diff options
82 files changed, 8463 insertions, 574 deletions
diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake index 799c117..ccd4fbc 100644 --- a/CMakeInstallation.cmake +++ b/CMakeInstallation.cmake @@ -189,7 +189,7 @@ HDF_README_PROPERTIES(HDF5_BUILD_FORTRAN) #----------------------------------------------------------------------------- # Configure the COPYING.txt file for the windows binary package #----------------------------------------------------------------------------- -if (WIN32 OR MINGW) +if (WIN32) configure_file (${HDF5_SOURCE_DIR}/COPYING ${HDF5_BINARY_DIR}/COPYING.txt @ONLY) endif () @@ -208,7 +208,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED) ${HDF5_SOURCE_DIR}/release_docs/COPYING ${HDF5_SOURCE_DIR}/release_docs/RELEASE.txt ) - if (WIN32 OR MINGW) + if (WIN32) set (release_files ${release_files} ${HDF5_SOURCE_DIR}/release_docs/USING_HDF5_VS.txt @@ -222,7 +222,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED) ${HDF5_SOURCE_DIR}/release_docs/HISTORY-1_8.txt ${HDF5_SOURCE_DIR}/release_docs/INSTALL ) - if (WIN32 OR MINGW) + if (WIN32) set (release_files ${release_files} ${HDF5_SOURCE_DIR}/release_docs/INSTALL_Windows.txt @@ -290,7 +290,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES) set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_EXT_DIR}/hdf.bmp") set (CPACK_GENERATOR "TGZ") - if (WIN32 OR MINGW) + if (WIN32) set (CPACK_GENERATOR "ZIP") if (NSIS_EXECUTABLE) @@ -455,7 +455,7 @@ The HDF5 data model, file format, API, library, and tools are open and distribut if (HDF5_PACKAGE_EXTLIBS) if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") if (ZLIB_FOUND AND ZLIB_USE_EXTERNAL) - if (WIN32 OR MINGW) + if (WIN32) set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;ALL;/") else () set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;libraries;/") @@ -464,7 +464,7 @@ The HDF5 data model, file format, API, library, and tools are open and distribut endif () endif () if (SZIP_FOUND AND SZIP_USE_EXTERNAL) - if (WIN32 OR MINGW) + if (WIN32) set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${SZIP_INCLUDE_DIR_GEN};SZIP;ALL;/") else () set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${SZIP_INCLUDE_DIR_GEN};SZIP;libraries;/") @@ -473,7 +473,7 @@ The HDF5 data model, file format, API, library, and tools are open and distribut endif () endif () if (PLUGIN_FOUND AND PLUGIN_USE_EXTERNAL) - if (WIN32 OR MINGW) + if (WIN32) set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${PLUGIN_BINARY_DIR};PLUGIN;ALL;/") else () set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${PLUGIN_BINARY_DIR};PLUGIN;libraries;/") diff --git a/CMakeLists.txt b/CMakeLists.txt index d0eebad..a2aeace 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -225,6 +225,7 @@ set (HDF5_JAVA_LIB_DIR ${HDF5_SOURCE_DIR}/java/lib) set (HDF5_JAVA_LOGGING_JAR ${HDF5_SOURCE_DIR}/java/lib/slf4j-api-1.7.25.jar) set (HDF5_JAVA_LOGGING_NOP_JAR ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-nop-1.7.25.jar) set (HDF5_JAVA_LOGGING_SIMPLE_JAR ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-simple-1.7.25.jar) +set (HDF5_DOXYGEN_DIR ${HDF5_SOURCE_DIR}/doxygen) #----------------------------------------------------------------------------- # parse the full version number from H5public.h and include in H5_VERS_INFO @@ -532,6 +533,20 @@ endif () # endif () #----------------------------------------------------------------------------- +# Option to build documentation +#----------------------------------------------------------------------------- +option (HDF5_BUILD_DOC "Build documentation" OFF) +if (HDF5_BUILD_DOC AND EXISTS "${HDF5_DOXYGEN_DIR}" AND IS_DIRECTORY "${HDF5_DOXYGEN_DIR}") +# check if Doxygen is installed + find_package(Doxygen) + if (DOXYGEN_FOUND) + message(STATUS "Doxygen version: ${DOXYGEN_VERSION}") + else () + message(STATUS "Doxygen needs to be installed to generate the doxygen documentation") + endif () +endif () + +#----------------------------------------------------------------------------- # Option to indicate using a memory checker #----------------------------------------------------------------------------- option (HDF5_ENABLE_USING_MEMCHECKER "Indicate that a memory checker is used" OFF) @@ -572,12 +587,15 @@ endif () # Certain systems may add /Debug or /Release to output paths # and we need to call the executable from inside the CMake configuration #----------------------------------------------------------------------------- -set (EXE_EXT "") -if (WIN32 OR MINGW) - set (EXE_EXT ".exe") - add_compile_definitions (_BIND_TO_CURRENT_VCLIBS_VERSION=1 _CRT_SECURE_NO_WARNINGS _CONSOLE) +if (WIN32) + add_compile_definitions (_CRT_SECURE_NO_WARNINGS) + if (MSVC) + add_compile_definitions (_BIND_TO_CURRENT_VCLIBS_VERSION=1 _CONSOLE) + endif () endif () +option (HDF5_MINGW_STATIC_GCC_LIBS "Statically link libgcc/libstdc++" OFF) + if (MSVC) set (CMAKE_MFC_FLAG 0) set (WIN_COMPILE_FLAGS "") @@ -777,7 +795,7 @@ endif () option (HDF5_ENABLE_THREADSAFE "Enable thread-safety" OFF) if (HDF5_ENABLE_THREADSAFE) # check for unsupported options - if (WIN32 OR MINGW) + if (WIN32) message (STATUS " **** thread-safety option not supported with static library **** ") message (STATUS " **** thread-safety option will not be used building static library **** ") endif () @@ -193,6 +193,30 @@ ./doc/code-conventions.md +./doxygen/aliases +./doxygen/Doxyfile.in +./doxygen/dox/H5Acreate.dox +./doxygen/dox/H5Aiterate.dox +./doxygen/dox/H5Fget_info.dox +./doxygen/dox/H5Lget_info_by_idx.dox +./doxygen/dox/H5Lget_info.dox +./doxygen/dox/H5Literate_by_name.dox +./doxygen/dox/H5Literate.dox +./doxygen/dox/H5Lvisit_by_name.dox +./doxygen/dox/H5Lvisit.dox +./doxygen/dox/H5Oget_info_by_idx.dox +./doxygen/dox/H5Oget_info_by_name.dox +./doxygen/dox/H5Oget_info.dox +./doxygen/dox/H5Ovisit_by_name.dox +./doxygen/dox/H5Ovisit.dox +./doxygen/dox/H5Sencode.dox +./doxygen/dox/mainpage.dox +./doxygen/dox/rm-template.dox +./doxygen/examples/H5Fclose.c +./doxygen/examples/H5Fcreate.c +./doxygen/examples/hello_hdf5.c +./doxygen/img/HDFG-logo.png + ./examples/Attributes.txt ./examples/Makefile.am ./examples/h5_chunk_read.c diff --git a/Makefile.am b/Makefile.am index 9cb5d02..21bc550 100644 --- a/Makefile.am +++ b/Makefile.am @@ -187,6 +187,16 @@ check-all-install: trace: @(cd src && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1; +# Run doxygen across source files. +# Currently, only invoke doxygen in the src directory. +doxygen: + @echo Invoking doxygen + for d in src; do \ + if test $$d != .; then \ + (cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1; \ + fi; \ + done + # Run tests with different Virtual File Drivers. # Currently, only invoke check-vfd in the test directory. check-vfd: @@ -75,6 +75,6 @@ Periodically development code snapshots are provided at the following URL: Source packages for current and previous releases are located at: https://portal.hdfgroup.org/display/support/Downloads -Development code is available at our BitBucket Server: - https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5/browse +Development code is available at our Github location: + https://github.com/HDFGroup/hdf5.git diff --git a/c++/examples/CMakeLists.txt b/c++/examples/CMakeLists.txt index 3035841..c50315f 100644 --- a/c++/examples/CMakeLists.txt +++ b/c++/examples/CMakeLists.txt @@ -41,7 +41,7 @@ foreach (example ${examples}) else () TARGET_C_PROPERTIES (cpp_ex_${example} SHARED) target_link_libraries (cpp_ex_${example} PRIVATE ${HDF5_CPP_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) - if (MINGW) + if (MINGW AND HDF5_MINGW_STATIC_GCC_LIBS) target_link_options (${HDF5_CPP_LIBSH_TARGET} PRIVATE -static-libgcc -static-libstdc++ ) @@ -66,7 +66,7 @@ foreach (example ${tutr_examples}) else () TARGET_C_PROPERTIES (cpp_ex_${example} SHARED) target_link_libraries (cpp_ex_${example} PRIVATE ${HDF5_CPP_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) - if (MINGW) + if (MINGW AND HDF5_MINGW_STATIC_GCC_LIBS) target_link_options (${HDF5_CPP_LIBSH_TARGET} PRIVATE -static-libgcc -static-libstdc++ ) diff --git a/c++/src/CMakeLists.txt b/c++/src/CMakeLists.txt index 04822cf..de2306e 100644 --- a/c++/src/CMakeLists.txt +++ b/c++/src/CMakeLists.txt @@ -117,7 +117,7 @@ if (BUILD_SHARED_LIBS) target_link_libraries (${HDF5_CPP_LIBSH_TARGET} PUBLIC ${HDF5_LIBSH_TARGET} ) - if (MINGW) + if (MINGW AND HDF5_MINGW_STATIC_GCC_LIBS) target_link_options (${HDF5_CPP_LIBSH_TARGET} PRIVATE -static-libgcc -static-libstdc++ ) diff --git a/c++/test/CMakeLists.txt b/c++/test/CMakeLists.txt index 550b7ea..1255e39 100644 --- a/c++/test/CMakeLists.txt +++ b/c++/test/CMakeLists.txt @@ -49,7 +49,7 @@ if (NOT BUILD_SHARED_LIBS) else () TARGET_C_PROPERTIES (cpp_testhdf5 SHARED) target_link_libraries (cpp_testhdf5 PRIVATE ${HDF5_CPP_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} ${HDF5_TEST_LIBSH_TARGET}) - if (MINGW) + if (MINGW AND HDF5_MINGW_STATIC_GCC_LIBS) target_link_options (${HDF5_CPP_LIBSH_TARGET} PRIVATE -static-libgcc -static-libstdc++ ) diff --git a/config/cmake/HDF5PluginMacros.cmake b/config/cmake/HDF5PluginMacros.cmake index 2c9e5e6..46d3979 100644 --- a/config/cmake/HDF5PluginMacros.cmake +++ b/config/cmake/HDF5PluginMacros.cmake @@ -26,7 +26,7 @@ macro (EXTERNAL_PLUGIN_LIBRARY compress_type) # the hdf5 settings -DHDF5_PACKAGE_NAME:STRING=hdf5 -DHDF5_HDF5_HEADER:STRING=h5pubconf.h - -DHDF5_LINK_LIBS:STRING=$<TARGET_FILE:${HDF5_LIBSH_TARGET}> + -DHDF5_LINK_LIBS:STRING=$<TARGET_LINKER_FILE:${HDF5_LIBSH_TARGET}> -DHDF5_INCLUDE_DIR:PATH=${HDF5_SRC_DIR}|${HDF5_SRC_BINARY_DIR} -DPL_PACKAGE_NAME:STRING=${PLUGIN_PACKAGE_NAME} -DH5PL_CPACK_ENABLE:BOOL=ON @@ -78,7 +78,7 @@ macro (EXTERNAL_PLUGIN_LIBRARY compress_type) # the hdf5 settings -DHDF5_PACKAGE_NAME:STRING=hdf5 -DHDF5_HDF5_HEADER:STRING=h5pubconf.h - -DHDF5_LINK_LIBS:STRING=$<TARGET_FILE:${HDF5_LIBSH_TARGET}> + -DHDF5_LINK_LIBS:STRING=$<TARGET_LINKER_FILE:${HDF5_LIBSH_TARGET}> -DHDF5_INCLUDE_DIR:PATH=${HDF5_SRC_DIR}|${HDF5_SRC_BINARY_DIR} -DPL_PACKAGE_NAME:STRING=${PLUGIN_PACKAGE_NAME} -DH5PL_CPACK_ENABLE:BOOL=ON diff --git a/config/cmake/cacheinit.cmake b/config/cmake/cacheinit.cmake index f8ab3a2..71c8b4a 100644 --- a/config/cmake/cacheinit.cmake +++ b/config/cmake/cacheinit.cmake @@ -40,6 +40,8 @@ set (HDF5_ENABLE_ALL_WARNINGS ON CACHE BOOL "Enable all warnings" FORCE) set (HDF_TEST_EXPRESS "2" CACHE STRING "Control testing framework (0-3)" FORCE) +set (HDF5_MINGW_STATIC_GCC_LIBS ON CACHE BOOL "Statically link libgcc/libstdc++" FORCE) + set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)" FORCE) set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ) diff --git a/config/cmake/jrunTest.cmake b/config/cmake/jrunTest.cmake index 41570eb..7d59ce5 100644 --- a/config/cmake/jrunTest.cmake +++ b/config/cmake/jrunTest.cmake @@ -49,7 +49,7 @@ endif () message (STATUS "COMMAND: ${TEST_TESTER} -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=${LOG_LEVEL} -Djava.library.path=\"${TEST_LIBRARY_DIRECTORY}\" -cp \"${TEST_CLASSPATH}\" ${TEST_ARGS} ${TEST_PROGRAM} ${ARGN}") -if (WIN32 OR MINGW) +if (WIN32) set (ENV{PATH} "$ENV{PATH}\\;${TEST_LIBRARY_DIRECTORY}") else () set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}") @@ -131,7 +131,7 @@ if (NOT TEST_SKIP_COMPARE) file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM) list (LENGTH TEST_STREAM