Remove exec flag

.project

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>FieldML</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+	</buildSpec>
+	<natures>
+	</natures>
+</projectDescription>

CMakeLists.txt

@@ -34,140 +34,92 @@
  # the terms of any one of the MPL, the GPL or the LGPL.
  #
  # ***** END LICENSE BLOCK ***** */
-
 
-# Set the minimum version of cmake required to 2.6
-CMAKE_MINIMUM_REQUIRED( VERSION 2.6 )
-
-# Set this nampspace to keep these options seperate from other project options
-SET( FIELDML_NAMESPACE_NAME FIELDML )
-PROJECT(fieldml)
-
-MACRO( OPTION_WITH_DEFAULT OPTION_NAME OPTION_STRING OPTION_DEFAULT )
-	IF( NOT DEFINED ${OPTION_NAME} )
-		SET( ${OPTION_NAME} ${OPTION_DEFAULT} )
-	ENDIF( NOT DEFINED ${OPTION_NAME} )
-
-	OPTION( ${OPTION_NAME} "${OPTION_STRING}" ${${OPTION_NAME}} )
-ENDMACRO( OPTION_WITH_DEFAULT OPTION_NAME OPTION_STRING OPTION_DEFAULT )
-
-MACRO( CACHE_VAR_WITH_DEFAULT OPTION_NAME OPTION_DEFAULT OPTION_TYPE OPTION_STRING )
-	IF( NOT DEFINED ${OPTION_NAME} )
-		SET( ${OPTION_NAME} ${OPTION_DEFAULT} )
-	ENDIF( NOT DEFINED ${OPTION_NAME} )
-
-	SET( ${OPTION_NAME} "${OPTION_DEFAULT}" CACHE ${OPTION_TYPE} "${OPTION_STRING}" )
-ENDMACRO( CACHE_VAR_WITH_DEFAULT OPTION_NAME OPTION_DEFAULT OPTION_TYPE OPTION_STRING )
-
-# Set up library options
-# Generic library options
-SET( LIBRARY_TARGET_NAME fieldml )
-
-STRING( TOUPPER ${LIBRARY_TARGET_NAME} UPPERCASE_LIBRARY_TARGET_NAME )
-SET( FIELDML_API_MAJOR_VERSION "0" )
-SET( FIELDML_API_MINOR_VERSION "5" )
-SET( FIELDML_API_PATCH_VERSION "0" )
-
-CACHE_VAR_WITH_DEFAULT( ${UPPERCASE_LIBRARY_TARGET_NAME}_BUILD_TYPE "Release" STRING 
-	"Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel" )
-SET( CMAKE_BUILD_TYPE ${${UPPERCASE_LIBRARY_TARGET_NAME}_BUILD_TYPE} CACHE
-	INTERNAL "Internalise this variable and manipulate with
-	${UPPERCASE_LIBRARY_TARGET_NAME}_BUILD_TYPE" FORCE )
-CACHE_VAR_WITH_DEFAULT( ${UPPERCASE_LIBRARY_TARGET_NAME}_INSTALL_PREFIX
-	"${CMAKE_INSTALL_PREFIX}" PATH 
-	"Install path prefix, prepended onto install directories." )
-SET( CMAKE_INSTALL_PREFIX ${${UPPERCASE_LIBRARY_TARGET_NAME}_INSTALL_PREFIX}
-	CACHE INTERNAL "Internalise this variable and manipulate with
-	${UPPERCASE_LIBRARY_TARGET_NAME}_INSTALL_PREFIX" FORCE )
-OPTION_WITH_DEFAULT( ${UPPERCASE_LIBRARY_TARGET_NAME}_BUILD_STATIC_LIB "Build static zlib" TRUE )
-
-OPTION_WITH_DEFAULT( ${UPPERCASE_LIBRARY_TARGET_NAME}_INSTALL_CONFIG "Do you want to install CMake configuration files?" TRUE )
-
-OPTION_WITH_DEFAULT( ${UPPERCASE_LIBRARY_TARGET_NAME}_USE_HDF5 "Do you want to use hdf5?" FALSE )
-
-OPTION_WITH_DEFAULT( ${UPPERCASE_LIBRARY_TARGET_NAME}_BUILD_JAVA "Do you want to build the Java bindings" FALSE )
-
-
-# Specific library options
-OPTION_WITH_DEFAULT( ${UPPERCASE_LIBRARY_TARGET_NAME}_BUILD_TEST "Build ${LIBRARY_TARGET_NAME} test application" FALSE )
-
-# Define library type settings
-IF( NOT ${UPPERCASE_LIBRARY_TARGET_NAME}_BUILD_TEST )
