pyEQL 1.4.0rc9__cp312-cp312-macosx_10_13_x86_64.whl

pyEQL/phreeqc/ext/README.md

@@ -0,0 +1,10 @@
+## External Dependencies
+
+### IPhreeqc
+
+The contents of the `iphreeqc-3.8.6-17100` folder are extracted from the IPhreeqc module ("Linux (any processor)")
+downloaded from `https://www.usgs.gov/software/phreeqc-version-3`.
+
+Specfically, at the time of writing (10/31/2025), the file
+`https://water.usgs.gov/water-resources/software/PHREEQC/iphreeqc-3.8.6-17100.tar.gz`
+(md5sum: `91d8485139b423d5f0382e9215d9aea1`)

pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/CMakeLists.txt

@@ -0,0 +1,476 @@
+# CMAKE_MSVC_RUNTIME_LIBRARY requires 3.15
+cmake_minimum_required(VERSION 3.20)
+
+project (
+  IPhreeqc
+  VERSION 3.8.6
+  LANGUAGES CXX C
+  )
+
+# check if this is the root project
+if (CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
+  set(STANDALONE_BUILD 1)
+else()
+  set(STANDALONE_BUILD 0)
+endif()
+
+if (STANDALONE_BUILD)
+  # Set a default build type if none was specified
+  set(default_build_type "Release")
+  if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+    set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
+      STRING "Choose the type of build." FORCE)
+    # Set the possible values of build type for cmake-gui
+    set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+      "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+  endif()
+endif()
+
+# override docdir on windows
+if (WIN32 AND NOT CMAKE_INSTALL_DOCDIR)
+  set(CMAKE_INSTALL_DOCDIR "" CACHE PATH "documentation root (doc)")
+  set(CMAKE_INSTALL_DOCDIR "doc")
+endif()
+
+# set standard directory locations
+include(GNUInstallDirs)
+
+if (STANDALONE_BUILD AND MSVC)
+  option (IPHREEQC_STATIC_RUNTIME "Build with a static runtime" OFF)
+  if (IPHREEQC_STATIC_RUNTIME)
+    # compile with static runtime
+    set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
+  endif()
+endif()
+
+# Fortran
+option (IPHREEQC_ENABLE_MODULE "Enable Fortran module" ON)
+if (STANDALONE_BUILD)
+  if (IPHREEQC_FORTRAN_TESTING)
+    enable_language(Fortran)
+  else()
+    if (CMAKE_Fortran_COMPILER)
+      option (IPHREEQC_FORTRAN_TESTING "Build Fortran test" ON)
+    else()
+      option (IPHREEQC_FORTRAN_TESTING "Build Fortran test" OFF)
+    endif()
+  endif()
+endif()
+
+# compile Var.c as c++
+set_source_files_properties(src/Var.c PROPERTIES LANGUAGE CXX)
+
+if (STANDALONE_BUILD)
+  option(BUILD_SHARED_LIBS "Build Shared Libraries" OFF)
+  set(LIB_TYPE STATIC)
+endif()
+
+if (STANDALONE_BUILD)
+  if (MSVC)
+    option(BUILD_CLR_LIBS "Build CLR Libraries" OFF)
+  endif()
+endif()
+
+if (BUILD_SHARED_LIBS)
+  set(LIB_TYPE SHARED)
+endif()
+
+add_library(IPhreeqc ${LIB_TYPE} src/IPhreeqc.cpp)
+
+target_sources(IPhreeqc
+  PRIVATE
+    src/CSelectedOutput.cpp
+    src/CSelectedOutput.hxx
+    src/CVar.hxx
+    src/Debug.h
+    src/ErrorReporter.hxx
+    src/IPhreeqc.h
+    src/IPhreeqc.hpp
+    src/IPhreeqc_interface_F.cpp
+    src/IPhreeqcCallbacks.h
+    src/IPhreeqcLib.cpp
