From 4a96b21fc4991bb6ce4f019107cb8b02b43e273c Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 13:13:55 -0700
Subject: [PATCH 01/39] cmake: reorg root CMakeLists; rm unused FindNetCDF;
 update FindUDUNITS2

---
 CMakeLists.txt                   | 419 ++++++++++++++++---------------
 cmake/FindNetCDF.cmake           | 131 ----------
 cmake/modules/FindUDUNITS2.cmake |  18 +-
 src/core/mediator/CMakeLists.txt |   4 +-
 4 files changed, 233 insertions(+), 339 deletions(-)
 delete mode 100644 cmake/FindNetCDF.cmake

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5e44af1020..b60bdf046f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,225 +1,198 @@
-cmake_minimum_required(VERSION 3.14)
+# Ensure CMake policies have defaults depending on the CMake version used
+# between the two versions specified. e.g. if 3.18 is used, then 3.18 defaults
+# will be used instead of 3.17 defaults.
+cmake_minimum_required(VERSION 3.17...3.26)
 
+# Policies ====================================================================
 
 # Use `LOCATION` for python lookup strategy
 # https://cmake.org/cmake/help/latest/policy/CMP0094.html
-if(POLICY CMP0094)
-    cmake_policy(SET CMP0094 NEW)
-endif()
+cmake_policy(SET CMP0094 NEW)
+
+# find_package() uses <PackageName>_ROOT variables.
+# https://cmake.org/cmake/help/latest/policy/CMP0074.html
+cmake_policy(SET CMP0074 NEW)
 
-if(MPI_ACTIVE)
-   set (CMAKE_CXX_COMPILER "mpicxx")
+# find_package() uses upper-case <PACKAGENAME>_ROOT variables.
+# https://cmake.org/cmake/help/latest/policy/CMP0144.html
+if(POLICY CMP0144)
+    cmake_policy(SET CMP0144 NEW)
 endif()
 
-########### Define project version and use via generated config header
+# Project Variables ===========================================================
+set(NGEN_ROOT_DIR "${CMAKE_CURRENT_LIST_DIR}")
+set(NGEN_SRC_DIR  "${NGEN_ROOT_DIR}/src")
+set(NGEN_INC_DIR  "${NGEN_ROOT_DIR}/include")
+set(NGEN_EXT_DIR  "${NGEN_ROOT_DIR}/extern")
+set(NGEN_MOD_DIR  "${NGEN_ROOT_DIR}/cmake")
+list(APPEND CMAKE_MODULE_PATH "${NGEN_MOD_DIR}/modules")
+
+# Provides:
+#   (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
+include(GitUpdateSubmodules)
+
+# Options =====================================================================
+include(CMakeDependentOption)
+
+option(NGEN_WITH_MPI         "Build with MPI support"             OFF)
+option(NGEN_WITH_NETCDF      "Build with NetCDF support"          ON)
+option(NGEN_WITH_SQLITE      "Build with SQLite3 support"         ON)
+option(NGEN_WITH_UDUNITS     "Build with UDUNITS2 support"        ON)
+option(NGEN_WITH_BMI_FORTRAN "Build with Fortran BMI support"     ON)
+option(NGEN_WITH_BMI_C       "Build with C BMI support"           ON)
+option(NGEN_WITH_PYTHON      "Build with embedded Python support" ON)
+option(NGEN_WITH_TESTS       "Build with unit tests"              ON)
+
+# These options require dependency on some of the above options
+# Syntax: cmake_dependent_option(<option> "<help_text>" <value> <depends> <force>)
+cmake_dependent_option(NGEN_WITH_ROUTING "Build with t-route integration" OFF "NGEN_WITH_PYTHON" OFF)
+cmake_dependent_option(NGEN_ISO_C_FORTRAN_BMI_LIB_PATH "Path to iso_c_fortran_bmi library" "" "NGEN_WITH_BMI_FORTRAN" "")
+cmake_dependent_option(NGEN_UPDATE_GIT_SUBMODULES "Update submodules on configure" ON "GIT_FOUND;NGEN_HAS_GIT_DIR" OFF)
+# Project =====================================================================
+
+# Define project version and use via generated config header
 project(ngen VERSION 0.1.0)
-configure_file(include/NGenConfig.h.in include/NGenConfig.h)
 
-if("${PROJECT_NAME}" STREQUAL "${CMAKE_PROJECT_NAME}")
-    option(PACKAGE_TESTS "Build automated tests" ON)
-else()
-    option(PACKAGE_TESTS "Build automated tests")
-endif()
-
-# https://www.intel.com/content/www/us/en/develop/documentation/oneapi-dpcpp-cpp-compiler-dev-guide-and-reference/top/compiler-setup/use-the-command-line/use-cmake-with-the-compiler.html
-if (INTEL_DPCPP)
-    find_package(IntelDPCPP REQUIRED)
-endif()
+# Dependencies ================================================================
 
+# -----------------------------------------------------------------------------
+# Set global C++ options
 set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 set(CMAKE_CXX_VISIBILITY_PRESET hidden)
 
-include(ExternalProject)
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/modules/")
+# -----------------------------------------------------------------------------
+# Check if NGen is the main project (e.g. development environment)
+if(PROJECT_NAME STREQUAL CMAKE_PROJECT_NAME)
+    set(NGEN_IS_MAIN_PROJECT ON)
+else()
+    set(NGEN_IS_MAIN_PROJECT OFF)
+endif()
+
+# -----------------------------------------------------------------------------
+# If MPI support is enabled, set the C++ compiler to "mpicxx"
+if(NGEN_WITH_MPI)
+    find_package(MPI REQUIRED QUIET)
+    add_compile_definitions(NGEN_MPI_ACTIVE)
+endif()
+
+# -----------------------------------------------------------------------------
+# FIXME: Is this needed for icpx? or even icpp? This only enables support for SYCL - Justin
+# https://www.intel.com/content/www/us/en/develop/documentation/oneapi-dpcpp-cpp-compiler-dev-guide-and-reference/top/compiler-setup/use-the-command-line/use-cmake-with-the-compiler.html
+if(INTEL_DPCPP)
+    find_package(IntelDPCPP REQUIRED QUIET)
+endif()
 
+# -----------------------------------------------------------------------------
 # Account for different OS and how that impacts shared lib file names
-if ("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
+# FIXME: What is this used for? - Justin
+if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
     set(SHARED_LIB_EXTENSION "dylib")
 elseif(WIN32)
-    error( "Windows platforms are not currently supported" )
+    error("Windows platforms are not currently supported")
 else()
     set(SHARED_LIB_EXTENSION "so")
 endif()
 
-find_package(Git QUIET)
-if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
-    # Update submodules as needed
-    option(GIT_SUBMODULE "Check submodules during build" ON)
-endif()
-function(git_update_submodule PATH)
-    if(GIT_SUBMODULE)
-        message(STATUS "Updating submodule ${PATH}")
-        execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init -- ${PATH}
-            WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
-            RESULT_VARIABLE GIT_SUBMOD_RESULT
-            )
-        if(NOT GIT_SUBMOD_RESULT EQUAL "0")
-            message(FATAL_ERROR "git submodule update --init for \"${PATH}\" failed with ${GIT_SUBMOD_RESULT}")
-        endif()
-    else()
-        message(FATAL_ERROR "Git not detected: cannot obtain submodule at \"${PATH}\" (but how is this even working?)")
-    endif()
-endfunction()
-
-set(PROJ_ROOT_INCLUDE_DIR ./include)
-set(PROJ_ROOT_MODELS_DIR ./models)
-
+# -----------------------------------------------------------------------------
 # Find the Boost library and configure usage
 set(Boost_USE_STATIC_LIBS OFF)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
-
 if(NOT DEFINED BOOST_ROOT AND NOT DEFINED ENV{BOOST_ROOT})
     # Look for version-specific Boost directory if available (known from Github Actions VM docs)
     if(DEFINED ENV{BOOST_ROOT_1_72_0})
         set(BOOST_ROOT $ENV{BOOST_ROOT_1_72_0})
-        message(STATUS "Using value of \$ENV{BOOST_ROOT_1_72_0} to set BOOST_ROOT=$ENV{BOOST_ROOT_1_72_0}")
-    else()
-        message(STATUS "No BOOST_ROOT set")
     endif()
 endif()
-
 find_package(Boost 1.72.0 REQUIRED)
 
-if(MPI_ACTIVE)
-    find_package(MPI)
-    add_compile_definitions(NGEN_MPI_ACTIVE)
-endif()
-
-find_package(SQLite3)
-if(SQLite3_FOUND)
-    set(NGEN_WITH_SQLITE3 ON)
+# -----------------------------------------------------------------------------
+if(NGEN_WITH_SQLITE)
+    find_package(SQLite3 REQUIRED)
     add_compile_definitions(NGEN_WITH_SQLITE3)
-else()
-    set(NGEN_WITH_SQLITE3 OFF)
-endif()
-message(INFO " SQLite3 support is ${NGEN_WITH_SQLITE3}")
-
-# UDUNITS
-# Since UDUNITS is currently not really optional (yet) let's make it default to on...
-if (NOT (DEFINED UDUNITS_ACTIVE))
-    message(INFO " UDUNITS_ACTIVE not defined")
-    if (DEFINED ENV{UDUNITS_ACTIVE})
-        message(INFO " set as $ENV{UDUNITS_ACTIVE}")
-        set(UDUNITS_ACTIVE $ENV{UDUNITS_ACTIVE})
-    else()
-        set(UDUNITS_ACTIVE true)
-    endif()
 endif()
 
-if(UDUNITS_ACTIVE)
+# -----------------------------------------------------------------------------
+if(NGEN_WITH_UDUNITS)
     find_package(UDUNITS2 REQUIRED)
-    if(UDUNITS2_LIBRARY)
-        #add_library(libudunits2 SHARED IMPORTED)
-        target_include_directories(libudunits2 INTERFACE ${UDUNITS2_INCLUDE})
-        #include_directories(${UDUNITS2_INCLUDE})
-        message("INFO Using UDUNITS2 at ${UDUNITS2_LIBRARY} and ${UDUNITS2_INCLUDE}")
-    endif()
-    #add_compile_definitions("NGEN_UDUNITS2_XML_PATH=\"${UDUNITS_INSTALL_DIR}/share/udunits/udunits2.xml\"")
+    add_compile_definitions(NGEN_WITH_UDUNITS)
+
+    add_library(udunits2 SHARED IMPORTED)
+    target_include_directories(udunits2 INTERFACE "${UDUNITS2_INCLUDE}")
+    set_target_properties(udunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
 endif()
 
-cmake_policy(SET CMP0074 NEW)
+# -----------------------------------------------------------------------------
 if(NETCDF_ACTIVE)
-    set (NETCDF_CXX "YES")
-    set (NETCDF_F77 "NO")
-    set (NETCDF_F90 "NO")
+    set(NETCDF_CXX "YES")
+    set(NETCDF_F77 "NO")
+    set(NETCDF_F90 "NO")
     find_package(NetCDF REQUIRED)
     add_compile_definitions(NETCDF_ACTIVE)
-    if(NETCDF_FOUND)
-        include_directories(${NETCDF_INCLUDE_DIRS})
-        if(NETCDF_HAS_PARALLEL)
-            message("INFO Using NETCDF (with parallel!) at ${NETCDF_LIBRARIES} and ${NETCDF_INCLUDE_DIRS}")
-        else()
-            message("INFO Using NETCDF (without parallel!) at ${NETCDF_LIBRARIES} and ${NETCDF_INCLUDE_DIRS}")
-        endif()
-    else()
-        message("INFO netCDF library not found")
-    endif()
+    
+    add_library(NetCDF SHARED IMPORTED)
+    target_include_directories(NetCDF INTERFACE "${NETCDF_INCLUDE_DIR}" "${NETCDF_CXX_INCLUDE_DIR}")
+    set_target_properties(NetCDF PROPERTIES IMPORTED_LOCATION "${NETCDF_LIBRARIES};${NETCDF_CXX_LIBRARY}")
 endif()
 
-add_executable(ngen
-    src/NGen.cpp
-    )
-
-# Natively support BMI C++ modules and pre-compile in the test_bmi_cpp mock/example.
-set(TEST_BMI_CPP_DIR ${PROJECT_SOURCE_DIR}/extern/test_bmi_cpp)
-git_update_submodule(${PROJECT_SOURCE_DIR}/extern/bmi-cxx)
-add_subdirectory(${TEST_BMI_CPP_DIR} ${TEST_BMI_CPP_DIR}/cmake_build)
-add_dependencies(ngen testbmicppmodel) # because our demo realizations will use it
-
+# -----------------------------------------------------------------------------
 # Handle several steps for BMI C library logic and dependencies, at top level, if functionality is turned on
-if(BMI_C_LIB_ACTIVE)
+if(NGEN_WITH_BMI_C)
     # Define associated preprocessor directive
     add_compile_definitions(NGEN_BMI_C_LIB_ACTIVE)
 endif()
 
+# -----------------------------------------------------------------------------
 # Configure whether Fortran BMI functionality is active
-if (${BMI_FORTRAN_ACTIVE})
+if(NGEN_WITH_BMI_FORTRAN)
     add_compile_definitions(NGEN_BMI_FORTRAN_ACTIVE)
 endif()
 
-#### Python stuff
-# First, define NGEN_ACTIVATE_PYTHON, if not already defined
-#   Use NGEN_ACTIVATE_PYTHON environment variable if available, or default to true
-if (NOT (DEFINED NGEN_ACTIVATE_PYTHON))
-    if (DEFINED ENV{NGEN_ACTIVATE_PYTHON})
-        message(INFO " NGEN_ACTIVATE_PYTHON set to '$ENV{NGEN_ACTIVATE_PYTHON}' from the environment")
-        set(NGEN_ACTIVATE_PYTHON $ENV{NGEN_ACTIVATE_PYTHON})
-    else()
-        message(INFO " NGEN_ACTIVATE_PYTHON set to 'true' by default")
-        set(NGEN_ACTIVATE_PYTHON true)
-    endif()
-endif()
-
-# If Python set to be active, run steps to make sure it is included properly, and set compiler definition to true
-if (${NGEN_ACTIVATE_PYTHON})
+# -----------------------------------------------------------------------------
+if(NGEN_WITH_PYTHON)
     add_compile_definitions(ACTIVATE_PYTHON=true)
-
     find_package(Python 3.6.8 REQUIRED COMPONENTS Interpreter Development NumPy)
-    #message(INFO " the final Py lib is ${Python_LIBRARY}")
-    #message(INFO " the final Py libraries are ${Python_LIBRARIES}")
-    #message(INFO " the final Py library dirs are ${Python_LIBRARY_DIRS}")
-    #message(INFO " the final Py runtime library dirs are ${Python_RUNTIME_LIBRARY_DIRS}")
-    #message(INFO " the final Py std lib is ${Python_STDLIB}")
-    #message(INFO " the rpath is ${CMAKE_INSTALL_RPATH}")
     set(PYTHON_EXECUTABLE ${Python_EXECUTABLE}) # Case-sensitive difference
     add_subdirectory(extern/pybind11)
 endif()
 
-target_include_directories(ngen PUBLIC
-        "${PROJECT_BINARY_DIR}/include" # For generated config header file in binary tree
-        )
-
-  
-# In some IDEs (e.g., CLion), it is easier to work with the code in the included example of an "external" shared library
-# when that code appears to be part of the main project, which can be done by add a statement like the ones below.
-#
-# However, these should be removed or commented out when running CMake builds and in the committed version of this file.
-#
-#add_subdirectory("extern/cfe")
-#add_subdirectory("extern/test_bmi_c")
-
-if(QUIET)
-set(UDUNITS_QUIET true)
-set(ET_QUIET true)
-set(NGEN_QUIET true)
+# -----------------------------------------------------------------------------
+if(NGEN_QUIET)
+    set(UDUNITS_QUIET true)
+    set(ET_QUIET true)
+    add_compile_definitions(NGEN_QUIET)
 endif()
 
 if(UDUNITS_QUIET)
-add_compile_definitions(UDUNITS_QUIET)
+    add_compile_definitions(UDUNITS_QUIET)
 endif()
 
+# FIXME: I don't think this is needed now? - Justin
 if(ET_QUIET)
-add_compile_definitions(ET_QUIET)
+    add_compile_definitions(ET_QUIET)
 endif()
 
-if(NGEN_QUIET)
-add_compile_definitions(NGEN_QUIET)
-endif()
+# -----------------------------------------------------------------------------
+
+# Natively support BMI C++ modules and pre-compile in the test_bmi_cpp mock/example.
+set(TEST_BMI_CPP_DIR ${NGEN_EXT_DIR}/test_bmi_cpp)
+git_update_submodule(${NGEN_EXT_DIR}/bmi-cxx)
+add_subdirectory(${TEST_BMI_CPP_DIR} ${TEST_BMI_CPP_DIR}/cmake_build) # FIXME: Why is this here? - Justin
+
+# -----------------------------------------------------------------------------
+# Project Targets
+# -----------------------------------------------------------------------------
+
+
+configure_file(include/NGenConfig.h.in include/NGenConfig.h)
+add_executable(ngen "${NGEN_SRC_DIR}/NGen.cpp")
+add_dependencies(ngen testbmicppmodel)
+target_include_directories(ngen PUBLIC "${PROJECT_BINARY_DIR}/include")
 
 add_subdirectory("src/core")
-add_dependencies(core libudunits2)
 add_subdirectory("src/geojson")
 
 if(NGEN_WITH_SQLITE3)
@@ -232,7 +205,8 @@ add_subdirectory("src/forcing")
 add_subdirectory("src/utilities/mdarray")
 add_subdirectory("src/utilities/mdframe")
 
-target_link_libraries(ngen PUBLIC
+target_link_libraries(ngen
+    PUBLIC
         NGen::core
         NGen::core_catchment
         NGen::core_nexus
@@ -240,29 +214,18 @@ target_link_libraries(ngen PUBLIC
         NGen::realizations_catchment
         NGen::forcing
         NGen::core_mediator
-        libudunits2
-        ${NETCDF_LIBRARIES}
-        )
-
-add_executable(partitionGenerator
-    src/partitionGenerator.cpp
-    )
+        udunits2
+        NetCDF
+)
 
-target_include_directories(partitionGenerator PUBLIC
-        "${PROJECT_BINARY_DIR}/include" # For generated config header file in binary tree
-        )
-
-    target_link_libraries(partitionGenerator PUBLIC
-       core
-       geojson
-       )
+add_executable(partitionGenerator src/partitionGenerator.cpp)
+target_include_directories(partitionGenerator PUBLIC "${PROJECT_BINARY_DIR}/include")
+target_link_libraries(partitionGenerator PUBLIC NGen::core NGen::geojson)
 
 if(NGEN_ACTIVATE_ROUTING)
     add_compile_definitions(NGEN_ROUTING_ACTIVE)
     add_subdirectory("src/routing")
-    target_link_libraries(ngen PUBLIC
-            NGen::routing
-           )
+    target_link_libraries(ngen PUBLIC NGen::routing)
 endif()
 
 # For automated testing with Google Test
@@ -272,6 +235,10 @@ if(PACKAGE_TESTS)
     add_subdirectory(test)
 endif()
 
+# -----------------------------------------------------------------------------
+# Build Summary
+# -----------------------------------------------------------------------------
+
 macro(message_if_defined PRINTNAME)
 if(${ARGN})
 message(STATUS "    ${PRINTNAME}: ${${ARGN}}")
@@ -291,37 +258,95 @@ message(STATUS "  System: ${CMAKE_SYSTEM_NAME}")
 message(STATUS "  C Compiler: ${CMAKE_C_COMPILER}")
 message(STATUS "  CXX Compiler: ${CMAKE_CXX_COMPILER}")
 message(STATUS "  Flags:")
-message_if_defined("NETCDF" NETCDF_ACTIVE)
-message_if_defined("SQLITE3" NGEN_WITH_SQLITE3)
-message_if_defined("UDUNITS" UDUNITS_ACTIVE)
-message_if_defined("MPI" MPI_ACTIVE)
-message_if_defined("BMI FORTRAN" BMI_FORTRAN_ACTIVE)
-message_if_defined("BMI C" BMI_C_LIB_ACTIVE)
-message_if_defined("PYTHON" NGEN_ACTIVATE_PYTHON)
-message_if_defined("ROUTING" NGEN_ACTIVATE_ROUTING)
-message_if_defined("TESTS" PACKAGE_TESTS)
-message_if_defined("QUIET" QUIET)
 
