ci2.yml

name: MODFLOW 6 continuous integration
on:
  push:
    branches:
      - master
      - develop
      - ci-diagnose*
      - ncci
    paths-ignore:
      - '**.md'
      - 'doc/**'
  pull_request:
    branches:
      - master
      - develop
    paths-ignore:
      - '**.md'
      - 'doc/**'
jobs:

  netcdf_test_win:
    name: netcdf4 testing
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ windows-2022 ]
        #hdf5: [ 1.12.2 ]
        #netcdf: [ v4.7.4, v4.8.1, v4.9.0, main ]
        #netcdf: [ v4.9.0, main ]
    defaults:
      run:
        shell: bash -l {0}
    env:
      FC: gfortran
      GCC_V: 12
    steps:

      - name: Checkout modflow6
        uses: actions/checkout@v3
        with:
          path: modflow6

      - name: Setup MSYS2
        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 GNU Fortran ${{ env.GCC_V }}
        uses: awvwgk/setup-fortran@main
        with:
          compiler: gcc
          version: ${{ env.GCC_V }}

      - name: Install System dependencies
        shell: msys2 {0}
        run: |
          pacman -Syu
          pacman -S --noconfirm --needed base-devel unzip mingw-w64-x86_64-toolchain mingw-w64-x86_64-libtool mingw-w64-x86_64-cmake

      - name: Install hdf5 and netcdf-c
        shell: msys2 {0}
        run: |
          pacman -U --noconfirm https://repo.msys2.org/mingw/mingw64/mingw-w64-x86_64-hdf5-1.12.2-2-any.pkg.tar.zst
          pacman -S --noconfirm --needed mingw-w64-x86_64-netcdf

      - name: Download netcdf-f
        run: |
          mkdir ncf
          #cd ncf
          #wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.zip
          #unzip v4.6.0.zip

      - name: Make netcdf-f
        shell: msys2 {0}
        working-directory: ncf
        run: |
          wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.zip
          unzip v4.6.0.zip
          cd netcdf-fortran-4.6.0
          #LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared --prefix=/mingw64
          LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared
          make install
          ls -l
          find . | grep -i libnetcdff

      - name: Setup Micromamba
        uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: modflow6/environment.yml
          create-args: >-
            pkg-config
          init-shell: >-
            bash
            powershell
          cache-environment: true
          cache-downloads: true

      - name: Build modflow6
        working-directory: modflow6
        run: |
          #echo "PKG_CONFIG_PATH=/D/a/_temp/msys64/mingw64/lib" >> $GITHUB_ENV
          #echo $PKG_CONFIG_PATH
          #sed -i "s|prefix=/mingw64|prefix=d:/a/_temp/msys64/mingw64|g" /D/a/_temp/msys64/mingw64/lib/pkgconfig/netcdf.pc
          #sed -i "s|prefix=/mingw64|prefix=d:/a/_temp/msys64/mingw64|g" /D/a/_temp/msys64/mingw64/lib/pkgconfig/netcdf-fortran.pc
          #echo "FIXED"
          #cat /D/a/_temp/msys64/mingw64/lib/pkgconfig/netcdf.pc
          #cat /D/a/_temp/msys64/mingw64/lib/pkgconfig/netcdf-fortran.pc
          echo "PWD:"
          pwd
          #echo "find libnetcdff:"
          #find ../ncf | grep -i libnetcdff
          #echo "find incdir:"
          #find .. | grep -i netcdf4_nf_interfaces.mod
          #find $GITHUB_WORKSPACE | grep -i netcdf4_nf_interfaces.mod
          echo "find mingw64:"
          #find .. -type d | grep -i mingw64
          #find .. -type d | grep -i include
          #find $GITHUB_WORKSPACE -type d | grep -i mingw64
          #find $GITHUB_WORKSPACE -type d | grep -i include
          find /d -type d | grep -i mingw64
          find /d -type d | grep -i include
          #echo "ls -l ../netcdf/lib/libnetcdff.a:"
          #ls -l ../netcdf/lib/libnetcdff.a
          #echo "GHWRK"
          #echo $GITHUB_WORKSPACE
          #ls $GITHUB_WORKSPACE
          which nf-config
          which nc-config
          nf-config --all
          nc-config --all
          nc-config --libdir
          echo "0:"
          echo $GITHUB_WORKSPACE
          meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin
          meson install -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
        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 --durations 0 -m "$markers"

