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/**"
  workflow_dispatch:
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true
env:
  PIXI_BETA_WARNING_OFF: true
jobs:
  lint:
    name: Check format
    runs-on: ubuntu-latest
    steps:
      - name: Checkout MF6
        uses: actions/checkout@v6

      - name: Setup pixi
        uses: prefix-dev/setup-pixi@v0.9.6
        with:
          pixi-version: v0.41.4

      - name: Check Fortran source formatting
        run: pixi run check-format

      - name: Check MSVS project files
        run: pixi run check-vfproj

      - name: Check python lint
        run: pixi run check-python-lint

      - name: Check python format
        run: pixi run check-python-format

      - name: Check CITATION.cff
        run: pixi run check-citations

      - name: Check generated Fortran IDM files are up to date
        run: |
          pixi run update-fortran-definitions
          if ! git diff --exit-code src/Idm/; then
            echo "::error::Generated Fortran IDM files are out of date!"
            echo "::error::Run 'pixi run update-fortran-definitions' and commit changes."
            git diff --stat src/Idm/
            exit 1
          fi

  build:
    name: Build
    runs-on: ubuntu-22.04
    env:
      FC: gfortran
      FC_V: 13
    steps:
      - name: Checkout MF6
        uses: actions/checkout@v6

      - name: Setup ${{ env.FC }} ${{ env.FC_V }}
        uses: fortran-lang/setup-fortran@v1
        with:
          compiler: gcc
          version: ${{ env.FC_V }}

      - name: Setup pixi
        uses: prefix-dev/setup-pixi@v0.9.6
        with:
          pixi-version: v0.41.4

      - name: Setup MF6
        run: pixi run setup -Dwerror=true builddir

      - name: Build MF6
        run: pixi run build builddir

      - name: Setup mf5to6
        run: pixi run setup-mf5to6 -Dwerror=true builddir

      - name: Build mf5to6
        run: pixi run build-mf5to6 builddir

      - name: Show build log
        if: failure()
        run: cat builddir/meson-logs/meson-log.txt

      - name: Unit test MF6
        run: pixi run test builddir

  pixi-gcc-extended-build:
    name: Pixi gcc-extended-build environment testing
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        include:
          - os: ubuntu-22.04
          - os: macos-14
    defaults:
      run:
        shell: bash
    steps:
      - name: Checkout MF6
        uses: actions/checkout@v6

      - name: Setup pixi
        uses: prefix-dev/setup-pixi@v0.9.6
        with:
          pixi-version: v0.41.4

      - name: Update netcdf-fortran.pc and test-drive
        run: |
          pixi run -e gcc-extended-build gcc-extended-build-update

      - name: Setup and build the extended MF6 build in the gcc-extended-build environment
        run: |
          pixi run -e gcc-extended-build setup builddir -Dextended=true
          pixi run -e gcc-extended-build build builddir

      - name: Show build log
        if: failure()
        run: cat builddir/meson-logs/meson-log.txt

      - name: Unit test the extended MF6 build in the gcc-extended-build environment
        run: pixi run -e gcc-extended-build test builddir
        
  build-static:
    name: Static gcc build
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        include:
          - os: ubuntu-22.04
          - os: windows-2022
    defaults:
      run:
        shell: bash
    env:
      FC: gfortran
      FC_V: 13
    steps:
      - name: Checkout MF6
        uses: actions/checkout@v6

      - name: Setup ${{ env.FC }} ${{ env.FC_V }}
        uses: fortran-lang/setup-fortran@v1
        with:
          compiler: gcc
          version: ${{ env.FC_V }}

      - name: Setup pixi
        uses: prefix-dev/setup-pixi@v0.9.6
        with:
          pixi-version: v0.41.4

      - name: Setup static MF6
        run: pixi run setup -Dwerror=true -Ddefault_library=static builddir

      - name: Build MF6
        run: pixi run build builddir

      - name: Show build log
        if: failure()
        run: cat builddir/meson-logs/meson-log.txt