+message(STATUS "    NGEN_WITH_MPI: ${NGEN_WITH_MPI}")
+message(STATUS "    NGEN_WITH_NETCDF: ${NGEN_WITH_NETCDF}")
+message(STATUS "    NGEN_WITH_SQLITE: ${NGEN_WITH_SQLITE}")
+message(STATUS "    NGEN_WITH_UDUNITS: ${NGEN_WITH_UDUNITS}")
+message(STATUS "    NGEN_WITH_BMI_FORTRAN: ${NGEN_WITH_BMI_FORTRAN}")
+message(STATUS "    NGEN_WITH_BMI_C: ${NGEN_WITH_BMI_C}")
+message(STATUS "    NGEN_WITH_PYTHON: ${NGEN_WITH_PYTHON}")
+message(STATUS "    NGEN_WITH_ROUTING: ${NGEN_WITH_ROUTING}")
+message(STATUS "    NGEN_WITH_TESTS: ${NGEN_WITH_TESTS}")
+message(STATUS "    NGEN_QUIET: ${NGEN_QUIET}")
+
+message(STATUS)
+
+message(STATUS "Environment summary:")
 message(STATUS)
 
-if(Python_FOUND)
-    message(STATUS "Python environment summary:")
-    message(STATUS "  Version: ${Python_VERSION}")
-    message(STATUS "  Executable: ${Python_EXECUTABLE}")
-    message(STATUS "  Interpreter Type: ${Python_INTERPRETER_ID}")
-    message(STATUS "  Site Library: ${Python_SITELIB}")
-    message(STATUS "  Include: ${Python_INCLUDE_DIRS}")
-    message(STATUS "  Runtime Library: ${Python_RUNTIME_LIBRARY_DIRS}")
-    message(STATUS "  NumPy Version: ${Python_NumPy_VERSION}")
-    message(STATUS "  NumPy Include: ${Python_NumPy_INCLUDE_DIRS}")
+message(STATUS "  Boost:")
+message(STATUS "    Version: ${Boost_VERSION}")
+message(STATUS "    Include: ${Boost_INCLUDE_DIRS}")
+message(STATUS)
+
+if(INTEL_DPCPP)
+message(STATUS "  Intel DPC++:")
+message(STATUS "    Version: ${SYCL_LANGUAGE_VERSION}")
+message(STATUS "    Include: ${SYCL_INCLUDE_DIR}")
+message(STATUS "    Implmentation: ${SYCL_IMPLEMENTATION_ID}")
+message(STATUS)
+endif()
+
+if(NGEN_WITH_MPI)
+message(STATUS "  MPI (CXX):")
+message(STATUS "    Version: ${MPI_CXX_VERSION}")
+message(STATUS "    Library: ${MPI_CXX_LIBRARIES}")
+message(STATUS "    Include: ${MPI_CXX_INCLUDE_DIRS}")
+message(STATUS)
 endif()
 
-if(pybind11_FOUND)
-    message(STATUS "  pybind11 configuration summary:")
-    message(STATUS "    Version: ${pybind11_VERSION}")
-    message(STATUS "    Include: ${pybind11_INCLUDE_DIRS}")
-    message(STATUS "    Definitions: ${pybind11_DEFINITIONS}")
-    message(STATUS "    Libraries: ${pybind11_LIBRARIES}")
+if(NGEN_WITH_NETCDF)
+message(STATUS "  NetCDF:")
+message(STATUS "    Library: ${NETCDF_LIBRARY}")
+message(STATUS "    Library (CXX): ${NETCDF_CXX_LIBRARIES}")
+message(STATUS "    Include: ${NETCDF_INCLUDE_DIR}")
+message(STATUS "    Parallel: ${NETCDF_HAS_PARALLEL}")
+message(STATUS)
+endif()
+
+if(NGEN_WITH_SQLITE)
+message(STATUS "  SQLite:")
+message(STATUS "    Version: ${SQLite3_VERSION}")
+message(STATUS "    Library: ${SQLite3_LIBRARIES}")
+message(STATUS "    Include: ${SQLite3_INCLUDE_DIRS}")
+message(STATUS)
+endif()
+
+if(NGEN_WITH_UDUNITS)
+message(STATUS "  UDUNITS2:")
+message(STATUS "    Library: ${UDUNITS2_LIBRARY}")
+message(STATUS "    Include: ${UDUNITS2_INCLUDE}")
+message(STATUS)
+endif()
+
+if(NGEN_WITH_BMI_FORTRAN)
+message(STATUS "  Fortran:")
+message(STATUS "    Fortran-C BMI Compat Library Path: ${NGEN_ISO_C_FORTRAN_BMI_LIB_PATH}")
+message(STATUS)
+endif()
+
+if(NGEN_WITH_PYTHON)
+    if(DEFINED ENV{VIRTUAL_ENV})
+        set(NGEN_CONFIGURED_VENV "$ENV{VIRTUAL_ENV}")
+    else()
+        set(NGEN_CONFIGURED_VENV "<none>")
+    endif()
+    message(STATUS "  Python:")
+    message(STATUS "    Version: ${Python_VERSION}")
+    message(STATUS "    Virtual Env: ${NGEN_CONFIGURED_VENV}")
+    message(STATUS "    Executable: ${Python_EXECUTABLE}")
+    message(STATUS "    Interpreter Type: ${Python_INTERPRETER_ID}")
+    message(STATUS "    Site Library: ${Python_SITELIB}")
+    message(STATUS "    Include: ${Python_INCLUDE_DIRS}")
+    message(STATUS "    Runtime Library: ${Python_RUNTIME_LIBRARY_DIRS}")
+    message(STATUS "    NumPy Version: ${Python_NumPy_VERSION}")
+    message(STATUS "    NumPy Include: ${Python_NumPy_INCLUDE_DIRS}")
+    if(pybind11_FOUND)
+        message(STATUS "    pybind11:")
+        message(STATUS "      Version: ${pybind11_VERSION}")
+        message(STATUS "      Include: ${pybind11_INCLUDE_DIR}")
+    endif()
 endif()
 message(STATUS "---------------------------------------------------------------------")
 
diff --git a/cmake/FindNetCDF.cmake b/cmake/FindNetCDF.cmake
deleted file mode 100644
index 194b1a0d32..0000000000
--- a/cmake/FindNetCDF.cmake
+++ /dev/null
@@ -1,131 +0,0 @@
-#[==[
-Provides the following variables:
-
-  * `NetCDF_FOUND`: Whether NetCDF was found or not.
-  * `NetCDF_INCLUDE_DIRS`: Include directories necessary to use NetCDF.
-  * `NetCDF_LIBRARIES`: Libraries necessary to use NetCDF.
-  * `NetCDF_VERSION`: The version of NetCDF found.
-  * `NetCDF::NetCDF`: A target to use with `target_link_libraries`.
-  * `NetCDF_HAS_PARALLEL`: Whether or not NetCDF was found with parallel IO support.
-#]==]
-
-function(FindNetCDF_get_is_parallel_aware include_dir)
-  file(STRINGS "${include_dir}/netcdf_meta.h" _netcdf_lines
-    REGEX "#define[ \t]+NC_HAS_PARALLEL[ \t]")
-  string(REGEX REPLACE ".*NC_HAS_PARALLEL[ \t]*([0-1]+).*" "\\1" _netcdf_has_parallel "${_netcdf_lines}")
-  if (_netcdf_has_parallel)
-    set(NetCDF_HAS_PARALLEL TRUE PARENT_SCOPE)
-  else()
-    set(NetCDF_HAS_PARALLEL FALSE PARENT_SCOPE)
-  endif()
-endfunction()
-
-# Try to find a CMake-built NetCDF.
-find_package(netCDF CONFIG QUIET)
-if (netCDF_FOUND)
-  # Forward the variables in a consistent way.
-  set(NetCDF_FOUND "${netCDF_FOUND}")
-  set(NetCDF_INCLUDE_DIRS "${netCDF_INCLUDE_DIR}")
-  set(NetCDF_LIBRARIES "${netCDF_LIBRARIES}")
-  set(NetCDF_VERSION "${NetCDFVersion}")
-
-  include(FindPackageHandleStandardArgs)
-  find_package_handle_standard_args(NetCDF
-    REQUIRED_VARS NetCDF_INCLUDE_DIRS NetCDF_LIBRARIES
-    VERSION_VAR NetCDF_VERSION)
-
-  if (NOT TARGET NetCDF::NetCDF)
-    add_library(NetCDF::NetCDF INTERFACE IMPORTED)
-    if (TARGET "netCDF::netcdf")
-      # 4.7.3
-      set_target_properties(NetCDF::NetCDF PROPERTIES
-        INTERFACE_LINK_LIBRARIES "netCDF::netcdf")
-    elseif (TARGET "netcdf")
-      set_target_properties(NetCDF::NetCDF PROPERTIES
-        INTERFACE_LINK_LIBRARIES "netcdf")
-    else ()
-      set_target_properties(NetCDF::NetCDF PROPERTIES
-        INTERFACE_LINK_LIBRARIES "${netCDF_LIBRARIES}")
-    endif ()
-  endif ()
-
-  FindNetCDF_get_is_parallel_aware("${NetCDF_INCLUDE_DIRS}")
-  # Skip the rest of the logic in this file.
-  return ()
-endif ()
-
-find_package(PkgConfig QUIET)
-if (PkgConfig_FOUND)
-  pkg_check_modules(_NetCDF QUIET netcdf IMPORTED_TARGET)
-  if (_NetCDF_FOUND)
-    # Forward the variables in a consistent way.
-    set(NetCDF_FOUND "${_NetCDF_FOUND}")
-    set(NetCDF_INCLUDE_DIRS "${_NetCDF_INCLUDE_DIRS}")
-    set(NetCDF_LIBRARIES "${_NetCDF_LIBRARIES}")
-    set(NetCDF_VERSION "${_NetCDF_VERSION}")
-
-    include(FindPackageHandleStandardArgs)
-    find_package_handle_standard_args(NetCDF
-      REQUIRED_VARS NetCDF_LIBRARIES
-      # This is not required because system-default include paths are not
-      # reported by `FindPkgConfig`, so this might be empty. Assume that if we
-      # have a library, the include directories are fine (if any) since
-      # PkgConfig reported that the package was found.
-      # NetCDF_INCLUDE_DIRS
-      VERSION_VAR NetCDF_VERSION)
-
-    if (NOT TARGET NetCDF::NetCDF)
-      add_library(NetCDF::NetCDF INTERFACE IMPORTED)
-      set_target_properties(NetCDF::NetCDF PROPERTIES
-        INTERFACE_LINK_LIBRARIES "PkgConfig::_NetCDF")
-    endif ()
-
-    FindNetCDF_get_is_parallel_aware("${_NetCDF_INCLUDEDIR}")
-    # Skip the rest of the logic in this file.
-    return ()
-  endif ()
-endif ()
-
-find_path(NetCDF_INCLUDE_DIR
-  NAMES netcdf.h
-  DOC "netcdf include directories")
-mark_as_advanced(NetCDF_INCLUDE_DIR)
-
-find_library(NetCDF_LIBRARY
-  NAMES netcdf
-  DOC "netcdf library")
-mark_as_advanced(NetCDF_LIBRARY)
-
-if (NetCDF_INCLUDE_DIR)
-  file(STRINGS "${NetCDF_INCLUDE_DIR}/netcdf_meta.h" _netcdf_version_lines
-    REGEX "#define[ \t]+NC_VERSION_(MAJOR|MINOR|PATCH|NOTE)")
-  string(REGEX REPLACE ".*NC_VERSION_MAJOR *\([0-9]*\).*" "\\1" _netcdf_version_major "${_netcdf_version_lines}")
-  string(REGEX REPLACE ".*NC_VERSION_MINOR *\([0-9]*\).*" "\\1" _netcdf_version_minor "${_netcdf_version_lines}")
-  string(REGEX REPLACE ".*NC_VERSION_PATCH *\([0-9]*\).*" "\\1" _netcdf_version_patch "${_netcdf_version_lines}")
-  string(REGEX REPLACE ".*NC_VERSION_NOTE *\"\([^\"]*\)\".*" "\\1" _netcdf_version_note "${_netcdf_version_lines}")
-  set(NetCDF_VERSION "${_netcdf_version_major}.${_netcdf_version_minor}.${_netcdf_version_patch}${_netcdf_version_note}")
-  unset(_netcdf_version_major)
-  unset(_netcdf_version_minor)
-  unset(_netcdf_version_patch)
-  unset(_netcdf_version_note)
-  unset(_netcdf_version_lines)
-
-  FindNetCDF_get_is_parallel_aware("${NetCDF_INCLUDE_DIR}")
-endif ()
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(NetCDF
-  REQUIRED_VARS NetCDF_LIBRARY NetCDF_INCLUDE_DIR
-  VERSION_VAR NetCDF_VERSION)
-
-if (NetCDF_FOUND)
-  set(NetCDF_INCLUDE_DIRS "${NetCDF_INCLUDE_DIR}")
-  set(NetCDF_LIBRARIES "${NetCDF_LIBRARY}")
-
-  if (NOT TARGET NetCDF::NetCDF)
-    add_library(NetCDF::NetCDF UNKNOWN IMPORTED)
-    set_target_properties(NetCDF::NetCDF PROPERTIES
-      IMPORTED_LOCATION "${NetCDF_LIBRARY}"
-      INTERFACE_INCLUDE_DIRECTORIES "${NetCDF_INCLUDE_DIR}")
-  endif ()
-endif ()
diff --git a/cmake/modules/FindUDUNITS2.cmake b/cmake/modules/FindUDUNITS2.cmake
index 158ddea2d9..5cb39f1da2 100644
--- a/cmake/modules/FindUDUNITS2.cmake
+++ b/cmake/modules/FindUDUNITS2.cmake
@@ -1,22 +1,22 @@
-message("Looking for UDUNITS-2...")
 find_path(UDUNITS2_INCLUDE 
     NAMES udunits2.h
     PATH_SUFFIXES udunits2
     DOC "UDUNITS-2 include directories"
 )
 mark_as_advanced(UDUNITS2_INCLUDE)
-if(UDUNITS2_INCLUDE)
-    include_directories(${UDUNITS2_INCLUDE})
-endif()
 
 find_library(UDUNITS2_LIBRARY
-    NAMES libudunits2.so libudunits2.dylib
+    NAMES
+        libudunits2.so
+        libudunits2.dylib
 )
 mark_as_advanced(UDUNITS2_LIBRARY)
-if(UDUNITS2_LIBRARY)
-    add_library(libudunits2 SHARED IMPORTED)
-    set_property(TARGET libudunits2 PROPERTY IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
+
+if(DEFINED UDUNITS2_INCLUDE)
+    set(UDUNITS2_FOUND ON)
+else()
+    set(UDUNITS2_FOUND OFF)
 endif()
 
 include(FindPackageHandleStandardArgs)
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(UDUNITS2 DEFAULT_MSG UDUNITS2_LIBRARY UDUNITS2_INCLUDE)
\ No newline at end of file
+find_package_handle_standard_args(UDUNITS2 DEFAULT_MSG UDUNITS2_LIBRARY UDUNITS2_INCLUDE)
diff --git a/src/core/mediator/CMakeLists.txt b/src/core/mediator/CMakeLists.txt
index da9167ae59..4a6b668ab8 100644
--- a/src/core/mediator/CMakeLists.txt
+++ b/src/core/mediator/CMakeLists.txt
@@ -5,8 +5,8 @@ dynamic_sourced_cxx_library(core_mediator "${CMAKE_CURRENT_SOURCE_DIR}")
 
 add_library(NGen::core_mediator ALIAS core_mediator)
 if(UDUNITS_ACTIVE)
-        add_dependencies(core_mediator libudunits2)
-        target_link_libraries(core_mediator PUBLIC libudunits2)
+        add_dependencies(core_mediator udunits2)
+        target_link_libraries(core_mediator PUBLIC udunits2)
 endif()
 
 find_package(Threads REQUIRED)

From 915041d61e1fdb60cbc9b83511e928faf3f2cab3 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 13:44:56 -0700
Subject: [PATCH 02/39] cmake: ensure build is okay with changes

---
 CMakeLists.txt                 | 229 +++++++++++++++------------------
 cmake/modules/FindNetCDF.cmake |   1 -
 2 files changed, 104 insertions(+), 126 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b60bdf046f..284f090741 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -74,7 +74,7 @@ endif()
 # -----------------------------------------------------------------------------
 # If MPI support is enabled, set the C++ compiler to "mpicxx"
 if(NGEN_WITH_MPI)
-    find_package(MPI REQUIRED QUIET)
+    find_package(MPI REQUIRED)
     add_compile_definitions(NGEN_MPI_ACTIVE)
 endif()
 
@@ -82,7 +82,7 @@ endif()
 # FIXME: Is this needed for icpx? or even icpp? This only enables support for SYCL - Justin
 # https://www.intel.com/content/www/us/en/develop/documentation/oneapi-dpcpp-cpp-compiler-dev-guide-and-reference/top/compiler-setup/use-the-command-line/use-cmake-with-the-compiler.html
 if(INTEL_DPCPP)
-    find_package(IntelDPCPP REQUIRED QUIET)
+    find_package(IntelDPCPP REQUIRED)
 endif()
 
 # -----------------------------------------------------------------------------
@@ -120,6 +120,7 @@ if(NGEN_WITH_UDUNITS)
     find_package(UDUNITS2 REQUIRED)
     add_compile_definitions(NGEN_WITH_UDUNITS)
 
+    # Create UDUNITS2 target
     add_library(udunits2 SHARED IMPORTED)
     target_include_directories(udunits2 INTERFACE "${UDUNITS2_INCLUDE}")
     set_target_properties(udunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
@@ -133,9 +134,13 @@ if(NETCDF_ACTIVE)
     find_package(NetCDF REQUIRED)
     add_compile_definitions(NETCDF_ACTIVE)
     
+    # Create NetCDF target
     add_library(NetCDF SHARED IMPORTED)
     target_include_directories(NetCDF INTERFACE "${NETCDF_INCLUDE_DIR}" "${NETCDF_CXX_INCLUDE_DIR}")
-    set_target_properties(NetCDF PROPERTIES IMPORTED_LOCATION "${NETCDF_LIBRARIES};${NETCDF_CXX_LIBRARY}")
+    set_target_properties(NetCDF
+        PROPERTIES
+            IMPORTED_LOCATION "${NETCDF_LIBRARY}"
+            IMPORTED_LOCATION "${NETCDF_CXX_LIBRARY}")
 endif()
 
 # -----------------------------------------------------------------------------
@@ -159,6 +164,11 @@ if(NGEN_WITH_PYTHON)
     add_subdirectory(extern/pybind11)
 endif()
 
+# -----------------------------------------------------------------------------
+if(NGEN_WITH_ROUTING)
+    add_compile_definitions(NGEN_ROUTING_ACTIVE)
+endif()
+
 # -----------------------------------------------------------------------------
 if(NGEN_QUIET)
     set(UDUNITS_QUIET true)
@@ -185,25 +195,19 @@ add_subdirectory(${TEST_BMI_CPP_DIR} ${TEST_BMI_CPP_DIR}/cmake_build) # FIXME: W
 # -----------------------------------------------------------------------------
 # Project Targets
 # -----------------------------------------------------------------------------
-
-
 configure_file(include/NGenConfig.h.in include/NGenConfig.h)
 add_executable(ngen "${NGEN_SRC_DIR}/NGen.cpp")
 add_dependencies(ngen testbmicppmodel)
-target_include_directories(ngen PUBLIC "${PROJECT_BINARY_DIR}/include")
+target_include_directories(ngen PUBLIC "${NGEN_INC_DIR}")
 
 add_subdirectory("src/core")
 add_subdirectory("src/geojson")
-
-if(NGEN_WITH_SQLITE3)
-    add_subdirectory("src/geopackage")
-    target_link_libraries(ngen PUBLIC NGen::geopackage)
-endif()
-
+add_subdirectory("src/geopackage")
 add_subdirectory("src/realizations/catchment")
 add_subdirectory("src/forcing")
 add_subdirectory("src/utilities/mdarray")
 add_subdirectory("src/utilities/mdframe")
+add_subdirectory("src/routing")
 
 target_link_libraries(ngen
     PUBLIC
@@ -211,9 +215,11 @@ target_link_libraries(ngen
         NGen::core_catchment
         NGen::core_nexus
         NGen::geojson
+        NGen::geopackage
         NGen::realizations_catchment
         NGen::forcing
         NGen::core_mediator
+        NGen::routing
         udunits2
         NetCDF
 )
@@ -222,15 +228,9 @@ add_executable(partitionGenerator src/partitionGenerator.cpp)
 target_include_directories(partitionGenerator PUBLIC "${PROJECT_BINARY_DIR}/include")
 target_link_libraries(partitionGenerator PUBLIC NGen::core NGen::geojson)
 