test_len) if (test_len GREATER 0) - if (WIN32 OR MINGW) + if (WIN32) configure_file(${TEST_FOLDER}/${TEST_REFERENCE} ${TEST_FOLDER}/${TEST_REFERENCE}.tmp NEWLINE_STYLE CRLF) if (EXISTS "${TEST_FOLDER}/${TEST_REFERENCE}.tmp") file(RENAME ${TEST_FOLDER}/${TEST_REFERENCE}.tmp ${TEST_FOLDER}/${TEST_REFERENCE}) @@ -202,7 +202,7 @@ if (NOT TEST_SKIP_COMPARE) file (READ ${TEST_FOLDER}/${TEST_ERRREF} TEST_STREAM) list (LENGTH TEST_STREAM test_len) if (test_len GREATER 0) - if (WIN32 OR MINGW) + if (WIN32) configure_file(${TEST_FOLDER}/${TEST_ERRREF} ${TEST_FOLDER}/${TEST_ERRREF}.tmp NEWLINE_STYLE CRLF) if (EXISTS "${TEST_FOLDER}/${TEST_ERRREF}.tmp") file(RENAME ${TEST_FOLDER}/${TEST_ERRREF}.tmp ${TEST_FOLDER}/${TEST_ERRREF}) diff --git a/config/cmake/jvolTest.cmake b/config/cmake/jvolTest.cmake index 3a3877b..bcd9dbd 100644 --- a/config/cmake/jvolTest.cmake +++ b/config/cmake/jvolTest.cmake @@ -54,7 +54,7 @@ message (STATUS "USING ${TEST_VOL} ON COMMAND: ${TEST_TESTER} -Xmx1024M -Dorg.sl set (ENV{HDF5_VOL_CONNECTOR} "${TEST_VOL}") -if (WIN32 OR MINGW) +if (WIN32) set (ENV{PATH} "$ENV{PATH}\\;${TEST_LIBRARY_DIRECTORY}") else () set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}") @@ -136,7 +136,7 @@ if (NOT TEST_SKIP_COMPARE) file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM) list(LENGTH TEST_STREAM test_len) if (test_len GREATER 0) - if (WIN32 OR MINGW) + if (WIN32) configure_file(${TEST_FOLDER}/${TEST_REFERENCE} ${TEST_FOLDER}/${TEST_REFERENCE}.tmp NEWLINE_STYLE CRLF) if (EXISTS "${TEST_FOLDER}/${TEST_REFERENCE}.tmp") file(RENAME ${TEST_FOLDER}/${TEST_REFERENCE}.tmp ${TEST_FOLDER}/${TEST_REFERENCE}) @@ -207,7 +207,7 @@ if (NOT TEST_SKIP_COMPARE) file (READ ${TEST_FOLDER}/${TEST_ERRREF} TEST_STREAM) list(LENGTH TEST_STREAM test_len) if (test_len GREATER 0) - if (WIN32 OR MINGW) + if (WIN32) configure_file(${TEST_FOLDER}/${TEST_ERRREF} ${TEST_FOLDER}/${TEST_ERRREF}.tmp NEWLINE_STYLE CRLF) if (EXISTS "${TEST_FOLDER}/${TEST_ERRREF}.tmp") file(RENAME ${TEST_FOLDER}/${TEST_ERRREF}.tmp ${TEST_FOLDER}/${TEST_ERRREF}) diff --git a/config/cmake_ext_mod/HDFMacros.cmake b/config/cmake_ext_mod/HDFMacros.cmake index eb0392e..8ca8159 100644 --- a/config/cmake_ext_mod/HDFMacros.cmake +++ b/config/cmake_ext_mod/HDFMacros.cmake @@ -143,8 +143,8 @@ macro (HDF_SET_LIB_OPTIONS libtarget libname libtype) endif () endif () - #----- Use MSVC Naming conventions for Shared Libraries - if (MINGW AND ${libtype} MATCHES "SHARED") + option (HDF5_MSVC_NAMING_CONVENTION "Use MSVC Naming conventions for Shared Libraries" OFF) + if (HDF5_MSVC_NAMING_CONVENTION AND MINGW AND ${libtype} MATCHES "SHARED") set_target_properties (${libtarget} PROPERTIES IMPORT_SUFFIX ".lib" IMPORT_PREFIX "" @@ -343,7 +343,7 @@ macro (HDF_DIR_PATHS package_prefix) set (${package_prefix}_INSTALL_INCLUDE_DIR include) endif () if (NOT ${package_prefix}_INSTALL_DATA_DIR) - if (NOT WIN32) + if (NOT MSVC) if (APPLE) if (${package_prefix}_BUILD_FRAMEWORKS) set (${package_prefix}_INSTALL_EXTRA_DIR ../SharedSupport) @@ -353,12 +353,13 @@ macro (HDF_DIR_PATHS package_prefix) set (${package_prefix}_INSTALL_FWRK_DIR ${CMAKE_INSTALL_FRAMEWORK_PREFIX}) endif () set (${package_prefix}_INSTALL_DATA_DIR share) - set (${package_prefix}_INSTALL_CMAKE_DIR share/cmake) else () set (${package_prefix}_INSTALL_DATA_DIR ".") - set (${package_prefix}_INSTALL_CMAKE_DIR cmake) endif () endif () + if (NOT ${package_prefix}_INSTALL_CMAKE_DIR) + set (${package_prefix}_INSTALL_CMAKE_DIR share/cmake) + endif () # Always use full RPATH, i.e. don't skip the full RPATH for the build tree set (CMAKE_SKIP_BUILD_RPATH FALSE) diff --git a/config/cmake_ext_mod/grepTest.cmake b/config/cmake_ext_mod/grepTest.cmake index b011ae8..758b62b 100644 --- a/config/cmake_ext_mod/grepTest.cmake +++ b/config/cmake_ext_mod/grepTest.cmake @@ -46,7 +46,7 @@ endif () message (STATUS "COMMAND: ${TEST_EMULATOR} ${TEST_PROGRAM} ${TEST_ARGS}") if (TEST_LIBRARY_DIRECTORY) - if (WIN32 OR MINGW) + if (WIN32) set (ENV{PATH} "$ENV{PATH};${TEST_LIBRARY_DIRECTORY}") else () set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}") @@ -105,7 +105,7 @@ if (TEST_ERRREF) file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM) list (LENGTH TEST_STREAM test_len) if (test_len GREATER 0) - if (WIN32 OR MINGW) + if (WIN32) configure_file(${TEST_FOLDER}/${TEST_REFERENCE} ${TEST_FOLDER}/${TEST_REFERENCE}.tmp NEWLINE_STYLE CRLF) if (EXISTS "${TEST_FOLDER}/${TEST_REFERENCE}.tmp") file(RENAME ${TEST_FOLDER}/${TEST_REFERENCE}.tmp ${TEST_FOLDER}/${TEST_REFERENCE}) diff --git a/config/cmake_ext_mod/runTest.cmake b/config/cmake_ext_mod/runTest.cmake index 2b8b6b0..baf15c0 100644 --- a/config/cmake_ext_mod/runTest.cmake +++ b/config/cmake_ext_mod/runTest.cmake @@ -38,7 +38,7 @@ endif () message (STATUS "COMMAND: ${TEST_EMULATOR} ${TEST_PROGRAM} ${TEST_ARGS}") if (TEST_LIBRARY_DIRECTORY) - if (WIN32 OR MINGW) + if (WIN32) set (ENV{PATH} "$ENV{PATH};${TEST_LIBRARY_DIRECTORY}") else () set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}") @@ -212,7 +212,7 @@ if (NOT TEST_SKIP_COMPARE) file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM) list (LENGTH TEST_STREAM test_len) if (test_len GREATER 0) - if (WIN32 OR MINGW) + if (WIN32) configure_file(${TEST_FOLDER}/${TEST_REFERENCE} ${TEST_FOLDER}/${TEST_REFERENCE}.tmp NEWLINE_STYLE CRLF) if (EXISTS "${TEST_FOLDER}/${TEST_REFERENCE}.tmp") file(RENAME ${TEST_FOLDER}/${TEST_REFERENCE}.tmp ${TEST_FOLDER}/${TEST_REFERENCE}) @@ -283,7 +283,7 @@ if (NOT TEST_SKIP_COMPARE) file (READ ${TEST_FOLDER}/${TEST_ERRREF} TEST_STREAM) list (LENGTH TEST_STREAM test_len) if (test_len GREATER 0) - if (WIN32 OR MINGW) + if (WIN32) configure_file(${TEST_FOLDER}/${TEST_ERRREF} ${TEST_FOLDER}/${TEST_ERRREF}.tmp NEWLINE_STYLE CRLF) if (EXISTS "${TEST_FOLDER}/${TEST_ERRREF}.tmp") file(RENAME ${TEST_FOLDER}/${TEST_ERRREF}.tmp ${TEST_FOLDER}/${TEST_ERRREF}) diff --git a/config/commence.am b/config/commence.am index 6e3d9a9..e73352c 100644 --- a/config/commence.am +++ b/config/commence.am @@ -96,9 +96,9 @@ CHECK_CLEANFILES=*.chkexe *.chklog *.clog *.clog2 # commands that should be executed even if a file with the same name already # exists. .PHONY: build-check-clean build-check-p build-check-s build-lib build-progs \ - build-tests check-clean check-install check-p check-s check-vfd \ - check-passthrough-vol install-doc lib progs tests uninstall-doc \ - _exec_check-s _test help + build-tests check-clean check-install check-p check-s check-vfd \ + check-passthrough-vol install-doc lib progs tests uninstall-doc \ + _exec_check-s _test help trace doxygen help: @$(top_srcdir)/bin/makehelp diff --git a/config/sanitizer/formatting.cmake b/config/sanitizer/formatting.cmake index 677a69a..5aaa2a6 100644 --- a/config/sanitizer/formatting.cmake +++ b/config/sanitizer/formatting.cmake @@ -90,55 +90,3 @@ function(clang_format TARGET_NAME) endif() endfunction() -# -# cmake-format -# -find_program(CMAKE_FORMAT_EXE "cmake-format") -mark_as_advanced(FORCE CMAKE_FORMAT_EXE) -if(CMAKE_FORMAT_EXE) - message(STATUS "cmake-format found: ${CMAKE_FORMAT_EXE}") -else() - message(STATUS "cmake-format not found!") -endif() - -# When called, this function will call 'cmake-format' program on all listed -# files (if both the program and the files exist and are found) -# ~~~ -# Required: -# TARGET_NAME - The name of the target to create. -# -# Optional: -# ARGN - Any arguments passed in will be considered as 'files' to perform the -# formatting on. Any items that are not files will be ignored. Both relative and -# absolute paths are accepted. -# ~~~ -function(cmake_format TARGET_NAME) - if(CMAKE_FORMAT_EXE) - set(FORMAT_FILES) - # Determine files that exist - foreach(iter IN LISTS ARGN) - if(EXISTS ${iter}) - set(FORMAT_FILES ${FORMAT_FILES} ${iter}) - elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${iter}) - set(FORMAT_FILES ${FORMAT_FILES} ${CMAKE_CURRENT_SOURCE_DIR}/${iter}) - endif() - endforeach() - - # Generate target - if(FORMAT_FILES) - if(TARGET ${TARGET_NAME}) - message( - ERROR - "Cannot create cmake-format target '${TARGET_NAME}', already exists.") - else() - add_custom_target(${TARGET_NAME} COMMAND ${CMAKE_FORMAT_EXE} -i - ${FORMAT_FILES}) - - if(NOT TARGET cmake-format) - add_custom_target(cmake-format) - endif() - add_dependencies(cmake-format ${TARGET_NAME}) - endif() - endif() - endif() -endfunction() diff --git a/config/sanitizer/tools.cmake b/config/sanitizer/tools.cmake index 2f73cce..242e33f 100644 --- a/config/sanitizer/tools.cmake +++ b/config/sanitizer/tools.cmake @@ -111,4 +111,4 @@ else() set(CMAKE_CXX_CPPCHECK "" CACHE STRING "" FORCE) # delete it -endif()
\ No newline at end of file +endif() diff --git a/configure.ac b/configure.ac index e7a65ce..13c23b7 100644 --- a/configure.ac +++ b/configure.ac @@ -296,7 +296,7 @@ AC_MSG_CHECKING([for clang sanitizer checks]) AC_ARG_ENABLE([sanitize-checks], [AS_HELP_STRING([--enable-sanitize-checks=address], [(clang/clang++ compilers only) Enable sanitize checks. - Address is useful for detecting issues dealing with + Address is useful for detecting issues dealing with memory. See AddressSanitizer in config/sanitizer/README.md for more information. [default=none] @@ -311,7 +311,7 @@ fi if test "X$CC_BASENAME" = "Xclang"; then AC_SUBST([CLANG_SANITIZE_CHECKS]) - # There are several sanitizer tools. At present we are testing + # There are several sanitizer tools. At present we are testing # and describing only -fsanitizer=address with autotools. case "X-$CLANG_SANITIZE_CHECKS" in X-no|X-none) @@ -328,8 +328,8 @@ if test "X$CC_BASENAME" = "Xclang"; then # The clang compiler doesn't support some of them; they should be # checked before adding them to the list in the help message. # The sanitizers/sanitizers.cmake file lists these options: - # address, memory, memoryWithOrigins, undefined, thread, leak, - # 'address;undefined'. Which and which combinations of these are + # address, memory, memoryWithOrigins, undefined, thread, leak, + # 'address;undefined'. Which and which combinations of these are # supported varies by compiler version, but unsupported options # or combinations will result in configure errors reported in config.log. # Comma separated lists of sanitize options wil be entered intact in @@ -1049,6 +1049,64 @@ if test "X$HDF5_TOOLS" = "Xno"; then fi ## ---------------------------------------------------------------------- +## Check if they would like to enable building doxygen files +## + +## This needs to be exposed for the library info file. +AC_SUBST([HDF5_DOXYGEN]) + +## Default is to not build DOXYGEN +HDF5_DOXYGEN=no + +AC_MSG_CHECKING([if building doxygen is enabled]) + +AC_ARG_ENABLE([doxygen], + [AS_HELP_STRING([--enable-doxygen], + [Compile the HDF5 doxygen files [default=no]])], + [HDF5_DOXYGEN=$enableval]) + +if test "X$HDF5_DOXYGEN" = "Xyes"; then + DX_DOXYGEN_FEATURE(ON) + DX_DOT_FEATURE(OFF) + DX_HTML_FEATURE(ON) + DX_CHM_FEATURE(OFF) + DX_CHI_FEATURE(OFF) + DX_MAN_FEATURE(OFF) + DX_RTF_FEATURE(OFF) + DX_XML_FEATURE(OFF) + DX_PDF_FEATURE(ON) + DX_PS_FEATURE(OFF) + + AC_SUBST([DOXYGEN_PACKAGE]) + AC_SUBST([DOXYGEN_VERSION_STRING]) + AC_SUBST([DOXYGEN_INCLUDE_ALIASES]) + AC_SUBST([DOXYGEN_PROJECT_LOGO]) + AC_SUBST([DOXYGEN_PROJECT_BRIEF]) + AC_SUBST([DOXYGEN_INPUT_DIRECTORY]) + AC_SUBST([DOXYGEN_OPTIMIZE_OUTPUT_FOR_C]) + AC_SUBST([DOXYGEN_MACRO_EXPANSION]) + AC_SUBST([DOXYGEN_OUTPUT_DIR]) + + DOXYGEN_PACKAGE=${PACKAGE_NAME} + DOXYGEN_VERSION_STRING=${PACKAGE_VERSION} + DOXYGEN_INCLUDE_ALIASES='$(SRCDIR)/doxygen/aliases' + DOXYGEN_PROJECT_LOGO='$(SRCDIR)/doxygen/img/HDFG-logo.png' + DOXYGEN_PROJECT_BRIEF="C-API