+    src/phreeqcpp/advection.cpp
+    src/phreeqcpp/basicsubs.cpp
+    src/phreeqcpp/cl1.cpp
+    src/phreeqcpp/common/Parser.cxx
+    src/phreeqcpp/common/Parser.h
+    src/phreeqcpp/common/PHRQ_base.cxx
+    src/phreeqcpp/common/PHRQ_base.h
+    src/phreeqcpp/common/PHRQ_exports.h
+    src/phreeqcpp/common/PHRQ_io.cpp
+    src/phreeqcpp/common/PHRQ_io.h
+    src/phreeqcpp/common/phrqtype.h
+    src/phreeqcpp/common/Utils.cxx
+    src/phreeqcpp/common/Utils.h
+    src/phreeqcpp/cvdense.cpp
+    src/phreeqcpp/cvdense.h
+    src/phreeqcpp/cvode.cpp
+    src/phreeqcpp/cvode.h
+    src/phreeqcpp/cxxKinetics.cxx
+    src/phreeqcpp/cxxKinetics.h
+    src/phreeqcpp/cxxMix.cxx
+    src/phreeqcpp/cxxMix.h
+    src/phreeqcpp/dense.cpp
+    src/phreeqcpp/dense.h
+    src/phreeqcpp/Dictionary.cpp
+    src/phreeqcpp/Dictionary.h
+    src/phreeqcpp/dumper.cpp
+    src/phreeqcpp/dumper.h
+    src/phreeqcpp/Exchange.cxx
+    src/phreeqcpp/Exchange.h
+    src/phreeqcpp/ExchComp.cxx
+    src/phreeqcpp/ExchComp.h
+    src/phreeqcpp/GasComp.cxx
+    src/phreeqcpp/GasComp.h
+    src/phreeqcpp/gases.cpp
+    src/phreeqcpp/GasPhase.cxx
+    src/phreeqcpp/GasPhase.h
+    src/phreeqcpp/global_structures.h
+    src/phreeqcpp/input.cpp
+    src/phreeqcpp/integrate.cpp
+    src/phreeqcpp/inverse.cpp
+    src/phreeqcpp/ISolution.cxx
+    src/phreeqcpp/ISolution.h
+    src/phreeqcpp/ISolutionComp.cxx
+    src/phreeqcpp/ISolutionComp.h
+    src/phreeqcpp/isotopes.cpp
+    src/phreeqcpp/kinetics.cpp
+    src/phreeqcpp/KineticsComp.cxx
+    src/phreeqcpp/KineticsComp.h
+    src/phreeqcpp/mainsubs.cpp
+    src/phreeqcpp/model.cpp
+    src/phreeqcpp/NA.h
+    src/phreeqcpp/NameDouble.cxx
+    src/phreeqcpp/NameDouble.h
+    src/phreeqcpp/NumKeyword.cxx
+    src/phreeqcpp/NumKeyword.h
+    src/phreeqcpp/nvector.cpp
+    src/phreeqcpp/nvector.h
+    src/phreeqcpp/nvector_serial.cpp
+    src/phreeqcpp/nvector_serial.h
+    src/phreeqcpp/parse.cpp
+    src/phreeqcpp/PBasic.cpp
+    src/phreeqcpp/PBasic.h
+    src/phreeqcpp/phqalloc.cpp
+    src/phreeqcpp/phqalloc.h
+    src/phreeqcpp/Phreeqc.cpp
+    src/phreeqcpp/Phreeqc.h
+    src/phreeqcpp/PhreeqcKeywords/Keywords.cpp
+    src/phreeqcpp/PhreeqcKeywords/Keywords.h
+    src/phreeqcpp/PHRQ_io_output.cpp
+    src/phreeqcpp/pitzer.cpp
+    src/phreeqcpp/pitzer_structures.cpp
+    src/phreeqcpp/PPassemblage.cxx
+    src/phreeqcpp/PPassemblage.h
+    src/phreeqcpp/PPassemblageComp.cxx
+    src/phreeqcpp/PPassemblageComp.h
+    src/phreeqcpp/prep.cpp
+    src/phreeqcpp/Pressure.cxx
+    src/phreeqcpp/Pressure.h
+    src/phreeqcpp/print.cpp
+    src/phreeqcpp/Reaction.cxx
+    src/phreeqcpp/Reaction.h
+    src/phreeqcpp/read.cpp
+    src/phreeqcpp/ReadClass.cxx
+    src/phreeqcpp/readtr.cpp
+    src/phreeqcpp/runner.cpp
+    src/phreeqcpp/runner.h
+    src/phreeqcpp/SelectedOutput.cpp
+    src/phreeqcpp/SelectedOutput.h
+    src/phreeqcpp/Serializer.cxx
+    src/phreeqcpp/Serializer.h
+    src/phreeqcpp/sit.cpp
+    src/phreeqcpp/smalldense.cpp
+    src/phreeqcpp/smalldense.h
