ci.yml

# -----------------------------------------------------------------------------
#
# Copyright (c) 2017-2025 Sam Cox, Roberto Sommariva, James Allsopp
#
# This file is part of the AtChem2 software package.
#
# This file is licensed under the MIT license, which can be found in the file
# `LICENSE` at the top level of the AtChem2 distribution.
#
# -----------------------------------------------------------------------------

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

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

  # Triggers when a pull request targeting the master branch is
  # created or updated
  pull_request:
    branches: [ master ]

  # Triggers when a push is made to the master branch by merging a
  # pull request (direct commits to master are disabled)
  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 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, with
    # three versions of gnu fortran
    #
    # RUNNERS: https://github.com/actions/runner-images
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-22.04, ubuntu-24.04]   # NB: macos testing temporarily deactivated
        fortran: [11, 12, 13]
        # compiler versions  not available for specific runners
        exclude:
        - os: ubuntu-22.04
          fortran: 13
      fail-fast: false
    permissions:
      contents: read

    # -------------------------------------------------------------
    # Sequence of tasks to be executed as part of the `ci_testing` job:
    # 1. Checkout repository
    # 2. Install gfortran, if not available
    # 3. Install AtChem2 dependencies
    # 4. Build AtChem2
    # 5. Run Testsuite with default settings
    # 6. Recompile AtChem2, run Testsuite for Codecov
    steps:

      # -------------------------------------------------------------
      # (1) Checkout the repository under $GITHUB_WORKSPACE
      #
      # ACTION: https://github.com/marketplace/actions/checkout

      - name: Checkout repo
        uses: actions/checkout@v4
        with:
          fetch-depth: 2

      # -------------------------------------------------------------
      # (2) Install gfortran, if not supplied with the runner

      # gfortran on ubuntu
      - name: Install gfortran-11 (ubuntu-24.04)
        if: matrix.os == 'ubuntu-24.04' && matrix.fortran == 11
        run: sudo apt-get install gfortran-11

      # gfortran on macos
      - name: Install gfortran-10 and gfortran-11 (macos-13)
        if: matrix.os == 'macos-13' && (matrix.fortran == 10 || matrix.fortran == 11)
        run: brew install gcc@${{ matrix.fortran }}

      # -------------------------------------------------------------
      # (3) Install the AtChem2 dependencies: CVODE, openlibm, numdiff, FRUIT
      #
      # NB: the current version of FRUIT (v3.4.3) does not work with the most
      #     recent versions of Ruby; as a temporary fix, Ruby v3.0 is used for
      #     all unit tests in this workflow
      #
      # ACTION: https://github.com/marketplace/actions/setup-ruby-jruby-and-truffleruby

      - 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: Setup Ruby
        uses: ruby/setup-ruby@v1
        with:
          ruby-version: '3.0'

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

      - name: Install Python and Fortran formatters
        run: pip install black fprettify

      # -------------------------------------------------------------
      # (4) Build AtChem2 using the standard compilation flags

      - name: Build AtChem2
        env:
          FORT_VERSION: ${{ matrix.fortran }}
        run: |
          cp tools/install/Makefile.skel Makefile
          ./build/build_atchem2.sh --mechanism=./model/mechanism.fac --shared_lib=./model/sharedlib --configuration=./model/configuration --mcm=v3.3.1

          # 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

      # -------------------------------------------------------------
      # (5) Run the Testsuite using the standard compilation flags and the
      #     default model settings, then upload the log files as artifacts
      #
      # ACTION: https://github.com/marketplace/actions/upload-a-build-artifact

      - name: Indent and Style tests
        run: |
          make indenttest
          make styletest
          make pythontest

      - name: Unit and Model tests
        env:
          FORT_VERSION: ${{ matrix.fortran }}
        # continue-on-error: true
        run: |
          export PATH=$PATH:$PWD/numdiff/bin
          make unittests
          make oldtests   # NB: oldtests will eventually be merged into modeltests
          make modeltests

      - name: Save log files
        uses: actions/upload-artifact@v4
        with:
          name: testsuite_${{ matrix.os }}_fortran-${{ matrix.fortran }}.log
          path: tests/*.log

      # -------------------------------------------------------------
      # (6) Recompile AtChem2 using the code coverage compilation flags,
      #     run the Testsuite and upload the gcov files to Codecov
      #
      # ACTION: https://github.com/marketplace/actions/codecov

      - name: Unit and Model tests (x Codecov)
        if: matrix.os == 'ubuntu-24.04' && matrix.fortran == 13
        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* ./   # for gcc>=11 handling of *.gcda, *.gcna files
          # model tests
          make modeltests CCOV=true   # run only the new Testsuite
          find ./ -name "*.gc*"

      - name: Upload coverage reports to Codecov
        if: matrix.os == 'ubuntu-24.04' && matrix.fortran == 13
        uses: codecov/codecov-action@v5