pyfabm: add ConservedQuantity with missing_value, restore Dependency.shape #538
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Build and test | |
| on: | |
| push: | |
| branches: | |
| - "**" | |
| pull_request: | |
| jobs: | |
| gfortran: | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| strategy: | |
| matrix: | |
| version: [9, 10, 11, 12] | |
| os: [ubuntu-latest] | |
| include: | |
| #- version: 4.8 | |
| # os: ubuntu-18.04 | |
| # cmake_args: -DFABM_USE_IEEE_ARITHMETIC=OFF | |
| #- version: 5 | |
| # os: ubuntu-18.04 | |
| #- version: 6 | |
| # os: ubuntu-18.04 | |
| - version: 7 | |
| os: ubuntu-20.04 | |
| - version: 8 | |
| os: ubuntu-20.04 | |
| cmake_args: -DFABM_USE_CONTIGUOUS=OFF | |
| - version: 13 | |
| os: ubuntu-24.04 | |
| - version: 14 | |
| os: ubuntu-24.04 | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| FFLAGS: -fcheck=all | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ">=3.7" | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pyyaml | |
| - name: Install compiler | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install gfortran-${{ matrix.version }} | |
| - name: Clone repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Run all test cases with host emulators | |
| run: python3 util/developers/run_all_testcases.py harness --show_logs --compiler gfortran-${{ matrix.version }} ${{ matrix.cmake_args }} | |
| - name: Run all test cases with pyfabm | |
| run: python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler gfortran-${{ matrix.version }} ${{ matrix.cmake_args }} | |
| ifort: | |
| # for available versions, see https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| strategy: | |
| matrix: | |
| include: | |
| - version: "2021.1.2.62" | |
| url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17508" | |
| # - version: "2022.2.1.16992" | |
| # url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18998" | |
| # - version: "2023.2.0.49254" | |
| # url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/237236c4-434b-4576-96ac-020ceeb22619" | |
| - version: "2024.2.0.426" | |
| url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/801143de-6c01-4181-9911-57e00fe40181" | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| env: | |
| FFLAGS: -check all | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ">=3.7" | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pyyaml | |
| - name: Install compiler | |
| run: | | |
| wget --no-verbose ${{ matrix.url_dir }}/l_fortran-compiler_p_${{ matrix.version }}_offline.sh | |
| /bin/sh l_fortran-compiler_p_${{ matrix.version }}_offline.sh -a --silent --cli --install-dir ${HOME}/intel --eula accept | |
| - name: Clone repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Run all test cases with host emulators | |
| run: | | |
| source ${HOME}/intel/setvars.sh | |
| python3 util/developers/run_all_testcases.py harness --show_logs --compiler ifort | |
| - name: Run all test cases with pyfabm | |
| run: | | |
| source ${HOME}/intel/setvars.sh | |
| python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler ifort | |
| env: | |
| FFLAGS: ${{ env.FFLAGS }} -fp-model precise -fp-model source | |
| ifx: | |
| # for available versions, see https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| strategy: | |
| matrix: | |
| include: | |
| - version: "2023.2.0.49254" | |
| url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/237236c4-434b-4576-96ac-020ceeb22619" | |
| fflags: -check all,nouninit,nocontiguous | |
| # nouninit because https://community.intel.com/t5/Intel-Fortran-Compiler/ifx-missing-clang-rt-msan-to-link-Fortran-program-in-debug-build/m-p/1536555 | |
| # nocontiguous because spurious errors occur when assigning null() to contiguous pointers, see https://community.intel.com/t5/Intel-Fortran-Compiler/ifx-2024-0-2-runtime-error-about-non-contiguous-target/m-p/1583909 | |
| #- version: "2024.0.2.28" | |
| # url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/41df6814-ec4b-4698-a14d-421ee2b02aa7" | |
| - version: "2024.2.0.426" | |
| url_dir: "https://registrationcenter-download.intel.com/akdlm/IRC_NAS/801143de-6c01-4181-9911-57e00fe40181" | |
| fflags: -check all,nouninit,nocontiguous | |
| # memory sanitizer (uninit) still seems broken, as it reports errors in libc.so (it should be auto-linked to sanitized libc, but apparently not) | |
