feat(idm): initial netcdf integration #2155
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| name: MODFLOW 6 continuous integration | |
| on: | |
| push: | |
| paths-ignore: | |
| - '**.md' | |
| - '**.pdf' | |
| - '**.tex' | |
| - '**.jpg' | |
| - '**.jpeg' | |
| - '**.png' | |
| - '**.bbl' | |
| - '**.bib' | |
| - 'doc/**.dat' | |
| - 'doc/**.ipynb' | |
| - 'doc/**.py' | |
| - 'doc/**.sh' | |
| - 'doc/**.xlsx' | |
| - '.hpc/**' | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| paths-ignore: | |
| - '**.md' | |
| - '**.pdf' | |
| - '**.tex' | |
| - '**.jpg' | |
| - '**.jpeg' | |
| - '**.png' | |
| - '**.bbl' | |
| - '**.bib' | |
| - 'doc/**.dat' | |
| - 'doc/**.ipynb' | |
| - 'doc/**.py' | |
| - 'doc/**.sh' | |
| - 'doc/**.xlsx' | |
| - '.hpc/**' | |
| jobs: | |
| lint: | |
| name: Check format | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Check Fortran source formatting | |
| run: python .github/common/fortran_format_check.py | |
| - name: Check MSVS project files | |
| run: python .github/common/msvs_vfproj_check.py | |
| - name: Check CITATION.cff | |
| uses: dieghernan/cff-validator@v3 | |
| build: | |
| name: Build | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| FC_V: 13 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.FC_V }} | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Meson setup | |
| run: meson setup builddir -Ddebug=false -Dwerror=true | |
| - name: Meson compile | |
| run: meson compile -C builddir | |
| - name: Show build log | |
| if: failure() | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Meson test | |
| run: meson test --verbose --no-rebuild -C builddir | |
| smoke_test: | |
| name: Smoke test | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| FC_V: 13 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Checkout test-drive | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: fortran-lang/test-drive | |
| path: test-drive | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.FC_V }} | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build test-drive | |
| working-directory: test-drive | |
| run: | | |
| meson setup builddir --prefix=$(pwd) --libdir=lib | |
| meson install -C builddir | |
| echo "PKG_CONFIG_PATH=$(pwd)/lib/pkgconfig:$PKG_CONFIG_PATH" >> $GITHUB_ENV | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| - name: Show build log | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Unit test programs | |
| working-directory: modflow6 | |
| run: meson test --verbose --no-rebuild -C builddir | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test programs | |
| working-directory: modflow6/autotest | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pytest -v -n auto --durations 0 -m "not slow and not regression and not developmode" --keep-failed .failed | |
| else | |
| pytest -v -n auto --durations 0 -S --keep-failed .failed | |
| fi | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-smoke-${{ runner.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed | |
| test_gfortran: | |
| name: Test gnu fortran | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-12, windows-2022 ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| FC_V: 13 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Checkout modflow6-testmodels | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-testmodels | |
| path: modflow6-testmodels | |
| - name: Checkout modflow6-examples | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-examples | |
| path: modflow6-examples | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.FC_V }} | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| - name: Show build log | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Unit test programs | |
| working-directory: modflow6 | |
| run: meson test --verbose --no-rebuild -C builddir | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test modflow6 | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pytest -v -n auto --durations 0 -m "not large and not developmode" --keep-failed .failed | |
| else | |
| pytest -v -n auto --durations 0 -m "not large" --keep-failed .failed | |
| fi | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed | |
| - name: Checkout usgslatex | |
| if: runner.os == 'Linux' | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/usgslatex | |
| path: usgslatex | |
| - name: Install TeX Live | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt install texlive-science \ | |
| texlive-latex-extra \ | |
| texlive-font-utils \ | |
| texlive-fonts-recommended \ | |
| texlive-fonts-extra | |
| - name: Install USGS LaTeX style files and Univers font | |
| if: runner.os == 'Linux' | |
| working-directory: usgslatex/usgsLaTeX | |
| run: sudo ./install.sh --all-users | |
| - name: Test distribution scripts | |
| working-directory: modflow6/distribution | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 | |
| test_intel_fortran: | |
| name: Test intel fortran | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| FC: intel-classic | |
| FC_V: "2021.7" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-22.04, macos-12, windows-2022] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Checkout modflow6-testmodels | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-testmodels | |
| path: modflow6-testmodels | |
| - name: Checkout modflow6-examples | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-examples | |
| path: modflow6-examples | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: ${{ env.FC }} | |
| version: ${{ env.FC_V }} | |
| - name: Update version files | |
| working-directory: modflow6/distribution | |
| run: python update_version.py | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| - name: Show build log | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Unit test programs | |
| working-directory: modflow6 | |
| run: meson test --verbose --no-rebuild -C builddir | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test programs | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pytest -v -n auto --durations 0 -m "not large and not developmode" --keep-failed .failed | |
| else | |
