coverage.yml

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: '3.10'
  PY_MID_VERSION: '3.11'
  PY_MAX_VERSION: '3.14'
  # The Linux runners have 4 cores:
  # https://docs.github.com/en/actions/using-github-hosted-runners/using-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
  CMAKE_BUILD_PARALLEL_LEVEL: '4'
  CTEST_PARALLEL_LEVEL: '4'
  CCACHE_DIR: ${{ github.workspace }}/ccache

jobs:
  coverage:
    runs-on: ubuntu-22.04

    name: Code Coverage

    timeout-minutes: 60

    env:
      DISPLAY: ${{ ':0' }}
      MUSIC_INSTALL_DIR: /opt/MUSIC
      # hash of commit containing mpi4py 4 fix
      MUSIC_VERSION: '13f312338dcccebfe74d391b1b24f1b6d816ac6c'

    steps:

      - name: Install apt packages
        run: |
          sudo apt-get update
          sudo apt-get install -y 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 libdw-dev binutils-dev
        shell: bash
        env:
          DEBIAN_FRONTEND: noninteractive

      - name: Install a new ccache
        run: |
          # versions older than 4.10 do not support -fprofile-update=atomic
          wget 'https://github.com/ccache/ccache/releases/download/v4.11.3/ccache-4.11.3-linux-x86_64.tar.xz'
          tar xf ccache-4.11.3-linux-x86_64.tar.xz
          sudo cp -a ccache-4.11.3-linux-x86_64/ccache /usr/bin/ccache
        working-directory: ${{runner.temp}}

      - name: Setup cmake
        uses: jwlawson/actions-setup-cmake@v2
        with:
          cmake-version : '3.19'

      - name: Setup Caliper profiler
        run: |
          git clone --branch v2.12.1 --depth 1 --recurse-submodules --shallow-submodules https://github.com/LLNL/Caliper.git
          cd Caliper
          cmake -B build -G Ninja .
          sudo cmake --build build --target install
        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

      # Restore (and later save) dependencies for min version of Python
      - name: Restore Python@${{ env.PY_MIN_VERSION }} dependencies
        id: cache-python-min-packages-restore
        uses: actions/cache/restore@v4
        with:
          path: ${{ github.workspace }}/pip_cache${{ env.PY_MIN_VERSION }}
          key: cache-${{ env.PY_MIN_VERSION }}-${{ hashFiles('ci/requirements.txt') }}

      - 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 -r ci/uv_requirements.txt
          python -m uv pip install -r ci/requirements.txt --cache-dir ${{ github.workspace }}/pip_cache${{ env.PY_MIN_VERSION }}

      - name: Save Python@${{ env.PY_MIN_VERSION }} dependencies
        id: cache-python-min-packages-save
        if: always() && steps.cache-python-min-packages-restore.outputs.cache-hit != 'true'
        uses: actions/cache/save@v4
        with:
          key: ${{ steps.cache-python-min-packages-restore.outputs.cache-primary-key }}
          path: ${{ github.workspace }}/pip_cache${{ env.PY_MIN_VERSION }}

      # Restore (and later save) dependencies for mid version of Python
      - name: Restore Python@${{ env.PY_MID_VERSION }} dependencies
        id: cache-python-mid-packages-restore
        uses: actions/cache/restore@v4
        with:
          path: ${{ github.workspace }}/pip_cache${{ env.PY_MID_VERSION }}
          key: cache-${{ env.PY_MID_VERSION }}-${{ hashFiles('ci/requirements.txt') }}

      - name: Set up Python@${{ env.PY_MID_VERSION }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ env.PY_MID_VERSION }}

      - name: Install Python@${{ env.PY_MID_VERSION }} dependencies
        working-directory: ${{runner.workspace}}/nrn
        run: |
          python -m pip install -r ci/uv_requirements.txt
          python -m uv pip install -r ci/requirements.txt --cache-dir ${{ github.workspace }}/pip_cache${{ env.PY_MID_VERSION }}