      - name: Unit test MF6
        run: pixi run test builddir

      - name: Confirm modflow6 has no dependencies (Linux)
        if: runner.os == 'Linux'
        run: |
          echo "Checking dependencies with ldd..."
          if ldd bin/mf6; then
              echo mf6 is dynamically linked
              exit 1
          else
              echo mf6 is statically linked
          fi

      - name: Clone ntldd repository and build
        if: runner.os == 'Windows'
        run: |
          git clone https://github.com/LRN/ntldd.git
          cd ntldd
          ./makeldd.sh
          ls -lha

      - name: Confirm modflow6 has no dependencies (Windows)
        if: runner.os == 'Windows'
        working-directory: ntldd
        run: |
          echo "Checking dependencies with ntldd..."
          set +e
          ./ntldd.exe ../bin/mf6.exe > mf6.dependencies.txt

          dep_count=$(grep -vc "KERNEL32.dll" mf6.dependencies.txt)
          echo "Number of dependencies: $dep_count"

          set -e
          if [ "$dep_count" -eq 0 ]; then
            echo mf6.exe is statically linked
          else
            echo mf6.exe is dynamically linked
            echo exit 1
          fi

  smoke_test:
    name: Smoke test
    runs-on: ubuntu-22.04
    defaults:
      run:
        shell: bash
    env:
      FC: gfortran
      FC_V: 13
    steps:
      - name: Checkout MF6
        uses: actions/checkout@v6
        with:
          path: modflow6

      - name: Setup ${{ env.FC }} ${{ env.FC_V }}
        uses: fortran-lang/setup-fortran@v1
        with:
          compiler: gcc
          version: ${{ env.FC_V }}

      - name: Setup pixi
        uses: prefix-dev/setup-pixi@v0.9.6
        with:
          pixi-version: v0.41.4
          manifest-path: "modflow6/pixi.toml"

      - name: Custom pixi install
        working-directory: modflow6
        run: pixi run install

      - name: Build MF6
        working-directory: modflow6
        run: |
          pixi run setup builddir
          pixi run build builddir
          pixi run setup-mf5to6 builddir
          pixi run build-mf5to6 builddir

      - name: Show build log
        if: failure()
        working-directory: modflow6
        run: cat builddir/meson-logs/meson-log.txt

      - name: Unit test MF6
        working-directory: modflow6
        run: pixi run test builddir

      - name: Update flopy
        working-directory: modflow6
        run: pixi run update-flopy

      - name: Get executables
        working-directory: modflow6
        env:
          GITHUB_TOKEN: ${{ github.token }}
        run: pixi run get-exes

      - name: Test MF6
        working-directory: modflow6
        run: |
          if [ "${{ github.ref_name }}" == "master" ]; then
            pixi run autotest -m "not slow and not regression and not developmode"
          else
            pixi run autotest --smoke
          fi

      - name: Upload failed test output
        if: failure()
        uses: actions/upload-artifact@v7
        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:
        include:
          # arm mac, release mode
          - os: macos-14
            debug: false
            xcode-version: '15.1.0'
          # arm mac, debug mode
          - os: macos-14
            debug: true
            xcode-version: '15.1.0'
          # ubuntu, release mode
          - os: ubuntu-22.04
            debug: false
          # ubuntu, debug mode
          - os: ubuntu-22.04
            debug: true
          # windows, release mode
          - os: windows-2022
            debug: false
    defaults:
      run:
        shell: bash
    env:
      FC: gfortran
      FC_V: 13
    steps:
      - name: Free disk space (Ubuntu)
        if: runner.os == 'Linux'
        uses: jlumbroso/free-disk-space@main
        with:
          tool-cache: true
          android: true
          dotnet: true
          haskell: true
          large-packages: true
          docker-images: true
          swap-storage: true

      - name: Checkout MF6
        uses: actions/checkout@v6
        with:
          path: modflow6

      - name: Checkout test models
        uses: actions/checkout@v6
        with:
          repository: MODFLOW-ORG/modflow6-testmodels
          path: modflow6-testmodels

      - name: Checkout examples
        uses: actions/checkout@v6
        with:
          repository: MODFLOW-ORG/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 pixi
        uses: prefix-dev/setup-pixi@v0.9.6
        with:
          pixi-version: v0.41.4
          manifest-path: "modflow6/pixi.toml"