-if(NGEN_ACTIVATE_ROUTING)
-    add_compile_definitions(NGEN_ROUTING_ACTIVE)
-    add_subdirectory("src/routing")
-    target_link_libraries(ngen PUBLIC NGen::routing)
-endif()
-
 # For automated testing with Google Test
-if(PACKAGE_TESTS)
-    enable_testing()
+if(NGEN_WITH_TESTS)
+    include(CTest) # calls enable_testing()
     include(GoogleTest)
     add_subdirectory(test)
 endif()
@@ -239,115 +239,94 @@ endif()
 # Build Summary
 # -----------------------------------------------------------------------------
 
-macro(message_if_defined PRINTNAME)
-if(${ARGN})
-message(STATUS "    ${PRINTNAME}: ${${ARGN}}")
-else()
-message(STATUS "    ${PRINTNAME}: OFF")
-endif()
-endmacro()
-
-message("")
-message(STATUS "---------------------------------------------------------------------")
-message(STATUS "NGen version: ${ngen_VERSION}")
-message(STATUS)
-message(STATUS "Build configuration summary:")
-message(STATUS "  Generator: ${CMAKE_GENERATOR}")
-message(STATUS "  Build type: ${CMAKE_BUILD_TYPE}")
-message(STATUS "  System: ${CMAKE_SYSTEM_NAME}")
-message(STATUS "  C Compiler: ${CMAKE_C_COMPILER}")
-message(STATUS "  CXX Compiler: ${CMAKE_CXX_COMPILER}")
-message(STATUS "  Flags:")
-
-message(STATUS "    NGEN_WITH_MPI: ${NGEN_WITH_MPI}")
-message(STATUS "    NGEN_WITH_NETCDF: ${NGEN_WITH_NETCDF}")
-message(STATUS "    NGEN_WITH_SQLITE: ${NGEN_WITH_SQLITE}")
-message(STATUS "    NGEN_WITH_UDUNITS: ${NGEN_WITH_UDUNITS}")
-message(STATUS "    NGEN_WITH_BMI_FORTRAN: ${NGEN_WITH_BMI_FORTRAN}")
-message(STATUS "    NGEN_WITH_BMI_C: ${NGEN_WITH_BMI_C}")
-message(STATUS "    NGEN_WITH_PYTHON: ${NGEN_WITH_PYTHON}")
-message(STATUS "    NGEN_WITH_ROUTING: ${NGEN_WITH_ROUTING}")
-message(STATUS "    NGEN_WITH_TESTS: ${NGEN_WITH_TESTS}")
-message(STATUS "    NGEN_QUIET: ${NGEN_QUIET}")
-
-message(STATUS)
-
-message(STATUS "Environment summary:")
-message(STATUS)
-
-message(STATUS "  Boost:")
-message(STATUS "    Version: ${Boost_VERSION}")
-message(STATUS "    Include: ${Boost_INCLUDE_DIRS}")
-message(STATUS)
-
-if(INTEL_DPCPP)
-message(STATUS "  Intel DPC++:")
-message(STATUS "    Version: ${SYCL_LANGUAGE_VERSION}")
-message(STATUS "    Include: ${SYCL_INCLUDE_DIR}")
-message(STATUS "    Implmentation: ${SYCL_IMPLEMENTATION_ID}")
-message(STATUS)
-endif()
-
-if(NGEN_WITH_MPI)
-message(STATUS "  MPI (CXX):")
-message(STATUS "    Version: ${MPI_CXX_VERSION}")
-message(STATUS "    Library: ${MPI_CXX_LIBRARIES}")
-message(STATUS "    Include: ${MPI_CXX_INCLUDE_DIRS}")
-message(STATUS)
-endif()
-
-if(NGEN_WITH_NETCDF)
-message(STATUS "  NetCDF:")
-message(STATUS "    Library: ${NETCDF_LIBRARY}")
-message(STATUS "    Library (CXX): ${NETCDF_CXX_LIBRARIES}")
-message(STATUS "    Include: ${NETCDF_INCLUDE_DIR}")
-message(STATUS "    Parallel: ${NETCDF_HAS_PARALLEL}")
-message(STATUS)
-endif()
-
-if(NGEN_WITH_SQLITE)
-message(STATUS "  SQLite:")
-message(STATUS "    Version: ${SQLite3_VERSION}")
-message(STATUS "    Library: ${SQLite3_LIBRARIES}")
-message(STATUS "    Include: ${SQLite3_INCLUDE_DIRS}")
-message(STATUS)
-endif()
-
-if(NGEN_WITH_UDUNITS)
-message(STATUS "  UDUNITS2:")
-message(STATUS "    Library: ${UDUNITS2_LIBRARY}")
-message(STATUS "    Include: ${UDUNITS2_INCLUDE}")
-message(STATUS)
+# Syntax: ngen_multiline_message("<message 1>" "<message 2>" ...)
+function(ngen_multiline_message)
+set(messages "${ARGN}")
+foreach(msg IN LISTS messages)
+    message(STATUS "${msg}")
+endforeach()
+endfunction()
+
+# Syntax: ngen_dependent_multiline_message(<variable> "<message 1>" "<message 2>" ...)
+function(ngen_dependent_multiline_message VARIABLE)
+if(${VARIABLE})
+    ngen_multiline_message(${ARGN})
 endif()
+endfunction()
 
-if(NGEN_WITH_BMI_FORTRAN)
-message(STATUS "  Fortran:")
-message(STATUS "    Fortran-C BMI Compat Library Path: ${NGEN_ISO_C_FORTRAN_BMI_LIB_PATH}")
-message(STATUS)
+# This is used purely for configuration output,
+# and does not affect the virtual environment used.
+if(DEFINED ENV{VIRTUAL_ENV})
+    set(NGEN_CONFIGURED_VENV "$ENV{VIRTUAL_ENV}")
+else()
+    set(NGEN_CONFIGURED_VENV "<none>")
 endif()
 
-if(NGEN_WITH_PYTHON)
-    if(DEFINED ENV{VIRTUAL_ENV})
-        set(NGEN_CONFIGURED_VENV "$ENV{VIRTUAL_ENV}")
-    else()
-        set(NGEN_CONFIGURED_VENV "<none>")
-    endif()
-    message(STATUS "  Python:")
-    message(STATUS "    Version: ${Python_VERSION}")
-    message(STATUS "    Virtual Env: ${NGEN_CONFIGURED_VENV}")
-    message(STATUS "    Executable: ${Python_EXECUTABLE}")
-    message(STATUS "    Interpreter Type: ${Python_INTERPRETER_ID}")
-    message(STATUS "    Site Library: ${Python_SITELIB}")
-    message(STATUS "    Include: ${Python_INCLUDE_DIRS}")
-    message(STATUS "    Runtime Library: ${Python_RUNTIME_LIBRARY_DIRS}")
-    message(STATUS "    NumPy Version: ${Python_NumPy_VERSION}")
-    message(STATUS "    NumPy Include: ${Python_NumPy_INCLUDE_DIRS}")
-    if(pybind11_FOUND)
-        message(STATUS "    pybind11:")
-        message(STATUS "      Version: ${pybind11_VERSION}")
-        message(STATUS "      Include: ${pybind11_INCLUDE_DIR}")
-    endif()
-endif()
+message(STATUS "---------------------------------------------------------------------")
+ngen_multiline_message(
+"NGen version: ${ngen_VERSION}"
+"Build configuration summary:"
+"  Generator: ${CMAKE_GENERATOR}"
+"  Build type: ${CMAKE_BUILD_TYPE}"
+"  System: ${CMAKE_SYSTEM_NAME}"
+"  C Compiler: ${CMAKE_C_COMPILER}"
+"  CXX Compiler: ${CMAKE_CXX_COMPILER}"
+"  Flags:"
+"    NGEN_WITH_MPI: ${NGEN_WITH_MPI}"
+"    NGEN_WITH_NETCDF: ${NGEN_WITH_NETCDF}"
+"    NGEN_WITH_SQLITE: ${NGEN_WITH_SQLITE}"
+"    NGEN_WITH_UDUNITS: ${NGEN_WITH_UDUNITS}"
+"    NGEN_WITH_BMI_FORTRAN: ${NGEN_WITH_BMI_FORTRAN}"
+"    NGEN_WITH_BMI_C: ${NGEN_WITH_BMI_C}"
+"    NGEN_WITH_PYTHON: ${NGEN_WITH_PYTHON}"
+"    NGEN_WITH_ROUTING: ${NGEN_WITH_ROUTING}"
+"    NGEN_WITH_TESTS: ${NGEN_WITH_TESTS}"
+"    NGEN_QUIET: ${NGEN_QUIET}"
+"Environment summary:"
+"  Boost:"
+"    Version: ${Boost_VERSION}"
+"    Include: ${Boost_INCLUDE_DIRS}")
+ngen_dependent_multiline_message(INTEL_DPCPP
+"  Intel DPC++:"
+"    Version: ${SYCL_LANGUAGE_VERSION}"
+"    Include: ${SYCL_INCLUDE_DIR}"
+"    Implmentation: ${SYCL_IMPLEMENTATION_ID}")
+ngen_dependent_multiline_message(NGEN_WITH_MPI
+"  MPI (CXX):"
+"    Version: ${MPI_CXX_VERSION}"
+"    Library: ${MPI_CXX_LIBRARIES}"
+"    Include: ${MPI_CXX_INCLUDE_DIRS}")
+ngen_dependent_multiline_message(NGEN_WITH_NETCDF
+"  NetCDF:"
+"    Library: ${NETCDF_LIBRARY}"
+"    Library (CXX): ${NETCDF_CXX_LIBRARIES}"
+"    Include: ${NETCDF_INCLUDE_DIR}"
+"    Parallel: ${NETCDF_HAS_PARALLEL}")
+ngen_dependent_multiline_message(NGEN_WITH_SQLITE
+"  SQLite:"
+"    Version: ${SQLite3_VERSION}"
+"    Library: ${SQLite3_LIBRARIES}"
+"    Include: ${SQLite3_INCLUDE_DIRS}")
+ngen_dependent_multiline_message(NGEN_WITH_UDUNITS
+"  UDUNITS2:"
+"    Library: ${UDUNITS2_LIBRARY}"
+"    Include: ${UDUNITS2_INCLUDE}")
+ngen_dependent_multiline_message(NGEN_WITH_BMI_FORTRAN
+"  Fortran:"
+"    Fortran-C BMI Compat Library Path: ${NGEN_ISO_C_FORTRAN_BMI_LIB_PATH}")
+ngen_dependent_multiline_message(NGEN_WITH_PYTHON
+"  Python:"
+"    Version: ${Python_VERSION}"
+"    Virtual Env: ${NGEN_CONFIGURED_VENV}"
+"    Executable: ${Python_EXECUTABLE}"
+"    Interpreter Type: ${Python_INTERPRETER_ID}"
+"    Site Library: ${Python_SITELIB}"
+"    Include: ${Python_INCLUDE_DIRS}"
+"    Runtime Library: ${Python_RUNTIME_LIBRARY_DIRS}"
+"    NumPy Version: ${Python_NumPy_VERSION}"
+"    NumPy Include: ${Python_NumPy_INCLUDE_DIRS}"
+"    pybind11 Version: ${pybind11_VERSION}"
+"    pybind11 Include: ${pybind11_INCLUDE_DIR}")
 message(STATUS "---------------------------------------------------------------------")
 
 #set_target_properties(ngen PROPERTIES LINKER_LANGUAGE CXX)
diff --git a/cmake/modules/FindNetCDF.cmake b/cmake/modules/FindNetCDF.cmake
index 7299948119..141268b26f 100644
--- a/cmake/modules/FindNetCDF.cmake
+++ b/cmake/modules/FindNetCDF.cmake
@@ -112,7 +112,6 @@ NetCDF_check_interface (F90 netcdf.mod  netcdff)
 list (APPEND NetCDF_libs "${NETCDF_C_LIBRARIES}")
 set (NETCDF_LIBRARIES ${NetCDF_libs})
 set (NETCDF_INCLUDE_DIRS ${NetCDF_includes})
-message("INFO find NETCDF at ${NETCDF_LIBRARIES} and ${NETCDF_INCLUDE_DIRS} in cmake/modules/FindNetCDF.cmake")
 
 # handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE if
 # all listed variables are TRUE

From 0df7fa778aea306354602ad178f9e544765923c0 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 13:58:03 -0700
Subject: [PATCH 03/39] git: update .gitignore; cmake: update cmake modules

- exclude cmake/**/*.cmake from .gitignore so that modules
  aren't ignored
- update dynamic library function to use file(GLOB ... CONFIGURE_DEPENDS ...)
  instead of executing a system command.
- move git submodule function into cmake module
- remove cmake/modules dir in favor of flattening
---
 .gitignore                             |  3 +++
 CMakeLists.txt                         |  2 +-
 cmake/{modules => }/FindNetCDF.cmake   |  0
 cmake/{modules => }/FindUDUNITS2.cmake |  0
 cmake/GitUpdateSubmodules.cmake        | 22 ++++++++++++++++++++++
 cmake/dynamic_sourced_library.cmake    | 10 +---------
 6 files changed, 27 insertions(+), 10 deletions(-)
 rename cmake/{modules => }/FindNetCDF.cmake (100%)
 rename cmake/{modules => }/FindUDUNITS2.cmake (100%)
 create mode 100644 cmake/GitUpdateSubmodules.cmake

diff --git a/.gitignore b/.gitignore
index d75b9abf4b..20ffa96238 100644
--- a/.gitignore
+++ b/.gitignore
@@ -99,6 +99,9 @@ CMakeCache.txt
 /build
 /cmake_build*
 
+# Prevent ignoring cmake modules
+!cmake/**/*.cmake
+
 # Static Headers
 include/bmi.hpp
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 284f090741..b92248f6ae 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,7 +25,7 @@ set(NGEN_SRC_DIR  "${NGEN_ROOT_DIR}/src")
 set(NGEN_INC_DIR  "${NGEN_ROOT_DIR}/include")
 set(NGEN_EXT_DIR  "${NGEN_ROOT_DIR}/extern")
 set(NGEN_MOD_DIR  "${NGEN_ROOT_DIR}/cmake")
-list(APPEND CMAKE_MODULE_PATH "${NGEN_MOD_DIR}/modules")
+list(APPEND CMAKE_MODULE_PATH "${NGEN_MOD_DIR}")
 
 # Provides:
 #   (1) finds Git package
diff --git a/cmake/modules/FindNetCDF.cmake b/cmake/FindNetCDF.cmake
similarity index 100%
rename from cmake/modules/FindNetCDF.cmake
rename to cmake/FindNetCDF.cmake
diff --git a/cmake/modules/FindUDUNITS2.cmake b/cmake/FindUDUNITS2.cmake
similarity index 100%
rename from cmake/modules/FindUDUNITS2.cmake
rename to cmake/FindUDUNITS2.cmake
diff --git a/cmake/GitUpdateSubmodules.cmake b/cmake/GitUpdateSubmodules.cmake
new file mode 100644
index 0000000000..d9ec78f38f
--- /dev/null
+++ b/cmake/GitUpdateSubmodules.cmake
@@ -0,0 +1,22 @@
+find_package(Git QUIET)
+
+if(EXISTS "${NGEN_ROOT_DIR}/.git")
+    set(NGEN_HAS_GIT_DIR ON)
+else()
+    set(NGEN_HAS_GIT_DIR OFF)
+endif()
+
+function(git_update_submodule PATH)
+    if(NGEN_UPDATE_GIT_SUBMODULES)
+        message(STATUS "Updating submodule ${PATH}")
+        execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init -- ${PATH}
+            WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+            RESULT_VARIABLE GIT_SUBMOD_RESULT
+            )
+        if(NOT GIT_SUBMOD_RESULT EQUAL "0")
+            message(FATAL_ERROR "git submodule update --init for \"${PATH}\" failed with ${GIT_SUBMOD_RESULT}")
+        endif()
+    else()
+        message(FATAL_ERROR "Git not detected: cannot obtain submodule at \"${PATH}\" (but how is this even working?)")
+    endif()
+endfunction()
diff --git a/cmake/dynamic_sourced_library.cmake b/cmake/dynamic_sourced_library.cmake
index 8352757cc0..67e492f66c 100644
--- a/cmake/dynamic_sourced_library.cmake
+++ b/cmake/dynamic_sourced_library.cmake
@@ -2,14 +2,6 @@
 ## Params: LIB_NAME, WORK_DIR
 ## Add/create a new library with the given name, passing as source files all the '*.cpp' files found in the given working directory for the library
 function(dynamic_sourced_cxx_library LIB_NAME WORK_DIR)
-    execute_process(COMMAND ls
-            COMMAND grep .cpp
-            WORKING_DIRECTORY "${WORK_DIR}"
-            OUTPUT_VARIABLE lib_CPP_FILES
-            )
-    string(REGEX REPLACE "\n$" "" lib_CPP_FILES "${lib_CPP_FILES}")
-    string(REPLACE "\n" ";" lib_CPP_FILES ${lib_CPP_FILES})
-    set(lib_CPP_FILES_LIST ${lib_CPP_FILES})
-
+    file(GLOB_RECURSE lib_CPP_FILES_LIST CONFIGURE_DEPENDS "*.cpp")
     add_library(${LIB_NAME} STATIC ${lib_CPP_FILES_LIST})
 endfunction()

From ecf0ae1e7cd1093eac5998f6452b7be2f42e9f40 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 14:00:06 -0700
Subject: [PATCH 04/39] cmake: rm min required calls in ngen::core

---
 src/core/CMakeLists.txt               | 2 --
 src/core/catchment/CMakeLists.txt     | 2 --
 src/core/hydrolocation/CMakeLists.txt | 2 --
 src/core/mediator/CMakeLists.txt      | 2 --
 4 files changed, 8 deletions(-)

diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
index b2379a8d61..fc067dffe5 100644
--- a/src/core/CMakeLists.txt
+++ b/src/core/CMakeLists.txt
@@ -1,5 +1,3 @@
-cmake_minimum_required(VERSION 3.10)
-
 include(${PROJECT_SOURCE_DIR}/cmake/dynamic_sourced_library.cmake)
 dynamic_sourced_cxx_library(core "${CMAKE_CURRENT_SOURCE_DIR}")
 
diff --git a/src/core/catchment/CMakeLists.txt b/src/core/catchment/CMakeLists.txt
index be2a4a7460..e0017d4d3f 100644
--- a/src/core/catchment/CMakeLists.txt
+++ b/src/core/catchment/CMakeLists.txt
@@ -1,5 +1,3 @@
-cmake_minimum_required(VERSION 3.10)
-
 include(${PROJECT_SOURCE_DIR}/cmake/dynamic_sourced_library.cmake)
 dynamic_sourced_cxx_library(core_catchment "${CMAKE_CURRENT_SOURCE_DIR}")
 
diff --git a/src/core/hydrolocation/CMakeLists.txt b/src/core/hydrolocation/CMakeLists.txt
index af22d82b79..057e6049b2 100644
--- a/src/core/hydrolocation/CMakeLists.txt
+++ b/src/core/hydrolocation/CMakeLists.txt
@@ -1,5 +1,3 @@
-cmake_minimum_required(VERSION 3.10)
-
 include(${PROJECT_SOURCE_DIR}/cmake/dynamic_sourced_library.cmake)
 dynamic_sourced_cxx_library(core_hydrolocation "${CMAKE_CURRENT_SOURCE_DIR}")
 
diff --git a/src/core/mediator/CMakeLists.txt b/src/core/mediator/CMakeLists.txt
index 4a6b668ab8..0cfbbdd211 100644
--- a/src/core/mediator/CMakeLists.txt
+++ b/src/core/mediator/CMakeLists.txt
@@ -1,5 +1,3 @@
-cmake_minimum_required(VERSION 3.10)
-
 include(${PROJECT_SOURCE_DIR}/cmake/dynamic_sourced_library.cmake)
 dynamic_sourced_cxx_library(core_mediator "${CMAKE_CURRENT_SOURCE_DIR}")
 

From 29e184e59797eafff65c09c77520219ce39bc96c Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 14:00:41 -0700
Subject: [PATCH 05/39] cmake: rm min required calls in ngen::forcing/geojson

