coverage.yml

name: NEURON Code Coverage

concurrency:
  group: ${{ github.workflow }}#${{ github.ref }}
  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@v3
        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@v4
        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

      - name: Set up Python@${{ env.PY_MID_VERSION }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ env.PY_MID_VERSION }}

      - name: Set up Python@${{ env.PY_MAX_VERSION }}
        uses: actions/setup-python@v4
        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

      - 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@v3
        with:
          directory: ./build
          fail_ci_if_error: true
          verbose: true
          token: ${{ secrets.CODECOV_TOKEN }}