Reference" + DOXYGEN_INPUT_DIRECTORY='$(SRCDIR) $(SRCDIR)/doxygen/dox' + DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES + DOXYGEN_MACRO_EXPANSION=YES + DOXYGEN_OUTPUT_DIR=hdf5lib_docs + + DX_INIT_DOXYGEN([HDF5], [doxygen/Doxyfile], [hdf5lib_docs]) + + #AC_SUBST([DOXYGEN_OUTPUT_DIR], [hdf5lib_docs]) + +else + echo "Doxygen support is disabled" +fi + + +## ---------------------------------------------------------------------- ## Create libtool. If shared/static libraries are going to be enabled ## or disabled, it should happen before these macros. LT_PREREQ([2.2]) @@ -3124,6 +3182,9 @@ if test "x$HAVE_LIBHDFS" = "xyes"; then [Proceed to build with libhdfs]) fi +## Read-only HDFS files are not built if not required. +AM_CONDITIONAL([HDFS_VFD_CONDITIONAL], [test "X$HAVE_LIBHDFS" = "Xyes"]) + ## Checkpoint the cache AC_CACHE_SAVE @@ -3863,6 +3924,7 @@ AM_CONDITIONAL([HAVE_SHARED_CONDITIONAL], [test "X$enable_shared" = "Xyes"]) AC_CONFIG_FILES([src/libhdf5.settings Makefile + doxygen/Doxyfile src/Makefile test/Makefile test/H5srcdir_str.h diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in new file mode 100644 index 0000000..711fa7a --- /dev/null +++ b/doxygen/Doxyfile.in @@ -0,0 +1,2544 @@ +# Doxyfile 1.8.18 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the configuration +# file that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# https://www.gnu.org/software/libiconv/ for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = @DOXYGEN_PACKAGE@ + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. This +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = @DOXYGEN_VERSION_STRING@ + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = @DOXYGEN_PROJECT_BRIEF@ + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = @DOXYGEN_PROJECT_LOGO@ + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = @DOXYGEN_OUTPUT_DIRECTORY@ + +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all generated output in the proper direction. +# Possible values are: None, LTR, RTL and Context. +# The default value is: None. + +OUTPUT_TEXT_DIRECTION = None + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = "The $name class" \ + "The $name widget" \ + "The $name file" \ + is \ + provides \ + specifies \ + contains \ + represents \ + a \ + an \ + the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line +# such as +# /*************** +# as being the beginning of a Javadoc-style comment "banner". If set to NO, the +# Javadoc-style will behave just like regular comments and it will not be +# interpreted by doxygen. +# The default value is: NO. + +JAVADOC_BANNER = NO + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines (in the resulting output). You can put ^^ in the value part of an +# alias to insert a newline as if a physical newline was in the original file. +# When you need a literal { or } or , in the value part of an alias you have to +# escape them by means of a backslash (\), this can lead to conflicts with the +# commands \{ and \} for these it is advised to use the version @{ and @} or use +# a double escape (\\{ and \\}) + +ALIASES = + +@INCLUDE = @DOXYGEN_INCLUDE_ALIASES@ + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = YES + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice +# sources only. Doxygen will then generate output that is more tailored for that +# language. For instance, namespaces will be presented as modules, types will be +# separated into more groups, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_SLICE = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, JavaScript, +# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL, +# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran: +# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser +# tries to guess whether the code is fixed or free formatted code, this is the +# default for Fortran type files). For instance to make doxygen treat .inc files +# as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See https://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up +# to that level are automatically included in the table of contents, even if +# they do not have an id attribute. +# Note: This feature currently applies only to Markdown headings. +# Minimum value: 0, maximum value: 99, default value: 5. +# This tag requires that the tag MARKDOWN_SUPPORT is set to YES. + +TOC_INCLUDE_HEADINGS = 5 + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# If one adds a struct or class to a group and this option is enabled, then also +# any nested class or struct is added to the same group. By default this option +# is disabled and one has to add nested compounds explicitly via \ingroup. +# The default value is: NO. + +GROUP_NESTED_COMPOUNDS = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = YES + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual +# methods of a class will be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIV_VIRTUAL = NO + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = NO + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# declarations. If set to NO, these declarations will be included in the +# documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# (including Cygwin) ands Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = NO + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = YES + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = YES + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if <section_label> ... \endif and \cond <section_label> +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. If +# EXTRACT_ALL is set to YES then this flag will automatically be disabled. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when +# a warning is encountered. +# The default value is: NO. + +WARN_AS_ERROR = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING +# Note: If this tag is empty the current directory is searched. + +INPUT = @DOXYGEN_INPUT_DIRECTORY@ + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: https://www.gnu.org/software/libiconv/) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# read by doxygen. +# +# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, +# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, +# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, +# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment), +# *.doc (to be provided as doxygen C comment), *.txt (to be provided as doxygen +# C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd, +# *.vhdl, *.ucf, *.qsf and *.ice. + +FILE_PATTERNS = H5*public.h \ + H5*module.h \ + H5VLconnector.h \ + H5VLconnector_passthru.h \ + H5VLnative.h \ + H5version.h \ + *.dox + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = examples + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = ../src ../examples ../test examples + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = *.c + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# <filter> <input-file> +# +# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# entity all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = NO + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see https://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = NO + +# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the +# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the +# cost of reduced performance. This can be particularly helpful with template +# rich C++ code for which doxygen's built-in parser lacks the necessary type +# information. +# Note: The availability of this option depends on whether or not doxygen was +# generated with the -Duse_libclang=ON option for CMake. +# The default value is: NO. + +CLANG_ASSISTED_PARSING = NO + +# If clang assisted parsing is enabled you can provide the compiler with command +# line options that you would normally use when invoking the compiler. Note that +# the include paths will already be set by doxygen for the files and directories +# specified with INPUT and INCLUDE_PATH. +# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES. + +CLANG_OPTIONS = + +# If clang assisted parsing is enabled you can provide the clang parser with the +# path to the compilation database (see: +# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) used when the files +# were built. This is equivalent to specifying the "-p" option to a clang tool, +# such as clang-check. These options will then be passed to the parser. +# Note: The availability of this option depends on whether or not doxygen was +# generated with the -Duse_libclang=ON option for CMake. + +CLANG_DATABASE_PATH = + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = H5 + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# https://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to YES can help to show when doxygen was last run and thus if the +# documentation is up to date. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = YES + +# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML +# documentation will contain a main index with vertical navigation menus that +# are dynamically created via JavaScript. If disabled, the navigation index will +# consists of multiple levels of tabs that are statically embedded in every HTML +# page. Disable this option to support browsers that do not have JavaScript, +# like the Qt help browser. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_MENUS = NO + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: https://developer.apple.com/xcode/), introduced with OSX +# 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy +# genXcode/_index.html for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: https://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = YES + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg +# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see +# https://inkscape.org) to generate formulas as SVG images instead of PNGs for +# the HTML output. These images will generally look nicer at scaled resolutions. +# Possible values are: png The default and svg Looks nicer but requires the +# pdf2svg tool. +# The default value is: png. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FORMULA_FORMAT = png + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANSPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands +# to create new LaTeX commands to be used in formulas as building blocks. See +# the section "Including formulas" for details. + +FORMULA_MACROFILE = + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# https://www.mathjax.org) which uses client side JavaScript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = NO + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from https://www.mathjax.org before deployment. +# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = https://cdn.jsdelivr.net/npm/mathjax@2 + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use <access key> + S +# (what the <access key> is depends on the OS and browser, but it is typically +# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down +# key> to jump into the search results window, the results can be navigated +# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel +# the search. The filter options can be selected when the cursor is inside the +# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys> +# to select a filter and <Enter> or <escape> to activate or cancel the filter +# option. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +SEARCHENGINE = NO + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be +# implemented using a web server instead of a web client using JavaScript. There +# are two flavors of web server based searching depending on the EXTERNAL_SEARCH +# setting. When disabled, doxygen will generate a PHP script for searching and +# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing +# and searching needs to be provided by external tools. See the section +# "External Indexing and Searching" for details. +# The default value is: NO. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SERVER_BASED_SEARCH = YES + +# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP +# script for searching. Instead the search results are written to an XML file +# which needs to be processed by an external indexer. Doxygen will invoke an +# external search engine pointed to by the SEARCHENGINE_URL option to obtain the +# search results. +# +# Doxygen ships with an example indexer (doxyindexer) and search engine +# (doxysearch.cgi) which are based on the open source search engine library +# Xapian (see: https://xapian.org/). +# +# See the section "External Indexing and Searching" for details. +# The default value is: NO. +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTERNAL_SEARCH = NO + +# The SEARCHENGINE_URL should point to a search engine hosted by a web server +# which will return the search results when EXTERNAL_SEARCH is enabled. +# +# Doxygen ships with an example indexer (doxyindexer) and search engine +# (doxysearch.cgi) which are based on the open source search engine library +# Xapian (see: https://xapian.org/). See the section "External Indexing and +# Searching" for details. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SEARCHENGINE_URL = + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed +# search data is written to a file for indexing by an external tool. With the +# SEARCHDATA_FILE tag the name of this file can be specified. +# The default file is: searchdata.xml. +# This tag requires that the tag SEARCHENGINE is set to YES. + +SEARCHDATA_FILE = searchdata.xml + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the +# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is +# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple +# projects and redirect the results back to the right project. +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTERNAL_SEARCH_ID = + +# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen +# projects other than the one defined by this configuration file, but that are +# all added to the same external search index. Each project needs to have a +# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of +# to a relative location where the documentation can be found. The format is: +# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ... +# This tag requires that the tag SEARCHENGINE is set to YES. + +EXTRA_SEARCH_MAPPINGS = + +#--------------------------------------------------------------------------- +# Configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output. +# The default value is: YES. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: latex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. +# +# Note that when not enabling USE_PDFLATEX the default is latex when enabling +# USE_PDFLATEX the default is pdflatex and when in the later case latex is +# chosen this is overwritten by pdflatex. For specific output languages the +# default can have been set differently, this depends on the implementation of +# the output language. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_CMD_NAME = + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate +# index for LaTeX. +# Note: This tag is used in the Makefile / make.bat. +# See also: LATEX_MAKEINDEX_CMD for the part in the generated output file +# (.tex). +# The default file is: makeindex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +MAKEINDEX_CMD_NAME = makeindex + +# The LATEX_MAKEINDEX_CMD tag can be used to specify the command name to +# generate index for LaTeX. In case there is no backslash (\) as first character +# it will be automatically added in the LaTeX code. +# Note: This tag is used in the generated output file (.tex). +# See also: MAKEINDEX_CMD_NAME for the part in the Makefile / make.bat. +# The default value is: makeindex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_MAKEINDEX_CMD = makeindex + +# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX +# documents. This may be useful for small projects and may help to save some +# trees in general. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used by the +# printer. +# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x +# 14 inches) and executive (7.25 x 10.5 inches). +# The default value is: a4. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +PAPER_TYPE = a4 + +# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names +# that should be included in the LaTeX output. The package can be specified just +# by its name or with the correct syntax as to be used with the LaTeX +# \usepackage command. To get the times font for instance you can specify : +# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times} +# To use the option intlimits with the amsmath package you can specify: +# EXTRA_PACKAGES=[intlimits]{amsmath} +# If left blank no extra packages will be included. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the +# generated LaTeX document. The header should contain everything until the first +# chapter. If it is left blank doxygen will generate a standard header. See +# section "Doxygen usage" for information on how to let doxygen write the +# default header to a separate file. +# +# Note: Only use a user-defined header if you know what you are doing! The +# following commands have a special meaning inside the header: $title, +# $datetime, $date, $doxygenversion, $projectname, $projectnumber, +# $projectbrief, $projectlogo. Doxygen will replace $title with the empty +# string, for the replacement values of the other commands the user is referred +# to HTML_HEADER. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_HEADER = + +# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the +# generated LaTeX document. The footer should contain everything after the last +# chapter. If it is left blank doxygen will generate a standard footer. See +# LATEX_HEADER for more information on how to generate a default footer and what +# special commands can be used inside the footer. +# +# Note: Only use a user-defined footer if you know what you are doing! +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_FOOTER = + +# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# LaTeX style sheets that are included after the standard style sheets created +# by doxygen. Using this option one can overrule certain style aspects. Doxygen +# will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_STYLESHEET = + +# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the LATEX_OUTPUT output +# directory. Note that the files will be copied as-is; there are no commands or +# markers available. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_FILES = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is +# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will +# contain links (just like the HTML output) instead of page references. This +# makes the output suitable for online browsing using a PDF viewer. +# The default value is: YES. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate +# the PDF file directly from the LaTeX files. Set this option to YES, to get a +# higher quality PDF documentation. +# The default value is: YES. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode +# command to the generated LaTeX files. This will instruct LaTeX to keep running +# if errors occur, instead of asking the user for help. This option is also used +# when generating formulas in HTML. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_BATCHMODE = NO + +# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the +# index chapters (such as File Index, Compound Index, etc.) in the output. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_HIDE_INDICES = NO + +# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source +# code with syntax highlighting in the LaTeX output. +# +# Note that which sources are shown also depends on other settings such as +# SOURCE_BROWSER. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_SOURCE_CODE = NO + +# The LATEX_BIB_STYLE tag can be used to specify the style to use for the +# bibliography, e.g. plainnat, or ieeetr. See +# https://en.wikipedia.org/wiki/BibTeX and \cite for more info. +# The default value is: plain. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_BIB_STYLE = plain + +# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated +# page will contain the date and time when the page was generated. Setting this +# to NO can help when comparing the output of multiple runs. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_TIMESTAMP = NO + +# The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute) +# path from which the emoji images will be read. If a relative path is entered, +# it will be relative to the LATEX_OUTPUT directory. If left blank the +# LATEX_OUTPUT directory will be used. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EMOJI_DIRECTORY = + +#--------------------------------------------------------------------------- +# Configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The +# RTF output is optimized for Word 97 and may not look too pretty with other RTF +# readers/editors. +# The default value is: NO. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: rtf. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF +# documents. This may be useful for small projects and may help to save some +# trees in general. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will +# contain hyperlink fields. The RTF file will contain links (just like the HTML +# output) instead of page references. This makes the output suitable for online +# browsing using Word or some other Word compatible readers that support those +# fields. +# +# Note: WordPad (write) and others do not support links. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# configuration file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. +# +# See also section "Doxygen usage" for information on how to generate the +# default style sheet that doxygen normally uses. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an RTF document. Syntax is +# similar to doxygen's configuration file. A template extensions file can be +# generated using doxygen -e rtf extensionFile. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_EXTENSIONS_FILE = + +# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code +# with syntax highlighting in the RTF output. +# +# Note that which sources are shown also depends on other settings such as +# SOURCE_BROWSER. +# The default value is: NO. +# This tag requires that the tag GENERATE_RTF is set to YES. + +RTF_SOURCE_CODE = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for +# classes and files. +# The default value is: NO. + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. A directory man3 will be created inside the directory specified by +# MAN_OUTPUT. +# The default directory is: man. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to the generated +# man pages. In case the manual section does not start with a number, the number +# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is +# optional. +# The default value is: .3. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_EXTENSION = .3 + +# The MAN_SUBDIR tag determines the name of the directory created within +# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by +# MAN_EXTENSION with the initial . removed. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_SUBDIR = + +# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it +# will generate one additional man file for each entity documented in the real +# man page(s). These additional files only source the real man page, but without +# them the man command would be unable to find the correct page. +# The default value is: NO. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that +# captures the structure of the code including all documentation. +# The default value is: NO. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: xml. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_OUTPUT = xml + +# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program +# listings (including syntax highlighting and cross-referencing information) to +# the XML output. Note that enabling this will significantly increase the size +# of the XML output. +# The default value is: YES. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_PROGRAMLISTING = YES + +# If the XML_NS_MEMB_FILE_SCOPE tag is set to YES, doxygen will include +# namespace members in file scope as well, matching the HTML output. +# The default value is: NO. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_NS_MEMB_FILE_SCOPE = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the DOCBOOK output +#--------------------------------------------------------------------------- + +# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files +# that can be used to generate PDF. +# The default value is: NO. + +GENERATE_DOCBOOK = NO + +# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in +# front of it. +# The default directory is: docbook. +# This tag requires that the tag GENERATE_DOCBOOK is set to YES. + +DOCBOOK_OUTPUT = docbook + +# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the +# program listings (including syntax highlighting and cross-referencing +# information) to the DOCBOOK output. Note that enabling this will significantly +# increase the size of the DOCBOOK output. +# The default value is: NO. +# This tag requires that the tag GENERATE_DOCBOOK is set to YES. + +DOCBOOK_PROGRAMLISTING = NO + +#--------------------------------------------------------------------------- +# Configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an +# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures +# the structure of the code including all documentation. Note that this feature +# is still experimental and incomplete at the moment. +# The default value is: NO. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# Configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module +# file that captures the structure of the code including all documentation. +# +# Note that this feature is still experimental and incomplete at the moment. +# The default value is: NO. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary +# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI +# output from the Perl module output. +# The default value is: NO. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely +# formatted so it can be parsed by a human reader. This is useful if you want to +# understand what is going on. On the other hand, if this tag is set to NO, the +# size of the Perl module output will be much smaller and Perl will parse it +# just the same. +# The default value is: YES. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file are +# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful +# so different doxyrules.make files included by the same Makefile don't +# overwrite each other's variables. +# This tag requires that the tag GENERATE_PERLMOD is set to YES. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all +# C-preprocessor directives found in the sources and include files. +# The default value is: YES. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names +# in the source code. If set to NO, only conditional compilation will be +# performed. Macro expansion can be done in a controlled way by setting +# EXPAND_ONLY_PREDEF to YES. +# The default value is: NO. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +MACRO_EXPANSION = YES + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then +# the macro expansion is limited to the macros specified with the PREDEFINED and +# EXPAND_AS_DEFINED tags. +# The default value is: NO. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES, the include files in the +# INCLUDE_PATH will be searched if a #include is found. +# The default value is: YES. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by the +# preprocessor. +# This tag requires that the tag SEARCH_INCLUDES is set to YES. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will be +# used. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that are +# defined before the preprocessor is started (similar to the -D option of e.g. +# gcc). The argument of the tag is a list of macros of the form: name or +# name=definition (no spaces). If the definition and the "=" are omitted, "=1" +# is assumed. To prevent a macro definition from being undefined via #undef or +# recursively expanded use the := operator instead of the = operator. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this +# tag can be used to specify a list of macro names that should be expanded. The +# macro definition that is found in the sources will be used. Use the PREDEFINED +# tag if you want to use a different macro definition that overrules the +# definition found in the source code. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will +# remove all references to function-like macros that are alone on a line, have +# an all uppercase name, and do not end with a semicolon. Such function macros +# are typically used for boiler-plate code, and will confuse the parser if not +# removed. +# The default value is: YES. +# This tag requires that the tag ENABLE_PREPROCESSING is set to YES. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES tag can be used to specify one or more tag files. For each tag +# file the location of the external documentation should be added. The format of +# a tag file without this location is as follows: +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where loc1 and loc2 can be relative or absolute paths or URLs. See the +# section "Linking to external documentation" for more information about the use +# of tag files. +# Note: Each tag file must have a unique name (where the name does NOT include +# the path). If a tag file is not located in the directory in which doxygen is +# run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create a +# tag file that is based on the input files it reads. See section "Linking to +# external documentation" for more information about the usage of tag files. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES, all external class will be listed in +# the class index. If set to NO, only the inherited external classes will be +# listed. +# The default value is: NO. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will be +# listed. +# The default value is: YES. + +EXTERNAL_GROUPS = YES + +# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in +# the related pages index. If set to NO, only the current project's pages will +# be listed. +# The default value is: YES. + +EXTERNAL_PAGES = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram +# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to +# NO turns the diagrams off. Note that this option also works with HAVE_DOT +# disabled, but it is recommended to install and use dot, since it yields more +# powerful graphs. +# The default value is: YES. + +CLASS_DIAGRAMS = YES + +# You can include diagrams made with dia in doxygen documentation. Doxygen will +# then run dia to produce the diagram and insert it in the documentation. The +# DIA_PATH tag allows you to specify the directory where the dia binary resides. +# If left empty dia is assumed to be found in the default search path. + +DIA_PATH = + +# If set to YES the inheritance and collaboration graphs will hide inheritance +# and usage relations if the target is undocumented or is not a class. +# The default value is: YES. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz (see: +# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent +# Bell Labs. The other options in this section have no effect if this option is +# set to NO +# The default value is: NO. + +HAVE_DOT = NO + +# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed +# to run in parallel. When set to 0 doxygen will base this on the number of +# processors available in the system. You can set it explicitly to a value +# larger than 0 to get control over the balance between CPU load and processing +# speed. +# Minimum value: 0, maximum value: 32, default value: 0. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_NUM_THREADS = 0 + +# When you want a differently looking font in the dot files that doxygen +# generates you can specify the font name using DOT_FONTNAME. You need to make +# sure dot is able to find the font, which can be done by putting it in a +# standard location or by setting the DOTFONTPATH environment variable or by +# setting DOT_FONTPATH to the directory containing the font. +# The default value is: Helvetica. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTNAME = Helvetica + +# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of +# dot graphs. +# Minimum value: 4, maximum value: 24, default value: 10. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the default font as specified with +# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set +# the path where dot can find it using this tag. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_FONTPATH = + +# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for +# each documented class showing the direct and indirect inheritance relations. +# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a +# graph for each documented class showing the direct and indirect implementation +# dependencies (inheritance, containment, and class references variables) of the +# class with other documented classes. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for +# groups, showing the direct groups dependencies. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +UML_LOOK = NO + +# If the UML_LOOK tag is enabled, the fields and methods are shown inside the +# class node. If there are many fields or methods and many nodes the graph may +# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the +# number of items for each type to make the size more manageable. Set this to 0 +# for no limit. Note that the threshold may be exceeded by 50% before the limit +# is enforced. So when you set the threshold to 10, up to 15 fields may appear, +# but if the number exceeds 15, the total amount of fields shown is limited to +# 10. +# Minimum value: 0, maximum value: 100, default value: 10. +# This tag requires that the tag HAVE_DOT is set to YES. + +UML_LIMIT_NUM_FIELDS = 10 + +# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and +# collaboration graphs will show the relations between templates and their +# instances. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +TEMPLATE_RELATIONS = NO + +# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to +# YES then doxygen will generate a graph for each documented file showing the +# direct and indirect include dependencies of the file with other documented +# files. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +INCLUDE_GRAPH = YES + +# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are +# set to YES then doxygen will generate a graph for each documented file showing +# the direct and indirect include dependencies of the file with other documented +# files. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH tag is set to YES then doxygen will generate a call +# dependency graph for every global function or class method. +# +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable call graphs for selected +# functions only using the \callgraph command. Disabling a call graph can be +# accomplished by means of the command \hidecallgraph. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller +# dependency graph for every global function or class method. +# +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable caller graphs for selected +# functions only using the \callergraph command. Disabling a caller graph can be +# accomplished by means of the command \hidecallergraph. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical +# hierarchy of all classes instead of a textual one. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the +# dependencies a directory has on other directories in a graphical way. The +# dependency relations are determined by the #include relations between the +# files in the directories. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. For an explanation of the image formats see the section +# output formats in the documentation of the dot tool (Graphviz (see: +# http://www.graphviz.org/)). +# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order +# to make the SVG files visible in IE 9+ (other browsers do not have this +# requirement). +# Possible values are: png, jpg, gif, svg, png:gd, png:gd:gd, png:cairo, +# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and +# png:gdiplus:gdiplus. +# The default value is: png. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_IMAGE_FORMAT = png + +# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to +# enable generation of interactive SVG images that allow zooming and panning. +# +# Note that this requires a modern browser other than Internet Explorer. Tested +# and working are Firefox, Chrome, Safari, and Opera. +# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make +# the SVG files visible. Older versions of IE do not have SVG support. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +INTERACTIVE_SVG = NO + +# The DOT_PATH tag can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the \dotfile +# command). +# This tag requires that the tag HAVE_DOT is set to YES. + +DOTFILE_DIRS = + +# The MSCFILE_DIRS tag can be used to specify one or more directories that +# contain msc files that are included in the documentation (see the \mscfile +# command). + +MSCFILE_DIRS = + +# The DIAFILE_DIRS tag can be used to specify one or more directories that +# contain dia files that are included in the documentation (see the \diafile +# command). + +DIAFILE_DIRS = + +# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the +# path where java can find the plantuml.jar file. If left blank, it is assumed +# PlantUML is not used or called during a preprocessing step. Doxygen will +# generate a warning when it encounters a \startuml command in this case and +# will not generate output for the diagram. + +PLANTUML_JAR_PATH = + +# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a +# configuration file for plantuml. + +PLANTUML_CFG_FILE = + +# When using plantuml, the specified paths are searched for files specified by +# the !include statement in a plantuml block. + +PLANTUML_INCLUDE_PATH = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes +# that will be shown in the graph. If the number of nodes in a graph becomes +# larger than this value, doxygen will truncate the graph, which is visualized +# by representing a node as a red box. Note that doxygen if the number of direct +# children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that +# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. +# Minimum value: 0, maximum value: 10000, default value: 50. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs +# generated by dot. A depth value of 3 means that only nodes reachable from the +# root by following a path via at most 3 edges will be shown. Nodes that lay +# further from the root node will be omitted. Note that setting this option to 1 +# or 2 may greatly reduce the computation time needed for large code bases. Also +# note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. +# Minimum value: 0, maximum value: 1000, default value: 0. +# This tag requires that the tag HAVE_DOT is set to YES. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not seem +# to support this out of the box. +# +# Warning: Depending on the platform used, enabling this option may lead to +# badly anti-aliased labels on the edges of a graph (i.e. they become hard to +# read). +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) support +# this, this feature is disabled by default. +# The default value is: NO. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page +# explaining the meaning of the various boxes and arrows in the dot generated +# graphs. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot +# files that are used to generate the various graphs. +# The default value is: YES. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_CLEANUP = YES diff --git a/doxygen/aliases b/doxygen/aliases new file mode 100644 index 0000000..aa22bd4 --- /dev/null +++ b/doxygen/aliases @@ -0,0 +1,184 @@ +################################################################################ +# Styling +################################################################################ + +ALIASES += Bold{1}="<b>\1</b>" +ALIASES += Emph{1}="<em>\1</em>" +ALIASES += Code{1}="<tt>\1</tt>" + +################################################################################ +# Return values +################################################################################ + +ALIASES += success{1}="\Bold{Success:} \1" +ALIASES += failure{1}="\Bold{Failure:} \1" + +ALIASES += herr_t="Returns a non-negative value if successful; otherwise returns a negative value." +ALIASES += hid_t{1}="Returns a \1 identifier if successful; otherwise returns #H5I_INVALID_HID. " +ALIASES += hid_ti{1}="Returns an \1 identifier if successful; otherwise returns #H5I_INVALID_HID. " +ALIASES += hid_tv{1}="Returns an \1 identifier if successful; otherwise returns a negative value. " +ALIASES += htri_t="Returns zero (false), a positive (true) or a negative (failure) value." + +################################################################################ +# General +################################################################################ + +ALIASES += idx_type="\param[in] idx_type Index type" +ALIASES += idx_type{1}="\param[in] \1 Index type" + +ALIASES += order="\param[in] order Iteration order" +ALIASES += order{1}="\param[in] \1 Iteration order" + +ALIASES += op="\param[in] op Callback function" +ALIASES += op{1}="\param[in] \1 Callback function" + +ALIASES += op_data="\param[in,out] op_data User-defined callback function context" +ALIASES += op_data{1}="\param[in,out] \1 User-defined callback function context" + +################################################################################ +# Attributes +################################################################################ + +ALIASES += attr_id="\param[in] attr_id Attribute identifier" +ALIASES += attr_id{1}="\param[in] \1 Attribute identifier" + +################################################################################ +# Dataset +################################################################################ + +ALIASES += dset_id="\param[in] dset_id Dataset identifier" +ALIASES += dset_id{1}="\param[in] \1 Dataset identifier" + +################################################################################ +# Dataspaces +################################################################################ + +ALIASES += space_id="\param[in] space_id Dataspace identifier" +ALIASES += space_id{1}="\param[in] \1 Dataspace identifier" + +################################################################################ +# Dataypes +################################################################################ + +ALIASES += dtype_id="\param[in] dtype_id Datatype identifier" +ALIASES += dtype_id{1}="\param[in] \1 Datatype identifier" + +ALIASES += file_type_id{1}="\param[in] \1 Datatype (in-file) identifier" +ALIASES += mem_type_id{1}="\param[in] \1 Datatype (in-memory) identifier" + +################################################################################ +# Files +################################################################################ + +ALIASES += file_id="\param[in] file_id File identifier" +ALIASES += file_id{1}="\param[in] \1 File identifier" + +ALIASES += fapl_id="\param[in] fapl_id File access property list identifier" +ALIASES += fapl_id{1}="\param[in] \1 File access property list identifier" + +ALIASES += fcpl_id="\param[in] fcpl_id File creation property list identifier" +ALIASES += fcpl_id{1}="\param[in] \1 File creation property list identifier" + +################################################################################ +# Groups +################################################################################ + +ALIASES += group_id="\param[in] group_id Group identifier" +ALIASES += group_id{1}="\param[in] \1 Group identifier" + +################################################################################ +# Locations +################################################################################ + +ALIASES += loc_id="\param[in] loc_id Location identifier" +ALIASES += loc_id{1}="\param[in] \1 Location identifier" + +ALIASES += fgdt_loc_id="\loc_id. The identifier may be that of a file, group, dataset, or named datatype." +ALIASES += fgdt_loc_id{1}="\loc_id{\1}. The identifier may be that of a file, group, dataset, or named datatype." + +ALIASES += fgdta_loc_id="\loc_id. The identifier may be that of a file, group, dataset, named datatype, or attribute." +ALIASES += fgdta_loc_id{1}="\loc_id{\1}. The