Merge commit '4e0cbe1b4fc5c07f40e5fdde480462152d945bdb'

Author: Darth Vader

src/phast/PhreeqcRM/.github/workflows/ci.yml

@@ -390,16 +390,15 @@ jobs:
         compiler: intel-classic
         version: '2021.10'
 
-    - name: Unset CC/CXX (Windows)
+    - name: Set CC/CXX (Windows)
       if: runner.os == 'Windows'
       shell: bash
       run: |
-        echo "CC=" >> $GITHUB_ENV
-        echo "CXX=" >> $GITHUB_ENV   
+        echo "CC=cl" >> $GITHUB_ENV
+        echo "CXX=cl" >> $GITHUB_ENV   
 
     - name: Install ninja valgrind (Linux)
       if: ${{ runner.os == 'Linux' }}
-      #run: sudo apt-get install -y ninja-build valgrind libyaml-cpp-dev python3-numpy
       run: |
         sudo apt-get -y update
         sudo apt-get install -y ninja-build valgrind
@@ -437,12 +436,6 @@ jobs:
         python -m pip install pytest
         # @todo if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
-    - name: Set up Visual Studio shell (Windows)
-      if: runner.os == 'Windows'
-      uses: egor-tensin/vs-shell@v2
-      with:
-        arch: x64
-
     - name: Extract tarball
       run: tar xvzf phreeqcrm-${{ env.VER_STRING }}.tar.gz
 

src/phast/PhreeqcRM/.github/workflows/wheels.yml

@@ -40,10 +40,12 @@ jobs:
           - [cp38, v141]
           - [cp39, v141]
           - [cp310, v141]
-          - [pp310, v141]
           - [cp311, v141]
+          - [cp312, v142]
           - [cp313, v142]
           # - [cp313t, v142]
+          - [pp310, v141]
+
         exclude:
           # cp313(i686) on ubuntu-20.04
           - buildplat: [ubuntu-20.04, manylinux_i686, i686]
@@ -88,11 +90,19 @@ jobs:
         run: |
           python --version
 
+      # free some space to prevent reaching GHA disk space limits
+      - name: Clean docker images
+        if: runner.os == 'Linux'
+        run: |
+          docker system prune -a -f
+          df -h
+
       - name: Setup QEMU
         if: runner.os == 'Linux'
         uses: docker/setup-qemu-action@v3
         with:
-          platforms: all
+          image: tonistiigi/binfmt:qemu-v8.1.5
+          #platforms: all
 
       - name: Build wheels (Linux)
         if: ${{ runner.os == 'Linux' }}

src/phast/PhreeqcRM/CMakeLists.txt

@@ -35,22 +35,12 @@ if(PHREEQCRM_FORTRAN_TESTING)
   enable_language(Fortran)
 endif()
 
+# Include FetchContent module
+include(FetchContent)
+
 if(DEFINED SKBUILD)
   # SKBUILD is defined when scikit-build-core is used to build python wheels (see pyproject.toml)
 