      - name: Custom pixi install
        working-directory: modflow6
        run: pixi run install

      - name: Set xcode version (macOS)
        if: runner.os == 'macOS'
        uses: maxim-lobanov/setup-xcode@v1
        with:
          xcode-version: ${{ matrix.xcode-version }}

      # static link gfortran libs
      - name: Hide dylibs (macOS)
        if: runner.os == 'macOS'
        run: |
          version="${{ env.FC_V }}"
          brew_prefix="$(brew --prefix)"
          libpath="$brew_prefix/opt/gcc@$version/lib/gcc/$version"
          mv $libpath/libgcc_s.1.1.dylib $libpath/libgcc_s.1.1.dylib.bak
          mv $libpath/libgfortran.5.dylib $libpath/libgfortran.5.dylib.bak
          mv $libpath/libquadmath.0.dylib $libpath/libquadmath.0.dylib.bak 

      # use classic xcode linker, static link libgcc
      - name: Set LDFLAGS (macOS)
        if: runner.os == 'macOS'
        run: |
          ldflags="$LDFLAGS -Wl,-ld_classic -static-libgcc"
          echo "LDFLAGS=$ldflags" >> $GITHUB_ENV

      - name: Update version files
        working-directory: modflow6
        run: pixi run update-version

      - name: Set setupargs
        run: |
          setupargs=""
          if [[ "${{ matrix.debug }}" == "true" ]]; then
            setupargs="-Ddebug=true -Doptimization=0"
          elif [[ "${{ matrix.os }}" == "macos-14" ]]; then
            setupargs="-Doptimization=1"
          fi
          echo "MESON_SETUP_ARGS=$setupargs" >> $GITHUB_ENV

      - name: Build MF6
        working-directory: modflow6
        run: |
          pixi run setup builddir $MESON_SETUP_ARGS
          pixi run build builddir

      - name: Build mf5to6 converter
        working-directory: modflow6
        run: |
          pixi run setup-mf5to6 builddir $MESON_SETUP_ARGS
          pixi run build-mf5to6 builddir

      - name: Show build log
        if: failure()
        working-directory: modflow6
        run: cat builddir/meson-logs/meson-log.txt

      - name: Upload build log
        if: failure()
        uses: actions/upload-artifact@v7
        with:
          name: ${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }}-meson-log.txt
          path: modflow6/builddir/meson-logs/meson-log.txt

      - name: Check arch/libs (macOS)
        if: runner.os == 'macOS'
        working-directory: modflow6/bin
        run: |
          otool -L mf6
          otool -L libmf6.dylib
          otool -L mf5to6
          otool -L zbud6
          lipo -info mf6 
          lipo -info libmf6.dylib
          lipo -info mf5to6
          lipo -info zbud6

      # TODO remove after next executables release. only necessary because
      # tests using gridgen were failing as the current gridgen depends on
      # some dylibs. new executables all statically link gcc/gfortran libs
      - name: Restore dylibs (macOS)
        if: runner.os == 'macOS'
        run: |
          version="${{ env.FC_V }}"
          brew_prefix="$(brew --prefix)"
          libpath="$brew_prefix/opt/gcc@$version/lib/gcc/$version"
          mv $libpath/libgcc_s.1.1.dylib.bak $libpath/libgcc_s.1.1.dylib
          mv $libpath/libgfortran.5.dylib.bak $libpath/libgfortran.5.dylib
          mv $libpath/libquadmath.0.dylib.bak $libpath/libquadmath.0.dylib

      - name: Unit test MF6
        working-directory: modflow6
        run: pixi run test builddir

      - name: Update flopy
        working-directory: modflow6
        run: pixi run update-flopy

      - name: Get executables
        working-directory: modflow6/autotest
        env:
          GITHUB_TOKEN: ${{ github.token }}
        run: pixi run get-exes

      - name: Set markers
        id: set_markers
        run: |
          markers=""
          if [[ "${{ github.ref_name }}" == "master" ]]; then
            markers="not large and not developmode"
          else
            markers="not large"
          fi
          echo "markers=$markers" >> $GITHUB_OUTPUT