-        SET( EXCLUDE_TEST EXCLUDE_FROM_ALL )
-ENDIF( NOT ${UPPERCASE_LIBRARY_TARGET_NAME}_BUILD_TEST )
-
-# Run ADD_SUBDIRECTORY command
-SET( LIBRARY_TARGET_NAME fieldml_api )
-SET( FIELDML_API_LIBRARY_TARGET_NAME ${LIBRARY_TARGET_NAME} )
-ADD_SUBDIRECTORY( core )
-SET( LIBRARY_TARGET_NAME fieldml_io_api )
-SET( FIELDML_IO_API_LIBRARY_TARGET_NAME ${LIBRARY_TARGET_NAME} )
-ADD_SUBDIRECTORY( io )
-GET_DIRECTORY_PROPERTY(HDF5_INCLUDE_DIRS DIRECTORY io DEFINITION HDF5_INCLUDE_DIRS)
-GET_DIRECTORY_PROPERTY(HDF5_MINE_LIBRARIES DIRECTORY io DEFINITION HDF5_MINE_LIBRARIES)
-GET_DIRECTORY_PROPERTY(MPI_LIBRARIES DIRECTORY io DEFINITION MPI_MINE_LIBRARIES)
-GET_DIRECTORY_PROPERTY(MPI_INCLUDE_DIRS DIRECTORY io DEFINITION MPI_INCLUDE_DIRS)
-GET_DIRECTORY_PROPERTY(HDF5_USE_MPI DIRECTORY io DEFINITION HDF5_USE_MPI)
-ADD_SUBDIRECTORY( test )
-
-foreach(arg ${MPI_LIBRARIES})
-	set(MPI_MINE_LIBRARIES "${MPI_MINE_LIBRARIES} ${arg}")
-endforeach(arg ${MPI_LIBRARIES})
-
-IF( ${FIELDML_NAMESPACE_NAME}_INSTALL_CONFIG )
-	SET( LIBRARY_CONFIG_FILE ${CMAKE_CURRENT_BINARY_DIR}/fieldml-config.cmake )
-	SET( CONFIG_FILE_CONTENTS 
-		"\nIF( NOT DEFINED _${FIELDML_NAMESPACE_NAME}_CONFIG_CMAKE )"
-		"\nSET( _${FIELDML_NAMESPACE_NAME}_CONFIG_CMAKE TRUE )"
-		"\nGET_FILENAME_COMPONENT( SELF_DIR \"\${CMAKE_CURRENT_LIST_FILE}\" PATH )"
-		"\nINCLUDE( \${SELF_DIR}/fieldml-targets.cmake )"
-		"\nGET_FILENAME_COMPONENT( ${FIELDML_NAMESPACE_NAME}_INCLUDE_DIRS \"\${SELF_DIR}/../../include\" ABSOLUTE )"
-		"\nSET( ${FIELDML_NAMESPACE_NAME}_INCLUDE_DIRS \"\${${FIELDML_NAMESPACE_NAME}_INCLUDE_DIRS}\" \"${LIBXML2_INCLUDE_DIR}\" \"${HDF5_INCLUDE_DIRS}\" \"${MPI_INCLUDE_DIRS}\" )"
-		"\nSET( ${FIELDML_NAMESPACE_NAME}_LIBRARIES ${FIELDML_API_LIBRARY_TARGET_NAME} ${FIELDML_IO_API_LIBRARY_TARGET_NAME} ${HDF5_MINE_LIBRARIES} ${MPI_MINE_LIBRARIES})"
-		"\nSET( ${FIELDML_NAMESPACE_NAME}_DEFINITIONS ${LIBXML2_DEFINITIONS} )"
-		"\nSET( ${FIELDML_NAMESPACE_NAME}_FOUND TRUE )" 
-		"\nENDIF( NOT DEFINED _${FIELDML_NAMESPACE_NAME}_CONFIG_CMAKE )" 
-		"\n" )
-	FILE( WRITE ${LIBRARY_CONFIG_FILE} ${CONFIG_FILE_CONTENTS} )
-	INSTALL( FILES ${LIBRARY_CONFIG_FILE} DESTINATION lib/cmake )
-	INSTALL( EXPORT fieldml-targets 
-		DESTINATION lib/cmake )
-ENDIF( ${FIELDML_NAMESPACE_NAME}_INSTALL_CONFIG )
-
-IF ( FIELDML_BUILD_JAVA )
-  FIND_PACKAGE(SWIG REQUIRED)
-  FIND_PACKAGE(JNI)
-  FIND_PACKAGE(Java)
-  INCLUDE_DIRECTORIES(${JNI_INCLUDE_DIRS})
-  INCLUDE_DIRECTORIES(io/src)
-  INCLUDE_DIRECTORIES(core/src)
-  INCLUDE(${SWIG_USE_FILE})
-
-  INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_PATH})
-  INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
-
-  SET(CMAKE_SWIG_FLAGS "-Iio/src;-Icore/src;-package;fieldml.jni")
-  SET(CMAKE_SWIG_OUTDIR "fieldml/jni")
-
-  SET_SOURCE_FILES_PROPERTIES(jni/fieldml_api.i PROPERTIES CPLUSPLUS ON)
-  SET_SOURCE_FILES_PROPERTIES(jni/fieldml_io.i PROPERTIES CPLUSPLUS ON)
-
-  # If you change these version, also change the .i files.