-  # Include FetchContent module
-  include(FetchContent)
-
-  # Fetch yaml-cpp
-  FetchContent_Declare(
-    yaml-cpp
-    URL https://github.com/jbeder/yaml-cpp/archive/refs/tags/0.8.0.tar.gz
-  )
-
-  # Make yaml-cpp available
-  FetchContent_MakeAvailable(yaml-cpp)
-
-
   # Fetch zlib
   FetchContent_Declare(
     zlib
@@ -68,10 +58,28 @@ if(DEFINED SKBUILD)
   # SKBUILD is defined when scikit-build-core is used to build python wheels (see pyproject.toml)
   set(PHREEQCRM_WITH_YAML_CPP ON)
 endif()
-if(PHREEQCRM_WITH_YAML_CPP AND NOT DEFINED SKBUILD)
+if(PHREEQCRM_WITH_YAML_CPP)
+  # Initialize a static build for yaml-cpp
+  # w/o the FORCE option the user can override using -DYAML_BUILD_SHARED_LIBS=ON
+  set(YAML_BUILD_SHARED_LIBS OFF CACHE STRING "")
+  # w/o the FORCE option the user can override using -DYAML_CPP_INSTALL=OFF
+  set(YAML_CPP_INSTALL ON CACHE STRING "")
+
+  # Fetch yaml-cpp
+  FetchContent_Declare(
+    yaml-cpp
+    URL https://github.com/jbeder/yaml-cpp/archive/refs/tags/0.8.0.tar.gz
+    OVERRIDE_FIND_PACKAGE
+  )
+
+  # The following will automatically forward through to FetchContent_MakeAvailable()
   find_package(yaml-cpp REQUIRED)
   if(yaml-cpp_FOUND)
-    message(STATUS "Found yaml-cpp: TRUE (found version \"${yaml-cpp_VERSION}\")")
+    if(DEFINED yaml-cpp_VERSION)
+      message(STATUS "Found yaml-cpp: TRUE (found version \"${yaml-cpp_VERSION}\")")
+    else()
+      message(STATUS "Found yaml-cpp: TRUE")
+    endif()
   endif()
 endif()
 
@@ -314,8 +322,8 @@ target_include_directories(PhreeqcRM
 include(GenerateExportHeader)
 generate_export_header(PhreeqcRM BASE_NAME IRM_DLL)
 
-# c++11
-target_compile_features(PhreeqcRM PUBLIC cxx_std_11)
+# c++14
+target_compile_features(PhreeqcRM PUBLIC cxx_std_14)
 
 # iphreeqc defs
 target_compile_definitions(PhreeqcRM PRIVATE SWIG_SHARED_OBJ)
@@ -526,13 +534,23 @@ if(STANDALONE_BUILD EQUAL 1 AND NOT DEFINED SKBUILD)
     DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/PhreeqcRM
   )
 
-  install(TARGETS PhreeqcRM
-    EXPORT   PhreeqcRMTargets
-    LIBRARY  DESTINATION ${CMAKE_INSTALL_LIBDIR}
-    ARCHIVE  DESTINATION ${CMAKE_INSTALL_LIBDIR}
-    RUNTIME  DESTINATION ${CMAKE_INSTALL_BINDIR}
-    INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
-  )
+  if(PHREEQCRM_WITH_YAML_CPP AND yaml-cpp_FOUND)
+    install(TARGETS PhreeqcRM yaml-cpp
+      EXPORT   PhreeqcRMTargets
+      LIBRARY  DESTINATION ${CMAKE_INSTALL_LIBDIR}
+      ARCHIVE  DESTINATION ${CMAKE_INSTALL_LIBDIR}
+      RUNTIME  DESTINATION ${CMAKE_INSTALL_BINDIR}
+      INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+    )
+  else()
+    install(TARGETS PhreeqcRM
+      EXPORT   PhreeqcRMTargets
+      LIBRARY  DESTINATION ${CMAKE_INSTALL_LIBDIR}
+      ARCHIVE  DESTINATION ${CMAKE_INSTALL_LIBDIR}
+      RUNTIME  DESTINATION ${CMAKE_INSTALL_BINDIR}
+      INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+    )
+  endif()
 
   install(EXPORT PhreeqcRMTargets
     FILE PhreeqcRMTargets.cmake

src/phast/PhreeqcRM/configure.ac

@@ -69,8 +69,8 @@ AC_PROG_AWK
 AC_PROG_CPP
 AC_PROG_LN_S
 
-# c++11 is required
-AX_CXX_COMPILE_STDCXX(11, [ext], [mandatory])
+# c++14 is required
+AX_CXX_COMPILE_STDCXX(14, [ext], [mandatory])
 