      - name: Save Python@${{ env.PY_MID_VERSION }} dependencies
        id: cache-python-mid-packages-save
        if: always() && steps.cache-python-mid-packages-restore.outputs.cache-hit != 'true'
        uses: actions/cache/save@v4
        with:
          key: ${{ steps.cache-python-mid-packages-restore.outputs.cache-primary-key }}
          path: ${{ github.workspace }}/pip_cache${{ env.PY_MID_VERSION }}

      # Restore (and later save) dependencies for max version of Python
      - name: Restore Python@${{ env.PY_MAX_VERSION }} dependencies
        id: cache-python-max-packages-restore
        uses: actions/cache/restore@v4
        with:
          path: ${{ github.workspace }}/pip_cache${{ env.PY_MAX_VERSION }}
          key: cache-${{ env.PY_MAX_VERSION }}-${{ hashFiles('ci/requirements.txt') }}

      - 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 -r ci/uv_requirements.txt
          python -m uv pip install -r ci/requirements.txt --cache-dir ${{ github.workspace }}/pip_cache${{ env.PY_MAX_VERSION }}

      - name: Save Python@${{ env.PY_MAX_VERSION }} dependencies
        id: cache-python-max-packages-save
        if: always() && steps.cache-python-max-packages-restore.outputs.cache-hit != 'true'
        uses: actions/cache/save@v4
        with:
          key: ${{ steps.cache-python-max-packages-restore.outputs.cache-primary-key }}
          path: ${{ github.workspace }}/pip_cache${{ env.PY_MAX_VERSION }}

      - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
        run: |
          python -m venv music-venv
          source music-venv/bin/activate
          python -m pip install -r ${{ github.workspace }}/ci/uv_requirements.txt
          python -m uv pip install -r ${{ github.workspace }}/ci/requirements.txt --cache-dir ${{ github.workspace }}/pip_cache${{ env.PY_MAX_VERSION }}
          sudo mkdir -p $MUSIC_INSTALL_DIR
          sudo chown -R $USER $MUSIC_INSTALL_DIR
          curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/${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}}

      # Restore (and later save) ccache
      - name: Restore compiler cache
        id: restore-compiler-cache
        uses: actions/cache/restore@v4
        with:
          path: ${{ github.workspace }}/ccache
          key: ccache-coverage-${{runner.os}}-${{github.ref_name}}
          restore-keys: |
            ccache-coverage-${{runner.os}}-master

      - 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);

          # Update all submodules with depth 1
          git submodule update --init --recursive --depth 1

          mkdir build && cd build;

          # CMake options & flags
          cmake_args=(-G Ninja \
                      -DCMAKE_BUILD_TYPE=Debug \
                      -DCMAKE_C_COMPILER="$CC" \
                      -DCMAKE_CXX_COMPILER="$CXX" \
                      -DCMAKE_C_COMPILER_LAUNCHER=ccache \
                      -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \
                      -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
          ccache -z
          ccache -s -v || ccache -s
          cmake --build .
          ccache -s -v || ccache -s
          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}" \
              "${python}" -c "from neuron import h; import neuron; neuron.test();neuron.test_rxd(); from neuron.tests import test_nmodl; test_nmodl.test_nmodl()"
          done
          cmake --build . --target cover_collect
          cmake --build . --target cover_combine
        env:
          MATRIX_EVAL: "CC=gcc CXX=g++"
          PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
          PYTHON_MID_NAME: "python${{ env.PY_MID_VERSION }}"
          PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}"

      - name: Upload build artifacts
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: coverage-${{runner.os}}
          path: |
            ${{runner.workspace}}/nrn/build/CMakeCache.txt
            ${{runner.workspace}}/nrn/build/build.ninja
            ${{runner.workspace}}/nrn/build/cmake_install.cmake

      - name: Save compiler cache
        id: save-compiler-cache
        if: always() && steps.restore-compiler-cache.outputs.cache-hit != 'true'
        uses: actions/cache/save@v4
        with:
          key: ${{ steps.restore-compiler-cache.outputs.cache-primary-key }}
          path: ${{ github.workspace }}/ccache

      # 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: ${{ contains(github.head_ref, 'dependabot/') && secrets.CODECOV_TOKEN || '' }}
          token: ${{ secrets.CODECOV_TOKEN }}