Merge pull request #2550 from MODFLOW-ORG/v6.6.3

Release 6.6.3

Author: wpbonelli

.build_rtd_docs/Doxyfile

@@ -37,7 +37,7 @@ PROJECT_NAME           = "MODFLOW 6"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "version 6.6.2"
+PROJECT_NUMBER         = "version 6.6.3"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

.build_rtd_docs/conf.py

@@ -91,6 +91,16 @@
 dst = os.path.join(dstdir, fpth)
 shutil.copy(src, dst)
 
+fpth = "README.md"
+src = os.path.join("..", "distribution", fpth)
+dst = os.path.join(dstdir, "DISTRIBUTION.md")
+shutil.copy(src, dst)
+
+fpth = "IDM.md"
+src = os.path.join("..", fpth)
+dst = os.path.join(dstdir, fpth)
+shutil.copy(src, dst)
+
 dstdir = "_migration"
 if os.path.isdir(dstdir):
     shutil.rmtree(dstdir)

.build_rtd_docs/dev.rst

@@ -11,5 +11,7 @@ This section contains developer documentation, including contributor conventions
    _dev/CONTRIBUTING.md
    _dev/DEVELOPER.md
    _dev/EXTENDED.md
+   _dev/DISTRIBUTION.md
    _dev/styleguide.md
    _dev/dfn.md
+   _dev/IDM.md

.codespell.ignore

@@ -2,6 +2,7 @@ Alph
 wel
 nam
 gage
+DisUtils
 drob
 delt
 lke
@@ -24,3 +25,4 @@ rin
 checkin
 exchng
 welp
+alog

.github/actions/build-netcdf-win/action.yml

@@ -17,18 +17,24 @@ runs:
     - name: Download NetCDF-C
       shell: bash
       run: |
-        mkdir -p netcdf/netCDF4.9.2-NC4-64
-        cd netcdf/netCDF4.9.2-NC4-64
-        curl https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netCDF4.9.2-NC4-64.exe -O -J
-        7z x netCDF4.9.2-NC4-64.exe -aou
+        mkdir -p netcdf/netCDF4.9.3-NC4-64
+        cd netcdf/netCDF4.9.3-NC4-64
+        curl https://downloads.unidata.ucar.edu/netcdf-c/4.9.3/netCDF4.9.3-NC4-64.exe -O -J
+        7z x netCDF4.9.3-NC4-64.exe -aou
+        # disable checks specific to standard install locations
+        sed -i '32,34s/^/#/' lib/cmake/netCDF/netCDFConfig.cmake
+        # disable system hdf5 library check
+        sed -i '67,70s/^/#/' lib/cmake/netCDF/netCDFConfig.cmake
 
     - name: Download NetCDF-Fortran
       shell: bash
       run: |
-        mkdir -p netcdf/netcdf-fortran-4.6.1/build
-        cd netcdf/netcdf-fortran-4.6.1
-        curl https://downloads.unidata.ucar.edu/netcdf-fortran/4.6.1/netcdf-fortran-4.6.1.zip -O -J
-        unzip netcdf-fortran-4.6.1.zip
+        mkdir -p netcdf/netcdf-fortran-4.6.2/build
+        cd netcdf/netcdf-fortran-4.6.2
+        curl https://downloads.unidata.ucar.edu/netcdf-fortran/4.6.2/netcdf-fortran-4.6.2.zip -O -J
+        unzip netcdf-fortran-4.6.2.zip
+        # disable system hdf5 library check
+        sed -i '485s/^/#/' netcdf-fortran-4.6.2/CMakeLists.txt
 
     - name: Setup oneAPI
       uses: ./modflow6/.github/actions/setup-par-oneapi
@@ -41,6 +47,6 @@ runs:
     - name: Update path for NetCDF libs
       shell: bash
       run: |
-        echo "$GITHUB_WORKSPACE/netcdf/netCDF4.9.2-NC4-64/bin" >> $GITHUB_PATH
-        echo "$GITHUB_WORKSPACE/netcdf/netCDF4.9.2-NC4-64/lib" >> $GITHUB_PATH
-        echo "$GITHUB_WORKSPACE/netcdf/netcdf-fortran-4.6.1/build/fortran" >> $GITHUB_PATH
+        echo "$GITHUB_WORKSPACE/netcdf/netCDF4.9.3-NC4-64/bin" >> $GITHUB_PATH
+        echo "$GITHUB_WORKSPACE/netcdf/netCDF4.9.3-NC4-64/lib" >> $GITHUB_PATH
+        echo "$GITHUB_WORKSPACE/netcdf/netcdf-fortran-4.6.2/build/fortran" >> $GITHUB_PATH

