ci.yml

# -----------------------------------------------------------------------------
#
# Copyright (c) 2017 Sam Cox, Roberto Sommariva
#
# This file is part of the AtChem2 software package.
#
# This file is covered by the MIT license which can be found in the file
# LICENSE.md at the top level of the AtChem2 distribution.
#
# -----------------------------------------------------------------------------

# Workflow for the continuous integration (CI) of AtChem2, using
# Github Actions and Codecov
#
# Acknowledgements: J. Allsopp
# -------------------------------------------------------------------- #
name: AtChem2 CI

# ------------------------------ EVENTS ------------------------------ #
# Controls when the workflow is activated
on:

  # Triggers when a pull request is created or updated (only on the
  # master branch)
  pull_request:
    branches: [ master ]

  # Triggers when a push is made to the master branch (either by
  # merging a pull request, or by direct commit)
  push:
    branches: [ master ]

  # Run manually from the Actions tab
  workflow_dispatch:

# ------------------------------ JOBS ------------------------------ #
# This workflow contains a single job called `ci_testing` which
# compiles the AtChem2 model, runs the Testsuite, and checks the code
# coverage using Codecov (https://app.codecov.io/gh/AtChem/AtChem2)
jobs:
  ci_testing:
    # The job runs on two versions of linux (ubuntu) and macos runner
    # images, with three versions of gnu fortran -- the runner images
    # are described here: https://github.com/actions/runner-images
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-20.04, ubuntu-22.04, macos-11, macos-12]
        fortran: [9, 10, 11]
        exclude: # TODO: gfortran-9 does not work on macos-12
        - os: macos-12
          fortran: 9
      fail-fast: false

    # -------------------------------------------------------------
    # Sequence of tasks to be executed as part of the `ci_testing` job:
    # 1. Checkout the repository
    # 2. Install gfortran, AtChem2 dependencies
    # 3. Compile AtChem2
    # 4. Run the Testsuite with default settings
    # 5. Recompile AtChem2, run unit and model tests for Codecov
    steps:

      # -------------------------------------------------------------
      # (1) Checkout the repository under $GITHUB_WORKSPACE
      - name: Checkout repo
        uses: actions/checkout@v4
        with:
          fetch-depth: 2

      # -------------------------------------------------------------
      # (2) Install gfortran, if not supplied with the runner image,
      # and the AtChem2 dependencies: CVODE, openlibm, numdiff, FRUIT

      # gfortran on ubuntu
      - name: Install gfortran-11 (ubuntu-20.04)
        if: matrix.os == 'ubuntu-20.04' && matrix.fortran == 11
        run: sudo apt-get install gfortran-11

      # gfortran on macos
      - name: Install gfortran-9 (macos-11)
        if: matrix.os == 'macos-11' && matrix.fortran == 9
        run: brew install gcc@${{ matrix.fortran }}

      - name: Install gfortran-9 and gfortran-10 (macos-12)
        if: matrix.os == 'macos-12' && (matrix.fortran == 9 || matrix.fortran == 10)
        run: brew install gcc@${{ matrix.fortran }}

      # AtChem2 dependencies
      - name: Install CVODE
        run: ./tools/install/install_cvode.sh $PWD $(which gfortran-${{ matrix.fortran }})

      - name: Install openlibm
        run: ./tools/install/install_openlibm.sh $PWD

      - name: Install numdiff
        run: ./tools/install/install_numdiff.sh $PWD

      - name: Install FRUIT
        run: sudo ./tools/install/install_fruit.sh $PWD

      # -------------------------------------------------------------
      # (3) Compile AtChem2 using the standard compilation flags
      - name: Build AtChem2
        # Set $FORT_VERSION for use with the `Makefile`, which is
        # called by the `build_atchem2.sh` script
        env:
          FORT_VERSION: ${{ matrix.fortran }}
        run: |
          cp tools/install/Makefile.skel Makefile
          ./build/build_atchem2.sh ./model/mechanism.fac ./model/configuration/ ./mcm/

          # macos only
          if [ $RUNNER_OS != "Linux" ] ; then
            install_name_tool -change libopenlibm.4.dylib $PWD/openlibm-0.8.1/libopenlibm.4.dylib atchem2 ;
            install_name_tool -change @rpath/libsundials_cvode.2.dylib $PWD/cvode/lib/libsundials_cvode.dylib atchem2 ;
            install_name_tool -change @rpath/libsundials_fnvecserial.2.dylib $PWD/cvode/lib/libsundials_fnvecserial.dylib atchem2 ;
            install_name_tool -change @rpath/libsundials_nvecserial.2.dylib $PWD/cvode/lib/libsundials_nvecserial.dylib atchem2 ;
          fi

      # -------------------------------------------------------------
      # (4) Run the Testsuite using the standard compilation flags and
      # default settings: indent, style, unit, model tests
      - name: Indent and Style tests
        run: |
          make indenttest
          make styletest

      - name: Unit and Model tests
        # Set $FORT_VERSION for use with the `Makefile`
        env:
          FORT_VERSION: ${{ matrix.fortran }}
        run: |
          export PATH=$PATH:$PWD/numdiff/bin
          make unittests
          make oldtests    # NB: oldtests will eventually be merged into modeltests
          #make modeltests  # TODO: temporarily deactivated (pass on linux, fail on macos)

      # -------------------------------------------------------------
      # (5) Recompile AtChem2 using the code coverage compilation
      # flags, then upload the gcov files to Codecov
      - name: Unit and Model tests (x Codecov)
        if: matrix.os == 'ubuntu-22.04' && matrix.fortran == 11
        # Set $FORT_VERSION for use with the `Makefile`
        env:
          FORT_VERSION: ${{ matrix.fortran }}
        run: |
          export PATH=$PATH:$PWD/numdiff/bin
          make clean
          # unit tests
          make unittests CCOV=true
          mv tests/unit_tests/*.gc* ./  # needed for GCC-11 handling of *.gcda, *.gcna files
          # model tests
          make modeltests CCOV=true     # run only the new Testsuite

      - name: Upload coverage reports to Codecov
        if: matrix.os == 'ubuntu-22.04' && matrix.fortran == 11
        uses: codecov/codecov-action@v3
        with:
          gcov: true