identifier may be that of a file, group, dataset, named datatype, or attribute." + +ALIASES += fg_loc_id="\loc_id. The identifier may be that of a file or group." +ALIASES += fg_loc_id{1}="\loc_id{\1}. The identifier may be that of a file or group." + +################################################################################ +# Property lists +################################################################################ + +ALIASES += aapl_id="\param[in] aapl_id Attribute access property list identifier" +ALIASES += aapl_id{1}="\param[in] \1 Attribute access property list identifier" + +ALIASES += acpl_id="\param[in] acpl_id Attribute creation property list identifier" +ALIASES += acpl_id{1}="\param[in] \1 Attribute creation property list identifier" + +ALIASES += dapl_id="\param[in] dapl_id Dataset access property list identifier" +ALIASES += dapl_id{1}="\param[in] \1 Dataset access property list identifier" + +ALIASES += dcpl_id="\param[in] dcpl_id Dataset creation property list identifier" +ALIASES += dcpl_id{1}="\param[in] \1 Dataset creation property list identifier" + +ALIASES += dxpl_id="\param[in] dxpl_id Dataset transfer property list identifier" +ALIASES += dxpl_id{1}="\param[in] \1 Dataset transfer property list identifier" + +ALIASES += gapl_id="\param[in] gapl_id Group access property list identifier" +ALIASES += gapl_id{1}="\param[in] \1 Group access property list identifier" + +ALIASES += gcpl_id="\param[in] gcpl_id Group creation property list identifier" +ALIASES += gcpl_id{1}="\param[in] \1 Group creation property list identifier" + +ALIASES += lapl_id="\param[in] lapl_id Link access property list identifier" +ALIASES += lapl_id{1}="\param[in] \1 Link access property list identifier" + +ALIASES += lcpl_id="\param[in] lcpl_id Link creation property list identifier" +ALIASES += lcpl_id{1}="\param[in] \1 Link creation property list identifier" + +ALIASES += vipl_id="\param[in] vipl_id VOL initialization property list identifier" +ALIASES += vipl_id{1}="\param[in] \1 vipl_id VOL initialization property list identifier" + +ALIASES += plist_id="\param[in] plist_id Property list identifier" +ALIASES += plist_id{1}="\param[in] \1 Property list identifier" + +ALIASES += plistcls_id="\param[in] plistcls_id Property list class identifier" +ALIASES += plistcls_id{1}="\param[in] \1 Property list class identifier" + +################################################################################ +# Objects +################################################################################ + +ALIASES += obj_id="\param[in] obj_id Object identifier" +ALIASES += obj_id{1}="\param[in] \1 Object identifier" +ALIASES += loc_obj_id{1}="\param[in] \1 Location identifier of object" + +ALIASES += fgdta_obj_id="\obj_id. The identifier may be that of a file, group, dataset, named datatype, or attribute." +ALIASES += fgdta_obj_id{1}="\obj_id{\1}. The identifier may be that of a file, group, dataset, named datatype, or attribute." +ALIASES += fgdta_loc_obj_id{1}="\loc_obj_id{\1}. The identifier may be that of a file, group, dataset, named datatype, or attribute." + +################################################################################ +# Others +################################################################################ + +ALIASES += estack_id="\param[in] estack_id Error stack identifier" +ALIASES += estack_id{1}="\param[in] \1 Error stack identifier" + +################################################################################ +# The Usual Suspects +################################################################################ + +ALIASES += csets="<table><tr><td>#H5T_CSET_ASCII</td><td>US ASCII</td></tr><tr><td>#H5T_CSET_UTF8</td><td>UTF-8 Unicode encoding</td></tr></table>" +ALIASES += datatype_class=" \li #H5T_INTEGER \li #H5T_FLOAT \li #H5T_STRING \li #H5T_BITFIELD \li #H5T_OPAQUE \li #H5T_COMPOUND \li #H5T_REFERENCE \li #H5T_ENUM \li #H5T_VLEN \li #H5T_ARRAY" +ALIASES += file_access="<table><tr><td>#H5F_ACC_RDWR</td><td>File was opened with read/write access.</td></tr><tr><td>#H5F_ACC_RDONLY</td><td>File was opened with read-only access.</td></tr><tr><td>#H5F_ACC_SWMR_WRITE</td><td>File was opened with read/write access for a single-writer/multiple-reader (SWMR) scenario. Note that the writer process must also open the file with the #H5F_ACC_RDWR flag.</td></tr><tr><td>#H5F_ACC_SWMR_READ</td><td>File was opened with read-only access for a single-writer/multiple-reader (SWMR) scenario. Note that the reader process must also open the file with the #H5F_ACC_RDONLY flag.</td></tr></table>" +ALIASES += id_types="<table><tr><td>#H5I_FILE</td><td>File</td></tr><tr><td>#H5I_GROUP</td><td>Group</td></tr><tr><td>#H5I_DATATYPE</td><td>Datatype</td></tr><tr><td>#H5I_DATASPACE</td><td>Dataspace</td></tr><tr><td>#H5I_DATASET</td><td>Dataset</td></tr><tr><td>#H5I_ATTR</td><td>Attribute</td></tr></table>" +ALIASES += indexes="<table><tr><td>#H5_INDEX_NAME</td><td>Lexicographic order on name</td></tr><tr><td>#H5_INDEX_CRT_ORDER</td><td>Index on creation order</td></tr></table>" +ALIASES += link_types="<table><tr><td>#H5L_TYPE_HARD</td><td>Hard link</td></tr><tr><td>#H5L_TYPE_SOFT</td><td>Soft link</td></tr><tr><td>#H5L_TYPE_EXTERNAL</td><td>External link</td></tr><tr><td>#H5L_TYPE_ERROR</td><td>Error</td></tr></table>" +ALIASES += mem_types="<table><tr><td>#H5FD_MEM_DEFAULT</td><td>The default file memory allocation type</td></tr><tr><td>#H5FD_MEM_SUPER</td><td>File memory allocated for Superblock</td></tr><tr><td>#H5FD_MEM_BTREE</td><td>File memory allocated for B-tree</td></tr><tr><td>#H5FD_MEM_DRAW</td><td>File memory allocated for raw data</td></tr><tr><td>#H5FD_MEM_GHEAP</td><td>File memory allocated for Global Heap</td></tr><tr><td>#H5FD_MEM_LHEAP</td><td>File memory allocated for Local Heap</td></tr><tr><td>#H5FD_MEM_OHDR</td><td>File memory allocated for Object Header</td></tr></table>" +ALIASES += norm_type="<table><tr><td>#H5T_NORM_IMPLIED</td><td>0</td><td>MSB of mantissa is not stored, always 1</td></tr><tr><td>#H5T_NORM_MSBSET</td><td>1</td><td>MSB of mantissa is always 1</td></tr><tr><td>#H5T_NORM_NONE</td><td>2</td><td>Mantissa is not normalized</td></tr></table>" +ALIASES += obj_types="<table><tr><td>#H5F_OBJ_FILE</td><td>Files only</td></tr><tr><td>#H5F_OBJ_DATASET</td><td>Datasets only</td></tr><tr><td>#H5F_OBJ_GROUP</td><td>Groups only</td></tr><tr><td>#H5F_OBJ_DATATYPE</td><td>Named datatypes only</td></tr><tr><td>#H5F_OBJ_ATTR</td><td>Attributes only</td></tr><tr><td>#H5F_OBJ_ALL</td><td>All of the above</td></tr></tr><tr><td>#H5F_OBJ_LOCAL</td><td>Restrict search to objects opened through current file identifier.</td></tr></table> \attention #H5F_OBJ_LOCAL does not stand alone; it is effective only when used in combination with one or more of the preceding types. For example, #H5F_OBJ_DATASET | #H5F_OBJ_GROUP | #H5F_OBJ_LOCAL would count all datasets and groups opened through the current file identifier." +ALIASES += orders="<table><tr><td>#H5_ITER_INC</td><td>Increasing order</td></tr><tr><td>#H5_ITER_DEC</td><td>Decreasing order</td></tr><tr><td>#H5_ITER_NATIVE</td><td>Fastest available order</td></tr></table>" +ALIASES += padding_type="<table><tr><td>#H5T_PAD_ZERO</td><td>0</td><td>Set background to zeros</td></tr><tr><td>#H5T_PAD_ONE</td><td>1</td><td>Set background to ones</td></tr><tr><td>#H5T_PAD_BACKGROUND</td><td>2</td><td>Leave background alone</td></tr></table>" +ALIASES += scopes="<table><tr><td>#H5F_SCOPE_GLOBAL</td><td>Flushes the entire virtual file</td></tr><tr><td>#H5F_SCOPE_LOCAL</td><td>Flushes only the specified file</td></tr></table>" +ALIASES += sign_prop="<table><tr><td>#H5T_SGN_NONE</td><td>0</td><td>Unsigned integer type</td></tr><tr><td>#H5T_SGN_2</td><td>1</td><td>Two's complement signed integer type</td></tr></table>" +ALIASES += storage_type="<table><tr><td>#H5G_STORAGE_TYPE_COMPACT</td><td>Compact storage</td></tr><tr><td>#H5G_STORAGE_TYPE_DENSE</td><td>Indexed storage</td></tr><tr><td>#H5G_STORAGE_TYPE_SYMBOL_TABLE</td><td>Symbol tables, the original HDF5 structure</td></tr></table>" +ALIASES += str_pad_type="<table><tr><td>#H5T_STR_NULLTERM</td><td>0</td><td>Null terminate (as C does)</td></tr><tr><td>#H5T_STR_NULLPAD</td><td>1</td><td>Pad with zeros</td></tr><tr><td>#H5T_STR_SPACEPAD</td><td>2</td><td>Pad with spaces (as FORTRAN does)</td></tr></table>" +ALIASES += virtual=" \see Supporting Functions: \li H5Pget_layout() \li H5Pset_layout() \li H5Sget_regular_hyperslab() \li H5Sis_regular_hyperslab() \li H5Sselect_hyperslab() \see VDS Functions: \li H5Pget_virtual_count() \li H5Pget_virtual_dsetname() \li H5Pget_virtual_filename() \li H5Pget_virtual_prefix() \li H5Pget_virtual_printf_gap() \li H5Pget_virtual_srcspace() \li H5Pget_virtual_view() \li H5Pget_virtual_vspace() \li H5Pset_virtual \li H5Pset_virtual_prefix() \li H5Pset_virtual_printf_gap() \li H5Pset_virtual_view()" +ALIASES += obj_info_fields="<table><tr><th>Flag</th><th>Purpose</th></tr><tr><td>#H5O_INFO_BASIC</td><td>Fill in the fileno, addr, type, and rc fields</td></tr><tr> <td>#H5O_INFO_TIME</td><td>Fill in the atime, mtime, ctime, and btime fields</td></tr><tr> <td>#H5O_INFO_NUM_ATTRS</td> <td>Fill in the num_attrs field</td></tr><tr><td>#H5O_INFO_HDR</td><td>Fill in the num_attrs field</td></tr><tr><td>#H5O_INFO_META_SIZE</td><td>Fill in the meta_size field</td></tr><tr><td>#H5O_INFO_ALL</td><td>#H5O_INFO_BASIC | #H5O_INFO_TIME | #H5O_INFO_NUM_ATTRS | #H5O_INFO_HDR | #H5O_INFO_META_SIZE</td></tr></table>" diff --git a/doxygen/dox/H5Acreate.dox b/doxygen/dox/H5Acreate.dox new file mode 100644 index 0000000..18d648f --- /dev/null +++ b/doxygen/dox/H5Acreate.dox @@ -0,0 +1,9 @@ +/** + * \ingroup H5A + * \def H5Acreate() + * H5Acreate() is a macro that is mapped to either H5Acreate1() or + * H5Acreate2(). + * + * + * \todo Standardize the way we describe these macros! + */ diff --git a/doxygen/dox/H5Aiterate.dox b/doxygen/dox/H5Aiterate.dox new file mode 100644 index 0000000..46b9bb4 --- /dev/null +++ b/doxygen/dox/H5Aiterate.dox @@ -0,0 +1,9 @@ +/** + * \ingroup H5A + * \def H5Aiterate() + * H5Aiterate() is a macro that is mapped to either H5Aiterate1() or + * H5Aiterate2(). + * + * + * \todo Standardize the way we describe these macros! + */ diff --git a/doxygen/dox/H5Fget_info.dox b/doxygen/dox/H5Fget_info.dox new file mode 100644 index 0000000..b2eeb6c --- /dev/null +++ b/doxygen/dox/H5Fget_info.dox @@ -0,0 +1,47 @@ +/** + * \ingroup H5F + * \def H5Fget_info() + * H5Fget_info() is a macro that is mapped to either H5Fget_info1() + * or H5Fget_info2(), depending on the needs of the application. + * Similarly, the macro for the \ref H5F_info_t struct is mapped to either + * H5F_info1_t or H5F_info2_t. + * + * Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in "API Compatibility + * Macros in HDF5". + * + * When both the HDF5 library and the application are built and installed with + * no specific compatibility flags, H5Fget_info() is mapped to the most recent + * version of the function, currently H5Fget_info2(). If the library and/or + * application is compiled for Release 1.8 emulation, H5Fget_info() will be + * mapped to H5Fget_info1(). Since there was no H5Fget_info() function in + * Release 1.6, if the library and/or application is compiled for Release 1.6 + * emulation, H5Fget_info() will