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/**'
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 modflow6
        uses: actions/checkout@v4

      - uses: prefix-dev/setup-pixi@v0.8.1
        with:
          pixi-version: v0.24.2

      - 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
        uses: dieghernan/cff-validator@v3

  build:
    name: Build
    runs-on: ubuntu-22.04
    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 }}

      - uses: prefix-dev/setup-pixi@v0.8.1
        with:
          pixi-version: v0.24.2

      - name: Meson setup
        run: pixi run setup -Dwerror=true builddir

      - name: Meson compile
        run: pixi run build builddir

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

      - name: Meson test
        run: pixi run test builddir

  smoke_test:
    name: Smoke test
    runs-on: ubuntu-22.04
    defaults:
      run:
        shell: bash
    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 pixi
        uses: prefix-dev/setup-pixi@v0.8.1
        with:
          pixi-version: v0.24.2
          manifest-path: "modflow6/pixi.toml"

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

      - name: Build test-drive
        working-directory: test-drive
        run: |
          pixi run --manifest-path=../modflow6/pixi.toml meson setup builddir --prefix=$(pwd) --libdir=lib
          pixi run --manifest-path=../modflow6/pixi.toml meson install -C builddir
          echo "PKG_CONFIG_PATH=$(pwd)/lib/pkgconfig:$PKG_CONFIG_PATH" >> $GITHUB_ENV

      - name: Build modflow6
        working-directory: modflow6
        run: |
          pixi run setup builddir
          pixi run build 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: 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 programs
        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@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, macos-14, windows-2022 ]
    defaults:
      run:
        shell: bash
    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 }} ${{ contains(fromJSON('["macos-14"]'), matrix.os) && 12 || env.FC_V }}
        uses: fortran-lang/setup-fortran@v1
        with:
          compiler: gcc
          version: ${{ contains(fromJSON('["macos-14"]'), matrix.os) && 12 || env.FC_V }}

      - name: Setup pixi
        uses: prefix-dev/setup-pixi@v0.8.1
        with:
          pixi-version: v0.24.2
          manifest-path: "modflow6/pixi.toml"

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

      - name: Set LDFLAGS (macOS)
        if: matrix.os == 'macos-14'
        run: |
          os_ver=$(sw_vers -productVersion | cut -d'.' -f1)
          if (( "$os_ver" > 12 )); then
            ldflags="$LDFLAGS -Wl,-ld_classic"
            echo "LDFLAGS=$ldflags" >> $GITHUB_ENV
          fi

      - name: Build modflow6
        working-directory: modflow6
        run: |
          setupargs=""
          if [[ "${{ matrix.os }}" == "macos-14" ]]; then
            setupargs="-Doptimization=1"
          fi
          pixi run setup builddir $setupargs
          pixi run build 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: 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: Test modflow6
        working-directory: modflow6
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: |
          markers=""
          if [[ "${{ github.ref_name }}" == "master" ]]; then
            markers="not large and not developmode"
          else
            markers="not large"
          fi

          filters=""
          if [[ "${{ matrix.os }}" == "macos-14" ]]; then
            # comparison fails on macos-14 with optimization=1
            filters="not test028_sfr_rewet"
          fi

          pixi run autotest -m "$markers" -k "$filters"
      
      - 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 bin/mf6 $(which mf6)
          cd ../modflow6-examples/autotest
          pytest -v -n auto test_scripts.py

      - 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
        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: "2021.7"
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-22.04, macos-12, windows-2022]
    defaults:
      run:
        shell: bash
    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 pixi
        uses: prefix-dev/setup-pixi@v0.8.1
        with:
          pixi-version: v0.24.2
          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 modflow6
        working-directory: modflow6
        run: |
          pixi run setup builddir
          pixi run build 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: 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 programs
        working-directory: modflow6
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: |
          if [ "${{ github.ref_name }}" == "master" ]; then
            pixi run autotest -m "not large and not developmode"
          else
            pixi run autotest -m "not large"
          fi

      - 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 bin/mf6 $(which mf6)
          cd ../modflow6-examples/autotest
          pytest -v -n auto test_scripts.py
      
      - 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
        env:
          GITHUB_TOKEN: ${{ github.token }}
        run: pixi run test-dist-scripts
        
  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
    
    steps:

      - name: Checkout modflow6
        uses: actions/checkout@v4
        with:
          path: modflow6

      - name: Setup pixi
        uses: prefix-dev/setup-pixi@v0.8.1
        with:
          pixi-version: v0.24.2
          manifest-path: "modflow6/pixi.toml"

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

      - name: Test parallel MF6
        if: runner.os != 'Windows'
        uses: ./modflow6/.github/actions/test-par

      - name: Test parallel MF6 (Windows)
        if: runner.os == 'Windows'
        uses: ./modflow6/.github/actions/test-par-win

      - name: Upload failed test output
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: failed-${{ matrix.os }}
          path: modflow6/autotest/.failed

  extended_test:
    name: Extended executable testing
    needs:
      - lint
      - build
      - smoke_test
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ ubuntu-22.04, macos-12 ]
    defaults:
      run:
        shell: bash

    steps:

      - name: Checkout modflow6
        uses: actions/checkout@v4
        with:
          path: modflow6

      - name: Setup pixi
        uses: prefix-dev/setup-pixi@v0.8.1
        with:
          pixi-version: v0.24.2
          manifest-path: "modflow6/pixi.toml"

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

      - name: Install additional netcdf testing packages
        working-directory: modflow6
        run: pixi run pip install xugrid xarray netcdf4

      - name: Test Extended MF6
        uses: ./modflow6/.github/actions/test-extended

      - name: Upload failed test output
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: failed-${{ matrix.os }}
          path: modflow6/autotest/.failed