---
 src/forcing/CMakeLists.txt | 5 -----
 src/geojson/CMakeLists.txt | 1 -
 2 files changed, 6 deletions(-)

diff --git a/src/forcing/CMakeLists.txt b/src/forcing/CMakeLists.txt
index 2ce80a97a2..13ab0f4a8f 100644
--- a/src/forcing/CMakeLists.txt
+++ b/src/forcing/CMakeLists.txt
@@ -1,8 +1,3 @@
-cmake_minimum_required(VERSION 3.10)
-#set(CMAKE_CXX_STANDARD 14)
-#set(CMAKE_CXX_STANDARD_REQUIRED True)
-#set(CMAKE_CXX_VISIBILITY_PRESET hidden)
-
 include(${PROJECT_SOURCE_DIR}/cmake/dynamic_sourced_library.cmake)
 dynamic_sourced_cxx_library(forcing "${CMAKE_CURRENT_SOURCE_DIR}")
 
diff --git a/src/geojson/CMakeLists.txt b/src/geojson/CMakeLists.txt
index 92315eb7c6..dc2ff4a83b 100644
--- a/src/geojson/CMakeLists.txt
+++ b/src/geojson/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 3.10)
 add_library(geojson STATIC
         JSONGeometry.cpp
         JSONProperty.cpp

From f0d4bae34eb2dfe7466ef6dfd8a38deb24989197 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 14:01:23 -0700
Subject: [PATCH 06/39] cmake: rm min required calls in remaining source dirs

---
 src/geopackage/CMakeLists.txt             | 3 ---
 src/realizations/catchment/CMakeLists.txt | 2 --
 src/routing/CMakeLists.txt                | 2 --
 3 files changed, 7 deletions(-)

diff --git a/src/geopackage/CMakeLists.txt b/src/geopackage/CMakeLists.txt
index 300b7b50db..574c516368 100644
--- a/src/geopackage/CMakeLists.txt
+++ b/src/geopackage/CMakeLists.txt
@@ -1,6 +1,3 @@
-cmake_minimum_required(VERSION 3.10)
-
-
 string(COMPARE EQUAL "${CMAKE_CXX_COMPILER_ID}" "IntelLLVM" _cmp)
 if (NOT _cmp)
     message(WARNING "[NGen::geopackage] wkb.cpp cannot be optimized with "
diff --git a/src/realizations/catchment/CMakeLists.txt b/src/realizations/catchment/CMakeLists.txt
index a3d1c6f7b1..121ce277e0 100644
--- a/src/realizations/catchment/CMakeLists.txt
+++ b/src/realizations/catchment/CMakeLists.txt
@@ -1,5 +1,3 @@
-cmake_minimum_required(VERSION 3.10)
-
 include(${PROJECT_SOURCE_DIR}/cmake/dynamic_sourced_library.cmake)
 dynamic_sourced_cxx_library(realizations_catchment "${CMAKE_CURRENT_SOURCE_DIR}")
 
diff --git a/src/routing/CMakeLists.txt b/src/routing/CMakeLists.txt
index 3b07ba038e..48993d72fe 100644
--- a/src/routing/CMakeLists.txt
+++ b/src/routing/CMakeLists.txt
@@ -1,5 +1,3 @@
-cmake_minimum_required(VERSION 3.10)
-
 include(${PROJECT_SOURCE_DIR}/cmake/dynamic_sourced_library.cmake)
 dynamic_sourced_cxx_library(routing "${CMAKE_CURRENT_SOURCE_DIR}")
 

From 3c4fa1f824501d0e1b5cc9ed2ea7f850161935b5 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 14:02:23 -0700
Subject: [PATCH 07/39] cmake: rm min required call in core_nexus

---
 src/core/nexus/CMakeLists.txt | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/core/nexus/CMakeLists.txt b/src/core/nexus/CMakeLists.txt
index 3102075d20..67b4440b59 100644
--- a/src/core/nexus/CMakeLists.txt
+++ b/src/core/nexus/CMakeLists.txt
@@ -1,5 +1,3 @@
-cmake_minimum_required(VERSION 3.10)
-
 include(${PROJECT_SOURCE_DIR}/cmake/dynamic_sourced_library.cmake)
 dynamic_sourced_cxx_library(core_nexus "${CMAKE_CURRENT_SOURCE_DIR}")
 

From f9b73169518ebe946b41423c59ebd8a01e1f9b50 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 14:12:21 -0700
Subject: [PATCH 08/39] cmake: revert changing udunits2 target name

---
 CMakeLists.txt                   | 8 ++++----
 src/core/mediator/CMakeLists.txt | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b92248f6ae..6926e140de 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -121,9 +121,9 @@ if(NGEN_WITH_UDUNITS)
     add_compile_definitions(NGEN_WITH_UDUNITS)
 
     # Create UDUNITS2 target
-    add_library(udunits2 SHARED IMPORTED)
-    target_include_directories(udunits2 INTERFACE "${UDUNITS2_INCLUDE}")
-    set_target_properties(udunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
+    add_library(libudunits2 SHARED IMPORTED)
+    target_include_directories(libudunits2 INTERFACE "${UDUNITS2_INCLUDE}")
+    set_target_properties(libudunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
 endif()
 
 # -----------------------------------------------------------------------------
@@ -220,7 +220,7 @@ target_link_libraries(ngen
         NGen::forcing
         NGen::core_mediator
         NGen::routing
-        udunits2
+        libudunits2
         NetCDF
 )
 
diff --git a/src/core/mediator/CMakeLists.txt b/src/core/mediator/CMakeLists.txt
index 0cfbbdd211..e871872821 100644
--- a/src/core/mediator/CMakeLists.txt
+++ b/src/core/mediator/CMakeLists.txt
@@ -3,8 +3,8 @@ dynamic_sourced_cxx_library(core_mediator "${CMAKE_CURRENT_SOURCE_DIR}")
 
 add_library(NGen::core_mediator ALIAS core_mediator)
 if(UDUNITS_ACTIVE)
-        add_dependencies(core_mediator udunits2)
-        target_link_libraries(core_mediator PUBLIC udunits2)
+        add_dependencies(core_mediator libudunits2)
+        target_link_libraries(core_mediator PUBLIC libudunits2)
 endif()
 
 find_package(Threads REQUIRED)

From 88dfd056dc42bde82fb0723bdf78b712e8a7afe0 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 14:46:49 -0700
Subject: [PATCH 09/39] cmake: rename (add_test -> ngen_add_test) and refactor

Refactor `ngen_add_test` using `cmake_parse_arguments` so that
the number of source files is not needed, and instead the
function derives the source files from the given multiarg option.

Also replaces all instances of `${NETCDF_LIBRARIES}` with the
NetCDF imported target.
---
 test/CMakeLists.txt | 386 ++++++++++++++++++++++++--------------------
 1 file changed, 209 insertions(+), 177 deletions(-)

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 115d5a86a8..b81317ce68 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -1,285 +1,313 @@
-project(test)
-
-include(CTest)
 add_subdirectory(googletest)
-include_directories(${gtest_SOURCE_DIR}/include ${gtest_SOURCE_DIR})
-include_directories(${gmock_SOURCE_DIR}/include ${gmock_SOURCE_DIR})
-include_directories(${PROJ_ROOT_INCLUDE_DIR})
+add_compile_definitions(NGEN_BMI_CPP_LIB_TESTS_ACTIVE)
 
-if (NGEN_ACTIVATE_PYTHON)
-    include_directories(${PROJECT_SOURCE_DIR}/extern/pybind11/include)
+if (NGEN_WITH_PYTHON)
     add_compile_definitions(NGEN_BMI_PY_TESTS_ACTIVE)
 endif()
 
-if(MPI_ACTIVE)
+if(NGEN_WITH_MPI)
     add_compile_definitions(NGEN_MPI_TESTS_ACTIVE)
 endif()
 
-add_compile_definitions(NGEN_BMI_CPP_LIB_TESTS_ACTIVE)
-
-if(BMI_C_LIB_ACTIVE)
+if(NGEN_WITH_BMI_C)
     add_compile_definitions(NGEN_BMI_C_LIB_TESTS_ACTIVE)
 endif()
 
-if(BMI_FORTRAN_ACTIVE)
+if(NGEN_WITH_BMI_FORTRAN)
     add_compile_definitions(NGEN_BMI_FORTRAN_LIB_TESTS_ACTIVE)
 endif()
 
-if(NGEN_ACTIVATE_ROUTING)
+if(NGEN_WITH_ROUTING)
     add_compile_definitions(ROUTING_PYBIND_TESTS_ACTIVE)
 endif()
 
-if(NETCDF_ACTIVE)
+if(NGEN_WITH_NETCDF)
     add_compile_definitions(NETCDF_ACTIVE)
 endif()
 
-# Add test source files (e.g., test1.cpp)
-#add_executable(test_hymod models/hymod/include/HymodTest.cpp)
-#target_link_libraries(test_hymod gtest gtest_main)
+#[==[
+ngen_add_test(<test name> SOURCES <source>...
+                          LIBRARIES <library>...
+                          [REQUIRES <varname>...])
+
+Adds an executable test (i.e. a target) called <test name>.
 
-function(add_test TESTNAME NUM_FILES)
-    math(EXPR NUM_LINKS "${ARGC} - ${NUM_FILES}")
-    list(SUBLIST ARGN 0 ${NUM_FILES} SOURCE_FILES)
-    list(SUBLIST ARGN ${NUM_FILES} ${NUM_LINKS} LINKED_LIBS)
+`SOURCES`
+    Source files containing the test cases/fixtures.
 
-    # Also link these testing libraries for anything
-    # TODO: verify these do not remove current value at i = 0, but instead push it forward
-    list(INSERT LINKED_LIBS 0 gtest gtest_main)
+`LIBRARIES`
+    Library targets that this test requires linking to.
 
-    # Sanity check for duplicates
-    list(REMOVE_DUPLICATES LINKED_LIBS)
+`REQUIRES`
+    Variable names that this test's creation is dependent on.
+    If a given variable is not defined or is FALSE/OFF/etc. then
+    the corresponding <test name> target is not created.
+#]==]
+function(ngen_add_test TESTNAME)
+    set(multiValueArgs OBJECTS LIBRARIES REQUIRES)
+    cmake_parse_arguments(NGEN_TEST "" "" "${multiValueArgs}" ${ARGN})
 
-    # Create the testing executable target and link the libraries
-    add_executable(${TESTNAME} ${SOURCE_FILES})
-    target_link_libraries(${TESTNAME} ${LINKED_LIBS})
+    list(REMOVE_DUPLICATES NGEN_TEST_LIBRARIES)
 
-    # Perform the final GoogleTest boilerplate steps
-    gtest_discover_tests(${TESTNAME}
+    set(NGEN_TEST_CREATE ON)
+    foreach(requirement_var IN LISTS NGEN_TEST_REQUIRES)
+        if(NOT ${requirement_var})
+            set(NGEN_TEST_CREATE OFF)
+            break()
+        endif()
+    endforeach()
+
+    if(NGEN_TEST_CREATE)
+        add_executable(${TESTNAME} ${NGEN_TEST_OBJECTS})
+        target_link_libraries(${TESTNAME} gtest gtest_main ${NGEN_TEST_LIBRARIES})
+        set_target_properties(${TESTNAME} PROPERTIES FOLDER test)
+        gtest_discover_tests(
+            ${TESTNAME}
             WORKING_DIRECTORY ${PROJECT_DIR}
-            PROPERTIES VS_DEBUGGER_WORKING_DIRECTORY "${PROJECT_DIR}"
-            )
-    set_target_properties(${TESTNAME} PROPERTIES FOLDER test)
+            PROPERTIES
+                VS_DEBUGGER_WORKING_DIRECTORY "${PROJECT_DIR}"
+        )
+    endif()
 endfunction()
 
 ########################## Individual tests ##########################
 
 ########################## GeoJSON Unit Tests
-add_test(test_geojson
-        4
+ngen_add_test(
+    test_geojson
+    OBJECTS
         geojson/JSONProperty_Test.cpp
         geojson/JSONGeometry_Test.cpp
         geojson/Feature_Test.cpp
         geojson/FeatureCollection_Test.cpp
+    LIBRARIES
         NGen::geojson
-        )
+)
 
 ########################## GeoPackage Unit Tests
-if(NGEN_WITH_SQLITE3)
-add_test(test_geopackage
-        3
+ngen_add_test(
+    test_geopackage
+    OBJECTS
         geopackage/WKB_Test.cpp
         geopackage/SQLite_Test.cpp
         geopackage/GeoPackage_Test.cpp
-        NGen::geopackage)
-endif()
+    LIBRARIES
+        NGen::geopackage
+    REQUIRES
+        NGEN_WITH_SQLITE
+)
 
 ########################## Realization Config Unit Tests
-add_test(test_realization_config
-        1
+ngen_add_test(
+    test_realization_config
+    OBJECTS
         realizations/Formulation_Manager_Test.cpp
+    LIBRARIES
         NGen::core
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
         libudunits2
         testbmicppmodel
-        ${NETCDF_LIBRARIES}
+        NetCDF
 )
 
 ########################## Series Unit Tests
-add_test(test_mdarray
-         4
-         utils/mdarray_Test.cpp
-         utils/mdframe_Test.cpp
-         utils/mdframe_netcdf_Test.cpp
-         utils/mdframe_csv_Test.cpp
-         NGen::mdarray
-         NGen::mdframe
-         ${NETCDF_LIBRARIES})
+ngen_add_test(
+    test_mdarray
+    OBJECTS
+        utils/mdarray_Test.cpp
+        utils/mdframe_Test.cpp
+        utils/mdframe_netcdf_Test.cpp
+        utils/mdframe_csv_Test.cpp
+    LIBRARIES
+        NGen::mdarray
+        NGen::mdframe
+        NetCDF
+)
 
 ########################## Nexus Tests
-add_test(
-        test_nexus
-        1
+ngen_add_test(
+    test_nexus
+    OBJECTS
         core/nexus/NexusTests.cpp
+    LIBRARIES
         NGen::core_nexus
 )
 
 ########################## MPI Remote Nexus Tests
-if(MPI_ACTIVE)
-   add_test(
-           test_remote_nexus
-           1
-           core/nexus/NexusRemoteTests.cpp
-           NGen::core_nexus
-   )
-endif()
+ngen_add_test(
+    test_remote_nexus
+    OBJECTS
+        core/nexus/NexusRemoteTests.cpp
+    LIBRARIES
+        NGen::core_nexus
+    REQUIRES
+        NGEN_WITH_MPI
+)
 
 ########################## Partitioning Tests
-#if(MPI_ACTIVE)
-   #TODO this test depends on a "reference hydrofabric" that is rather large
-   #and the path to that reference is absolute in the test code.  Need to rethink this.
-   add_test(
-           test_partition
-           1
-           utils/Partition_Test.cpp
-           NGen::core
-           NGen::geojson
+ngen_add_test(
+    test_partition
+    OBJECTS
+        utils/Partition_Test.cpp
+    LIBRARIES
+        NGen::core
+        NGen::geojson
+    # REQUIRES
+    #   NGEN_WITH_MPI
 )
-#endif()
 
 ########################## BMI C++ Tests
-add_test(
-        test_bmi_cpp
-        2
+ngen_add_test(
+    test_bmi_cpp
+    OBJECTS
         realizations/catchments/Bmi_Cpp_Adapter_Test.cpp
         realizations/catchments/Bmi_Cpp_Formulation_Test.cpp
+    LIBRARIES
         NGen::core
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
         libudunits2
-        ${NETCDF_LIBRARIES}
+        NetCDF
 )
 
 ########################## BMI C Tests
-if(BMI_C_LIB_ACTIVE)
-    add_test(
-            test_bmi_c
-            2
-            realizations/catchments/Bmi_C_Adapter_Test.cpp
-            realizations/catchments/Bmi_C_Formulation_Test.cpp
-            NGen::core
-            NGen::realizations_catchment
-            NGen::core_mediator
-            NGen::forcing
-            libudunits2
-            ${NETCDF_LIBRARIES}
-    )
-endif()
+ngen_add_test(
+    test_bmi_c
+    OBJECTS
+        realizations/catchments/Bmi_C_Adapter_Test.cpp
+        realizations/catchments/Bmi_C_Formulation_Test.cpp
+    LIBRARIES
+        NGen::core
+        NGen::realizations_catchment
+        NGen::core_mediator
+        NGen::forcing
+        libudunits2
+        NetCDF
+    REQUIRES
+        NGEN_WITH_BMI_C
+)
 
 ########################## BMI Fortran Tests
-if (${BMI_FORTRAN_ACTIVE})
-    add_test(
-            test_bmi_fortran
-            2
-            realizations/catchments/Bmi_Fortran_Adapter_Test.cpp
-            realizations/catchments/Bmi_Fortran_Formulation_Test.cpp
-            NGen::core
-            NGen::realizations_catchment
-            NGen::core_mediator
-            NGen::forcing
-            libudunits2
-            ${NETCDF_LIBRARIES}
-    )
-endif()
+ngen_add_test(
+    test_bmi_fortran
+    OBJECTS
+        realizations/catchments/Bmi_Fortran_Adapter_Test.cpp
+        realizations/catchments/Bmi_Fortran_Formulation_Test.cpp
+    LIBRARIES
+        NGen::core
+        NGen::realizations_catchment
+        NGen::core_mediator
+        NGen::forcing
+        libudunits2
+        NetCDF
+    REQUIRES
+        NGEN_WITH_BMI_FORTRAN
+)
 
 ########################## BMI Python Tests
-if (${NGEN_ACTIVATE_PYTHON})
-    add_test(
-            test_bmi_python
-            2
-            realizations/catchments/Bmi_Py_Adapter_Test.cpp
-            realizations/catchments/Bmi_Py_Formulation_Test.cpp
-            NGen::core
-            NGen::realizations_catchment
-            NGen::core_mediator
-            NGen::forcing
-            libudunits2
-            ${NETCDF_LIBRARIES}
-    )
-endif()
+ngen_add_test(
+    test_bmi_python
+    OBJECTS
+        realizations/catchments/Bmi_Py_Adapter_Test.cpp
+        realizations/catchments/Bmi_Py_Formulation_Test.cpp
+    LIBRARIES
+        NGen::core
+        NGen::realizations_catchment
+        NGen::core_mediator
+        NGen::forcing
+        libudunits2
+        NetCDF
+    REQUIRES
+        NGEN_WITH_PYTHON
+)
 
 ########################## BMI Multi Tests
 add_test(
-        test_bmi_multi
-        2
+    test_bmi_multi
+    OBJECTS
         realizations/catchments/Bmi_Multi_Formulation_Test.cpp
         realizations/catchments/Bmi_Cpp_Multi_Array_Test.cpp
+    LIBRARIES
         NGen::core
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
         libudunits2
-        ${NETCDF_LIBRARIES}
+        NetCDF
 )
 
 ########################## All BMI Unit Tests
-if(BMI_C_LIB_ACTIVE)
-    if (${BMI_FORTRAN_ACTIVE})
-        if (${NGEN_ACTIVATE_PYTHON})
-            add_test(
-                    test_bmi_unit_all
-                    7
-                    realizations/catchments/Bmi_C_Adapter_Test.cpp
-                    realizations/catchments/Bmi_C_Formulation_Test.cpp
-                    realizations/catchments/Bmi_Fortran_Adapter_Test.cpp
-                    realizations/catchments/Bmi_Fortran_Formulation_Test.cpp
-                    realizations/catchments/Bmi_Py_Adapter_Test.cpp
-                    realizations/catchments/Bmi_Py_Formulation_Test.cpp
-                    realizations/catchments/Bmi_Multi_Formulation_Test.cpp
-                    NGen::core
-                    NGen::realizations_catchment
-                    NGen::core_mediator
-                    NGen::forcing
-                    libudunits2
-                    ${NETCDF_LIBRARIES}
-            )
-        endif()
-    endif()
-endif()
+ngen_add_test(
+    test_bmi_unit_all
+    OBJECTS
+        realizations/catchments/Bmi_C_Adapter_Test.cpp
+        realizations/catchments/Bmi_C_Formulation_Test.cpp
+        realizations/catchments/Bmi_Fortran_Adapter_Test.cpp
+        realizations/catchments/Bmi_Fortran_Formulation_Test.cpp
+        realizations/catchments/Bmi_Py_Adapter_Test.cpp
+        realizations/catchments/Bmi_Py_Formulation_Test.cpp
+        realizations/catchments/Bmi_Multi_Formulation_Test.cpp
+    LIBRARIES
+        NGen::core
+        NGen::realizations_catchment
+        NGen::core_mediator
+        NGen::forcing
+        libudunits2
+        NetCDF
+    REQUIRES
+        NGEN_WITH_BMI_C
+        NGEN_WITH_BMI_FORTRAN
+        NGEN_WITH_PYTHON
+)
 