| # contiguous check still broken, to be fixed in 2025.x as per https://community.intel.com/t5/Intel-Fortran-Compiler/ifx-2024-0-2-runtime-error-about-non-contiguous-target/m-p/1583909 | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ">=3.7" | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pyyaml | |
| - name: Install compiler | |
| run: | | |
| wget --no-verbose ${{ matrix.url_dir }}/l_fortran-compiler_p_${{ matrix.version }}_offline.sh | |
| /bin/sh l_fortran-compiler_p_${{ matrix.version }}_offline.sh -a --silent --cli --install-dir ${HOME}/intel --eula accept | |
| - name: Clone repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Run all test cases with host emulators | |
| run: | | |
| source ${HOME}/intel/setvars.sh | |
| python3 util/developers/run_all_testcases.py harness --show_logs --compiler ifx | |
| env: | |
| FFLAGS: ${{ matrix.fflags }} | |
| - name: Run all test cases with pyfabm | |
| run: | | |
| source ${HOME}/intel/setvars.sh | |
| python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler ifx | |
| env: | |
| FFLAGS: ${{ matrix.fflags }} -fp-model=precise | |
| nvfortran: | |
| # for available versions, see https://developer.nvidia.com/nvidia-hpc-sdk-releases | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| strategy: | |
| matrix: | |
| include: | |
| - version: "20.7" # released 2020-08 | |
| exe: nvhpc_2020_207_Linux_x86_64_cuda_11.0 | |
| # - version: "20.9" # released 2020-10 | |
| # exe: nvhpc_2020_209_Linux_x86_64_cuda_11.0 | |
| # - version: "22.9" # released 2022-10 | |
| # exe: nvhpc_2022_229_Linux_x86_64_cuda_11.7 | |
| # - version: "23.7" # released 2023-07 | |
| # exe: nvhpc_2023_237_Linux_x86_64_cuda_12.2 | |
| - version: "24.5" # released 2024-05 | |
| exe: nvhpc_2024_245_Linux_x86_64_cuda_12.4 | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| env: | |
| FFLAGS: -Mbounds -Mchkptr | |
| steps: | |
| - name: Free up disk space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ">=3.7" | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pyyaml | |
| - name: Install compiler | |
| run: | | |
| wget --no-verbose https://developer.download.nvidia.com/hpc-sdk/${{ matrix.version }}/${{ matrix.exe }}.tar.gz | |
| tar xpzf ${{ matrix.exe }}.tar.gz | |
| rm ${{ matrix.exe }}.tar.gz | |
| ${{ matrix.exe }}/install | |
| env: | |
| NVHPC_SILENT: true | |
| NVHPC_INSTALL_DIR: /home/runner/nvhpc | |
| NVHPC_INSTALL_TYPE: single | |
| - name: Clone repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Run all test cases with host emulators | |
| run: python3 util/developers/run_all_testcases.py harness --show_logs --compiler /home/runner/nvhpc/Linux_x86_64/${{ matrix.version }}/compilers/bin/pgfortran | |
| - name: Run all test cases with pyfabm | |
| run: python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler /home/runner/nvhpc/Linux_x86_64/${{ matrix.version }}/compilers/bin/pgfortran | |
| aocc: | |
| # for available versions, see https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/aocc/package.py | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| strategy: | |
| matrix: | |
| include: | |
| - version: "3.2.0" # released 2021-12-02 (LLVM 13.0) | |
| pyfabm_cmake_args: -DCMAKE_Fortran_FLAGS_DEBUG= # skip -g as that triggers segfault | |
| url_dir: https://download.amd.com/developer/eula/aocc-compiler | |
| # - version: "4.0.0" # released 2022-11-10 (LLVM 14.0.6) | |
| # url_dir: https://download.amd.com/developer/eula/aocc-compiler | |
| # - version: "4.1.0" # released 2023-08-04 (LLVM 16.0.3) | |
| # url_dir: https://download.amd.com/developer/eula/aocc/aocc-4-1 | |
| - version: "4.2.0" # released 2024-02-27 (LLVM 16.0.3) | |
| url_dir: https://download.amd.com/developer/eula/aocc/aocc-4-2 | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ">=3.7" | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pyyaml | |
| - name: Install compiler | |
| run: | | |
| cd /home/runner | |
| wget --no-verbose ${{ matrix.url_dir }}/aocc-compiler-${{ matrix.version }}.tar | |
| tar xpf aocc-compiler-${{ matrix.version }}.tar | |
| rm aocc-compiler-${{ matrix.version }}.tar | |
| ./aocc-compiler-${{ matrix.version }}/install.sh | |
| - name: Clone repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Run all test cases with host emulators | |
| run: | | |
| source /home/runner/setenv_AOCC.sh | |
| python3 util/developers/run_all_testcases.py harness --show_logs --compiler flang | |
| - name: Run all test cases with pyfabm | |
| run: | | |
| source /home/runner/setenv_AOCC.sh | |
| python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler flang ${{ matrix.pyfabm_cmake_args }} | |