.github/actions/test-extended-win/action.yml

@@ -23,19 +23,12 @@ runs:
       run: |
         unix2dos -n "%GITHUB_WORKSPACE%\modflow6\.github\common\test_modflow6_extended.bat" "%TEMP%\test_modflow6_extended.bat"
 
-    - name: Test programs (extended)
-      if: github.ref_name != 'master'
-      shell: cmd
-      env:
-        REPOS_PATH: ${{ github.workspace }}
-      run: |
-        "%ONEAPI_ROOT%\setvars.bat" intel64 vs2022 && "%TEMP%\test_modflow6_extended.bat"
-
     - name: Test programs (extended)
       if: github.ref_name == 'master'
       shell: cmd
       env:
         REPOS_PATH: ${{ github.workspace }}
-        MARKERS: not developmode
+        MARKERS: ${{ env.MARKERS }}
+        FILTERS: ${{ env.FILTERS }}
       run: |
         "%ONEAPI_ROOT%\setvars.bat" intel64 vs2022 && "%TEMP%\test_modflow6_extended.bat"

.github/actions/test-extended/action.yml

@@ -3,7 +3,28 @@ description: Build and test Extended MODFLOW 6
 runs:
   using: "composite"
   steps:
+    - name: Install netcdf
+      if: runner.os == 'Linux'
+      shell: bash
+      run: |
+        sudo apt-get update
+        sudo apt-get install build-essential \
+          libnetcdf-dev \
+          libnetcdff-dev \
+          netcdf-bin
+        nc-config --all
+        nf-config --all
+
+    - name: Install netcdf
+      if: runner.os == 'macOS'
+      shell: bash
+      run: |
+        brew install netcdf-fortran
+        nc-config --all
+        nf-config --all
+
     - name: Setup GNU Fortran
+      if: runner.os != 'macOS'
       uses: fortran-lang/setup-fortran@v1
       with:
         compiler: gcc
@@ -20,6 +41,7 @@ runs:
       shell: bash
       run: |
         echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/arch-gcc-opt/lib/pkgconfig" >> $GITHUB_ENV
+        echo "LD_LIBRARY_PATH=$GITHUB_WORKSPACE/petsc/arch-gcc-opt/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         echo "$GITHUB_WORKSPACE/petsc/arch-gcc-opt/bin" >> $GITHUB_PATH
 
     - name: Configure PETSc
@@ -30,26 +52,6 @@ runs:
         sudo ./configure PETSC_ARCH=arch-gcc-opt --download-fblaslapack --download-openmpi=$GITHUB_WORKSPACE/petsc/openmpi-5.0.2.tar.gz --with-debugging=0
         sudo make all
 
-    - name: Install netcdf
-      if: runner.os == 'Linux'
-      shell: bash
-      run: |
-        sudo apt-get update
-        sudo apt-get install build-essential \
-          libnetcdf-dev \
-          libnetcdff-dev \
-          netcdf-bin
-        nc-config --all
-        nf-config --all
-
-    - name: Install netcdf
-      if: runner.os == 'macOS'
-      shell: bash
-      run: |
-        brew install netcdf-fortran
-        nc-config --all
-        nf-config --all
-
     - name: Build modflow6
       shell: bash
       working-directory: modflow6

.github/common/check_format.py

@@ -24,7 +24,11 @@
 ]
 
 # exclude these files from checks
-excludefiles = [PROJ_ROOT / "src" / "Idm" / "gwf-stoidm.f90"]
+excludefiles = [
+    PROJ_ROOT / "src" / "Idm" / "gwf-csubidm.f90",
+    PROJ_ROOT / "src" / "Idm" / "gwf-stoidm.f90",
+    PROJ_ROOT / "src" / "Idm" / "gwf-vscidm.f90",
+]
 