 ########################## Comparison tests for the BMI PET implementation
 # TODO: this probably needs to be added to integration testing also
-add_test(
-        compare_pet
-        1
+ngen_add_test(
+    compare_pet
+    OBJECTS
         realizations/catchments/Bmi_C_Pet_IT.cpp
+    LIBRARIES
         NGen::core
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
         libudunits2
-        ${NETCDF_LIBRARIES}
+        NetCDF
 )
 
 ########################## Routing Tests
-if(NGEN_ACTIVATE_ROUTING)
-    add_test(
-            test_routing_pybind
-            1
-            routing/Routing_Py_Bind_Test.cpp
-            NGen::core # for filechecker utility
-            NGen::routing
-            pybind11::embed
-    )
-endif()
+ngen_add_test(
+    test_routing_pybind
+    OBJECTS
+        routing/Routing_Py_Bind_Test.cpp
+    LIBRARIES
+        NGen::core # for filechecker utility
+        NGen::routing
+        pybind11::embed
+    REQUIRES
+        NGEN_WITH_ROUTING
+)
 
 ########################## Network Class Tests
-add_test(
-        test_network
-        1
+ngen_add_test(
+    test_network
+    OBJECTS
         core/NetworkTests.cpp
+    LIBRARIES
         NGen::core
         NGen::geojson
 )
 
 ########################### Netcdf Forcing Tests
 #if(NETCDF_ACTIVE)
-add_test(
-        test_netcdf_forcing
-        1
+ngen_add_test(
+    test_netcdf_forcing
+    OBJECTS
         forcing/NetCDFPerFeatureDataProvider_Test.cpp
+    LIBRARIES
         NGen::core
         NGen::core_nexus
         NGen::core_mediator
@@ -287,14 +315,16 @@ add_test(
         NGen::geojson
         NGen::realizations_catchment
         libudunits2
-        ${NETCDF_LIBRARIES}
+        NetCDF
+    REQUIRES
+        NGEN_WITH_NETCDF
 )
 #endif()
 
 ########################## Primary Combined Unit Test Target
-add_test(
-        test_unit
-        17
+ngen_add_test(
+    test_unit
+    OBJECTS
         geojson/JSONProperty_Test.cpp
         geojson/JSONGeometry_Test.cpp
         geojson/Feature_Test.cpp
@@ -312,6 +342,7 @@ add_test(
         utils/mdframe_Test.cpp
         utils/mdframe_netcdf_Test.cpp
         utils/mdframe_csv_Test.cpp
+    LIBRARIES
         NGen::core
         NGen::core_nexus
         NGen::core_mediator
@@ -322,13 +353,13 @@ add_test(
         NGen::mdframe
         libudunits2
         testbmicppmodel
-        ${NETCDF_LIBRARIES}
+        NetCDF
 )
 
 # All automated tests
-add_test(
-        test_all
-        16
+ngen_add_test(
+    test_all
+    OBJECTS
         geojson/JSONProperty_Test.cpp
         geojson/JSONGeometry_Test.cpp
         geojson/Feature_Test.cpp
@@ -345,6 +376,7 @@ add_test(
         utils/mdframe_Test.cpp
         utils/mdframe_netcdf_Test.cpp
         utils/mdframe_csv_Test.cpp
+    LIBRARIES
         NGen::core
         gmock
         NGen::core_nexus
@@ -356,5 +388,5 @@ add_test(
         NGen::mdframe
         libudunits2
         testbmicppmodel
-        ${NETCDF_LIBRARIES}
+        NetCDF
 )

From 40f9bd4ab1c44ec7ca4e019e44f7769f9cb53179 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 16:30:19 -0700
Subject: [PATCH 10/39] cmake: add deprecated options for compat [no ci]

---
 CMakeLists.txt                |  2 ++
 cmake/DeprecatedOptions.cmake | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+)
 create mode 100644 cmake/DeprecatedOptions.cmake

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6926e140de..d7c4753721 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -50,6 +50,8 @@ option(NGEN_WITH_TESTS       "Build with unit tests"              ON)
 cmake_dependent_option(NGEN_WITH_ROUTING "Build with t-route integration" OFF "NGEN_WITH_PYTHON" OFF)
 cmake_dependent_option(NGEN_ISO_C_FORTRAN_BMI_LIB_PATH "Path to iso_c_fortran_bmi library" "" "NGEN_WITH_BMI_FORTRAN" "")
 cmake_dependent_option(NGEN_UPDATE_GIT_SUBMODULES "Update submodules on configure" ON "GIT_FOUND;NGEN_HAS_GIT_DIR" OFF)
+
+include(DeprecatedOptions)
 # Project =====================================================================
 
 # Define project version and use via generated config header
diff --git a/cmake/DeprecatedOptions.cmake b/cmake/DeprecatedOptions.cmake
new file mode 100644
index 0000000000..3cfb1b7b4d
--- /dev/null
+++ b/cmake/DeprecatedOptions.cmake
@@ -0,0 +1,19 @@
+macro(deprecated_option)
+    set(options INCLUDE_ENV)
+    set(oneValueArgs NEW OLD)
+    cmake_parse_arguments(DEPRECATED_OPTION "${options}" "${oneValueArgs}" "" ${ARGN})
+
+    if(DEFINED ${DEPRECATED_OPTION_OLD})
+        message(DEPRECATION "Deprecated option ${DEPRECATED_OPTION_OLD} defined; setting ${DEPRECATED_OPTION_NEW} to ${DEPRECATED_OPTION_OLD} (aka ${${DEPRECATED_OPTION_OLD}})")
+        set(${DEPRECATED_OPTION_NEW} ${${DEPRECATED_OPTION_OLD}})
+    endif()
+
+    if(DEPRECATED_OPTION_INCLUDE_ENV)
+        if(DEFINED ENV{${DEPRECATED_OPTION_OLD}})
+            message(DEPRECATION "Deprecated environment variable ${DEPRECATED_OPTION_OLD} defined; setting ${DEPRECATED_OPTION_NEW} to ENV{${DEPRECATED_OPTION_OLD}} (aka $ENV{${DEPRECATED_OPTION_OLD}})")
+            set(${DEPRECATED_OPTION_NEW} $ENV{${DEPRECATED_OPTION_OLD}})
+        endif()
+    endif()
+endmacro()
+
+deprecated_option(OLD MPI_ACTIVE NEW NGEN_WITH_MPI INCLUDE_ENV)

From 19a1cf32798c55f92623b4248599d6d3c50e6ccd Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Wed, 6 Sep 2023 16:40:16 -0700
Subject: [PATCH 11/39] cmake: fix incorrect docstring for ngen_add_test [no
 ci]

---
 test/CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index b81317ce68..12c8acd995 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -26,13 +26,13 @@ if(NGEN_WITH_NETCDF)
 endif()
 
 #[==[
-ngen_add_test(<test name> SOURCES <source>...
+ngen_add_test(<test name> OBJECTS <source>...
                           LIBRARIES <library>...
                           [REQUIRES <varname>...])
 
 Adds an executable test (i.e. a target) called <test name>.
 
-`SOURCES`
+`OBJECTS`
     Source files containing the test cases/fixtures.
 
 `LIBRARIES`

From 489dec73b6049989e0c2597ae2f524e5fdad577c Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 07:14:50 -0700
Subject: [PATCH 12/39] cmake: add deprecated options

---
 CMakeLists.txt                | 10 ++++++++++
 cmake/DeprecatedOptions.cmake | 13 +++++++++++--
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d7c4753721..e90955d812 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -44,6 +44,7 @@ option(NGEN_WITH_BMI_FORTRAN "Build with Fortran BMI support"     ON)
 option(NGEN_WITH_BMI_C       "Build with C BMI support"           ON)
 option(NGEN_WITH_PYTHON      "Build with embedded Python support" ON)
 option(NGEN_WITH_TESTS       "Build with unit tests"              ON)
+option(NGEN_QUIET            "Silence output"                     OFF)
 
 # These options require dependency on some of the above options
 # Syntax: cmake_dependent_option(<option> "<help_text>" <value> <depends> <force>)
@@ -52,6 +53,15 @@ cmake_dependent_option(NGEN_ISO_C_FORTRAN_BMI_LIB_PATH "Path to iso_c_fortran_bm
 cmake_dependent_option(NGEN_UPDATE_GIT_SUBMODULES "Update submodules on configure" ON "GIT_FOUND;NGEN_HAS_GIT_DIR" OFF)
 
 include(DeprecatedOptions)
+deprecated_option(OLD MPI_ACTIVE            NEW NGEN_WITH_MPI     INCLUDE_ENV)
+deprecated_option(OLD UDUNITS_ACTIVE        NEW NGEN_WITH_UDUNITS INCLUDE_ENV)
+deprecated_option(OLD NGEN_ACTIVATE_PYTHON  NEW NGEN_WITH_PYTHON  INCLUDE_ENV)
+deprecated_option(OLD NGEN_ACTIVATE_ROUTING NEW NGEN_WITH_ROUTING)
+deprecated_option(OLD NETCDF_ACTIVE         NEW NGEN_WITH_NETCDF)
+deprecated_option(OLD BMI_C_LIB_ACTIVE      NEW NGEN_WITH_BMI_C)
+deprecated_option(OLD BMI_FORTRAN_ACTIVE    NEW NGEN_WITH_BMI_FORTRAN)
+deprecated_option(OLD QUIET                 NEW NGEN_QUIET)
+deprecated_option(OLD PACKAGE_TESTS         NEW NGEN_WITH_TESTS)
 # Project =====================================================================
 
 # Define project version and use via generated config header
diff --git a/cmake/DeprecatedOptions.cmake b/cmake/DeprecatedOptions.cmake
index 3cfb1b7b4d..4cd27eeee5 100644
--- a/cmake/DeprecatedOptions.cmake
+++ b/cmake/DeprecatedOptions.cmake
@@ -1,3 +1,14 @@
+#[==[
+deprecated_option(NEW <variable> OLD <variable> [INCLUDE_ENV])
+
+Adds a CMake option that will output a deprecation message on use.
+
+The `NEW` variable is the option that should be used when building.
+
+The `OLD` variable is the deprecated option that corresponds to a new option.
+
+The `INCLUDE_ENV` flag also checks the environment variables for a variable named `OLD`, i.e. ENV{<OLD variable>}.
+#]==]
 macro(deprecated_option)
     set(options INCLUDE_ENV)
     set(oneValueArgs NEW OLD)
@@ -15,5 +26,3 @@ macro(deprecated_option)
         endif()
     endif()
 endmacro()
-
-deprecated_option(OLD MPI_ACTIVE NEW NGEN_WITH_MPI INCLUDE_ENV)

From 1a1bef38182a4abbed6964d294fe9a960e6aa9b9 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 07:21:28 -0700
Subject: [PATCH 13/39] cmake: default NGEN_WITH_ROUTING to ON

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e90955d812..d7cd3a2382 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -48,7 +48,7 @@ option(NGEN_QUIET            "Silence output"                     OFF)
 
 # These options require dependency on some of the above options
 # Syntax: cmake_dependent_option(<option> "<help_text>" <value> <depends> <force>)
-cmake_dependent_option(NGEN_WITH_ROUTING "Build with t-route integration" OFF "NGEN_WITH_PYTHON" OFF)
+cmake_dependent_option(NGEN_WITH_ROUTING "Build with t-route integration" ON "NGEN_WITH_PYTHON" OFF)
 cmake_dependent_option(NGEN_ISO_C_FORTRAN_BMI_LIB_PATH "Path to iso_c_fortran_bmi library" "" "NGEN_WITH_BMI_FORTRAN" "")
 cmake_dependent_option(NGEN_UPDATE_GIT_SUBMODULES "Update submodules on configure" ON "GIT_FOUND;NGEN_HAS_GIT_DIR" OFF)
 

From 7e9d2ed6308a015dcdd9f2bf7cf02291b365f402 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 08:37:28 -0700
Subject: [PATCH 14/39] cmake: see extended commit

- Add dependent options for `BMI_FORTRAN_ISO_C_LIB_{DIR/NAME}`
- Add target `bmi_fortran_compat` for ISO C compatibility with BMI Fortran
- Modify target linking semantics. NGen targets should link to dependencies
  as needed, and other targets should not duplicate dependencies.

  > e.g. test targets now link only to NGen components or GTest targets
  >      instead of to direct dependencies, since the components publicize
  >      their dependency links.

- Ensure new option names are being used in various CMakeLists
---
 CMakeLists.txt                            | 25 +++++++++++++++++-----
 src/core/CMakeLists.txt                   |  2 +-
 src/core/hydrolocation/CMakeLists.txt     |  4 ----
 src/core/mediator/CMakeLists.txt          |  2 +-
 src/core/nexus/CMakeLists.txt             |  4 ----
 src/forcing/CMakeLists.txt                |  6 +++++-
 src/realizations/catchment/CMakeLists.txt | 12 +++--------
 src/utilities/mdframe/CMakeLists.txt      |  6 +++++-
 test/CMakeLists.txt                       | 26 +++--------------------
 9 files changed, 38 insertions(+), 49 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d7cd3a2382..425ddc69b3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -49,8 +49,20 @@ option(NGEN_QUIET            "Silence output"                     OFF)
 # These options require dependency on some of the above options
 # Syntax: cmake_dependent_option(<option> "<help_text>" <value> <depends> <force>)
 cmake_dependent_option(NGEN_WITH_ROUTING "Build with t-route integration" ON "NGEN_WITH_PYTHON" OFF)
-cmake_dependent_option(NGEN_ISO_C_FORTRAN_BMI_LIB_PATH "Path to iso_c_fortran_bmi library" "" "NGEN_WITH_BMI_FORTRAN" "")
 cmake_dependent_option(NGEN_UPDATE_GIT_SUBMODULES "Update submodules on configure" ON "GIT_FOUND;NGEN_HAS_GIT_DIR" OFF)
+cmake_dependent_option(BMI_FORTRAN_ISO_C_LIB_DIR
+    "Directory hint for middleware Fortran shared lib handling iso_c_binding"
+    "${PROJECT_SOURCE_DIR}/extern/iso_c_fortran_bmi/cmake_build"
+    "NGEN_WITH_BMI_FORTRAN"
+    ""
+)
+
+cmake_dependent_option(BMI_FORTRAN_ISO_C_LIB_NAME
+    "Name for middleware Fortran shared lib handling iso_c_binding"
+    "iso_c_bmi"
+    "NGEN_WITH_BMI_FORTRAN"
+    ""
+)
 
 include(DeprecatedOptions)
 deprecated_option(OLD MPI_ACTIVE            NEW NGEN_WITH_MPI     INCLUDE_ENV)
@@ -67,6 +79,8 @@ deprecated_option(OLD PACKAGE_TESTS         NEW NGEN_WITH_TESTS)
 # Define project version and use via generated config header
 project(ngen VERSION 0.1.0)
 
+add_executable(ngen "${NGEN_SRC_DIR}/NGen.cpp")
+
 # Dependencies ================================================================
 
 # -----------------------------------------------------------------------------
@@ -139,7 +153,7 @@ if(NGEN_WITH_UDUNITS)
 endif()
 
 # -----------------------------------------------------------------------------
-if(NETCDF_ACTIVE)
+if(NGEN_WITH_NETCDF)
     set(NETCDF_CXX "YES")
     set(NETCDF_F77 "NO")
     set(NETCDF_F90 "NO")
@@ -166,6 +180,10 @@ endif()
 # Configure whether Fortran BMI functionality is active
 if(NGEN_WITH_BMI_FORTRAN)
     add_compile_definitions(NGEN_BMI_FORTRAN_ACTIVE)
+    find_library(BMI_FORTRAN_ISO_C_LIB_PATH "${BMI_FORTRAN_ISO_C_LIB_NAME}" PATHS "${BMI_FORTRAN_ISO_C_LIB_DIR}" REQUIRED)
+    message("BMI Fortran: ${BMI_FORTRAN_ISO_C_LIB_PATH}")
+    add_library(bmi_fortran_compat SHARED IMPORTED)
+    set_target_properties(bmi_fortran_compat PROPERTIES IMPORTED_LOCATION "${BMI_FORTRAN_ISO_C_LIB_PATH}")
 endif()
 
 # -----------------------------------------------------------------------------
@@ -208,7 +226,6 @@ add_subdirectory(${TEST_BMI_CPP_DIR} ${TEST_BMI_CPP_DIR}/cmake_build) # FIXME: W
 # Project Targets
 # -----------------------------------------------------------------------------
 configure_file(include/NGenConfig.h.in include/NGenConfig.h)
-add_executable(ngen "${NGEN_SRC_DIR}/NGen.cpp")
 add_dependencies(ngen testbmicppmodel)
 target_include_directories(ngen PUBLIC "${NGEN_INC_DIR}")
 
@@ -232,8 +249,6 @@ target_link_libraries(ngen
         NGen::forcing
         NGen::core_mediator
         NGen::routing
-        libudunits2
-        NetCDF
 )
 
 add_executable(partitionGenerator src/partitionGenerator.cpp)
diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
index fc067dffe5..101ff43d8a 100644
--- a/src/core/CMakeLists.txt
+++ b/src/core/CMakeLists.txt
@@ -18,7 +18,7 @@ target_include_directories(core PUBLIC
         ${PROJECT_SOURCE_DIR}/extern/pybind11/include
         )
 
-if (${NGEN_ACTIVATE_PYTHON})
+if (NGEN_WITH_PYTHON)
     target_include_directories(core PUBLIC
             ${PROJECT_SOURCE_DIR}/include
             ${PROJECT_SOURCE_DIR}/include/simulation_time
diff --git a/src/core/hydrolocation/CMakeLists.txt b/src/core/hydrolocation/CMakeLists.txt
index 057e6049b2..c6446c8810 100644
--- a/src/core/hydrolocation/CMakeLists.txt
+++ b/src/core/hydrolocation/CMakeLists.txt
@@ -14,7 +14,3 @@ target_include_directories(core_hydrolocation PUBLIC
 target_link_libraries(core_hydrolocation PUBLIC
         Boost::boost                # Headers-only Boost
         )
-
-if(MPI_ACTIVE)
-    add_compile_definitions(NGEN_MPI_ACTIVE)
-endif()
diff --git a/src/core/mediator/CMakeLists.txt b/src/core/mediator/CMakeLists.txt
index e871872821..b1c336cd67 100644
--- a/src/core/mediator/CMakeLists.txt
+++ b/src/core/mediator/CMakeLists.txt
@@ -2,7 +2,7 @@ include(${PROJECT_SOURCE_DIR}/cmake/dynamic_sourced_library.cmake)
 dynamic_sourced_cxx_library(core_mediator "${CMAKE_CURRENT_SOURCE_DIR}")
 
 add_library(NGen::core_mediator ALIAS core_mediator)
-if(UDUNITS_ACTIVE)
+if(NGEN_WITH_UDUNITS)
         add_dependencies(core_mediator libudunits2)
         target_link_libraries(core_mediator PUBLIC libudunits2)
 endif()
diff --git a/src/core/nexus/CMakeLists.txt b/src/core/nexus/CMakeLists.txt
index 67b4440b59..078a2b55d7 100644
--- a/src/core/nexus/CMakeLists.txt
+++ b/src/core/nexus/CMakeLists.txt
@@ -15,7 +15,3 @@ target_include_directories(core_nexus PUBLIC
 target_link_libraries(core_nexus PUBLIC
         Boost::boost                # Headers-only Boost
         )
-
-if(MPI_ACTIVE)
-    add_compile_definitions(NGEN_MPI_ACTIVE)
-endif()
diff --git a/src/forcing/CMakeLists.txt b/src/forcing/CMakeLists.txt
index 13ab0f4a8f..0390ac3389 100644
--- a/src/forcing/CMakeLists.txt
+++ b/src/forcing/CMakeLists.txt
@@ -16,6 +16,10 @@ target_include_directories(forcing PUBLIC
 target_link_libraries(forcing PUBLIC
         Boost::boost                # Headers-only Boost
         Threads::Threads
-        )
+)
+
+if(NGEN_WITH_NETCDF)
+    target_link_libraries(forcing PUBLIC NetCDF)
+endif()
 