| flang-new: | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| strategy: | |
| matrix: | |
| os: [windows-latest] | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: cmd /C call {0} | |
| env: | |
| CMAKE_GENERATOR: Ninja | |
| steps: | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| - name: Install Python dependencies | |
| run: conda install -c conda-forge pyyaml flang>=19.0 ninja c-compiler | |
| - name: Clone repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Run all test cases with host emulators | |
| run: | | |
| set CMAKE_GENERATOR_PLATFORM= | |
| set CMAKE_GENERATOR_TOOLSET= | |
| python util/developers/run_all_testcases.py harness --show_logs --compiler flang-new | |
| - name: Run all test cases with pyfabm | |
| run: | | |
| set CMAKE_GENERATOR_PLATFORM= | |
| set CMAKE_GENERATOR_TOOLSET= | |
| python util/developers/run_all_testcases.py pyfabm --show_logs --compiler flang-new -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE | |
| pyfabm: | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] | |
| fail-fast: false | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Clone repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Set up Python ${{ matrix.python-version }} with conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge | |
| - name: Install dependencies | |
| run: conda install pip python-build | |
| - name: Build distribution | |
| run: python -m build | |
| - name: Install | |
| run: python -m pip install -v . | |
| - name: Test | |
| run: | | |
| python -c "import pyfabm;print('pyfabm version =', getattr(pyfabm, '__version__', None))" | |
| for f in testcases/*.yaml; do fabm_describe_model $f; done | |
| for f in testcases/*.yaml; do fabm_complete_yaml --add_missing $f; done | |
| - name: Run notebooks | |
| if: matrix.python-version != '3.7' # due to https://github.com/conda-forge/webcolors-feedstock/issues/26 | |
| run: | | |
| conda install ipython jupyterlab ipympl matplotlib scipy | |
| cd testcases/python | |
| for f in *.ipynb; do ipython --gui qt -c "%run $f"; done | |
| - name: Install with customization via command line arguments | |
| run: | | |
| rm -rf build | |
| python -m pip install -v -C--build-option=build_ext -C--build-option="--cmake-opts=-DFABM_INSTITUTES=examples" . | |
| - name: Install with customization via setup.cfg | |
| run: | | |
| rm -rf build | |
| echo "[build_ext]" > setup.cfg | |
| echo "cmake_opts=-DFABM_INSTITUTES=examples" >> setup.cfg | |
| python -m pip install -v . | |
| fabm0d: | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install NetCDF | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libnetcdff-dev | |
| - name: Clone FABM | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Clone GOTM | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: gotm-model/code | |
| ref: v6.0 | |
| path: gotm | |
| submodules: recursive | |
| - name: Build | |
| run: | | |
| cmake -S src/drivers/0d -B build -DGOTM_BASE=gotm | |
| cmake --build build --target install | |
| stat ~/local/fabm/0d/bin/fabm0d | |
| cmake: | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| strategy: | |
| matrix: | |
| cmake-version: ["3.13"] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Clone FABM | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Download and extract cmake | |
| run: | | |
| wget --no-verbose https://cmake.org/files/v${{ matrix.cmake-version }}/cmake-${{ matrix.cmake-version }}.0-Linux-x86_64.tar.gz | |
| tar -xvf cmake-${{ matrix.cmake-version }}.0-Linux-x86_64.tar.gz | |
| - name: Build | |
| run: | | |
| cmake-${{ matrix.cmake-version }}.0-Linux-x86_64/bin/cmake -S . -B build | |
| cmake-${{ matrix.cmake-version }}.0-Linux-x86_64/bin/cmake --build build --target install | |
| ninja: | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Clone FABM | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Install Ninja | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install ninja-build | |
| - name: Build | |
| run: | | |
| cmake -S . -B build -G Ninja | |
| cmake --build build --target install | |
| binder: | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Clone repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Set up Python with conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| environment-file: .binder/environment.yml | |
| activate-environment: fabm | |
| - name: Install | |
| run: .binder/postBuild | |
| env: | |
| REPO_DIR: . |