+    src/phreeqcpp/Solution.cxx
+    src/phreeqcpp/Solution.h
+    src/phreeqcpp/SolutionIsotope.cxx
+    src/phreeqcpp/SolutionIsotope.h
+    src/phreeqcpp/spread.cpp
+    src/phreeqcpp/SS.cxx
+    src/phreeqcpp/SS.h
+    src/phreeqcpp/SSassemblage.cxx
+    src/phreeqcpp/SSassemblage.h
+    src/phreeqcpp/SScomp.cxx
+    src/phreeqcpp/SScomp.h
+    src/phreeqcpp/step.cpp
+    src/phreeqcpp/StorageBin.cxx
+    src/phreeqcpp/StorageBin.h
+    src/phreeqcpp/StorageBinList.cpp
+    src/phreeqcpp/StorageBinList.h
+    src/phreeqcpp/structures.cpp
+    src/phreeqcpp/sundialsmath.cpp
+    src/phreeqcpp/sundialsmath.h
+    src/phreeqcpp/sundialstypes.h
+    src/phreeqcpp/Surface.cxx
+    src/phreeqcpp/Surface.h
+    src/phreeqcpp/SurfaceCharge.cxx
+    src/phreeqcpp/SurfaceCharge.h
+    src/phreeqcpp/SurfaceComp.cxx
+    src/phreeqcpp/SurfaceComp.h
+    src/phreeqcpp/System.cxx
+    src/phreeqcpp/System.h
+    src/phreeqcpp/tally.cpp
+    src/phreeqcpp/Temperature.cxx
+    src/phreeqcpp/Temperature.h
+    src/phreeqcpp/tidy.cpp
+    src/phreeqcpp/transport.cpp
+    src/phreeqcpp/Use.cpp
+    src/phreeqcpp/Use.h
+    src/phreeqcpp/UserPunch.cpp
+    src/phreeqcpp/UserPunch.h
+    src/phreeqcpp/utilities.cpp
+    src/thread.h
+    src/Var.c
+    src/Var.h
+    src/Version.h
+)
+
+target_include_directories(IPhreeqc
+  PUBLIC
+    $<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src>
+    $<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src/phreeqcpp>
+    $<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src/phreeqcpp/common>
+    $<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src/phreeqcpp/PhreeqcKeywords>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+  )
+
+target_compile_definitions(IPhreeqc PRIVATE SWIG_SHARED_OBJ)
+target_compile_definitions(IPhreeqc PRIVATE USE_PHRQ_ALLOC)
+
+if (NOT IPHREEQC_ENABLE_MODULE)
+  target_compile_definitions(IPhreeqc
+    PUBLIC
+      IPHREEQC_NO_FORTRAN_MODULE
+  )
+
+  target_sources(IPhreeqc
+    PRIVATE
+      src/fimpl.h
+      src/fwrap.cpp
+      src/fwrap1.cpp
+      src/fwrap2.cpp
+      src/fwrap3.cpp
+      src/fwrap4.cpp
+      src/fwrap5.cpp
+      src/fwrap6.cpp
+      src/fwrap7.cpp
+      src/fwrap8.cpp
+  )
+endif()
+
+if (${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC)
+  target_compile_options(IPhreeqc PRIVATE /wd4251 /wd4275 /wd4793)
+endif()
+
+# Disable deprecation warnings for standard C and STL functions in VS2005
+# and later
+if (MSVC_VERSION EQUAL 1400 OR MSVC_VERSION GREATER 1400)
+  target_compile_definitions(IPhreeqc PUBLIC _CRT_SECURE_NO_DEPRECATE)
+  target_compile_definitions(IPhreeqc PUBLIC _SCL_SECURE_NO_WARNINGS)
+endif()
+
+if (WIN32 AND BUILD_SHARED_LIBS)
+  # Required to build IMPLIB
+  # (Seems to be automatically set when using Visual Studio as the generator)
+  target_compile_definitions(IPhreeqc PRIVATE _WINDLL)
+endif()
+
+# Allow user to override POSTFIX properties (but mandate them so that
+# all builds can be installed to the same directory)