 #target_compile_options(forcing PUBLIC -std=c++14 -Wall)
diff --git a/src/realizations/catchment/CMakeLists.txt b/src/realizations/catchment/CMakeLists.txt
index 121ce277e0..c4d340ca5c 100644
--- a/src/realizations/catchment/CMakeLists.txt
+++ b/src/realizations/catchment/CMakeLists.txt
@@ -19,16 +19,10 @@ target_link_libraries(realizations_catchment PUBLIC
         NGen::geojson
         )
 
-if(NGEN_ACTIVATE_PYTHON)
+if(NGEN_WITH_PYTHON)
    target_link_libraries(realizations_catchment PUBLIC pybind11::embed)
 endif()
 
-##### Logic for Fortran integration
-# Go ahead and set these two cache variables, regardless of whether active currently
-SET(BMI_FORTRAN_ISO_C_LIB_DIR "${PROJECT_SOURCE_DIR}/extern/iso_c_fortran_bmi/cmake_build" CACHE STRING "Directory hint for middleware Fortran shared lib handling iso_c_binding")
-SET(BMI_FORTRAN_ISO_C_LIB_NAME "iso_c_bmi" CACHE STRING "Name for middleware Fortran shared lib handling iso_c_binding")
-# If Fortran is active, include linking to middleware shared library
-if (${BMI_FORTRAN_ACTIVE})
-   find_library(BMI_FORTRAN_ISO_C_LIB_PATH "${BMI_FORTRAN_ISO_C_LIB_NAME}" PATHS "${BMI_FORTRAN_ISO_C_LIB_DIR}")
-   target_link_libraries(realizations_catchment PRIVATE "${BMI_FORTRAN_ISO_C_LIB_PATH}")
+if(NGEN_WITH_BMI_FORTRAN)
+    target_link_libraries(realizations_catchment PUBLIC bmi_fortran_compat)
 endif()
diff --git a/src/utilities/mdframe/CMakeLists.txt b/src/utilities/mdframe/CMakeLists.txt
index a4bd75e49d..1188f90b43 100644
--- a/src/utilities/mdframe/CMakeLists.txt
+++ b/src/utilities/mdframe/CMakeLists.txt
@@ -1,4 +1,8 @@
 add_library(mdframe handler_csv.cpp handler_netcdf.cpp)
 add_library(NGen::mdframe ALIAS mdframe)
 target_include_directories(mdframe PUBLIC ${PROJECT_SOURCE_DIR}/include/utilities)
-target_link_libraries(mdframe PRIVATE NGen::mdarray Boost::boost)
+target_link_libraries(mdframe PUBLIC NGen::mdarray Boost::boost)
+
+if(NGEN_WITH_NETCDF)
+    target_link_libraries(mdframe PUBLIC NetCDF)
+endif()
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 12c8acd995..e01d2766ca 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -107,9 +107,8 @@ ngen_add_test(
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
-        libudunits2
         testbmicppmodel
-        NetCDF
+        
 )
 
 ########################## Series Unit Tests
@@ -123,7 +122,7 @@ ngen_add_test(
     LIBRARIES
         NGen::mdarray
         NGen::mdframe
-        NetCDF
+        
 )
 
 ########################## Nexus Tests
@@ -169,8 +168,6 @@ ngen_add_test(
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
-        libudunits2
-        NetCDF
 )
 
 ########################## BMI C Tests
@@ -184,8 +181,6 @@ ngen_add_test(
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
-        libudunits2
-        NetCDF
     REQUIRES
         NGEN_WITH_BMI_C
 )
@@ -201,8 +196,6 @@ ngen_add_test(
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
-        libudunits2
-        NetCDF
     REQUIRES
         NGEN_WITH_BMI_FORTRAN
 )
@@ -218,8 +211,6 @@ ngen_add_test(
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
-        libudunits2
-        NetCDF
     REQUIRES
         NGEN_WITH_PYTHON
 )
@@ -235,8 +226,6 @@ add_test(
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
-        libudunits2
-        NetCDF
 )
 
 ########################## All BMI Unit Tests
@@ -255,8 +244,6 @@ ngen_add_test(
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
-        libudunits2
-        NetCDF
     REQUIRES
         NGEN_WITH_BMI_C
         NGEN_WITH_BMI_FORTRAN
@@ -274,8 +261,6 @@ ngen_add_test(
         NGen::realizations_catchment
         NGen::core_mediator
         NGen::forcing
-        libudunits2
-        NetCDF
 )
 
 ########################## Routing Tests
@@ -314,8 +299,6 @@ ngen_add_test(
         NGen::forcing
         NGen::geojson
         NGen::realizations_catchment
-        libudunits2
-        NetCDF
     REQUIRES
         NGEN_WITH_NETCDF
 )
@@ -351,9 +334,8 @@ ngen_add_test(
         NGen::realizations_catchment
         NGen::mdarray
         NGen::mdframe
-        libudunits2
         testbmicppmodel
-        NetCDF
+        
 )
 
 # All automated tests
@@ -386,7 +368,5 @@ ngen_add_test(
         NGen::realizations_catchment
         NGen::mdarray
         NGen::mdframe
-        libudunits2
         testbmicppmodel
-        NetCDF
 )

From 514e40f105b404ca109be4fe3b67200a75f69d2b Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 08:46:28 -0700
Subject: [PATCH 15/39] cmake: conditionalize NGen::routing again

---
 CMakeLists.txt | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 425ddc69b3..a826c699ea 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -236,7 +236,6 @@ add_subdirectory("src/realizations/catchment")
 add_subdirectory("src/forcing")
 add_subdirectory("src/utilities/mdarray")
 add_subdirectory("src/utilities/mdframe")
-add_subdirectory("src/routing")
 
 target_link_libraries(ngen
     PUBLIC
@@ -248,9 +247,13 @@ target_link_libraries(ngen
         NGen::realizations_catchment
         NGen::forcing
         NGen::core_mediator
-        NGen::routing
 )
 
+if(NGEN_WITH_ROUTING)
+    add_subdirectory("src/routing")
+    target_link_libraries(ngen PUBLIC NGen::routing)
+endif()
+
 add_executable(partitionGenerator src/partitionGenerator.cpp)
 target_include_directories(partitionGenerator PUBLIC "${PROJECT_BINARY_DIR}/include")
 target_link_libraries(partitionGenerator PUBLIC NGen::core NGen::geojson)

From 128951632405498ac6129f08e55023518b27fc9d Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 09:14:52 -0700
Subject: [PATCH 16/39] cmake: default MPI builds; better searching for BMI
 iso_c handling

---
 CMakeLists.txt | 46 ++++++++++++++++++++++++++++++----------------
 1 file changed, 30 insertions(+), 16 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index a826c699ea..ecb0a1a99c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -36,7 +36,7 @@ include(GitUpdateSubmodules)
 # Options =====================================================================
 include(CMakeDependentOption)
 
-option(NGEN_WITH_MPI         "Build with MPI support"             OFF)
+option(NGEN_WITH_MPI         "Build with MPI support"             ON)
 option(NGEN_WITH_NETCDF      "Build with NetCDF support"          ON)
 option(NGEN_WITH_SQLITE      "Build with SQLite3 support"         ON)
 option(NGEN_WITH_UDUNITS     "Build with UDUNITS2 support"        ON)
@@ -50,19 +50,9 @@ option(NGEN_QUIET            "Silence output"                     OFF)
 # Syntax: cmake_dependent_option(<option> "<help_text>" <value> <depends> <force>)
 cmake_dependent_option(NGEN_WITH_ROUTING "Build with t-route integration" ON "NGEN_WITH_PYTHON" OFF)
 cmake_dependent_option(NGEN_UPDATE_GIT_SUBMODULES "Update submodules on configure" ON "GIT_FOUND;NGEN_HAS_GIT_DIR" OFF)
-cmake_dependent_option(BMI_FORTRAN_ISO_C_LIB_DIR
-    "Directory hint for middleware Fortran shared lib handling iso_c_binding"
-    "${PROJECT_SOURCE_DIR}/extern/iso_c_fortran_bmi/cmake_build"
-    "NGEN_WITH_BMI_FORTRAN"
-    ""
-)
 
-cmake_dependent_option(BMI_FORTRAN_ISO_C_LIB_NAME
-    "Name for middleware Fortran shared lib handling iso_c_binding"
-    "iso_c_bmi"
-    "NGEN_WITH_BMI_FORTRAN"
-    ""
-)
+option(BMI_FORTRAN_ISO_C_LIB_DIR "Directory hint for middleware Fortran shared lib handling iso_c_binding" "${NGEN_ROOT_DIR}/extern/iso_c_fortran_bmi/cmake_build")
+option(BMI_FORTRAN_ISO_C_LIB_NAME "Name for middleware Fortran shared lib handling iso_c_binding" "iso_c_bmi")
 
 include(DeprecatedOptions)
 deprecated_option(OLD MPI_ACTIVE            NEW NGEN_WITH_MPI     INCLUDE_ENV)
@@ -180,8 +170,25 @@ endif()
 # Configure whether Fortran BMI functionality is active
 if(NGEN_WITH_BMI_FORTRAN)
     add_compile_definitions(NGEN_BMI_FORTRAN_ACTIVE)
-    find_library(BMI_FORTRAN_ISO_C_LIB_PATH "${BMI_FORTRAN_ISO_C_LIB_NAME}" PATHS "${BMI_FORTRAN_ISO_C_LIB_DIR}" REQUIRED)
-    message("BMI Fortran: ${BMI_FORTRAN_ISO_C_LIB_PATH}")
+
+    # Searches for ISO C BMI library, defaults to
+    # known development directories in the event the BMI_FORTRAN_ISO_C_*
+    # variables are not set.
+    find_library(BMI_FORTRAN_ISO_C_LIB_PATH
+        NAMES
+            "${BMI_FORTRAN_ISO_C_LIB_NAME}"
+            "iso_c_bmi"
+        HINTS # Searched before paths
+            "${BMI_FORTRAN_ISO_C_LIB_DIR}" 
+        PATHS
+            ENV BMI_FORTRAN_ISO_C_LIB_DIR
+            "${NGEN_ROOT_DIR}/extern/iso_c_fortran_bmi/cmake_build"
+            "${NGEN_ROOT_DIR}/extern/iso_c_fortran_bmi/build"
+        DOC "Path to middleware Fortran shared lib handling iso_c_binding"
+        NO_CACHE
+        REQUIRED
+    )
+    
     add_library(bmi_fortran_compat SHARED IMPORTED)
     set_target_properties(bmi_fortran_compat PROPERTIES IMPORTED_LOCATION "${BMI_FORTRAN_ISO_C_LIB_PATH}")
 endif()
@@ -322,6 +329,11 @@ ngen_dependent_multiline_message(INTEL_DPCPP
 "    Include: ${SYCL_INCLUDE_DIR}"
 "    Implmentation: ${SYCL_IMPLEMENTATION_ID}")
 ngen_dependent_multiline_message(NGEN_WITH_MPI
+"  MPI (C):"
+"    Version: ${MPI_C_VERSION}"
+"    Library: ${MPI_C_LIBRARIES}"
+"    Include: ${MPI_C_INCLUDE_DIRS}")
+ngen_dependent_multiline_message(NGEN_WITH_MPI
 "  MPI (CXX):"
 "    Version: ${MPI_CXX_VERSION}"
 "    Library: ${MPI_CXX_LIBRARIES}"
@@ -343,7 +355,9 @@ ngen_dependent_multiline_message(NGEN_WITH_UDUNITS
 "    Include: ${UDUNITS2_INCLUDE}")
 ngen_dependent_multiline_message(NGEN_WITH_BMI_FORTRAN
 "  Fortran:"
-"    Fortran-C BMI Compat Library Path: ${NGEN_ISO_C_FORTRAN_BMI_LIB_PATH}")
+"    BMI_FORTRAN_ISO_C_LIB_PATH: ${BMI_FORTRAN_ISO_C_LIB_PATH}"
+"    BMI_FORTRAN_ISO_C_LIB_NAME: ${BMI_FORTRAN_ISO_C_LIB_NAME}"
+"    BMI_FORTRAN_ISO_C_LIB_DIR: ${BMI_FORTRAN_ISO_C_LIB_DIR}")
 ngen_dependent_multiline_message(NGEN_WITH_PYTHON
 "  Python:"
 "    Version: ${Python_VERSION}"

From 7a99b44feae749ba4e79b6155ba6acfffaa0177d Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 09:15:29 -0700
Subject: [PATCH 17/39] cmake: link MPI-based builds to the MPI targets

---
 src/core/CMakeLists.txt       | 4 ++++
 src/core/nexus/CMakeLists.txt | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
index 101ff43d8a..668d30877d 100644
--- a/src/core/CMakeLists.txt
+++ b/src/core/CMakeLists.txt
@@ -58,6 +58,10 @@ else ()
             )
 endif ()
 
+if(NGEN_WITH_MPI)
+    target_link_libraries(core PUBLIC MPI::MPI_C MPI::MPI_CXX)
+endif()
+
 add_subdirectory("catchment")
 add_subdirectory("nexus")
 add_subdirectory("hydrolocation")
diff --git a/src/core/nexus/CMakeLists.txt b/src/core/nexus/CMakeLists.txt
index 078a2b55d7..567ef9a6ea 100644
--- a/src/core/nexus/CMakeLists.txt
+++ b/src/core/nexus/CMakeLists.txt
@@ -15,3 +15,7 @@ target_include_directories(core_nexus PUBLIC
 target_link_libraries(core_nexus PUBLIC
         Boost::boost                # Headers-only Boost
         )
+
+if(NGEN_WITH_MPI)
+    target_link_libraries(core_nexus PUBLIC MPI::MPI_C MPI::MPI_CXX)
+endif()

From a85badc09123a1757d81283888d1465fd5730242 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 09:31:28 -0700
Subject: [PATCH 18/39] cmake: fix missing call to ngen_add_test

---
 test/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index e01d2766ca..d6fd26351d 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -216,7 +216,7 @@ ngen_add_test(
 )
 
 ########################## BMI Multi Tests
-add_test(
+ngen_add_test(
     test_bmi_multi
     OBJECTS
         realizations/catchments/Bmi_Multi_Formulation_Test.cpp

From 73bcc7117297433173c369ef5d8849cedb9fe718 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 09:51:07 -0700
Subject: [PATCH 19/39] cmake: change defaults again; attempt to fix CI issues

---
 CMakeLists.txt                   | 11 ++++++-----
 src/core/mediator/CMakeLists.txt |  4 ++--
 test/CMakeLists.txt              |  4 +++-
 3 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ecb0a1a99c..6260c6b905 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -36,13 +36,13 @@ include(GitUpdateSubmodules)
 # Options =====================================================================
 include(CMakeDependentOption)
 
-option(NGEN_WITH_MPI         "Build with MPI support"             ON)
+option(NGEN_WITH_MPI         "Build with MPI support"             OFF)
 option(NGEN_WITH_NETCDF      "Build with NetCDF support"          ON)
 option(NGEN_WITH_SQLITE      "Build with SQLite3 support"         ON)
 option(NGEN_WITH_UDUNITS     "Build with UDUNITS2 support"        ON)
-option(NGEN_WITH_BMI_FORTRAN "Build with Fortran BMI support"     ON)
-option(NGEN_WITH_BMI_C       "Build with C BMI support"           ON)
-option(NGEN_WITH_PYTHON      "Build with embedded Python support" ON)
+option(NGEN_WITH_BMI_FORTRAN "Build with Fortran BMI support"     OFF)
+option(NGEN_WITH_BMI_C       "Build with C BMI support"           OFF)
+option(NGEN_WITH_PYTHON      "Build with embedded Python support" OFF)
 option(NGEN_WITH_TESTS       "Build with unit tests"              ON)
 option(NGEN_QUIET            "Silence output"                     OFF)
 
@@ -69,6 +69,8 @@ deprecated_option(OLD PACKAGE_TESTS         NEW NGEN_WITH_TESTS)
 # Define project version and use via generated config header
 project(ngen VERSION 0.1.0)
 
+configure_file("${NGEN_INC_DIR}/NGenConfig.h.in" "${NGEN_INC_DIR}/NGenConfig.h")
+
 add_executable(ngen "${NGEN_SRC_DIR}/NGen.cpp")
 
 # Dependencies ================================================================
@@ -232,7 +234,6 @@ add_subdirectory(${TEST_BMI_CPP_DIR} ${TEST_BMI_CPP_DIR}/cmake_build) # FIXME: W
 # -----------------------------------------------------------------------------
 # Project Targets
 # -----------------------------------------------------------------------------
-configure_file(include/NGenConfig.h.in include/NGenConfig.h)
 add_dependencies(ngen testbmicppmodel)
 target_include_directories(ngen PUBLIC "${NGEN_INC_DIR}")
 
diff --git a/src/core/mediator/CMakeLists.txt b/src/core/mediator/CMakeLists.txt
index b1c336cd67..6384473db5 100644
--- a/src/core/mediator/CMakeLists.txt
+++ b/src/core/mediator/CMakeLists.txt
@@ -2,9 +2,9 @@ include(${PROJECT_SOURCE_DIR}/cmake/dynamic_sourced_library.cmake)
 dynamic_sourced_cxx_library(core_mediator "${CMAKE_CURRENT_SOURCE_DIR}")
 
 add_library(NGen::core_mediator ALIAS core_mediator)
+
 if(NGEN_WITH_UDUNITS)
-        add_dependencies(core_mediator libudunits2)
-        target_link_libraries(core_mediator PUBLIC libudunits2)
+    target_link_libraries(core_mediator PUBLIC libudunits2)
 endif()
 
 find_package(Threads REQUIRED)
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index d6fd26351d..44046d32ae 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -59,7 +59,7 @@ function(ngen_add_test TESTNAME)
 
     if(NGEN_TEST_CREATE)
         add_executable(${TESTNAME} ${NGEN_TEST_OBJECTS})
-        target_link_libraries(${TESTNAME} gtest gtest_main ${NGEN_TEST_LIBRARIES})
+        target_link_libraries(${TESTNAME} PUBLIC gtest gtest_main ${NGEN_TEST_LIBRARIES})
         set_target_properties(${TESTNAME} PROPERTIES FOLDER test)
         gtest_discover_tests(
             ${TESTNAME}
@@ -177,6 +177,7 @@ ngen_add_test(
         realizations/catchments/Bmi_C_Adapter_Test.cpp
         realizations/catchments/Bmi_C_Formulation_Test.cpp
     LIBRARIES
+        gmock
         NGen::core
         NGen::realizations_catchment
         NGen::core_mediator
@@ -326,6 +327,7 @@ ngen_add_test(
         utils/mdframe_netcdf_Test.cpp
         utils/mdframe_csv_Test.cpp
     LIBRARIES
+        gmock
         NGen::core
         NGen::core_nexus
         NGen::core_mediator

From dbb4c60ac50eac84f95faecd7b77f9d378af791a Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 10:28:53 -0700
Subject: [PATCH 20/39] cmake: attempt to fix udunits macOS inclusion

---
 CMakeLists.txt | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6260c6b905..aec76afbcb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -140,8 +140,11 @@ if(NGEN_WITH_UDUNITS)
 
     # Create UDUNITS2 target
     add_library(libudunits2 SHARED IMPORTED)
-    target_include_directories(libudunits2 INTERFACE "${UDUNITS2_INCLUDE}")
+    target_include_directories(libudunits2 SYSTEM INTERFACE "${UDUNITS2_INCLUDE}")
     set_target_properties(libudunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
+
+    get_target_property(_SUMMARY_UDUNITS_INCLUDE libudunits2 INTERFACE_INCLUDE_DIRECTORIES)
+    get_target_property(_SUMMARY_UDUNITS_SYS_INCLUDE libudunits2 INTERFACE_SYSTEM_INCLUDE_DIRECTORIES)
 endif()
 
 # -----------------------------------------------------------------------------
@@ -187,9 +190,11 @@ if(NGEN_WITH_BMI_FORTRAN)
             "${NGEN_ROOT_DIR}/extern/iso_c_fortran_bmi/cmake_build"
             "${NGEN_ROOT_DIR}/extern/iso_c_fortran_bmi/build"
         DOC "Path to middleware Fortran shared lib handling iso_c_binding"
-        NO_CACHE
-        REQUIRED
     )
+
+    if("${BMI_FORTRAN_ISO_C_LIB_PATH}" STREQUAL "BMI_FORTRAN_ISO_C_LIB_PATH-NOTFOUND")
+        message(FATAL_ERROR "Failed to find BMI_FORTRAN_ISO_C_LIB_PATH:\n  BMI_FORTRAN_ISO_C_LIB_NAME: ${BMI_FORTRAN_ISO_C_LIB_NAME}\n  BMI_FORTRAN_ISO_C_LIB_DIR: ${BMI_FORTRAN_ISO_C_LIB_DIR}")
+    endif()
     
     add_library(bmi_fortran_compat SHARED IMPORTED)
     set_target_properties(bmi_fortran_compat PROPERTIES IMPORTED_LOCATION "${BMI_FORTRAN_ISO_C_LIB_PATH}")
@@ -300,6 +305,9 @@ else()
     set(NGEN_CONFIGURED_VENV "<none>")
 endif()
 
