clone --branch=${{ env.NEURON_BRANCH }} https://github.com/neuronsimulator/nrn.git | |
| cd nrn | |
| git checkout ${{ env.NEURON_COMMIT_ID }} | |
| cd .. | |
| else | |
| git clone --branch=${{ env.NEURON_BRANCH }} https://github.com/neuronsimulator/nrn.git --depth=1 | |
| fi | |
| python -m pip install --upgrade pip -r nrn/nrn_requirements.txt | |
| cmake -B nrn/build -S nrn -G Ninja \ | |
| -DPYTHON_EXECUTABLE=$(which python) \ | |
| -DCMAKE_INSTALL_PREFIX=$(pwd)/nrn/build/install \ | |
| -DNRN_ENABLE_MPI=ON \ | |
| -DNRN_ENABLE_INTERVIEWS=OFF \ | |
| -DNRN_ENABLE_CORENEURON=ON \ | |
| -DCMAKE_C_COMPILER=gcc \ | |
| -DCMAKE_CXX_COMPILER=g++ \ | |
| -DCORENRN_ENABLE_REPORTING=ON \ | |
| -DCMAKE_PREFIX_PATH=$SONATAREPORT_DIR | |
| cmake --build nrn/build --parallel | |
| cmake --build nrn/build --target install | |
| - name: Install mpi4py | |
| if: steps.cache-venv.outputs.cache-hit != 'true' | |
| run: | | |
| pip install mpi4py | |
| - name: Build h5py with the local hdf5 | |
| run: | | |
| CC="mpicc" HDF5_MPI="ON" HDF5_INCLUDEDIR=/usr/include/hdf5/mpich HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu/hdf5/mpich \ | |
| pip install --no-cache-dir --no-binary=h5py h5py --no-build-isolation | |
| - name: Install neurodamus | |
| run: | | |
| pip install .[full] | |
| - name: Build neocortex models | |
| run: | | |
| export SONATAREPORT_DIR=$(pwd)/libsonatareport/build/install | |
| export PATH=$(pwd)/nrn/build/install/bin:$PATH | |
| # Clone neurodamus-models repository | |
| git clone --branch=${{ env.NEURODAMUS_MODELS_BRANCH }} https://github.com/BlueBrain/neurodamus-models.git | |
| # Build neocortex model | |
| DATADIR=$(python -c "import neurodamus; from pathlib import Path; print(Path(neurodamus.__file__).parent / 'data')") | |
| cmake -B neurodamus-models/build -S neurodamus-models/ \ | |
| -DCMAKE_INSTALL_PREFIX=$PWD/neurodamus-models/install \ | |
| -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON \ | |
| -DCMAKE_PREFIX_PATH=$SONATAREPORT_DIR \ | |
| -DNEURODAMUS_CORE_DIR=${DATADIR} \ | |
| -DNEURODAMUS_MECHANISMS=neocortex \ | |
| -DNEURODAMUS_NCX_V5=ON | |
| cmake --build neurodamus-models/build | |
| cmake --install neurodamus-models/build | |
| echo "NEURODAMUS_NEOCORTEX_ROOT=$(pwd)/neurodamus-models/install" >> $GITHUB_ENV; | |
| # Build neocortex-multiscale model | |
| echo "build neurodamus-neocortex-multiscale model" | |
| cmake -B neurodamus-models/build_multiscale -S neurodamus-models/ \ | |
| -DCMAKE_INSTALL_PREFIX=$PWD/neurodamus-models/install_multiscale \ | |
| -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON \ | |
| -DCMAKE_PREFIX_PATH=$SONATAREPORT_DIR \ | |
| -DNEURODAMUS_CORE_DIR=${DATADIR} \ | |
| -DNEURODAMUS_MECHANISMS=neocortex \ | |
| -DNEURODAMUS_NCX_METABOLISM=ON \ | |
| -DNEURODAMUS_NCX_NGV=ON \ | |
| -DNEURODAMUS_ENABLE_CORENEURON=OFF | |
| cmake --build neurodamus-models/build_multiscale | |
| cmake --install neurodamus-models/build_multiscale | |
| echo "NEURODAMUS_NEOCORTEX_MULTISCALE_ROOT=$(pwd)/neurodamus-models/install_multiscale" >> $GITHUB_ENV; | |
| - name: load neocortex model | |
| run: | | |
| export PYTHONPATH=$(pwd)/nrn/build/install/lib/python:$PYTHONPATH | |
| export HOC_LIBRARY_PATH=$NEURODAMUS_NEOCORTEX_ROOT/share/neurodamus_neocortex/hoc | |
| export NEURODAMUS_PYTHON=$(pwd)/neurodamus/data | |
| export CORENEURONLIB=$NEURODAMUS_NEOCORTEX_ROOT/lib/libcorenrnmech.so | |
| export NRNMECH_LIB_PATH=$NEURODAMUS_NEOCORTEX_ROOT/lib/libnrnmech.so | |
| export PATH=$NEURODAMUS_NEOCORTEX_ROOT/bin:$PATH | |
| echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV; | |
| echo "HOC_LIBRARY_PATH=$HOC_LIBRARY_PATH" >> $GITHUB_ENV; | |
| echo "CORENEURONLIB=$CORENEURONLIB" >> $GITHUB_ENV; | |
| echo "NRNMECH_LIB_PATH=$NRNMECH_LIB_PATH" >> $GITHUB_ENV; | |
| echo "NEURODAMUS_PYTHON=$NEURODAMUS_PYTHON" >> $GITHUB_ENV; | |
| which special | |
| # launch simulation with NEURON | |
| cd tests/simulations/usecase3/ | |
| mpirun -np 2 special -mpi -python $NEURODAMUS_PYTHON/init.py --configFile=simulation_sonata.json | |
| ls reporting/*.h5 | |
| # launch simulation with CORENEURON | |
| mpirun -np 2 special -mpi -python $NEURODAMUS_PYTHON/init.py --configFile=simulation_sonata_coreneuron.json | |
| ls reporting_coreneuron/*.h5 | |
| - name: Install test dependencies | |
| run: | | |
| pip install -r tests/requirements.txt | |
| - name: test-unit | |
| run: | | |
| pytest tests/unit | |
| - name: test-integration | |
| run: | | |
| pytest -x --forked tests/integration | |
| - name: test-integration-e2e | |
| run: | | |
| pytest -s -x --forked --durations=5 --durations-min=15 tests/integration-e2e | |
| - name: test-scientific | |
| run: | | |
| pytest -s -x --forked --durations=5 --durations-min=15 tests/scientific | |
| - name: test-scientific-ngv | |
| run: | | |
| export HOC_LIBRARY_PATH=$NEURODAMUS_NEOCORTEX_MULTISCALE_ROOT/share/neurodamus_neocortex/hoc | |
| export NRNMECH_LIB_PATH=$NEURODAMUS_NEOCORTEX_MULTISCALE_ROOT/lib/libnrnmech.so | |
| unset CORENEURONLIB | |
| pytest -s -x --forked --durations=5 --durations-min=15 tests/scientific-ngv | |
| - name: live debug session, comment out | |
| if: failure() | |
| uses: mxschmitt/action-tmate@v3 | |
| with: | |
| timeout-minutes: 60 # or any other value you need |