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
          which cygpath
          #ln -s /usr/bin/cygpath.exe /bin/cygpath
          ls -l /usr/bin/ | grep -i cygpath
          ls -l /bin/ | grep -i cygpath

      - name: Prepare netcdf build
        run: |
          mkdir ncc
          mkdir ncf

      - name: Install hdf5 and netcdf-c
        shell: msys2 {0}
        working-directory: ncc
        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
          echo "PWD:"
          pwd
          echo "LD_LIBRARY_PATH:"
          echo $LD_LIBRARY_PATH
          echo "PATH:"
          echo $PATH
          echo "LIBS:"
          echo $LIBS
          #wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.0.zip
          wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.zip
          #wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.8.1.zip
          unzip v4.9.2.zip
          cd netcdf-c-4.9.2
          #LDFLAGS="-Wl,-no-undefined" ./configure --enable-shared --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets
          LDFLAGS="-Wl,-no-undefined,--export-all-symbols" ./configure --enable-shared --disable-dap --disable-testsets --disable-examples --disable-libxml2
          #LDFLAGS="-Wl,-no-undefined" ./configure --enable-shared --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets
          echo "LD_LIBRARY_PATH=/d/a/_temp/msys64/mingw64/lib" >> $GITHUB_ENV
          echo "PATH=/d/a/_temp/msys64/mingw64/usr/bin:/d/a/_temp/msys64/mingw64/bin:/d/a/modflow6/modflow6/ncc/include:/d/a/modflow6/modflow6/ncf/netcdf-fortran-4.6.1/fortran/.libs:/d/a/modflow6/modflow6/modflow6/bin" >> $GITHUB_ENV
          ln -s /usr/bin/cygpath.exe /d/a/modflow6/modflow6/ncc/include/cygpath
          which cygpath
          sed -i.bak -e "s/\(allow_undefined=\)yes/\1no/" libtool
          echo "grep:"
          grep -nrIl nc_inq_libvers .
          echo "ls -al:"
          ls -la
          echo "find:"
          find . | grep netcdf
          echo "find derror:"
          find . | grep -i derror
          echo "find ncdispatch.h:"
          find . | grep -i ncdispatch.h
          make install
          which ldd
          ls /mingw64/bin | grep netcdf
          ldd /mingw64/bin/libnetcdf-19.dll
          nc-config --all

      - name: Make netcdf-f
        shell: msys2 {0}
        working-directory: ncf
        run: |
          #echo "LD_LIBRARY_PATH=/d/a/_temp/msys64/mingw64/lib" >> $GITHUB_ENV
          #echo "PATH=/d/a/_temp/msys64/mingw64/bin:/d/a/modflow6/modflow6/modflow6/bin:/d/a/modflow6/modflow6/ncf/netcdf-fortran-4.6.0/fortran/.libs" >> $GITHUB_ENV
          #wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.zip
          wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.1.zip
          unzip v4.6.1.zip
          cd netcdf-fortran-4.6.1
          #LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared --prefix=/mingw64
          #LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared
          LDFLAGS="-Wl,-no-undefined" LIBS="$(nc-config --libs)" ./configure --enable-shared
          sed -i.bak -e "s/\(allow_undefined=\)yes/\1no/" libtool
          make install
          #ldconfig
          ls fortran/.libs
          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
          log-level: 'trace'

      - name: Build modflow6
        working-directory: modflow6
        run: |
          #echo "LD_LIBRARY_PATH=/d/a/_temp/msys64/mingw64/lib" >> $GITHUB_ENV
          #echo "PATH=/d/a/_temp/msys64/mingw64/bin" >> $GITHUB_ENV
          #echo "PATH=/d/a/_temp/msys64/mingw64/bin:/d/a/modflow6/modflow6/modflow6/bin:/d/a/modflow6/modflow6/ncf/netcdf-fortran-4.6.0/fortran/.libs" >> $GITHUB_ENV
          echo "PWD:"
          pwd
          echo "ls cmake/netCDF:"
          ls -l /d/a/_temp/msys64/mingw64/lib/cmake/netCDF
          echo "find netcdf:"
          find /d/a/_temp/msys64/mingw64 | grep -i netcdf
          echo "find netcdf2:"
          find ../ncf/netcdf-fortran-4.6.1/fortran/.libs | grep -i netcdf
          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
          #echo "PATH=/d/a/modflow6/modflow6/modflow6/bin" >> $GITHUB_ENV
          #ln -sf /d/a/_temp/msys64/mingw64/bin/libnetcdf.dll bin/libnetcdf.dll

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

      - name: Check exe
        working-directory: modflow6/autotest
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: |
          which dumpbin
          which dumpbin.exe
          echo "LD_LIBRARY_PATH:"
          echo $LD_LIBRARY_PATH
          echo "PATH:"
          echo $PATH
          ls -l /d/a/modflow6/modflow6/modflow6/bin
          echo "FILE:"
          file /d/a/modflow6/modflow6/modflow6/bin/mf6.exe
          echo "LDD1:"
          ldd /d/a/modflow6/modflow6/modflow6/bin/mf6.exe
          #echo "LDD hdf:"
          #ldd /d/a/_temp/msys64/mingw64/bin
          echo "LDD nc:"
          ldd /d/a/_temp/msys64/mingw64/bin/libnetcdf.dll
          echo "LDD ncf:"
          ldd /d/a/_temp/msys64/mingw64/bin/libnetcdff-7.dll
          #/d/a/modflow6/modflow6/modflow6/bin/mf6.exe --version
          which mf6.exe
          #mf6.exe
          mf6.exe --version

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

      - 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: Check exe
        if: runner.os == 'Linux'
        working-directory: modflow6/autotest
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: |
          echo "LD_LIBRARY_PATH:"
          echo $LD_LIBRARY_PATH
          echo "PATH:"
          echo $PATH
          ls -l /home/runner/work/modflow6/modflow6/modflow6/bin
          echo "FILE:"
          file /home/runner/work/modflow6/modflow6/modflow6/bin/mf6
          echo "LDD1:"
          ldd /home/runner/work/modflow6/modflow6/modflow6/bin/mf6
          #/d/a/modflow6/modflow6/modflow6/bin/mf6 --version
          #which mf6
          #mf6
          /home/runner/work/modflow6/modflow6/modflow6/bin/mf6 --version

      - name: Check exe
        if: runner.os == 'macOS'
        working-directory: modflow6/autotest
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: |
          echo "LD_LIBRARY_PATH:"
          echo $LD_LIBRARY_PATH
          echo "PATH:"
          echo $PATH
          ls -l /Users/runner/work/modflow6/modflow6/modflow6/bin
          echo "FILE:"
          file /Users/runner/work/modflow6/modflow6/modflow6/bin/mf6
          echo "LDD1:"
          ldd /Users/runner/work/modflow6/modflow6/modflow6/bin/mf6
          #/d/a/modflow6/modflow6/modflow6/bin/mf6 --version
          #which mf6
          #mf6
          /Users/runner/work/modflow6/modflow6/modflow6/bin/mf6 --version

      - 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 nc4 program
        working-directory: modflow6/autotest
        env:
          REPOS_PATH: ${{ github.workspace }}
        run: |
          pytest -v test_gwf_chd01.py -s --keep temp
          ls -l temp
          ls -l temp/test_mf6model[chd01]0
          cat temp/test_mf6model[chd01]0/mfsim.lst | grep -i netcdf
          #ls -l /tmp

      - 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"