      - name: Test nc4 program
        working-directory: modflow6/autotest
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: |
          pytest -v test_gwf_chd01.py -s --keep temp
          cat test_mf6model[chd01]0/mfsim.list

  netcdf_test_mac:
    name: netcdf4 testing
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ macos-12 ]
        hdf5: [ 1.12.2 ]
        #netcdf: [ v4.9.0 ]
        netcdf: [ main ]
    defaults:
      run:
        shell: bash -l {0}
    env:
      FC: gfortran
      GCC_V: 13
    steps:

      - name: Checkout modflow6
        uses: actions/checkout@v3
        with:
          path: modflow6

      - name: Setup gfortran ${{ env.GCC_V }}
        uses: awvwgk/setup-fortran@main
        with:
          compiler: gcc
          version: ${{ env.GCC_V }}

        ###
        # Set Environmental Variables
        ###
      - run: echo "FCFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV
      - run: echo "FFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV
      - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV

      - run: echo "CPPFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV
      - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV
      - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV
      - run: echo "DYLD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV
      - run: echo "PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/bin:${PATH}" >> $GITHUB_ENV

      - run: brew install automake libaec
        ###
        # Installing libhdf4 and libhdf5
        ###
      - name: Cache libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }}
        id: cache-hdf5
        uses: actions/cache@v2
        with:
          path: ~/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}
          key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}


      - name: Build libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }}
        #if: steps.cache-hdf5.outputs.cache-hit != 'true'
        run: |
          cd $HOME
          wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(echo ${{ matrix.hdf5 }} | cut -d. -f 1,2)/hdf5-${{ matrix.hdf5 }}/src/hdf5-${{ matrix.hdf5 }}.tar.bz2
          tar -jxf hdf5-${{ matrix.hdf5 }}.tar.bz2
          cd hdf5-${{ matrix.hdf5 }}
          ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --enable-hl --with-szlib
          make -j
          make install -j

      - name: Build 2 libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }}
        #if: steps.cache-hdf5.outputs.cache-hit != 'true'
        run: |
          cd $HOME
          git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c
          cd netcdf-c
          autoreconf -if
          CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}
          make -j
          make install -j

      - run: echo "FCFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV
      - run: echo "FFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV

      - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV
      - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV
      - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV
      - run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf}}" >> $GITHUB_ENV

      - run: brew install automake

      - name: Perform out-of-directory build
        shell: bash -l {0}
        run: |
              cd $HOME
              pwd
              LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake -S netcdf-c -B build -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH}

#      - name: Print Summary
#        shell: bash -l {0}
#        run: |
#              #cd build
#              #cat libnetcdff.settings
#              find . | grep -i libnetcdff.settings

      - name: Build All
        shell: bash -l {0}
        run: |
              cd $HOME
              cd build
              LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j 12
        if: ${{ success() }}

      - name: Run Tests
        shell: bash -l {0}
        run: |
              cd $HOME
              cd build
              LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest -j 1 .
        if: ${{ success() }}

      - name: Look at LastTest.log if error
        shell: bash -l {0}
        run: |
          cat /home/runner/work/netcdf-fortran/netcdf-fortran/build/Testing/Temporary/LastTest.log
          cd build
          LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest --rerun-failed --output-on-failure

        if: ${{ failure() }}

      - name: Setup Micromamba
        uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: modflow6/environment.yml
          create-args: >-
            pkg-config
          init-shell: >-
            bash
            powershell
          cache-environment: true
          cache-downloads: true

      - name: Build modflow6
        working-directory: modflow6
        run: |
          nf-config --all
          nc-config --all
          nc-config --libdir
          echo "PKG_CONFIG_PATH=$(nc-config --libdir)" >> $GITHUB_ENV
          meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin
          meson install -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
        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 --durations 0 -m "$markers"

  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: awvwgk/setup-fortran@main
        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
          create-args: >-
            netcdf-fortran
            pkg-config
          init-shell: >-
            bash
            powershell
          cache-environment: true
          cache-downloads: true

      - name: Edit netcdf-fortran.pc
        if: runner.os == 'Linux'
        working-directory: modflow6
        run: sed -i "s|libdir=/home/runner/micromamba/envs/modflow6//home/runner/micromamba/envs/modflow6/lib|libdir=/home/runner/micromamba/envs/modflow6/lib|g" /home/runner/micromamba/envs/modflow6/lib/pkgconfig/netcdf-fortran.pc

      - name: Edit netcdf-fortran.pc
        if: runner.os == 'macOS'
        working-directory: modflow6
        run: sed -i '' -e "s|libdir=/Users/runner/micromamba/envs/modflow6//Users/runner/micromamba/envs/modflow6/lib|libdir=/Users/runner/micromamba/envs/modflow6/lib|g" /Users/runner/micromamba/envs/modflow6/lib/pkgconfig/netcdf-fortran.pc

      - 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"