-  SWIG_ADD_MODULE(fieldml_jni_0.5 java jni/fieldml_api.i)
-  SWIG_ADD_MODULE(fieldml_io_0.5 java jni/fieldml_io.i)
-  SWIG_LINK_LIBRARIES(fieldml_jni_0.5 fieldml_api fieldml_io_api)
-  SWIG_LINK_LIBRARIES(fieldml_io_0.5 fieldml_api fieldml_io_api)
-
-  # Also make the jar file...
-  SET(javafiles "fieldml/jni/FieldmlApiConstants.java;fieldml/jni/FieldmlApi.java;fieldml/jni/FieldmlApiJNI.java;fieldml/jni/FieldmlDataDescriptionType.java;fieldml/jni/FieldmlDataResourceType.java;fieldml/jni/FieldmlDataSourceType.java;fieldml/jni/FieldmlEnsembleMembersType.java;fieldml/jni/FieldmlHandleType.java;fieldml/jni/FieldmlIo.java;fieldml/jni/FieldmlIoJNI.java;fieldml/jni/SWIGTYPE_p_FmlBoolean.java;fieldml/jni/SWIGTYPE_p_FmlObjectHandle.java;fieldml/jni/SWIGTYPE_p_FmlSessionHandle.java;fieldml/jni/SWIGTYPE_p_int32_t.java")
-  SET(classfiles "fieldml/jni/FieldmlApi.class;fieldml/jni/FieldmlApiConstants.class;fieldml/jni/FieldmlApiJNI.class;fieldml/jni/FieldmlDataDescriptionType.class;fieldml/jni/FieldmlDataDescriptionType\\$$SwigNext.class;fieldml/jni/FieldmlDataResourceType.class;fieldml/jni/FieldmlDataResourceType\\$$SwigNext.class;fieldml/jni/FieldmlDataSourceType.class;fieldml/jni/FieldmlDataSourceType\\$$SwigNext.class;fieldml/jni/FieldmlEnsembleMembersType.class;fieldml/jni/FieldmlEnsembleMembersType\\$$SwigNext.class;fieldml/jni/FieldmlHandleType.class;fieldml/jni/FieldmlHandleType\\$$SwigNext.class;fieldml/jni/FieldmlIoConstants.class;fieldml/jni/FieldmlIo.class;fieldml/jni/FieldmlIoConstants.class;fieldml/jni/FieldmlIoJNI.class;fieldml/jni/SWIGTYPE_p_FmlBoolean.class;fieldml/jni/SWIGTYPE_p_FmlObjectHandle.class;fieldml/jni/SWIGTYPE_p_FmlSessionHandle.class;fieldml/jni/SWIGTYPE_p_int32_t.class")
-
-  ADD_CUSTOM_COMMAND(OUTPUT ${classfiles}
-                     COMMAND ${Java_JAVAC_EXECUTABLE} ARGS ${javafiles}
-                     DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/jni/fieldml_apiJAVA_wrap.cxx)
-  ADD_CUSTOM_COMMAND(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/jni/fieldml.jar
-                     COMMAND ${Java_JAR_EXECUTABLE} ARGS cf ${CMAKE_CURRENT_BINARY_DIR}/jni/fieldml.jar ${classfiles}
-                     DEPENDS ${classfiles})
-  ADD_CUSTOM_TARGET(jnijar ALL DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/jni/fieldml.jar)
-
-ENDIF ( FIELDML_BUILD_JAVA )
+# Set the minimum version of cmake required to 3.0
+cmake_minimum_required( VERSION 3.0 )
+
+# Set this namespace to keep these options seperate from other project options
+set( FIELDML_NAMESPACE_NAME FIELDML )
+project(fieldml VERSION 0.5.0 LANGUAGES CXX)
+enable_language(Fortran OPTIONAL)
+
+option(USE_HDF5 "Do you want to use netgen (HDF5)?" NO)
+option(HDF5_WITH_MPI "Do you want to use MPI with HDF5?" NO)
+option(BUILD_TESTS "Build tests" ON)
+option(FORTRAN_BINDINGS "Do you want to build the Fortran bindings" YES)
+if (FORTRAN_BINDINGS AND NOT CMAKE_Fortran_COMPILER)
+    set(FORTRAN_BINDINGS NO)
+    message(WARNING "No Fortran compiler found but FORTRAN_BINDINGS requested. Disabling.")