+if (NOT CMAKE_DEBUG_POSTFIX)
+  set_target_properties(IPhreeqc PROPERTIES DEBUG_POSTFIX "d")
+endif()
+
+if (NOT CMAKE_MINSIZEREL_POSTFIX)
+  set_target_properties(IPhreeqc PROPERTIES MINSIZEREL_POSTFIX "msr")
+endif()
+
+if (NOT CMAKE_RELWITHDEBINFO_POSTFIX)
+  set_target_properties(IPhreeqc PROPERTIES RELWITHDEBINFO_POSTFIX "rwd")
+endif()
+
+set(IPhreeqc_Headers
+  ${PROJECT_SOURCE_DIR}/src/IPhreeqc.h
+  ${PROJECT_SOURCE_DIR}/src/IPhreeqc.hpp
+  ${PROJECT_SOURCE_DIR}/src/IPhreeqcCallbacks.h
+  ${PROJECT_SOURCE_DIR}/src/phreeqcpp/PhreeqcKeywords/Keywords.h
+  ${PROJECT_SOURCE_DIR}/src/phreeqcpp/common/PHRQ_exports.h
+  ${PROJECT_SOURCE_DIR}/src/phreeqcpp/common/PHRQ_io.h
+  ${PROJECT_SOURCE_DIR}/src/Var.h
+  )
+
+if (IPHREEQC_ENABLE_MODULE)
+  set(IPhreeqc_SRC
+    ${PROJECT_SOURCE_DIR}/src/IPhreeqc_interface.F90
+    ${PROJECT_SOURCE_DIR}/src/README.Fortran
+    )
+else()
+  # always install README.Fortran
+  set(IPhreeqc_SRC
+    ${PROJECT_SOURCE_DIR}/src/README.Fortran
+    )
+  # install old fortran include files
+  set(IPhreeqc_Headers
+    ${IPhreeqc_Headers}
+    ${PROJECT_SOURCE_DIR}/src/IPhreeqc.f.inc
+    ${PROJECT_SOURCE_DIR}/src/IPhreeqc.f90.inc
+    )
+endif()
+
+# Setup references for /CLR
+if (MSVC AND BUILD_SHARED_LIBS AND BUILD_CLR_LIBS)
+  if (MSVC_VERSION LESS 1600)
+    message(FATAL_ERROR "CLR options must be set manually for versions prior to Visual Studio 2010")
+  endif()
+  set_target_properties(IPhreeqc PROPERTIES VS_DOTNET_REFERENCES "System;System.Drawing;System.Windows.Forms;${CMAKE_CURRENT_SOURCE_DIR}/src/phreeqcpp/ZedGraph.dll")
+  set_target_properties(IPhreeqc PROPERTIES COMMON_LANGUAGE_RUNTIME "")
+  target_compile_definitions(IPhreeqc PRIVATE "MULTICHART")
+endif()
+
+set_target_properties(IPhreeqc PROPERTIES
+  VERSION "${IPhreeqc_VERSION}"
+  SOVERSION "${IPhreeqc_VERSION_MAJOR}"
+  )
+
+# install
+if (STANDALONE_BUILD)
+
+  include(CMakePackageConfigHelpers)
+
+  configure_package_config_file(IPhreeqcConfig.cmake.in
+    ${CMAKE_CURRENT_BINARY_DIR}/IPhreeqcConfig.cmake
+    INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/IPhreeqc
+    )
+
+  write_basic_package_version_file("IPhreeqcConfigVersion.cmake"
+    VERSION ${IPhreeqc_VERSION}
+    COMPATIBILITY SameMajorVersion
+    )
+
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/IPhreeqcConfig.cmake ${CMAKE_CURRENT_BINARY_DIR}/IPhreeqcConfigVersion.cmake
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/IPhreeqc
+    )
+
+  install(TARGETS  IPhreeqc
+    EXPORT   IPhreeqcTargets
+    LIBRARY  DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    ARCHIVE  DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    RUNTIME  DESTINATION ${CMAKE_INSTALL_BINDIR}
+    INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+    )
+  install(EXPORT IPhreeqcTargets
+    FILE IPhreeqcTargets.cmake
+    NAMESPACE IPhreeqc::
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/IPhreeqc
+    )
+
+  install(FILES ${IPhreeqc_Headers} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+  if (WIN32)
