simulation_test.yml

name: neurodamus build and test
on:
  schedule:
    # every evening at 20:00 UTC
    - cron: '0 20 * * *'
  pull_request:
    branches:
      - main
  workflow_dispatch:
    inputs:
      NEURON_BRANCH:
        description: 'NEURON branch to use'
        required: false
      LIBSONATA_REPORT_BRANCH:
        description: 'libsonatareport branch to use'
        required: false

jobs:
  simulation:
    runs-on: ubuntu-22.04

    steps:
    - name: Checkout neurodamus repository
      uses: actions/checkout@v4
      with:
        ref: ${{ github.event.pull_request.head.sha }}
        fetch-depth: 0

    - 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

    - name: Install hdf5-mpich
      run: |
        sudo apt-get update
        sudo apt-get install mpich libmpich-dev libhdf5-mpich-dev hdf5-tools

    - name: Install libsonata
      run: |
        CC=mpicc CXX=mpic++ pip install git+https://github.com/BlueBrain/libsonata

    - name: Install libsonatareport
      run: |
        git clone --branch="${LIBSONATA_REPORT_BRANCH:-master}" https://github.com/BlueBrain/libsonatareport.git --recursive --depth=1
        cd libsonatareport
        mkdir build && cd build
        cmake -DCMAKE_INSTALL_PREFIX=$(pwd)/install -DCMAKE_BUILD_TYPE=Release -DSONATA_REPORT_ENABLE_SUBMODULES=ON -DSONATA_REPORT_ENABLE_MPI=ON ..
        cmake --build . --parallel
        cmake --build . --target install

    - name: Install NEURON
      run: |
        sudo apt-get install flex libfl-dev bison ninja-build
        pip install -U pip setuptools
        pip install "cython<3" pytest sympy
        export SONATAREPORT_DIR=$(pwd)/libsonatareport/build/install
        git clone --branch="${NEURON_BRANCH:-master}" https://github.com/neuronsimulator/nrn.git --depth=1
        cd nrn
        mkdir build && cd build
        cmake -G Ninja -DPYTHON_EXECUTABLE=$(which python) -DCMAKE_INSTALL_PREFIX=$(pwd)/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 . --parallel
        cmake --build . --target install

    - name: Build h5py with the local hdf5
      run: |
        pip install -U pip setuptools
        pip install cython numpy wheel pkgconfig
        MPICC="mpicc -shared" pip install --no-cache-dir --no-binary=mpi4py mpi4py
        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 .

    - name: Build models
      run: |
        export SONATAREPORT_DIR=$(pwd)/libsonatareport/build/install
        export PATH=$(pwd)/nrn/build/install/bin:$PATH
        # copy mod files from the Zenodo link
        wget --output-document="O1_mods.xz" --quiet "https://zenodo.org/record/8026353/files/O1_mods.xz?download=1"
        tar -xf O1_mods.xz
        cp -r mod tests/share/
        cp neurodamus/data/mod/*.mod tests/share/mod/
        ./docker/build_neurodamus.sh tests/share/mod

    - name: Example run
      run: |
        export PYTHONPATH=$(pwd)/nrn/build/lib/python:$PYTHONPATH
        cp neurodamus/data/hoc/* tests/share/hoc/
        export HOC_LIBRARY_PATH=$(pwd)/tests/share/hoc
        # launch simulation with NEURON
        mpirun -np 2 ./x86_64/special -mpi -python neurodamus/data/init.py --configFile=tests/simulations/usecase3/simulation_sonata.json
        ls tests/simulations/usecase3/reporting/*.h5
        # launch simulation with CORENEURON
        mpirun -np 2 ./x86_64/special -mpi -python neurodamus/data/init.py --configFile=tests/simulations/usecase3/simulation_sonata_coreneuron.json
        ls tests/simulations/usecase3/reporting_coreneuron/*.h5

    # - name: live debug session, comment out
    #   if: failure()
    #   uses: mxschmitt/action-tmate@v3