test-as-submodule.yml

name: NEURON submodule

concurrency:
  group: ${{ github.workflow }}#${{ github.ref }}
  cancel-in-progress: true

on:
  push:
    branches:
      - master
      - release/**
  pull_request:
    branches:
      - master
      - release/**

jobs:
  ci:
    name: ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        include:
          - os: ubuntu-20.04
            cores: 2
          - os: macOS-11
            cores: 3
      fail-fast: false
    env:
      CMAKE_BUILD_PARALLEL_LEVEL: ${{matrix.cores}}
      SDK_ROOT: $(xcrun --sdk macosx --show-sdk-path)

    steps:

      - name: Install homebrew packages
        if: startsWith(matrix.os, 'macOS')
        run: |
          brew install bison coreutils flex ninja openmpi
          python3 -m pip install --upgrade numpy pytest pytest-cov
          echo /usr/local/opt/flex/bin:/usr/local/opt/bison/bin >> $GITHUB_PATH
          echo "CC=gcc" >> $GITHUB_ENV
          echo "CXX=g++" >> $GITHUB_ENV

      - name: Install apt packages
        if: startsWith(matrix.os, 'ubuntu')
        run: |
          sudo apt-get update
          sudo apt-get install bison cython3 flex libfl-dev libopenmpi-dev \
            ninja-build openmpi-bin python3-dev
          python3 -m pip install --upgrade numpy pytest pytest-cov
          echo "CC=gcc" >> $GITHUB_ENV
          echo "CXX=g++" >> $GITHUB_ENV

      - name: Set NEURON branch
        id: vars
        env:
          GITHUB_PR_BODY: ${{ github.event.pull_request.body }}
        run: |
          nrn_branch=$(echo "${GITHUB_PR_BODY}" | grep "^CI_BRANCHES" \
                      | awk -F '[:,]{1}NEURON_BRANCH=' '{print $2}' \
                      | awk -F ',' '{print $1}')
          if [ -z "$nrn_branch" ]; then
              nrn_branch=master
          fi
          echo "Will use neuron branch: $nrn_branch"
          echo ::set-output name=neuron_branch::"${nrn_branch}"

      - uses: actions/checkout@v3
        name: Checkout NEURON
        with:
          path: nrn
          repository: neuronsimulator/nrn
          ref: ${{ steps.vars.outputs.neuron_branch }}

      - name: Update CoreNEURON submodule
        run: |
          cd ${GITHUB_WORKSPACE}/nrn
          coreneuron_sha=${{github.event.pull_request.head.sha}}
          if [[ -z ${coreneuron_sha} ]]; then
          # presumably we're running on a push event
          coreneuron_sha=${{github.sha}}
          fi
          echo "Using CoreNEURON SHA ${coreneuron_sha}"
          # https://stackoverflow.com/a/33575837
          git update-index --cacheinfo 160000,${coreneuron_sha},external/coreneuron
          git submodule update --init external/coreneuron
          echo "NEURON status"
          git status
          git log -n 1
          cd external/coreneuron
          echo "CoreNEURON status"
          git status
          git log -n 1

      - name: Configure NEURON
        run: |
          cd ${GITHUB_WORKSPACE}/nrn
          mkdir build install
          cd build
          # NEURON CMake assumes this is defined.
          export SHELL=$(command -v bash)
          openMP=" -DCORENRN_ENABLE_OPENMP=ON"
          if [[ "${{ startsWith(matrix.os, 'macOS') }}" = "true" ]]; then
            openMP=" -DCORENRN_ENABLE_OPENMP=OFF"
          fi
          cmake .. -G Ninja \
            -DCMAKE_BUILD_TYPE=RelWithDebInfo \
            -DCMAKE_INSTALL_PREFIX=../install \
            -DPYTHON_EXECUTABLE=$(command -v python3) \
            -DNRN_ENABLE_CORENEURON=ON \
            -DNRN_ENABLE_INTERVIEWS=OFF \
            -DNRN_ENABLE_RX3D=OFF \
            -DNRN_ENABLE_MPI_DYNAMIC=ON \
            -DNRN_ENABLE_TESTS=ON ${openMP}

      - name: Build NEURON
        run: |
          cd ${GITHUB_WORKSPACE}/nrn/build
          cmake --build . --parallel

      - name: Test NEURON
        run: |
          cd ${GITHUB_WORKSPACE}/nrn/build
          ctest --output-on-failure

      - name: Install NEURON
        run: |
          cd ${GITHUB_WORKSPACE}/nrn/build
          cmake --build . --target install

      # 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/workflows/test-as-submodule.yml`)
        if: failure() && contains(github.event.pull_request.title, 'live-debug-ci')
        uses: mxschmitt/action-tmate@v3