      - name: Set filters
        id: set_filters
        run: |
          filters=""
          if [[ "${{ matrix.os }}" == "macos-14" ]]; then
            # comparison fails on macos-14 with optimization=1
            filters="not test028_sfr_rewet"
          fi
          echo "filters=$filters" >> $GITHUB_OUTPUT

      - name: Test MF6
        working-directory: modflow6
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: pixi run autotest -m "${{ steps.set_markers.outputs.markers }} and not external" -k "${{ steps.set_filters.outputs.filters }}"

      - name: Test MF6 models
        working-directory: modflow6
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: pixi run autotest -m "${{ steps.set_markers.outputs.markers }} and external" -k "${{ steps.set_filters.outputs.filters }}" --models-path ../../modflow6-testmodels/mf6

      - name: Test converter models
        working-directory: modflow6
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: pixi run autotest -m "${{ steps.set_markers.outputs.markers }} and external" -k "${{ steps.set_filters.outputs.filters }}" --models-path ../../modflow6-testmodels/mf5to6 --namefile-pattern "*.nam"

      - name: Install executables
        uses: modflowpy/install-modflow-action@v1

      - name: Test examples
        working-directory: modflow6
        if: runner.os != 'Windows'
        shell: pixi run bash -e {0}
        run: |
          cp -R bin/* ~/.local/bin/modflow/
          cd ../modflow6-examples/autotest
          pytest -v -n auto test_scripts.py

      - name: Test examples
        working-directory: modflow6
        if: runner.os == 'Windows'
        run: |
          cp -R bin/* /c/Users/runneradmin/.local/bin/modflow/
          cd ../modflow6-examples/autotest
          pixi run --manifest-path ../../modflow6/pixi.toml pytest -v -n auto test_scripts.py

      - name: Upload failed test output
        if: failure()
        uses: actions/upload-artifact@v7
        with:
          name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }}
          path: modflow6/autotest/.failed

      - name: Checkout usgslatex
        if: runner.os == 'Linux'
        uses: actions/checkout@v6
        with:
          repository: MODFLOW-ORG/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
        env:
          GITHUB_TOKEN: ${{ github.token }}
        run: pixi run test-dist-scripts

  test_intel_fortran:
    name: Test Intel fortran
    needs:
      - lint
      - build
      - smoke_test
    runs-on: ${{ matrix.os }}
    env:
      FC: intel-classic
      FC_V: "2021.6"
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-22.04, windows-2022]
    defaults:
      run:
        shell: bash
    steps:
      - name: Free disk space (Ubuntu)
        if: runner.os == 'Linux'
        uses: jlumbroso/free-disk-space@main
        with:
          tool-cache: true
          android: true
          dotnet: true
          haskell: true
          large-packages: true
          docker-images: true
          swap-storage: true

      - name: Checkout MF6
        uses: actions/checkout@v6
        with:
          path: modflow6

      - name: Checkout test models
        uses: actions/checkout@v6
        with:
          repository: MODFLOW-ORG/modflow6-testmodels
          path: modflow6-testmodels

      - name: Checkout examples
        uses: actions/checkout@v6
        with:
          repository: MODFLOW-ORG/modflow6-examples
          path: modflow6-examples

      - name: Setup pixi
        uses: prefix-dev/setup-pixi@v0.9.6
        with:
          pixi-version: v0.41.4
          manifest-path: "modflow6/pixi.toml"

      - name: Custom pixi install
        working-directory: modflow6
        run: pixi run install

      - 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
        run: pixi run update-version

      - name: Build MF6
        working-directory: modflow6
        run: |
          pixi run setup builddir
          pixi run build builddir
          pixi run setup-mf5to6 builddir
          pixi run build-mf5to6 builddir

      - name: Show build log
        if: failure()
        working-directory: modflow6
        run: cat builddir/meson-logs/meson-log.txt

      - name: Unit test MF6
        working-directory: modflow6
        run: pixi run test builddir

