ci.yml

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: 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