+# MPI CXX libraries output both C and CXX libs
+string(REPLACE ";" "," _MPI_CXX_LIBS "${MPI_CXX_LIBRARIES}")
+
 message(STATUS "---------------------------------------------------------------------")
 ngen_multiline_message(
 "NGen version: ${ngen_VERSION}"
@@ -337,7 +345,7 @@ ngen_dependent_multiline_message(NGEN_WITH_MPI
 ngen_dependent_multiline_message(NGEN_WITH_MPI
 "  MPI (CXX):"
 "    Version: ${MPI_CXX_VERSION}"
-"    Library: ${MPI_CXX_LIBRARIES}"
+"    Library: ${_MPI_CXX_LIBS}"
 "    Include: ${MPI_CXX_INCLUDE_DIRS}")
 ngen_dependent_multiline_message(NGEN_WITH_NETCDF
 "  NetCDF:"
@@ -353,7 +361,8 @@ ngen_dependent_multiline_message(NGEN_WITH_SQLITE
 ngen_dependent_multiline_message(NGEN_WITH_UDUNITS
 "  UDUNITS2:"
 "    Library: ${UDUNITS2_LIBRARY}"
-"    Include: ${UDUNITS2_INCLUDE}")
+"    Include: ${_SUMMARY_UDUNITS_INCLUDE}"
+"    System Include: ${_SUMMARY_UDUNITS_SYS_INCLUDE}")
 ngen_dependent_multiline_message(NGEN_WITH_BMI_FORTRAN
 "  Fortran:"
 "    BMI_FORTRAN_ISO_C_LIB_PATH: ${BMI_FORTRAN_ISO_C_LIB_PATH}"

From 4d5baa8d54f1aede89e20febb748dcb504ac004a Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 11:00:21 -0700
Subject: [PATCH 21/39] cmake: another attempt at fixing udunits inclusion

---
 CMakeLists.txt | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index aec76afbcb..d543dfc5d0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -139,12 +139,13 @@ if(NGEN_WITH_UDUNITS)
     add_compile_definitions(NGEN_WITH_UDUNITS)
 
     # Create UDUNITS2 target
-    add_library(libudunits2 SHARED IMPORTED)
-    target_include_directories(libudunits2 SYSTEM INTERFACE "${UDUNITS2_INCLUDE}")
+    # Note: GLOBAL is required here in order to extent the scope of
+    #       included directories.
+    #       see: https://stackoverflow.com/a/46491758/6891484
+    add_library(libudunits2 SHARED IMPORTED GLOBAL)
+    target_include_directories(libudunits2 INTERFACE "${UDUNITS2_INCLUDE}")
     set_target_properties(libudunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
-
     get_target_property(_SUMMARY_UDUNITS_INCLUDE libudunits2 INTERFACE_INCLUDE_DIRECTORIES)
-    get_target_property(_SUMMARY_UDUNITS_SYS_INCLUDE libudunits2 INTERFACE_SYSTEM_INCLUDE_DIRECTORIES)
 endif()
 
 # -----------------------------------------------------------------------------
@@ -156,7 +157,7 @@ if(NGEN_WITH_NETCDF)
     add_compile_definitions(NETCDF_ACTIVE)
     
     # Create NetCDF target
-    add_library(NetCDF SHARED IMPORTED)
+    add_library(NetCDF SHARED IMPORTED GLOBAL)
     target_include_directories(NetCDF INTERFACE "${NETCDF_INCLUDE_DIR}" "${NETCDF_CXX_INCLUDE_DIR}")
     set_target_properties(NetCDF
         PROPERTIES
@@ -361,8 +362,7 @@ ngen_dependent_multiline_message(NGEN_WITH_SQLITE
 ngen_dependent_multiline_message(NGEN_WITH_UDUNITS
 "  UDUNITS2:"
 "    Library: ${UDUNITS2_LIBRARY}"
-"    Include: ${_SUMMARY_UDUNITS_INCLUDE}"
-"    System Include: ${_SUMMARY_UDUNITS_SYS_INCLUDE}")
+"    Include: ${_SUMMARY_UDUNITS_INCLUDE}")
 ngen_dependent_multiline_message(NGEN_WITH_BMI_FORTRAN
 "  Fortran:"
 "    BMI_FORTRAN_ISO_C_LIB_PATH: ${BMI_FORTRAN_ISO_C_LIB_PATH}"

From 76ba4ee3e3c4a4131230cef5bc1c44e771b46f70 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 11:20:03 -0700
Subject: [PATCH 22/39] cmake: workaround for udunits2 inclusion on macOS

---
 CMakeLists.txt                   | 6 +++---
 src/core/mediator/CMakeLists.txt | 5 +++++
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d543dfc5d0..1d5453ea01 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -139,12 +139,12 @@ if(NGEN_WITH_UDUNITS)
     add_compile_definitions(NGEN_WITH_UDUNITS)
 
     # Create UDUNITS2 target
-    # Note: GLOBAL is required here in order to extent the scope of
-    #       included directories.
+    # Note: GLOBAL is required here in order to extend the scope of the target.
     #       see: https://stackoverflow.com/a/46491758/6891484
     add_library(libudunits2 SHARED IMPORTED GLOBAL)
-    target_include_directories(libudunits2 INTERFACE "${UDUNITS2_INCLUDE}")
+    target_include_directories(libudunits2 SYSTEM INTERFACE "${UDUNITS2_INCLUDE}")
     set_target_properties(libudunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
+        
     get_target_property(_SUMMARY_UDUNITS_INCLUDE libudunits2 INTERFACE_INCLUDE_DIRECTORIES)
 endif()
 
diff --git a/src/core/mediator/CMakeLists.txt b/src/core/mediator/CMakeLists.txt
index 6384473db5..f0319ab049 100644
--- a/src/core/mediator/CMakeLists.txt
+++ b/src/core/mediator/CMakeLists.txt
@@ -5,6 +5,11 @@ add_library(NGen::core_mediator ALIAS core_mediator)
 
 if(NGEN_WITH_UDUNITS)
     target_link_libraries(core_mediator PUBLIC libudunits2)
+
+    # FIXME: workaround for now... there is an issue with macOS linking to
+    #        the shared imported udunits2 target, such that header include
+    #        directories aren't correctly propogated. - Justin
+    target_include_directories(core_mediator PUBLIC "${UDUNITS2_INCLUDE}")
 endif()
 
 find_package(Threads REQUIRED)

From e2eecc55a5e6b9550fc06311ea00263f6d495b19 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 11:35:47 -0700
Subject: [PATCH 23/39] cmake: set sqlite3 support default to OFF

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1d5453ea01..c0c7f3d9e4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -38,7 +38,7 @@ include(CMakeDependentOption)
 
 option(NGEN_WITH_MPI         "Build with MPI support"             OFF)
 option(NGEN_WITH_NETCDF      "Build with NetCDF support"          ON)
-option(NGEN_WITH_SQLITE      "Build with SQLite3 support"         ON)
+option(NGEN_WITH_SQLITE      "Build with SQLite3 support"         OFF)
 option(NGEN_WITH_UDUNITS     "Build with UDUNITS2 support"        ON)
 option(NGEN_WITH_BMI_FORTRAN "Build with Fortran BMI support"     OFF)
 option(NGEN_WITH_BMI_C       "Build with C BMI support"           OFF)

From 2dc180e3b8daca124646a7e59858f7998cd1301c Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 13:50:24 -0700
Subject: [PATCH 24/39] cmake: another attempt

---
 CMakeLists.txt                   | 9 ++++++---
 src/core/mediator/CMakeLists.txt | 5 -----
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c0c7f3d9e4..db8054bd8a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -141,9 +141,12 @@ if(NGEN_WITH_UDUNITS)
     # Create UDUNITS2 target
     # Note: GLOBAL is required here in order to extend the scope of the target.
     #       see: https://stackoverflow.com/a/46491758/6891484
-    add_library(libudunits2 SHARED IMPORTED GLOBAL)
-    target_include_directories(libudunits2 SYSTEM INTERFACE "${UDUNITS2_INCLUDE}")
-    set_target_properties(libudunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
+    add_library(libudunits2::library SHARED IMPORTED GLOBAL)
+    set_target_properties(libudunits2::library PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
+
+    add_library(libudunits2 INTERFACE IMPORTED)
+    target_include_directories(libudunits2 INTERFACE "${UDUNITS2_INCLUDE}")
+    target_link_libraries(libudunits2 INTERFACE libudunits2::library)
         
     get_target_property(_SUMMARY_UDUNITS_INCLUDE libudunits2 INTERFACE_INCLUDE_DIRECTORIES)
 endif()
diff --git a/src/core/mediator/CMakeLists.txt b/src/core/mediator/CMakeLists.txt
index f0319ab049..6384473db5 100644
--- a/src/core/mediator/CMakeLists.txt
+++ b/src/core/mediator/CMakeLists.txt
@@ -5,11 +5,6 @@ add_library(NGen::core_mediator ALIAS core_mediator)
 
 if(NGEN_WITH_UDUNITS)
     target_link_libraries(core_mediator PUBLIC libudunits2)
-
-    # FIXME: workaround for now... there is an issue with macOS linking to
-    #        the shared imported udunits2 target, such that header include
-    #        directories aren't correctly propogated. - Justin
-    target_include_directories(core_mediator PUBLIC "${UDUNITS2_INCLUDE}")
 endif()
 
 find_package(Threads REQUIRED)

From 98d567d99e47b3ad34ef378b8399f648619cc0d1 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Thu, 7 Sep 2023 21:40:19 -0700
Subject: [PATCH 25/39] cmake: revert some changes; include UDUNITS2_INCLUDE at
 compiler level

---
 CMakeLists.txt           | 7 ++-----
 cmake/FindUDUNITS2.cmake | 5 +++++
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index db8054bd8a..2573a0b5d1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -141,12 +141,9 @@ if(NGEN_WITH_UDUNITS)
     # Create UDUNITS2 target
     # Note: GLOBAL is required here in order to extend the scope of the target.
     #       see: https://stackoverflow.com/a/46491758/6891484
-    add_library(libudunits2::library SHARED IMPORTED GLOBAL)
-    set_target_properties(libudunits2::library PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
-
-    add_library(libudunits2 INTERFACE IMPORTED)
+    add_library(libudunits2 SHARED IMPORTED GLOBAL)
+    set_target_properties(libudunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
     target_include_directories(libudunits2 INTERFACE "${UDUNITS2_INCLUDE}")
-    target_link_libraries(libudunits2 INTERFACE libudunits2::library)
         
     get_target_property(_SUMMARY_UDUNITS_INCLUDE libudunits2 INTERFACE_INCLUDE_DIRECTORIES)
 endif()
diff --git a/cmake/FindUDUNITS2.cmake b/cmake/FindUDUNITS2.cmake
index 5cb39f1da2..30d1fca367 100644
--- a/cmake/FindUDUNITS2.cmake
+++ b/cmake/FindUDUNITS2.cmake
@@ -20,3 +20,8 @@ endif()
 
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(UDUNITS2 DEFAULT_MSG UDUNITS2_LIBRARY UDUNITS2_INCLUDE)
+
+# Based on: https://stackoverflow.com/questions/26834553/osx-10-10-cmake-3-0-2-and-clang-wont-find-local-headers
+if(UDUNITS2_FOUND)
+    include_directories(${UDUNITS2_INCLUDE})
+endif()

From dae6d1562d6ebc963c78bfdf996592aa636ca508 Mon Sep 17 00:00:00 2001
From: Phil Miller <philip.miller@noaa.gov>
Date: Fri, 8 Sep 2023 07:33:22 -0700
Subject: [PATCH 26/39] Move C++ standards options before declaring project and
 main executable, so that they're applied to that

---
 CMakeLists.txt | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2573a0b5d1..c1b18faca2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -66,6 +66,12 @@ deprecated_option(OLD QUIET                 NEW NGEN_QUIET)
 deprecated_option(OLD PACKAGE_TESTS         NEW NGEN_WITH_TESTS)
 # Project =====================================================================
 
+# -----------------------------------------------------------------------------
+# Set global C++ options
+set(CMAKE_CXX_STANDARD 14)
+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)
 
@@ -75,12 +81,6 @@ add_executable(ngen "${NGEN_SRC_DIR}/NGen.cpp")
 
 # Dependencies ================================================================
 
-# -----------------------------------------------------------------------------
-# Set global C++ options
-set(CMAKE_CXX_STANDARD 14)
-set(CMAKE_CXX_STANDARD_REQUIRED True)
-set(CMAKE_CXX_VISIBILITY_PRESET hidden)
-
 # -----------------------------------------------------------------------------
 # Check if NGen is the main project (e.g. development environment)
 if(PROJECT_NAME STREQUAL CMAKE_PROJECT_NAME)

From 8cada60e12831dd70a230aebbf40221c84244fe5 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Fri, 8 Sep 2023 07:41:16 -0700
Subject: [PATCH 27/39] cmake: remove unnecessary comments; gh: update action
 to default sqlite support

---
 .github/actions/ngen-build/action.yaml | 7 ++++++-
 CMakeLists.txt                         | 6 ------
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/.github/actions/ngen-build/action.yaml b/.github/actions/ngen-build/action.yaml
index da90a7352e..b81e389d02 100644
--- a/.github/actions/ngen-build/action.yaml
+++ b/.github/actions/ngen-build/action.yaml
@@ -39,6 +39,10 @@ inputs:
       required: false
       description: 'Activate NetCDF Lumped Forcing Support'
       default: 'ON'
+    use_sqlite:
+      required: false
+      description: 'Activate SQLite3 suppport for GeoPackage'
+      default: 'ON'
     use_troute:
       required: false
       description: 'Enable t-route integration support'
@@ -176,7 +180,8 @@ runs:
               -DBMI_FORTRAN_ACTIVE:BOOL=${{ inputs.bmi_fortran }} \
               -DNGEN_ACTIVATE_ROUTING:BOOL=${{ inputs.use_troute }} \
               -DNETCDF_ACTIVE:BOOL=${{ inputs.use_netcdf }} \
-              -DMPI_ACTIVE:BOOL=${{ inputs.use_mpi }} -S .
+              -DNGEN_WITH_SQLITE:BOOL=${{ inputs.use_sqlite }} \
+              -DMPI_ACTIVE:BOOL=${{ inputs.use_mpi }} -S . \
             echo "build-dir=$(echo ${{ inputs.build-dir }})" >> $GITHUB_OUTPUT
           shell: bash
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index c1b18faca2..b80e2a252c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -382,9 +382,3 @@ ngen_dependent_multiline_message(NGEN_WITH_PYTHON
 "    pybind11 Version: ${pybind11_VERSION}"
 "    pybind11 Include: ${pybind11_INCLUDE_DIR}")
 message(STATUS "---------------------------------------------------------------------")
-
-#set_target_properties(ngen PROPERTIES LINKER_LANGUAGE CXX)
-#
-#target_compile_options(ngen PUBLIC -std=c++14 -Wall)
-#target_compile_features(ngen PUBLIC cxx_std_14)
-#add_subdirectory("src/geojson")

From e30a8ec683544673a43e2040b503666d14f06c19 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Fri, 8 Sep 2023 07:47:03 -0700
Subject: [PATCH 28/39] gh: rm accidental slash

---
 .github/actions/ngen-build/action.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/ngen-build/action.yaml b/.github/actions/ngen-build/action.yaml
index b81e389d02..dd7ecdebef 100644
--- a/.github/actions/ngen-build/action.yaml
+++ b/.github/actions/ngen-build/action.yaml
@@ -181,7 +181,7 @@ runs:
               -DNGEN_ACTIVATE_ROUTING:BOOL=${{ inputs.use_troute }} \
               -DNETCDF_ACTIVE:BOOL=${{ inputs.use_netcdf }} \
               -DNGEN_WITH_SQLITE:BOOL=${{ inputs.use_sqlite }} \
-              -DMPI_ACTIVE:BOOL=${{ inputs.use_mpi }} -S . \
+              -DMPI_ACTIVE:BOOL=${{ inputs.use_mpi }} -S .
             echo "build-dir=$(echo ${{ inputs.build-dir }})" >> $GITHUB_OUTPUT
           shell: bash
 

From 9eb556a9346dc4da4197cea570cf499edd56be8a Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Fri, 8 Sep 2023 07:51:07 -0700
Subject: [PATCH 29/39] docker: deactivate netcdf support

---
 docker/CENTOS_NGEN_RUN.dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/CENTOS_NGEN_RUN.dockerfile b/docker/CENTOS_NGEN_RUN.dockerfile
index 5009c74454..14548125f6 100644
--- a/docker/CENTOS_NGEN_RUN.dockerfile
+++ b/docker/CENTOS_NGEN_RUN.dockerfile
@@ -30,7 +30,7 @@ RUN git submodule update --init --recursive -- extern/pybind11
 
 WORKDIR /ngen
 
-RUN cmake -B /ngen -S .
+RUN cmake -DNGEN_WITH_NETCDF:BOOL=OFF -B /ngen -S .
 
 RUN cmake --build . --target ngen
 

From c9dc6d227908e644a26d1fe7fd6aa6de88548d89 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Fri, 8 Sep 2023 08:22:28 -0700
Subject: [PATCH 30/39] docker: disable sqlite for example run

---
 docker/CENTOS_NGEN_RUN.dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docker/CENTOS_NGEN_RUN.dockerfile b/docker/CENTOS_NGEN_RUN.dockerfile
index 14548125f6..a2dbe92817 100644
--- a/docker/CENTOS_NGEN_RUN.dockerfile
+++ b/docker/CENTOS_NGEN_RUN.dockerfile
@@ -30,7 +30,9 @@ RUN git submodule update --init --recursive -- extern/pybind11
 
 WORKDIR /ngen
 
-RUN cmake -DNGEN_WITH_NETCDF:BOOL=OFF -B /ngen -S .
+RUN cmake -DNGEN_WITH_NETCDF:BOOL=OFF \
+          -DNGEN_WITH_SQLITE:BOOL=OFF \
+          -B /ngen -S .
 