| pytest -v -n auto --durations 0 -m "not large" --keep-failed .failed | |
| fi | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed | |
| - name: Test scripts | |
| working-directory: modflow6/distribution | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 | |
| parallel_test: | |
| name: Parallel testing | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-12 ] #, windows-2022 ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| FC_V: 12 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Setup MSYS2 | |
| if: runner.os == 'Windows' | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: | | |
| git | |
| make | |
| mingw-w64-x86_64-gcc | |
| mingw-w64-x86_64-python | |
| mingw-w64-x86_64-python-pip | |
| mingw-w64-x86_64-python-pytest | |
| - name: Setup MPI | |
| if: runner.os == 'Windows' | |
| uses: mpi4py/setup-mpi@v1 | |
| with: | |
| mpi: msmpi | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.FC_V }} | |
| - name: Cache PETSc | |
| id: cache-petsc | |
| uses: actions/cache@v4 | |
| with: | |
| path: petsc | |
| key: ${{ runner.os }}-petsc | |
| - name: Clone PETSc | |
| if: runner.os != 'Windows' && steps.cache-petsc.outputs.cache-hit != 'true' | |
| run: git clone -b release https://gitlab.com/petsc/petsc.git petsc | |
| - name: Download PETSc | |
| if: runner.os == 'Windows' | |
| run: | | |
| curl https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.18.4.tar.gz -O -J | |
| mkdir petsc | |
| tar -xzf petsc-3.18.4.tar.gz -C petsc --strip-components=1 | |
| - name: Configure environment | |
| if: runner.os == 'Linux' | |
| run: | | |
| echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/linux-gnu/lib/pkgconfig" >> $GITHUB_ENV | |
| echo "$GITHUB_WORKSPACE/petsc/linux-gnu/bin" >> $GITHUB_PATH | |
| - name: Configure environment | |
| if: runner.os == 'macOS' | |
| run: | | |
| echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/lib/pkgconfig" >> $GITHUB_ENV | |
| echo "$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/bin" >> $GITHUB_PATH | |
| - name: Configure PETSc | |
| if: runner.os == 'Linux' | |
| working-directory: petsc | |
| run: | | |
| sudo ./configure PETSC_ARCH=linux-gnu --download-fblaslapack --download-openmpi | |
| sudo make all | |
| - name: Configure PETSc | |
| if: runner.os == 'macOS' | |
| working-directory: petsc | |
| run: | | |
| sudo ./configure PETSC_DIR="$GITHUB_WORKSPACE/petsc" PETSC_ARCH=arch-darwin-gcc-debug --download-fblaslapack --download-openmpi | |
| sudo make all | |
| - name: Configure PETSc | |
| if: runner.os == 'Windows' | |
| shell: msys2 {0} | |
| working-directory: petsc | |
| run: | | |
| pacman -Syu | |
| pacman -Sy --noconfirm autoconf automake-wrapper bison bsdcpio make git \ | |
| mingw-w64-x86_64-toolchain patch python flex \ | |
| pkg-config pkgfile tar unzip mingw-w64-x86_64-cmake \ | |
| mingw-w64-x86_64-msmpi mingw-w64-x86_64-openblas mingw-w64-x86_64-jq | |
| /usr/bin/python ./configure --with-mpiexec='/C/Program\ Files/Microsoft\ MPI/Bin/mpiexec' --with-shared-libraries=0 | |
| make all | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false -Dparallel=true --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Show Meson logs | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test programs (parallel) | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| branch="${{ github.ref_name }}" | |
| marker="not large" | |
| markers=$([ "$branch" == "master" ] && echo "$marker and not developmode" || echo "$marker") | |
| pytest -v -n auto --parallel --durations 0 -m "$markers" --keep-failed .failed | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed | |
| netcdf_test: | |
| name: NetCDF testing | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-12 ] #, windows-2022 ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| FC_V: 12 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.FC_V }} | |
| - name: Cache PETSc | |
| id: cache-petsc | |
| uses: actions/cache@v4 | |
| with: | |
| path: petsc | |
| key: ${{ runner.os }}-petsc | |
| - name: Clone PETSc | |
| if: runner.os != 'Windows' && steps.cache-petsc.outputs.cache-hit != 'true' | |
| run: git clone -b release https://gitlab.com/petsc/petsc.git petsc | |
| - name: Configure environment | |
| if: runner.os == 'Linux' | |
| run: | | |
| echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/linux-gnu/lib/pkgconfig" >> $GITHUB_ENV | |
| echo "$GITHUB_WORKSPACE/petsc/linux-gnu/bin" >> $GITHUB_PATH | |
| - name: Configure environment | |
| if: runner.os == 'macOS' | |
| run: | | |
| echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/lib/pkgconfig" >> $GITHUB_ENV | |
| echo "$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/bin" >> $GITHUB_PATH | |
| - name: Configure PETSc | |
| if: runner.os == 'Linux' | |
| working-directory: petsc | |
| run: | | |
| sudo ./configure PETSC_ARCH=linux-gnu --download-fblaslapack --download-openmpi | |
| sudo make all | |
| - name: Configure PETSc | |
| if: runner.os == 'macOS' | |
| working-directory: petsc | |
| run: | | |
| sudo ./configure PETSC_DIR="$GITHUB_WORKSPACE/petsc" PETSC_ARCH=arch-darwin-gcc-debug --download-fblaslapack --download-openmpi | |
| sudo make all | |
| - name: Install netcdf | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install build-essential \ | |
| libnetcdf-dev \ | |
| libnetcdff-dev \ | |
| netcdf-bin | |
| nc-config --all | |
| nf-config --all | |
| - name: Install netcdf | |
| if: runner.os == 'macOS' | |
| run: | | |
| bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" | |
| brew install netcdf-fortran | |
| brew install gcc | |
| nc-config --all | |
| nf-config | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment-nctest.yml | |
| create-args: >- | |
| netcdf4 | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false -Dextended=true --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Show Meson logs | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test programs (netcdf) | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| pytest -v -n auto -m netcdf --netcdf --parallel --durations 0 --keep-failed .failed | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed |