DONT MERGE, JUST TESTING RUNNERS

.github/actions/ngen-build/action.yaml

@@ -82,11 +82,11 @@ runs:
             elif [ ${{ runner.os }} == 'macOS' ]
             then
               brew install netcdf netcdf-cxx netcdf-fortran
-              echo "LIBRARY_PATH=/usr/local/lib/:$LIBRARY_PATH" >> $GITHUB_ENV
-              echo "LD_LIBRARY_PATH=/usr/local/lib/:$LD_LIBRARY_PATH" >> $GITHUB_ENV
-              echo "LDFLAGS=-L/usr/local/lib" >> $GITHUB_ENV
+              echo "LIBRARY_PATH=$(brew --prefix)/lib/:$LIBRARY_PATH" >> $GITHUB_ENV
+              echo "LD_LIBRARY_PATH=$(brew --prefix)/lib/:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+              echo "LDFLAGS=-L$(brew --prefix)/lib" >> $GITHUB_ENV
               echo "LIB=$LD_LIBRARY_PATH" >> $GITHUB_ENV
-              echo "NETCDF=/usr/local" >> $GITHUB_ENV
+              echo "NETCDF=$(brew --prefix)" >> $GITHUB_ENV
             fi
           shell: bash
 
@@ -110,14 +110,20 @@ runs:
           id: cache-boost-dep
           uses: actions/cache@v4
           with:
-            path: boost_1_79_0
+            path: boost_1_86_0
             key: unix-boost-dep
 
         - name: Get Boost Dependency
           if: steps.cache-boost-dep.outputs.cache-hit != 'true'
           run: |
-            curl -L -o boost_1_79_0.tar.bz2 https://sourceforge.net/projects/boost/files/boost/1.79.0/boost_1_79_0.tar.bz2/download
-            tar xjf boost_1_79_0.tar.bz2
+            curl -L -o boost_1_86_0.tar.bz2 https://sourceforge.net/projects/boost/files/boost/1.86.0/boost_1_86_0.tar.bz2/download
+            tar xjf boost_1_86_0.tar.bz2
+          shell: bash
+
+        - name: Set Pip Constraints
+          run: |
+            echo "numpy<2.0" > $GITHUB_WORKSPACE/constraints.txt
+            echo "PIP_CONSTRAINT=$GITHUB_WORKSPACE/constraints.txt" >> $GITHUB_ENV
           shell: bash
 
         - name: Cache Python Dependencies
@@ -179,12 +185,19 @@ runs:
 
         - name: Cmake Initialization
           id: cmake_init
+          # NOTE: -DCMAKE_POLICY_VERSION_MINIMUM=3.5 is required to use cmake version 4
+          # and with older pybind11 versions, the minimum cmake version is set to 3.4
+          # which causes cmake configuration to fail.
           run: |
-            export BOOST_ROOT="$(pwd)/boost_1_79_0"
+            which apt && sudo apt update && sudo apt install clang-17 && export CC=clang && export CXX=clang++ && echo "USING CLANG"
+            export BOOST_ROOT="$(pwd)/boost_1_86_0"
             export CFLAGS="-fsanitize=address -O1 -g -fno-omit-frame-pointer -Werror"
-            export CXXFLAGS="-fsanitize=address -O1 -g -fno-omit-frame-pointer -pedantic-errors -Werror -Wpessimizing-move -Wparentheses -Wrange-loop-construct"
+            export CXXFLAGS="-fsanitize=address -O1 -g -fno-omit-frame-pointer -pedantic-errors -Werror -Wpessimizing-move -Wparentheses -Wrange-loop-construct -Wsuggest-override"
             . .venv/bin/activate
             [ ! -d "$BOOST_ROOT" ] && echo "Error: no Boost root found at $BOOST_ROOT" && exit 1
+            echo "Cmake Version:"
+            which cmake
+            cmake --version
             cmake -B ${{ inputs.build-dir }} \
               -DNGEN_WITH_BMI_C:BOOL=${{ inputs.bmi_c }} \
               -DNGEN_WITH_PYTHON:BOOL=${{ inputs.use_python }} \
@@ -193,7 +206,9 @@ runs:
               -DNGEN_WITH_ROUTING:BOOL=${{ inputs.use_troute }} \
               -DNGEN_WITH_NETCDF:BOOL=${{ inputs.use_netcdf }} \
               -DNGEN_WITH_SQLITE:BOOL=${{ inputs.use_sqlite }} \
-              -DNGEN_WITH_MPI:BOOL=${{ inputs.use_mpi }} -S .
+              -DNGEN_WITH_MPI:BOOL=${{ inputs.use_mpi }} \
+              -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -S .
+
             echo "build-dir=$(echo ${{ inputs.build-dir }})" >> $GITHUB_OUTPUT
           shell: bash
 

.github/actions/ngen-submod-build/action.yaml

@@ -42,7 +42,9 @@ runs:
           if: |
             runner.os == 'macOS'
           run: |
-            echo "FC=gfortran-11" >> $GITHUB_ENV
+            # see macOS image readmes for supported versions
+            # https://github.com/actions/runner-images/tree/main/images/macos
+            echo FC="gfortran-12" >> $GITHUB_ENV
           shell: bash
 
         - name: Cmake Initialization

.github/workflows/Example_model_run.yml

@@ -1,8 +1,10 @@
 name: Build and Run NGEN on example data
 
 on:
+  push:
+    branches: [ release-* ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, release-* ]
 jobs:
     Build_and_Run_Model:
       runs-on: ubuntu-latest

.github/workflows/documentation.yml

@@ -6,7 +6,7 @@ name: Documentation
 # events but only for the master branch
 on:
   push:
-    branches: [ master ]
+    branches: [ master, release-* ]
   #pull_request:
     #branches: [ master ]
 

.github/workflows/module_integration.yml

@@ -3,9 +3,9 @@ name: Module Integration Tests
 # Controls when the action will run.
 on:
   push:
-    branches: [ master, dev, notreal ]
+    branches: [ master, dev, notreal, release-* ]
   pull_request:
-    branches: [ master, dev, notreal ]
+    branches: [ master, dev, notreal, release-* ]
   workflow_dispatch:
 
 env:
@@ -22,7 +22,7 @@ jobs:
     # The type of runner that the job will run on
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12]
+        os: [ubuntu-22.04, macos-15]
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -43,11 +43,13 @@ jobs:
       - name: Run surfacebmi plus cfebmi
         run: |
           inputfile='data/example_bmi_multi_realization_config.json'
+          ./cmake_build/ngen || true
           ./cmake_build/ngen data/catchment_data.geojson "cat-27" data/nexus_data.geojson "nex-26" $inputfile
 
       - name: Run surfacebmi, cfebmi and petbmi
         run: |
           inputfile='data/example_bmi_multi_realization_config_w_noah_pet_cfe.json'
+          ./cmake_build/ngen || true
           ./cmake_build/ngen data/catchment_data.geojson "cat-27" data/nexus_data.geojson "nex-26" $inputfile
 
 # Run t-route/pybind integration test
@@ -117,14 +119,10 @@ jobs:
             export LIBRARY_PATH=/usr/local/lib/gcc/11/
             export LD_LIBRARY_PATH=/usr/local/lib/gcc/11/
           fi
-          sed -i.bak 's/NETCDF}"/NETCDF}\/include"/' compiler.sh
+          export NETCDFALTERNATIVE=${NETCDF}/include
           export FC=gfortran
           export F90=gfortran 
-          ./compiler.sh
-          cd src
-          pip install troute-nwm/
-          pip install --install-option="--use-cython" troute-network/
-          pip install --install-option="--use-cython" troute-routing/
+          ./compiler.sh no-e
 
           deactivate
 

.github/workflows/test_and_validate.yml

@@ -5,9 +5,9 @@ name: Testing and Validation
 # Controls when the action will run.
 on:
   push:
-    branches: [ master, dev, notreal ]
+    branches: [ master, dev, notreal, release-* ]
   pull_request:
-    branches: [ master, dev, notreal ]
+    branches: [ master, dev, notreal, release-* ]
   workflow_dispatch:
 
 env:
@@ -24,7 +24,7 @@ jobs:
     # The type of runner that the job will run on
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12]
+        os: [ubuntu-22.04, macos-15]
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -59,7 +59,7 @@ jobs:
     # The type of runner that the job will run on
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12]
+        os: [ubuntu-22.04, macos-15]
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -116,7 +116,7 @@ jobs:
     # The type of runner that the job will run on
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12]
+        os: [ubuntu-24.04, macos-26]
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -139,6 +139,7 @@ jobs:
       - name: Run Tests
         run: |
           cd ./cmake_build/test/
+          export ASAN_OPTIONS=${ASAN_OPTIONS}:detect_odr_violation=0
           ./test_bmi_cpp
           cd ../../
         timeout-minutes: 15
@@ -151,7 +152,7 @@ jobs:
     # The type of runner that the job will run on
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12]
+        os: [ubuntu-22.04, macos-15]
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -182,7 +183,7 @@ jobs:
     # The type of runner that the job will run on
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12]
+        os: [ubuntu-22.04, macos-15]
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -215,7 +216,7 @@ jobs:
     # The type of runner that the job will run on
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12]
+        os: [ubuntu-22.04, macos-15]
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -250,7 +251,7 @@ jobs:
     # The type of runner that the job will run on
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12]
+        os: [ubuntu-22.04, macos-15]
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -272,12 +273,43 @@ jobs:
       - name: Run Unit Tests
         run: |
           . .venv/bin/activate
+          export ASAN_OPTIONS=${ASAN_OPTIONS}:detect_odr_violation=0
           ./cmake_build/test/test_bmi_multi
         timeout-minutes: 15
 
       - name: Clean Up Unit Test Build
         uses: ./.github/actions/clean-build
 
+  # Run BMI protocol tests in linux/unix environment
+  test_bmi_protocols:
+    # The type of runner that the job will run on
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, macos-15]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      - name: Build BMI Protocol Unit Tests
+        uses: ./.github/actions/ngen-build
+        with:
+          targets: "test_bmi_protocols"
+          build-cores: ${{ env.LINUX_NUM_PROC_CORES }}
+
+      - name: run_bmi_protocol_tests
+        run: |
+          cd ./cmake_build/test/
+          export ASAN_OPTIONS=${ASAN_OPTIONS}:detect_odr_violation=0
+          ./test_bmi_protocols
+          cd ../../
+        timeout-minutes: 15
+
+      - name: Clean Up BMI Protocol Unit Test Build
+        uses: ./.github/actions/clean-build
 
   # TODO: fails due to compilation error, at least in large part due to use of POSIX functions not supported on Windows.
   # TODO: Need to determine whether Windows support (in particular, development environment support) is necessary.

.gitignore

@@ -127,7 +127,6 @@ data/hydrofabric/huc01_demo/
 # NGen build-related items
 .venv
 boost_*
-include/NGenConfig.h
 
 # Large Example Datasets for certain tests #
 ############################################

.gitpod.yml

@@ -32,7 +32,7 @@ tasks:
       ./compiler.sh
       popd
       pip install pyyaml bmipy
-      cmake -S . -B cmake_build -DBMI_C_LIB_ACTIVE=1 -DBMI_FORTRAN_ACTIVE=1 -DNGEN_ACTIVATE_ROUTING=1
+      cmake -S . -B cmake_build -DNGEN_WITH_BMI_C=ON -DNGEN_WITH_BMI_FORTRAN=ON -DNGEN_ACTIVATE_ROUTING=1
       cmake --build cmake_build --target all
   - name: Workshell
     before: |

CMakeLists.txt

@@ -31,6 +31,7 @@ list(APPEND CMAKE_MODULE_PATH "${NGEN_MOD_DIR}")
 #   (1) finds Git package
 #   (2) Sets ${NGEN_HAS_GIT_DIR} to ON/OFF if ${NGEN_ROOT_DIR}/.git exists
 #   (3) Function `git_update_submodule` which updates a given submodule
+#   (4) Sets ${NGEN_GIT_COMMIT} to the current commit hash if available
 include(GitUpdateSubmodules)
 
 # NGen CMake module for automating external subdirectory builds (i.e. testbmicpp)
@@ -113,7 +114,7 @@ set(CMAKE_CXX_STANDARD_REQUIRED True)
 set(CMAKE_CXX_VISIBILITY_PRESET hidden)
 
 # Define project version and use via generated config header
-project(ngen VERSION 0.1.0)
+project(ngen VERSION 0.3.0)
 
 add_executable(ngen "${NGEN_SRC_DIR}/NGen.cpp")
 
@@ -139,7 +140,6 @@ endif()
 # If MPI support is enabled, set the C++ compiler to "mpicxx"
 if(NGEN_WITH_MPI)
     find_package(MPI REQUIRED)
-    add_compile_definitions(NGEN_MPI_ACTIVE)
 endif()
 
 # -----------------------------------------------------------------------------
@@ -165,7 +165,7 @@ add_compile_definitions(NGEN_SHARED_LIB_EXTENSION)
 set(Boost_USE_STATIC_LIBS OFF)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
-find_package(Boost 1.79.0 REQUIRED)
+find_package(Boost 1.86.0 REQUIRED)
 
 # -----------------------------------------------------------------------------
 if(NGEN_WITH_SQLITE)
@@ -196,8 +196,6 @@ if(NGEN_WITH_NETCDF)
         set(NetCDF_CXX_LIBRARY "${PROJECT_BINARY_DIR}/extern-libs/netcdf-cxx4/libnetcdf-cxx4.a")
         target_link_libraries(NetCDF INTERFACE netcdf-cxx4)
     endif()
-
-    add_compile_definitions(NETCDF_ACTIVE)
 endif()
 
 if(NGEN_WITH_EXTERN_SLOTH)
@@ -216,8 +214,6 @@ endif()
 # -----------------------------------------------------------------------------
 # Handle several steps for BMI C library logic and dependencies, at top level, if functionality is turned on
 if(NGEN_WITH_BMI_C)
-    add_compile_definitions(NGEN_BMI_C_LIB_ACTIVE)
-
     if(NGEN_WITH_EXTERN_TOPMODEL)
         add_external_subdirectory(
             SOURCE     "${NGEN_EXT_DIR}/topmodel"
@@ -249,8 +245,6 @@ endif()
 # -----------------------------------------------------------------------------
 # Configure whether Fortran BMI functionality is active
 if(NGEN_WITH_BMI_FORTRAN)
-    add_compile_definitions(NGEN_BMI_FORTRAN_ACTIVE)
-
     add_external_subdirectory(
         SOURCE  "${NGEN_EXT_DIR}/iso_c_fortran_bmi"
         OUTPUT  "${NGEN_EXT_DIR}/iso_c_fortran_bmi/cmake_build"
@@ -269,17 +263,14 @@ endif()
 
 # -----------------------------------------------------------------------------
 if(NGEN_WITH_PYTHON)
-    add_compile_definitions(ACTIVATE_PYTHON=true)
     find_package(Python 3.6.8 REQUIRED COMPONENTS Interpreter Development NumPy)
+    if(${Python_NumPy_VERSION} VERSION_GREATER_EQUAL 2)
+        message(FATAL_ERROR "Found numpy version \"${Python_NumPy_VERSION}\"; numpy>=2.0.0 is not currently supported")
+    endif()
     set(PYTHON_EXECUTABLE ${Python_EXECUTABLE}) # Case-sensitive difference
     add_subdirectory(extern/pybind11 pybind11)
 endif()
 
-# -----------------------------------------------------------------------------
-if(NGEN_WITH_ROUTING)
-    add_compile_definitions(NGEN_ROUTING_ACTIVE)
-endif()
-
 # -----------------------------------------------------------------------------
 if(NGEN_QUIET)
     set(UDUNITS_QUIET true)
@@ -416,7 +407,10 @@ ngen_multiline_message(
 "  C Compiler: ${CMAKE_C_COMPILER}"
 "  C Flags: ${CMAKE_C_FLAGS}"
 "  CXX Compiler: ${CMAKE_CXX_COMPILER}"
-"  CXX Flags: ${CMAKE_CXX_FLAGS}"
+"  CXX Flags: ${CMAKE_CXX_FLAGS}")
+ngen_dependent_multiline_message(NGEN_HAS_GIT_DIR
+"  Git Commit ID: ${NGEN_GIT_COMMIT}")
+ngen_multiline_message(
 "  Flags:"
 "    NGEN_WITH_MPI: ${NGEN_WITH_MPI}"
 "    NGEN_WITH_NETCDF: ${NGEN_WITH_NETCDF}"