Revision of the manual #365
Workflow file for this run
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| # ----------------------------------------------------------------------------- | |
| # | |
| # 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-12, macos-13] | |
| fortran: [10, 11, 12] | |
| exclude: # gfortran-11, gfortran-12 not available for ubuntu-20.04 | |
| - os: ubuntu-20.04 | |
| fortran: 11 | |
| - os: ubuntu-20.04 | |
| fortran: 12 | |
| 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 $GITHUB_WORKSPACE | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 # https://github.com/marketplace/actions/checkout | |
| with: | |
| fetch-depth: 2 | |
| # ------------------------------------------------------------- | |
| # (2) Install gfortran, if not supplied with the runner image, | |
| # and the AtChem2 dependencies: CVODE, openlibm, numdiff, FRUIT | |
| # gfortran on ubuntu | |
| # - name: Install gfortran-11 (ubuntu-20.04) | |
| # if: matrix.os == 'ubuntu-20.04' && matrix.fortran == 11 | |
| # run: sudo apt-get install gfortran-11 | |
| # gfortran on macos | |
| - name: Install gfortran-10 (macos-12) | |
| if: matrix.os == 'macos-12' && (matrix.fortran == 10) # || matrix.fortran == 11) | |
| run: brew install gcc@${{ matrix.fortran }} | |
| - 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 }} | |
| # 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 == 12 | |
| # 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* ./ # 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 # TODO: update codecov action | |
| if: matrix.os == 'ubuntu-22.04' && matrix.fortran == 12 | |
| uses: codecov/codecov-action@v3 # https://github.com/marketplace/actions/codecov | |
| with: | |
| gcov: true |