feat(idm): extend input framework with netcdf4 loaders (incomplete) #1311
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: 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 | |
| build: | |
| name: Build | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| GCC_V: 13 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| - name: Setup gfortran ${{ env.GCC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC_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 | |
| GCC: 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 GNU Fortran ${{ env.GCC }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC }} | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build test-drive | |
| working-directory: test-drive | |
| run: | | |
| meson setup builddir --prefix=$(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" | |
| else | |
| pytest -v -n auto --durations 0 -S | |
| fi | |
| 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 | |
| GCC: 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 GNU Fortran ${{ env.GCC }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC }} | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false --prefix=$(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" | |
| else | |
| pytest -v -n auto --durations 0 -m "not large" | |
| fi | |
| - 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 }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - {os: ubuntu-22.04, compiler: intel-classic, version: 2021.7} | |
| - {os: macos-12, compiler: intel-classic, version: 2021.7} | |
| - {os: windows-2022, compiler: intel-classic, version: 2021.7} | |
| 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: 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 Intel Fortran | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: ${{ matrix.compiler }} | |
| version: ${{ matrix.version }} | |
| - name: Update version files | |
| working-directory: modflow6/distribution | |
| run: python update_version.py | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false --prefix=$(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" | |
| else | |
| pytest -v -n auto --durations 0 -m "not large" | |
| fi | |
| - 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 | |
| GCC_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 GNU Fortran ${{ env.GCC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC_V }} | |
| - name: Cache PETSc | |
| id: cache-petsc | |
| uses: actions/cache@v3 | |
| 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" | |