 # Check if the fortran test should be included
 AC_MSG_CHECKING([if Fortran test is added])

src/phast/PhreeqcRM/mamba.environment.yml

@@ -8,5 +8,4 @@ dependencies:
 - python
 - pyyaml
 - swig
-- yaml-cpp
 - cmake

src/phast/PhreeqcRM/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "phreeqcrm"
-version = "0.0.12"
+version = "0.0.14"
 description = "A reaction module for transport simulators based on the geochemical model PHREEQC."
 readme = "README.md"
 requires-python = ">=3.8"

src/phast/PhreeqcRM/src/BMIPhreeqcRM.cpp

@@ -149,10 +149,10 @@ void BMIPhreeqcRM::ClearBMISelectedOutput(void)
 	assert(this->var_man);
 	this->var_man->BMISelectedOutput.clear();
 }
-void BMIPhreeqcRM::Construct(PhreeqcRM::Initializer i)
+void BMIPhreeqcRM::Construct()
 {
 	if (constructed) return;
-	this->PhreeqcRM::Construct(i);
+	this->PhreeqcRM::Construct();
 	this->var_man = new VarManager((PhreeqcRM*)this);
 #if defined(WITH_PYBIND11)
 	this->_initialized = true;
@@ -180,13 +180,13 @@ void BMIPhreeqcRM::Initialize(std::string config_file)
 			std::string keyword = it1++->second.as<std::string>();
 			if (keyword == "SetGridCellCount")
 			{
-				this->initializer.nxyz_arg = it1++->second.as<int>();
+				set_nxyz(it1++->second.as<int>());
 				found_nxyz = true;
 			}
 			if (keyword == "ThreadCount")
 			{
 #if !defined(USE_MPI)
-				this->initializer.data_for_parallel_processing = it1++->second.as<int>();
+				set_data_for_parallel_processing(it1++->second.as<int>());
 #endif
 				found_threads = true;
 			}
@@ -195,7 +195,7 @@ void BMIPhreeqcRM::Initialize(std::string config_file)
 	}
 #endif
 
-	this->Construct(this->initializer);
+	this->Construct();
 	constructed = true;
 #ifdef USE_YAML
 	if (config_file.size() != 0)
@@ -1321,6 +1321,14 @@ RMVARS BMIPhreeqcRM::GetEnum(const std::string name)
 	return RMVARS::NotFound;
 };
 
-//////////////////
+/* ---------------------------------------------------------------------- */
+IRM_RESULT
+BMIPhreeqcRM::LoadDatabase(const std::string& database)
+/* ---------------------------------------------------------------------- */
+{
+	// reqd for swig-python
+	return this->PhreeqcRM::LoadDatabase(database);
+}
 
+//////////////////
 

src/phast/PhreeqcRM/src/BMIPhreeqcRM.h

@@ -1271,6 +1271,8 @@ class IRM_DLL_EXPORT BMIPhreeqcRM : public bmi::Bmi, public PhreeqcRM
     //  std::set<std::string> UpdateMap;
     // std::set<std::string>& GetUpdateMap() { return UpdateMap; }
 
+    IRM_RESULT                          LoadDatabase(const std::string& database) override;
+
 #if defined(WITH_PYBIND11)
 
     py::array BMIPhreeqcRM::get_value(std::string name, py::array arr);
@@ -1297,7 +1299,7 @@ class IRM_DLL_EXPORT BMIPhreeqcRM : public bmi::Bmi, public PhreeqcRM
 #endif
 
 protected:
-    void Construct(Initializer initializer) override;
+    void Construct(void) override;
 
 private:
     //friend class RM_interface;

src/phast/PhreeqcRM/src/PhreeqcRM.cpp

@@ -69,6 +69,19 @@
 	const MP_TYPE PhreeqcRM::default_data_for_parallel_processing = -1;
 #endif
 