      - name: Update flopy
        working-directory: modflow6
        run: pixi run update-flopy

      - name: Get executables
        working-directory: modflow6
        env:
          GITHUB_TOKEN: ${{ github.token }}
        run: pixi run get-exes

      - name: Set markers
        id: set_markers
        run: |
          markers=""
          if [[ "${{ github.ref_name }}" == "master" ]]; then
            markers="not large and not developmode"
          else
            markers="not large"
          fi
          echo "markers=$markers" >> $GITHUB_OUTPUT

      - name: Test MF6
        working-directory: modflow6
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: pixi run autotest -m "${{ steps.set_markers.outputs.markers }} and not external"

      - name: Test MF6 models
        working-directory: modflow6
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: pixi run autotest -m "${{ steps.set_markers.outputs.markers }} and external" --models-path ../../modflow6-testmodels/mf6

      - name: Test converter models
        working-directory: modflow6
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: pixi run autotest -m "${{ steps.set_markers.outputs.markers }} and external" --models-path ../../modflow6-testmodels/mf5to6 --namefile-pattern "*.nam"

      # if on linux, test example models too
      - name: Install executables
        if: runner.os == 'Linux'
        uses: modflowpy/install-modflow-action@v1

      - name: Test MF6 examples
        if: runner.os == 'Linux'
        working-directory: modflow6
        shell: pixi run bash -e {0}
        run: |
          cp -R bin/* ~/.local/bin/modflow/
          cd ../modflow6-examples/autotest
          pytest -v -n auto test_scripts.py

      - name: Upload failed test output
        if: failure()
        uses: actions/upload-artifact@v7
        with:
          name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }}
          path: modflow6/autotest/.failed

      - name: Test scripts
        working-directory: modflow6
        env:
          GITHUB_TOKEN: ${{ github.token }}
        run: pixi run test-dist-scripts

  extended_test:
    name: Extended testing
    needs:
      - lint
      - build
      - smoke_test
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-22.04, macos-14, windows-2022]
    defaults:
      run:
        shell: bash

    steps:
      - name: Free disk space (Ubuntu)
        if: runner.os == 'Linux'
        uses: jlumbroso/free-disk-space@main
        with:
          tool-cache: true
          android: true
          dotnet: true
          haskell: true
          large-packages: true
          docker-images: true
          swap-storage: true

      - name: Checkout MF6
        uses: actions/checkout@v6
        with:
          path: modflow6

      - name: Setup gfortran
        if: runner.os != 'Windows'
        uses: fortran-lang/setup-fortran@v1
        with:
          compiler: gcc
          version: 13

      - name: Setup pixi
        uses: prefix-dev/setup-pixi@v0.9.6
        with:
          pixi-version: v0.41.4
          manifest-path: "modflow6/pixi.toml"

      - name: Custom pixi install
        working-directory: modflow6
        run: pixi run install

      - name: Set LDFLAGS (macOS)
        if: runner.os == 'macOS'
        run: |
          ldflags="$LDFLAGS -Wl,-ld_classic -static-libgcc"
          echo "LDFLAGS=$ldflags" >> $GITHUB_ENV

      - name: Set markers
        id: set_markers
        run: echo "markers=not large" >> $GITHUB_OUTPUT

      - name: Set filters
        id: set_filters
        run: echo "filters=test_par or test_netcdf" >> $GITHUB_OUTPUT

      - name: Test extended MF6
        if: runner.os != 'Windows'
        uses: ./modflow6/.github/actions/test-extended
        env:
          MARKERS: ${{ steps.set_markers.outputs.markers }}
          FILTERS: ${{ steps.set_filters.outputs.filters }}

      - name: Test extended MF6
        if: runner.os == 'Windows'
        uses: ./modflow6/.github/actions/test-extended-win
        env:
          MARKERS: ${{ steps.set_markers.outputs.markers }}
          FILTERS: ${{ steps.set_filters.outputs.filters }}

      - name: Upload failed test output
        if: failure()
        uses: actions/upload-artifact@v7
        with:
          name: failed-${{ matrix.os }}-ext
          path: modflow6/autotest/.failed