 RUN cmake --build . --target ngen
 

From ba6c71e44a98a8ce1e14757f1982f3bdd114db77 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Fri, 8 Sep 2023 08:33:59 -0700
Subject: [PATCH 31/39] cmake: only add geopackage if SQLite is enabled

---
 CMakeLists.txt | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b80e2a252c..dbe74161d2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -245,7 +245,6 @@ target_include_directories(ngen PUBLIC "${NGEN_INC_DIR}")
 
 add_subdirectory("src/core")
 add_subdirectory("src/geojson")
-add_subdirectory("src/geopackage")
 add_subdirectory("src/realizations/catchment")
 add_subdirectory("src/forcing")
 add_subdirectory("src/utilities/mdarray")
@@ -257,12 +256,16 @@ target_link_libraries(ngen
         NGen::core_catchment
         NGen::core_nexus
         NGen::geojson
-        NGen::geopackage
         NGen::realizations_catchment
         NGen::forcing
         NGen::core_mediator
 )
 
+if(NGEN_WITH_SQLITE)
+    add_subdirectory("src/geopackage")
+    target_link_libraries(ngen PUBLIC NGen::geopackage)
+endif()
+
 if(NGEN_WITH_ROUTING)
     add_subdirectory("src/routing")
     target_link_libraries(ngen PUBLIC NGen::routing)

From 57135c1ed8764f49722898bd6239cc9446ebeae7 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Fri, 8 Sep 2023 12:07:28 -0700
Subject: [PATCH 32/39] cmake: UDUNITS2_FOUND only if library is found also

Co-authored-by: Phil Miller - NOAA <philip.miller@noaa.gov>
---
 cmake/FindUDUNITS2.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/FindUDUNITS2.cmake b/cmake/FindUDUNITS2.cmake
index 30d1fca367..ec41ba2281 100644
--- a/cmake/FindUDUNITS2.cmake
+++ b/cmake/FindUDUNITS2.cmake
@@ -12,7 +12,7 @@ find_library(UDUNITS2_LIBRARY
 )
 mark_as_advanced(UDUNITS2_LIBRARY)
 
-if(DEFINED UDUNITS2_INCLUDE)
+if(DEFINED UDUNITS2_INCLUDE AND DEFINED UDUNITS2_LIBRARY)
     set(UDUNITS2_FOUND ON)
 else()
     set(UDUNITS2_FOUND OFF)

From 47b9a4817265fd1cdbf31a8ed8474622b03cf574 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Fri, 8 Sep 2023 12:13:29 -0700
Subject: [PATCH 33/39] cmake: changes per review

Co-authored-by: Phil Miller - NOAA <philip.miller@noaa.gov>
---
 CMakeLists.txt                | 27 +++++++--------------------
 cmake/DeprecatedOptions.cmake |  4 ++--
 test/CMakeLists.txt           |  6 ++++++
 3 files changed, 15 insertions(+), 22 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index dbe74161d2..e940ef5602 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -41,7 +41,7 @@ option(NGEN_WITH_NETCDF      "Build with NetCDF support"          ON)
 option(NGEN_WITH_SQLITE      "Build with SQLite3 support"         OFF)
 option(NGEN_WITH_UDUNITS     "Build with UDUNITS2 support"        ON)
 option(NGEN_WITH_BMI_FORTRAN "Build with Fortran BMI support"     OFF)
-option(NGEN_WITH_BMI_C       "Build with C BMI support"           OFF)
+option(NGEN_WITH_BMI_C       "Build with C BMI support"           ON)
 option(NGEN_WITH_PYTHON      "Build with embedded Python support" OFF)
 option(NGEN_WITH_TESTS       "Build with unit tests"              ON)
 option(NGEN_QUIET            "Silence output"                     OFF)
@@ -105,14 +105,14 @@ endif()
 
 # -----------------------------------------------------------------------------
 # Account for different OS and how that impacts shared lib file names
-# FIXME: What is this used for? - Justin
-if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
-    set(SHARED_LIB_EXTENSION "dylib")
-elseif(WIN32)
-    error("Windows platforms are not currently supported")
+if(WIN32)
+    message(FATAL_ERROR "Windows platforms are not currently supported")
+elseif("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
+    set(NGEN_SHARED_LIB_EXTENSION "dylib")
 else()
-    set(SHARED_LIB_EXTENSION "so")
+    set(NGEN_SHARED_LIB_EXTENSION "so")
 endif()
+add_compile_definitions(NGEN_SHARED_LIB_EXTENSION)
 
 # -----------------------------------------------------------------------------
 # Find the Boost library and configure usage
@@ -217,7 +217,6 @@ endif()
 # -----------------------------------------------------------------------------
 if(NGEN_QUIET)
     set(UDUNITS_QUIET true)
-    set(ET_QUIET true)
     add_compile_definitions(NGEN_QUIET)
 endif()
 
@@ -225,22 +224,10 @@ if(UDUNITS_QUIET)
     add_compile_definitions(UDUNITS_QUIET)
 endif()
 
-# FIXME: I don't think this is needed now? - Justin
-if(ET_QUIET)
-    add_compile_definitions(ET_QUIET)
-endif()
-
-# -----------------------------------------------------------------------------
-
-# Natively support BMI C++ modules and pre-compile in the test_bmi_cpp mock/example.
-set(TEST_BMI_CPP_DIR ${NGEN_EXT_DIR}/test_bmi_cpp)
-git_update_submodule(${NGEN_EXT_DIR}/bmi-cxx)
-add_subdirectory(${TEST_BMI_CPP_DIR} ${TEST_BMI_CPP_DIR}/cmake_build) # FIXME: Why is this here? - Justin
 
 # -----------------------------------------------------------------------------
 # Project Targets
 # -----------------------------------------------------------------------------
-add_dependencies(ngen testbmicppmodel)
 target_include_directories(ngen PUBLIC "${NGEN_INC_DIR}")
 
 add_subdirectory("src/core")
diff --git a/cmake/DeprecatedOptions.cmake b/cmake/DeprecatedOptions.cmake
index 4cd27eeee5..806912b61d 100644
--- a/cmake/DeprecatedOptions.cmake
+++ b/cmake/DeprecatedOptions.cmake
@@ -9,7 +9,7 @@ The `OLD` variable is the deprecated option that corresponds to a new option.
 
 The `INCLUDE_ENV` flag also checks the environment variables for a variable named `OLD`, i.e. ENV{<OLD variable>}.
 #]==]
-macro(deprecated_option)
+function(deprecated_option)
     set(options INCLUDE_ENV)
     set(oneValueArgs NEW OLD)
     cmake_parse_arguments(DEPRECATED_OPTION "${options}" "${oneValueArgs}" "" ${ARGN})
@@ -25,4 +25,4 @@ macro(deprecated_option)
             set(${DEPRECATED_OPTION_NEW} $ENV{${DEPRECATED_OPTION_OLD}})
         endif()
     endif()
-endmacro()
+endfunction()
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 44046d32ae..bfa060ff37 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -1,6 +1,12 @@
 add_subdirectory(googletest)
 add_compile_definitions(NGEN_BMI_CPP_LIB_TESTS_ACTIVE)
 
+# Natively support BMI C++ modules and pre-compile in the test_bmi_cpp mock/example.
+set(TEST_BMI_CPP_DIR ${NGEN_EXT_DIR}/test_bmi_cpp)
+git_update_submodule(${NGEN_EXT_DIR}/bmi-cxx)
+add_subdirectory(${TEST_BMI_CPP_DIR} ${TEST_BMI_CPP_DIR}/cmake_build)
+add_dependencies(ngen testbmicppmodel)
+
 if (NGEN_WITH_PYTHON)
     add_compile_definitions(NGEN_BMI_PY_TESTS_ACTIVE)
 endif()

From 4778e541a793ad883d25827365394406fddeb529 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Fri, 8 Sep 2023 12:18:45 -0700
Subject: [PATCH 34/39] cmake: fix deprecated options scope

---
 cmake/DeprecatedOptions.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cmake/DeprecatedOptions.cmake b/cmake/DeprecatedOptions.cmake
index 806912b61d..f5c82776f0 100644
--- a/cmake/DeprecatedOptions.cmake
+++ b/cmake/DeprecatedOptions.cmake
@@ -16,13 +16,13 @@ function(deprecated_option)
 
     if(DEFINED ${DEPRECATED_OPTION_OLD})
         message(DEPRECATION "Deprecated option ${DEPRECATED_OPTION_OLD} defined; setting ${DEPRECATED_OPTION_NEW} to ${DEPRECATED_OPTION_OLD} (aka ${${DEPRECATED_OPTION_OLD}})")
-        set(${DEPRECATED_OPTION_NEW} ${${DEPRECATED_OPTION_OLD}})
+        set(${DEPRECATED_OPTION_NEW} ${${DEPRECATED_OPTION_OLD}} PARENT_SCOPE)
     endif()
 
     if(DEPRECATED_OPTION_INCLUDE_ENV)
         if(DEFINED ENV{${DEPRECATED_OPTION_OLD}})
             message(DEPRECATION "Deprecated environment variable ${DEPRECATED_OPTION_OLD} defined; setting ${DEPRECATED_OPTION_NEW} to ENV{${DEPRECATED_OPTION_OLD}} (aka $ENV{${DEPRECATED_OPTION_OLD}})")
-            set(${DEPRECATED_OPTION_NEW} $ENV{${DEPRECATED_OPTION_OLD}})
+            set(${DEPRECATED_OPTION_NEW} $ENV{${DEPRECATED_OPTION_OLD}} PARENT_SCOPE)
         endif()
     endif()
 endfunction()

From 96737eebe700f6b77be5e2a88fbeb719e33be0ed Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Mon, 11 Sep 2023 09:49:04 -0700
Subject: [PATCH 35/39] cmake: create targets in cmake modules instead of root
 cmakelists

---
 CMakeLists.txt                            | 41 +----------------------
 cmake/FindBMI_FORTRAN_ISO_C.cmake         | 23 +++++++++++++
 cmake/FindNetCDF.cmake                    | 10 ++++++
 cmake/FindUDUNITS2.cmake                  |  9 ++++-
 src/realizations/catchment/CMakeLists.txt |  2 +-
 5 files changed, 43 insertions(+), 42 deletions(-)
 create mode 100644 cmake/FindBMI_FORTRAN_ISO_C.cmake

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e940ef5602..93e44a83ec 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -137,14 +137,6 @@ endif()
 if(NGEN_WITH_UDUNITS)
     find_package(UDUNITS2 REQUIRED)
     add_compile_definitions(NGEN_WITH_UDUNITS)
-
-    # Create UDUNITS2 target
-    # Note: GLOBAL is required here in order to extend the scope of the target.
-    #       see: https://stackoverflow.com/a/46491758/6891484
-    add_library(libudunits2 SHARED IMPORTED GLOBAL)
-    set_target_properties(libudunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
-    target_include_directories(libudunits2 INTERFACE "${UDUNITS2_INCLUDE}")
-        
     get_target_property(_SUMMARY_UDUNITS_INCLUDE libudunits2 INTERFACE_INCLUDE_DIRECTORIES)
 endif()
 
@@ -155,20 +147,11 @@ if(NGEN_WITH_NETCDF)
     set(NETCDF_F90 "NO")
     find_package(NetCDF REQUIRED)
     add_compile_definitions(NETCDF_ACTIVE)
-    
-    # Create NetCDF target
-    add_library(NetCDF SHARED IMPORTED GLOBAL)
-    target_include_directories(NetCDF INTERFACE "${NETCDF_INCLUDE_DIR}" "${NETCDF_CXX_INCLUDE_DIR}")
-    set_target_properties(NetCDF
-        PROPERTIES
-            IMPORTED_LOCATION "${NETCDF_LIBRARY}"
-            IMPORTED_LOCATION "${NETCDF_CXX_LIBRARY}")
 endif()
 
 # -----------------------------------------------------------------------------
 # Handle several steps for BMI C library logic and dependencies, at top level, if functionality is turned on
 if(NGEN_WITH_BMI_C)
-    # Define associated preprocessor directive
     add_compile_definitions(NGEN_BMI_C_LIB_ACTIVE)
 endif()
 
@@ -176,29 +159,7 @@ endif()
 # Configure whether Fortran BMI functionality is active
 if(NGEN_WITH_BMI_FORTRAN)
     add_compile_definitions(NGEN_BMI_FORTRAN_ACTIVE)
-
-    # Searches for ISO C BMI library, defaults to
-    # known development directories in the event the BMI_FORTRAN_ISO_C_*
-    # variables are not set.
-    find_library(BMI_FORTRAN_ISO_C_LIB_PATH
-        NAMES
-            "${BMI_FORTRAN_ISO_C_LIB_NAME}"
-            "iso_c_bmi"
-        HINTS # Searched before paths
-            "${BMI_FORTRAN_ISO_C_LIB_DIR}" 
-        PATHS
-            ENV BMI_FORTRAN_ISO_C_LIB_DIR
-            "${NGEN_ROOT_DIR}/extern/iso_c_fortran_bmi/cmake_build"
-            "${NGEN_ROOT_DIR}/extern/iso_c_fortran_bmi/build"
-        DOC "Path to middleware Fortran shared lib handling iso_c_binding"
-    )
-
-    if("${BMI_FORTRAN_ISO_C_LIB_PATH}" STREQUAL "BMI_FORTRAN_ISO_C_LIB_PATH-NOTFOUND")
-        message(FATAL_ERROR "Failed to find BMI_FORTRAN_ISO_C_LIB_PATH:\n  BMI_FORTRAN_ISO_C_LIB_NAME: ${BMI_FORTRAN_ISO_C_LIB_NAME}\n  BMI_FORTRAN_ISO_C_LIB_DIR: ${BMI_FORTRAN_ISO_C_LIB_DIR}")
-    endif()
-    
-    add_library(bmi_fortran_compat SHARED IMPORTED)
-    set_target_properties(bmi_fortran_compat PROPERTIES IMPORTED_LOCATION "${BMI_FORTRAN_ISO_C_LIB_PATH}")
+    find_package(BMI_FORTRAN_ISO_C REQUIRED)
 endif()
 
 # -----------------------------------------------------------------------------
diff --git a/cmake/FindBMI_FORTRAN_ISO_C.cmake b/cmake/FindBMI_FORTRAN_ISO_C.cmake
new file mode 100644
index 0000000000..48d2a0e435
--- /dev/null
+++ b/cmake/FindBMI_FORTRAN_ISO_C.cmake
@@ -0,0 +1,23 @@
+# Searches for ISO C BMI library, defaults to
+# known development directories in the event the BMI_FORTRAN_ISO_C_*
+# variables are not set.
+find_library(BMI_FORTRAN_ISO_C_LIB_PATH
+    NAMES
+        "${BMI_FORTRAN_ISO_C_LIB_NAME}"
+        "iso_c_bmi"
+    HINTS # Searched before paths
+        "${BMI_FORTRAN_ISO_C_LIB_DIR}" 
+    PATHS
+        ENV BMI_FORTRAN_ISO_C_LIB_DIR
+        "${NGEN_ROOT_DIR}/extern/iso_c_fortran_bmi/cmake_build"
+        "${NGEN_ROOT_DIR}/extern/iso_c_fortran_bmi/build"
+    DOC "Path to middleware Fortran shared lib handling iso_c_binding"
+)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(BMI_FORTRAN_ISO_C DEFAULT_MSG BMI_FORTRAN_ISO_C_LIB_PATH)
+
+if(BMI_FORTRAN_ISO_C_FOUND)
+    add_library(bmi_fortran_iso_c SHARED IMPORTED)
+    set_target_properties(bmi_fortran_iso_c PROPERTIES IMPORTED_LOCATION "${BMI_FORTRAN_ISO_C_LIB_PATH}")
+endif()
diff --git a/cmake/FindNetCDF.cmake b/cmake/FindNetCDF.cmake
index 141268b26f..4a9debf5c4 100644
--- a/cmake/FindNetCDF.cmake
+++ b/cmake/FindNetCDF.cmake
@@ -133,3 +133,13 @@ endfunction()
 if (NETCDF_INCLUDE_DIR)
   FindNetCDF_get_is_parallel_aware("${NETCDF_INCLUDE_DIR}")
 endif ()
+
+if(NETCDF_FOUND)
+  # Create NetCDF target
+  add_library(NetCDF SHARED IMPORTED GLOBAL)
+  target_include_directories(NetCDF INTERFACE "${NETCDF_INCLUDE_DIR}" "${NETCDF_CXX_INCLUDE_DIR}")
+  set_target_properties(NetCDF
+      PROPERTIES
+          IMPORTED_LOCATION "${NETCDF_LIBRARY}"
+          IMPORTED_LOCATION "${NETCDF_CXX_LIBRARY}")
+endif()
diff --git a/cmake/FindUDUNITS2.cmake b/cmake/FindUDUNITS2.cmake
index ec41ba2281..643157c588 100644
--- a/cmake/FindUDUNITS2.cmake
+++ b/cmake/FindUDUNITS2.cmake
@@ -21,7 +21,14 @@ endif()
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(UDUNITS2 DEFAULT_MSG UDUNITS2_LIBRARY UDUNITS2_INCLUDE)
 
-# Based on: https://stackoverflow.com/questions/26834553/osx-10-10-cmake-3-0-2-and-clang-wont-find-local-headers
 if(UDUNITS2_FOUND)
+    # Create UDUNITS2 target
+    # Note: GLOBAL is required here in order to extend the scope of the target.
+    #       see: https://stackoverflow.com/a/46491758/6891484
+    add_library(libudunits2 SHARED IMPORTED GLOBAL)
+    set_target_properties(libudunits2 PROPERTIES IMPORTED_LOCATION "${UDUNITS2_LIBRARY}")
+    target_include_directories(libudunits2 INTERFACE "${UDUNITS2_INCLUDE}")
+
+    # Based on: https://stackoverflow.com/questions/26834553/osx-10-10-cmake-3-0-2-and-clang-wont-find-local-headers
     include_directories(${UDUNITS2_INCLUDE})
 endif()
diff --git a/src/realizations/catchment/CMakeLists.txt b/src/realizations/catchment/CMakeLists.txt
index c4d340ca5c..d62626d267 100644
--- a/src/realizations/catchment/CMakeLists.txt
+++ b/src/realizations/catchment/CMakeLists.txt
@@ -24,5 +24,5 @@ if(NGEN_WITH_PYTHON)
 endif()
 
 if(NGEN_WITH_BMI_FORTRAN)
-    target_link_libraries(realizations_catchment PUBLIC bmi_fortran_compat)
+    target_link_libraries(realizations_catchment PUBLIC bmi_fortran_iso_c)
 endif()

From cc00b903aac03b1ef38cf64171d8a01c5c7c196b Mon Sep 17 00:00:00 2001
From: Phil Miller <philip.miller@noaa.gov>
Date: Fri, 15 Sep 2023 05:35:36 -0700
Subject: [PATCH 36/39] Add missing gmock dependency in individual test

---
 test/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index bfa060ff37..9e3834e946 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -157,6 +157,7 @@ ngen_add_test(
     OBJECTS
         utils/Partition_Test.cpp
     LIBRARIES
+        gmock
         NGen::core
         NGen::geojson
     # REQUIRES

From 2a273d3b98a405f7f2c2619e38f104da0374dd77 Mon Sep 17 00:00:00 2001
From: program-- <justin@justinsingh.me>
Date: Fri, 15 Sep 2023 07:18:59 -0700
Subject: [PATCH 37/39] cmake: update comments for clarity

---
 CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 93e44a83ec..88cab046e7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -13,7 +13,7 @@ cmake_policy(SET CMP0094 NEW)
 # https://cmake.org/cmake/help/latest/policy/CMP0074.html
 cmake_policy(SET CMP0074 NEW)
 
-# find_package() uses upper-case <PACKAGENAME>_ROOT variables.
+# find_package() uses upper-case <PACKAGENAME>_ROOT variables in conjunction with CMP0074.
 # https://cmake.org/cmake/help/latest/policy/CMP0144.html
 if(POLICY CMP0144)
     cmake_policy(SET CMP0144 NEW)
@@ -97,7 +97,7 @@ if(NGEN_WITH_MPI)
 endif()
 
 # -----------------------------------------------------------------------------
-# FIXME: Is this needed for icpx? or even icpp? This only enables support for SYCL - Justin
+# TODO: Used for compatibility on Hera. Refactor this in the future.
 # https://www.intel.com/content/www/us/en/develop/documentation/oneapi-dpcpp-cpp-compiler-dev-guide-and-reference/top/compiler-setup/use-the-command-line/use-cmake-with-the-compiler.html
 if(INTEL_DPCPP)
     find_package(IntelDPCPP REQUIRED)

From aaa50719b4b86a482a30378bfded932d84369be3 Mon Sep 17 00:00:00 2001
From: Phil Miller <philip.miller@noaa.gov>
Date: Fri, 15 Sep 2023 08:13:12 -0700
Subject: [PATCH 38/39] Add another missing dependence on gmock

---
 test/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 9e3834e946..d2c3d178b1 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -248,6 +248,7 @@ ngen_add_test(
         realizations/catchments/Bmi_Py_Formulation_Test.cpp
         realizations/catchments/Bmi_Multi_Formulation_Test.cpp
     LIBRARIES
+        gmock
         NGen::core
         NGen::realizations_catchment
         NGen::core_mediator

From f88b74bf2c53184bb24c139a12677ac84212adf9 Mon Sep 17 00:00:00 2001
From: "Justin Singh-M. - NOAA" <jsingh.school@gmail.com>
Date: Fri, 15 Sep 2023 12:32:45 -0700
Subject: [PATCH 39/39] cmake: fix FindNetCDF linkage

Co-authored-by: Phil Miller - NOAA <unmobile+gh@gmail.com>
---
 cmake/FindNetCDF.cmake | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cmake/FindNetCDF.cmake b/cmake/FindNetCDF.cmake
index 4a9debf5c4..954e76003c 100644
--- a/cmake/FindNetCDF.cmake
+++ b/cmake/FindNetCDF.cmake
@@ -138,6 +138,7 @@ if(NETCDF_FOUND)
   # Create NetCDF target
   add_library(NetCDF SHARED IMPORTED GLOBAL)
   target_include_directories(NetCDF INTERFACE "${NETCDF_INCLUDE_DIR}" "${NETCDF_CXX_INCLUDE_DIR}")
+  target_link_libraries(NetCDF INTERFACE "${NETCDF_LIBRARY}" "${NETCDF_CXX_LIBRARY}")
   set_target_properties(NetCDF
       PROPERTIES
           IMPORTED_LOCATION "${NETCDF_LIBRARY}"