+endif()
+option(JAVA_BINDINGS "Do you want to build the Java bindings" NO)
+set(PACKAGE_CONFIG_DIR "lib/cmake" CACHE STRING "Directory for package config files (relative to CMAKE_INSTALL_PREFIX)")
+# Further options:
+# CMAKE_POSITION_INDEPENDENT_CODE=YES for -fPIC constant (is also passed in from OpenCMISS-main build script)
+
+find_package(LibXml2 REQUIRED)
+if(USE_HDF5)
+    # See the FindHDF5 description
+    if (BUILD_SHARED_LIBS)
+        set(HDF5_USE_STATIC_LIBRARIES NO)
+    else()
+        set(HDF5_USE_STATIC_LIBRARIES YES)
+    endif()
+	find_package(HDF5 REQUIRED CXX)
+	if(HDF5_WITH_MPI)
+		find_package(MPI REQUIRED)
+    endif()
+endif()
+
+if (NOT CMAKE_DEBUG_POSTFIX)
+    SET(CMAKE_DEBUG_POSTFIX d)
+endif()
+
+# Add actual fieldml code and io
+add_subdirectory(core)
+add_subdirectory(io)
+
+if (FORTRAN_BINDINGS)
+    include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/FortranBindings.cmake)
+endif()
+
+# Create interface library for easy inclusion
+add_library(fieldml-api INTERFACE)
+target_link_libraries(fieldml-api INTERFACE fieldml-core fieldml-io)
+if (HAVE_Fortran_BINDINGS)
+    target_link_libraries(fieldml-api INTERFACE fieldml-fortran)
+endif()
+install(TARGETS fieldml-api
+    EXPORT fieldml-api-config
+    INCLUDES DESTINATION include)
+
+# Tests
+if (BUILD_TESTS)
+    add_subdirectory(test)
+endif()
+
+if(JAVA_BINDINGS)
+  include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/JavaBindings.cmake)
+endif()
+
+include(CMakePackageConfigHelpers)
+install(EXPORT fieldml-api-config
+	DESTINATION ${PACKAGE_CONFIG_DIR})
+WRITE_BASIC_PACKAGE_VERSION_FILE(${CMAKE_CURRENT_BINARY_DIR}/fieldml-api-config-version.cmake
+	COMPATIBILITY AnyNewerVersion)
+file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/fieldml-api-config-dependencies.cmake 
+    "include(CMakeFindDependencyMacro)\r\n"
+    "set(${PROJECT_NAME}_IMPORT_PREFIX \${_IMPORT_PREFIX})\r\n"
+)
+file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/fieldml-api-config-dependencies.cmake "find_dependency(LibXml2 ${LIBXML2_VERSION})\r\n")
+if (USE_HDF5)
+    file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/fieldml-api-config-dependencies.cmake "find_dependency(HDF5 ${HDF5_VERSION})\r\n")
+endif()
+if (JAVA_BINDINGS)
+    # TODO
+    #file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/fieldml-api-config-dependencies.cmake "find_dependency(OpenMP)\r\n")
+endif()
+file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/fieldml-api-config-dependencies.cmake "set(_IMPORT_PREFIX \${${PROJECT_NAME}_IMPORT_PREFIX})")
+install(FILES 
+    ${CMAKE_CURRENT_BINARY_DIR}/fieldml-api-config-version.cmake
+    ${CMAKE_CURRENT_BINARY_DIR}/fieldml-api-config-dependencies.cmake
+    DESTINATION ${PACKAGE_CONFIG_DIR})