+    install(FILES ${IPhreeqc_SRC} DESTINATION src)
+  else()
+    install(FILES ${IPhreeqc_SRC} DESTINATION ${CMAKE_INSTALL_DOCDIR}/src)
+  endif()
+  if (BUILD_CLR_LIBS)
+    install(FILES "${PROJECT_SOURCE_DIR}/src/phreeqcpp/ZedGraph.dll" DESTINATION ${CMAKE_INSTALL_BINDIR})
+  endif()
+endif()
+
+if (BUILD_CLR_LIBS)
+  if (NOT BUILD_SHARED_LIBS)
+    message(FATAL_ERROR "BUILD_CLR_LIBS requires that BUILD_SHARED_LIBS be set")
+  endif()
+
+  if (IPHREEQC_STATIC_RUNTIME)
+    message(FATAL_ERROR "BUILD_CLR_LIBS and IPHREEQC_STATIC_RUNTIME are mutually exclusive")
+  endif()
+
+  # CLR files
+  target_sources(IPhreeqc
+    PRIVATE
+      src/phreeqcpp/ChartHandler.cpp
+      src/phreeqcpp/ChartHandler.h
+      src/phreeqcpp/ChartObject.cpp
+      src/phreeqcpp/ChartObject.h
+      src/phreeqcpp/CurveObject.cpp
+      src/phreeqcpp/CurveObject.h
+  )
+
+endif()
+
+include (CTest)
+
+if (STANDALONE_BUILD)
+
+  add_subdirectory(database)
+  add_subdirectory(doc)
+  add_subdirectory(examples)
+
+  if (BUILD_TESTING)
+    add_subdirectory(tests)
+  endif()
+
+
+  if (BUILD_TESTING)  # may need to add MSVC version check
+    include(FetchContent)
+
+    # Avoid warning about DOWNLOAD_EXTRACT_TIMESTAMP in CMake 3.24:
+    if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0")
+      cmake_policy(SET CMP0135 NEW)
+    endif()    
+
+    FetchContent_Declare(
+      googletest
+      URL https://github.com/google/googletest/archive/release-1.12.1.tar.gz
+      )
+
+    mark_as_advanced(
+      FETCHCONTENT_BASE_DIR
+      FETCHCONTENT_FULLY_DISCONNECTED
+      FETCHCONTENT_QUIET
+      FETCHCONTENT_SOURCE_DIR_GOOGLETEST
+      FETCHCONTENT_UPDATES_DISCONNECTED
+      FETCHCONTENT_UPDATES_DISCONNECTED_GOOGLETEST
+      )
+
+    # Prevent GoogleTest from overriding our compiler/linker options
+    # when building with Visual Studio
+    set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
+
+    set(BUILD_GTEST ON CACHE BOOL "" FORCE)
+    set(BUILD_GMOCK ON CACHE BOOL "" FORCE)
+
+    set(INSTALL_GTEST OFF CACHE BOOL "" FORCE)
+    set(INSTALL_GMOCK OFF CACHE BOOL "" FORCE)
+
+    mark_as_advanced(
+      BUILD_GTEST
+      BUILD_GMOCK
+      INSTALL_GTEST
+      INSTALL_GMOCK
+      gmock_build_tests
+      gtest_build_tests
+      gtest_build_samples
+      gtest_disable_pthreads
+      gtest_force_shared_crt
+      gtest_hide_internal_symbols
+      )
+
+    FetchContent_GetProperties(googletest)
+    if (NOT googletest_POPULATED)
+      # Always build googletest static
+      set(SAVE_BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS})
+      set(BUILD_SHARED_LIBS OFF)
+      FetchContent_MakeAvailable(googletest)
+      set(BUILD_SHARED_LIBS ${SAVE_BUILD_SHARED_LIBS})
+    endif()
+
+    add_subdirectory(gtest)
+  endif()
+endif()
+
+# get_cmake_property(_variableNames VARIABLES)
+# list (SORT _variableNames)
+# foreach (_variableName ${_variableNames})
+#   message(STATUS "${_variableName}=${${_variableName}}")
+# endforeach()