+// Pimpl for initialization
+class PhreeqcRM::Initializer
+{
+
+public:
+	Initializer() : nxyz_arg(default_nxyz), data_for_parallel_processing(default_data_for_parallel_processing), io(nullptr) {}
+	Initializer(int nxyz, MP_TYPE data, PHRQ_io *pio) : nxyz_arg(nxyz), data_for_parallel_processing(data), io(pio) {}
+
+public:
+	int nxyz_arg;
+	MP_TYPE data_for_parallel_processing;
+	PHRQ_io *io;
+};
 
 //// static PhreeqcRM methods
 /* ---------------------------------------------------------------------- */
@@ -169,7 +182,7 @@ PhreeqcRM::PhreeqcRM(int nxyz_arg, MP_TYPE data_for_parallel_processing, PHRQ_io
 , mpi_worker_callback_c( nullptr )
 , mpi_worker_callback_cookie( nullptr )
 , species_save_on( false )
-, initializer( nxyz_arg, data_for_parallel_processing, io )
+, initializer(std::make_unique<PhreeqcRM::Initializer>(nxyz_arg, data_for_parallel_processing, io))
 {
 #ifdef USE_MPI
 	phreeqcrm_comm = data_for_parallel_processing;
@@ -188,24 +201,24 @@ PhreeqcRM::PhreeqcRM(int nxyz_arg, MP_TYPE data_for_parallel_processing, PHRQ_io
 #ifdef USE_MPI
 		if (mpi_myself == 0)
 		{
-			this->Construct(this->initializer);
+			this->Construct();
 			MpiWorkerBreak();
 		}
 		else
 		{
 			MpiWorker();
 		}
 #else
-		this->Construct(this->initializer);
+		this->Construct();
 #endif
 	}
 }
 
-void PhreeqcRM::Construct(PhreeqcRM::Initializer i)
+void PhreeqcRM::Construct()
 {
-	int nxyz_arg = i.nxyz_arg;
-	MP_TYPE data_for_parallel_processing = i.data_for_parallel_processing;
-	//PHRQ_io *io = i.io;
+	int nxyz_arg                         = this->initializer->nxyz_arg;
+	MP_TYPE data_for_parallel_processing = this->initializer->data_for_parallel_processing;
+	//PHRQ_io* io                          = this->initializer->io;
 #ifdef USE_MPI
 	if (mpi_myself == 0)
 	{
@@ -5631,7 +5644,8 @@ IRM_RESULT		PhreeqcRM::InitializeYAML(std::string config)
 			if (keyword == "LoadDatabase")
 			{
 				std::string file = it1++->second.as< std::string >();
-				this->LoadDatabase(file);
+				// no need to check for initialization just call base class
+				this->PhreeqcRM::LoadDatabase(file);
 				continue;
 			}
 			if (keyword == "OpenFiles")
@@ -7035,7 +7049,7 @@ PhreeqcRM::MpiWorker()
 			case METHOD_CONSTRUCT:
 				if (debug_worker) std::cerr << "METHOD_CONSTRUCT" << std::endl;
 				{
-					this->Construct(this->initializer);
+					this->Construct();
 				}
 				break;
 			case METHOD_CREATEMAPPING:
@@ -13028,6 +13042,27 @@ PhreeqcRM::WarningMessage(const std::string &str)
 		this->phreeqcrm_io->warning_msg(str.c_str());
 	}
 }
+/* ---------------------------------------------------------------------- */
+void
+PhreeqcRM::set_data_for_parallel_processing(int value)
+/* ---------------------------------------------------------------------- */
+{
+	this->initializer->data_for_parallel_processing = value;
+}
+/* ---------------------------------------------------------------------- */
+void
+PhreeqcRM::set_nxyz(int value)
+/* ---------------------------------------------------------------------- */
+{
+	this->initializer->nxyz_arg = value;
+}
+/* ---------------------------------------------------------------------- */
+void
+PhreeqcRM::set_io(PHRQ_io *value)
+/* ---------------------------------------------------------------------- */
+{
+	this->initializer->io = value;
+}