 # commands
 fprettify = "fprettify -c .fprettify.yaml"

.github/common/compile_netcdf.bat

@@ -1,11 +1,11 @@
-cd "%GITHUB_WORKSPACE%\netcdf\netcdf-fortran-4.6.1\build"
+cd "%GITHUB_WORKSPACE%\netcdf\netcdf-fortran-4.6.2\build"
 
 :: build/install static libs
-cmake --fresh -G Ninja -DCMAKE_Fortran_COMPILER="C:/Program Files (x86)/Intel/oneAPI/compiler/latest/bin/ifort.exe" -DCMAKE_BUILD_TYPE=Release -DNETCDF_C_LIBRARY="%GITHUB_WORKSPACE%/netcdf/netCDF4.9.2-NC4-64/lib/netcdf.lib" -DNETCDF_C_INCLUDE_DIR="%GITHUB_WORKSPACE%/netcdf/netCDF4.9.2-NC4-64/include" -DBUILD_SHARED_LIBS=0 -DCMAKE_INSTALL_PREFIX="%GITHUB_WORKSPACE%/netcdf/netcdf-fortran-4.6.1/build" ../netcdf-fortran-4.6.1
+cmake --fresh -G Ninja -DCMAKE_Fortran_COMPILER="C:/Program Files (x86)/Intel/oneAPI/compiler/latest/bin/ifort.exe" -DCMAKE_BUILD_TYPE=Release -DNETCDF_C_LIBRARY="%GITHUB_WORKSPACE%/netcdf/netCDF4.9.3-NC4-64/lib/netcdf.lib" -DNETCDF_C_INCLUDE_DIR="%GITHUB_WORKSPACE%/netcdf/netCDF4.9.3-NC4-64/include" -DBUILD_SHARED_LIBS=0 -DCMAKE_INSTALL_PREFIX="%GITHUB_WORKSPACE%/netcdf/netcdf-fortran-4.6.2/build" ../netcdf-fortran-4.6.2
 cmake --build .
 cmake –-install .
 
 :: build/install shared libs
-cmake --fresh -G Ninja -DCMAKE_Fortran_COMPILER="C:/Program Files (x86)/Intel/oneAPI/compiler/latest/bin/ifort.exe" -DCMAKE_BUILD_TYPE=Release -DNETCDF_C_LIBRARY="%GITHUB_WORKSPACE%/netcdf/netCDF4.9.2-NC4-64/lib/netcdf.lib" -DNETCDF_C_INCLUDE_DIR="%GITHUB_WORKSPACE%/netcdf/netCDF4.9.2-NC4-64/include" -DBUILD_SHARED_LIBS=1 -DCMAKE_INSTALL_PREFIX="%GITHUB_WORKSPACE%/netcdf/netcdf-fortran-4.6.1/build" ../netcdf-fortran-4.6.1
+cmake --fresh -G Ninja -DCMAKE_Fortran_COMPILER="C:/Program Files (x86)/Intel/oneAPI/compiler/latest/bin/ifort.exe" -DCMAKE_BUILD_TYPE=Release -DNETCDF_C_LIBRARY="%GITHUB_WORKSPACE%/netcdf/netCDF4.9.3-NC4-64/lib/netcdf.lib" -DNETCDF_C_INCLUDE_DIR="%GITHUB_WORKSPACE%/netcdf/netCDF4.9.3-NC4-64/include" -DBUILD_SHARED_LIBS=1 -DCMAKE_INSTALL_PREFIX="%GITHUB_WORKSPACE%/netcdf/netcdf-fortran-4.6.2/build" ../netcdf-fortran-4.6.2
 cmake --build .
 cmake –-install .

.github/common/test_modflow6_extended.bat

@@ -1,2 +1,2 @@
 cd "%GITHUB_WORKSPACE%\modflow6\autotest"
-pixi run autotest -m "%MARKERS%" --netcdf --parallel
+pixi run autotest -m "%MARKERS%" -k "%FILTERS%" --netcdf --parallel