be mapped to the most recent version of the + * function, currently H5Fget_info2(). Function-specific flags are available to + * override these settings on a function-by-function basis when the application + * is compiled. + * + * Specific compile-time compatibility flags and the resulting + * mappings are as follows: + * + * \Bold{Global settings}\n + * \li No compatibility flag: H5Fget_info2() and H5F_info2_t + * \li Enable deprecated symbols: H5Fget_info2() and H5F_info2_t + * \li Disable deprecated symbols: H5Fget_info2() and H5F_info2_t + * \li Emulate Release 1.6 interface: H5Fget_info2() and H5F_info2_t + * \li Emulate Release 1.8 interface: H5Fget_info1() and H5F_info1_t + * + * \Bold{Function- and struct-level macros}\n + * \li \Code{H5Fget_info_vers=2}: H5Fget_info2() + * \li \Code{H5Fget_info_vers=1}: H5Fget_info1() + * \li \Code{H5F_info_t_vers=2}: H5F_info2_t + * \li \Code{H5F_info_t_vers=1}: H5F_info1_t + * + * \todo Fix the reference. + * + * \version 1.10.0 The C function H5Fget_info() and H5F_info_t renamed to + * H5Fget_info1() and H5F_info1_t, respectively, and deprecated + * in this release. The C macro #H5Fget_info, the C function + * H5Fget_info2(), and the struct H5F_info2_t introduced in this + * release. + */ diff --git a/doxygen/dox/H5Lget_info.dox b/doxygen/dox/H5Lget_info.dox new file mode 100644 index 0000000..686dfe4 --- /dev/null +++ b/doxygen/dox/H5Lget_info.dox @@ -0,0 +1,18 @@ + /** + * \ingroup LMGT + * \def H5Lget_info() + * H5Lget_info() is a macro that is mapped to either H5Lget_info1() + * or H5Lget_info2() Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in Compatibility + * Macros in HDF5. If the library and/or application is compiled for Release + * 1.12 emulation, H5Lget_info() will be mapped to H5Lget_info2() and + * H5Lget_info1() is deprecated. With earlier versions, H5Lget_info() is mapped to + * H5Lget_info1(). Specific compile-time compatibility flags and the resulting + * mappings are as follows: + * \li No compatibility flag: H5Lget_info2() (using 1.12 source) H5Lget_info1() + * (using 1.10 or 1.8 source) + * \li Emulate Release 1.12: H5Lget_info2() + * \li Emulate Release 1.8 or 1.10 interface: H5Lget_info1() + * + * \todo Fix the reference. + */ diff --git a/doxygen/dox/H5Lget_info_by_idx.dox b/doxygen/dox/H5Lget_info_by_idx.dox new file mode 100644 index 0000000..8f1511e --- /dev/null +++ b/doxygen/dox/H5Lget_info_by_idx.dox @@ -0,0 +1,18 @@ + /** + * \ingroup LMGT + * \def H5Lget_info_by_idx() + * H5Lget_info_by_idx() is a macro that is mapped to either H5Lget_info_by_idx1() + * or H5Lget_info_by_idx2() Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in Compatibility + * Macros in HDF5. If the library and/or application is compiled for Release + * 1.12 emulation, H5Lget_info_by_idx() will be mapped to H5Lget_info_by_idx2() and + * H5Lget_info_by_idx1() is deprecated. With earlier versions, H5Lget_infoby_idx() is mapped to + * H5Lget_info_by_idx1(). Specific compile-time compatibility flags and the resulting + * mappings are as follows: + * \li No compatibility flag: H5Lget_info_by_idx2() (using 1.12 source) H5Lget_info_by_idx1() + * (using 1.10 or 1.8 source) + * \li Emulate Release 1.12: H5Lget_info_by_idx2() + * \li Emulate Release 1.8 or 1.10 interface: H5Lget_info_by_idx1() + * + * \todo Fix the reference. + */ diff --git a/doxygen/dox/H5Literate.dox b/doxygen/dox/H5Literate.dox new file mode 100644 index 0000000..4d3a8dc --- /dev/null +++ b/doxygen/dox/H5Literate.dox @@ -0,0 +1,22 @@ +/** + * \ingroup TRAV + * \def H5Literate() + * H5Literate() is a macro that is mapped to either H5Literate1() or + * H5Literate2() Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in + * Compatibility Macros in HDF5. If the library and/or application is + * compiled for Release 1.12 emulation, H5Literate() will be mapped to + * H5Literate2() and H5Literate1() is deprecated. With earlier versions, + * H5Literate() is mapped to H5Literate1(). Specific compile-time compatibility + * flags and the resulting mappings are as follows: + * \li No compatibility flag: H5Literate2() (using 1.12 source) H5Literate1() + * (using 1.10 or 1.8 source) + * \li Emulate Release 1.12: H5Literate2() + * \li Emulate Release 1.8 or 1.10 interface: H5Literate1() + * + * \todo Fix the reference. + * + * \version 1.12.0 The function H5Literate() was renamed to H5Literate1() and + * deprecated in this release. The macro H5Literate() and the + * function H5Literate2() were introduced in this release. + */ diff --git a/doxygen/dox/H5Literate_by_name.dox b/doxygen/dox/H5Literate_by_name.dox new file mode 100644 index 0000000..174157a --- /dev/null +++ b/doxygen/dox/H5Literate_by_name.dox @@ -0,0 +1,23 @@ +/** + * \ingroup TRAV + * \def H5Literate_by_name() + * H5Literate_by_name() is a macro that is mapped to either + * H5Literate_by_name1() or H5Literate_by_name2() Such macros are provided to + * facilitate application compatibility. Their use and mappings are fully + * described in Compatibility Macros in HDF5. If the library and/or application is + * compiled for Release 1.12 emulation, H5Literate_by_name() will be mapped to + * H5Literate_by_name2() and H5Literate_by_name1() is deprecated. With earlier + * versions, H5Literate_by_name() is mapped to H5Literate_by_name1(). + * Specific compile-time compatibility flags and the resulting mappings are as + * follows: + * \li No compatibility flag: H5Literate_by_name2() (using 1.12 source) + * H5Literate_by_name1() (using 1.10 or 1.8 source) + * \li Emulate Release 1.12: H5Literate_by_name2() + * \li Emulate Release 1.8 or 1.10 interface: H5Literate_by_name1() + * + * \todo Fix the reference. + * + * \version 1.12.0 The function H5Literate_by_name() was renamed to H5Literate_by_name1() and + * deprecated in this release. The macro H5Literate_by_name() and the + * function H5Literate_by_name2() were introduced in this release. + */ diff --git a/doxygen/dox/H5Lvisit.dox b/doxygen/dox/H5Lvisit.dox new file mode 100644 index 0000000..e356576 --- /dev/null +++ b/doxygen/dox/H5Lvisit.dox @@ -0,0 +1,22 @@ +/** + * \ingroup TRAV + * \def H5Lvisit() + * H5Lvisit() is a macro that is mapped to either H5Lvisit1() or + * H5Lvisit2() Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in + * Compatibility Macros in HDF5. If the library and/or application is + * compiled for Release 1.12 emulation, H5Lvisit() will be mapped to + * H5Lvisit2() and H5Lvisit1() is deprecated. With earlier versions, + * H5Lvisit() is mapped to H5Lvisit1(). Specific compile-time compatibility + * flags and the resulting mappings are as follows: + * \li No compatibility flag: H5Lvisit2() (using 1.12 source) H5Lvisit1() + * (using 1.10 or 1.8 source) + * \li Emulate Release 1.12: H5Lvisit2() + * \li Emulate Release 1.8 or 1.10 interface: H5Lvisit1() + * + * \todo Fix the reference. + * + * \version 1.12.0 The function H5Lvisit() was renamed to H5Lvisit1() and + * deprecated in this release. The macro H5Lvisit() and the + * function H5Lvisit2() were introduced in this release. + */ diff --git a/doxygen/dox/H5Lvisit_by_name.dox b/doxygen/dox/H5Lvisit_by_name.dox new file mode 100644 index 0000000..0bb482e --- /dev/null +++ b/doxygen/dox/H5Lvisit_by_name.dox @@ -0,0 +1,22 @@ +/** + * \ingroup TRAV + * \def H5Lvisit_by_name() + * H5Lvisit_by_name() is a macro that is mapped to either H5Lvisit_by_name1() or + * H5Lvisit_by_name2() Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in + * Compatibility Macros in HDF5. If the library and/or application is + * compiled for Release 1.12 emulation, H5Lvisit_by_name() will be mapped to + * H5Lvisit_by_name2() and H5Lvisit_by_name1() is deprecated. With earlier versions, + * H5Lvisit_by_name() is mapped to H5Lvisit_by_name1(). Specific compile-time + * compatibility flags and the resulting mappings are as follows: + * \li No compatibility flag: H5Lvisit_by_name2() (using 1.12 source) H5Lvisit_by_name1() + * (using 1.10 or 1.8 source) + * \li Emulate Release 1.12: H5Lvisit_by_name2() + * \li Emulate Release 1.8 or 1.10 interface: H5Lvisit_by_name1() + * + * \todo Fix the reference. + * + * \version 1.12.0 The function H5Lvisit_by_name() was renamed to H5Lvisit_by_name1() and + * deprecated in this release. The macro H5Lvisit_by_name() and the + * function H5Lvisit_by_name2() were introduced in this release. + */ diff --git a/doxygen/dox/H5Oget_info.dox b/doxygen/dox/H5Oget_info.dox new file mode 100644 index 0000000..e8b7afa --- /dev/null +++ b/doxygen/dox/H5Oget_info.dox @@ -0,0 +1,121 @@ +/** + * \ingroup H5O + * \def H5Oget_info() + * + * #H5Oget_info is a macro that is mapped to: + * \li H5Oget_info3() + * \li H5Oget_info1() + * + * \details Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in + * API Compatibility Macros in HDF5; we urge you to read that + * document closely. + * + * In HDF5 versions 1.12 and after, #H5Oget_info is mapped to + * \ref H5Oget_info3() and \ref H5Oget_info1() is deprecated. + * In version 1.10 #H5Oget_info is identical to \ref H5Oget_info1(). + * + * Specific compile-time compatibility flags and the resulting + * mappings are as follows: + * \par + * <table> + * <tr> + * <th>Compatibility setting</th> + * <th>H5Oget_info</th> + * </tr> + * <tr> + * <td>No compatibility flag</td> + * <td>\ref H5Oget_info3() (in release 1.12)</td> + * </tr> + * <tr> + <td></td> + * <td>\ref H5Oget_info1() (in 1.8 or 1.10)</td> + * </tr> + * <tr> + * <td>Emulate Release 1.12</td> + * <td>\ref H5Oget_info3()</td> + * </tr> + * <tr> + * <td>Emulate Release 1.10/1.8 interface</td> + * <td>\ref H5Oget_info1()</td> + * </tr> + * </table> + * + * \note If you are iterating through a lot of different objects to + * retrieve information via the H5Oget_info() family of routines, + * you may see memory building up. This can be due to memory + * allocation for metadata such as object headers and messages + * when the iterated objects are put into the metadata cache. + * \note + * If the memory buildup is not desirable, you can configure a + * smaller cache via H5Fset_mdc_config() or set the file access + * property list via H5Pset_mdc_config(). A smaller sized cache + * will force metadata entries to be evicted from the cache, + * thus freeing the memory associated with the entries. + * + * \todo Fix reference to the document + * + * \par Version + * <table> + * <tr> + * <th>Release</th> + * <th>Change</th> + * </tr> + * <tr> + * <td>1.12.0</td> + * <td>The macro #H5Oget_info and the function \ref H5Oget_info3() were added, + * and \ref H5Oget_info1() was deprecated.</td> + * </tr> + * <tr> + * <td>1.10.5</td> + * <td>The macro #H5Oget_info was removed.</td> + * </tr> + * <tr> + * <td></td> + * <td>The functions \ref H5Oget_info1() and + * #H5Oget_info are identical in this release.</td> + * </tr> + * <tr> + * <td></td> + * <td>This change was added to restore the broken API compatibility + * introduced in HDF5-1.10.3.</td> + * </tr> + * <tr> + * <td>1.10.3</td> + * <td>The function \ref H5Oget_info() was renamed \ref H5Oget_info1.</td> + * </tr> + * <tr> + * <td></td> + * <td>The macro #H5Oget_info and the function \ref H5Oget_info2() were + * introduced in this release.</td> + * </tr> + * <tr> + * <td>1.8.15</td> + * <td>Added a note about the valid values for the \c version field in + * the \ref H5O_hdr_info_t structure.</td> + * </tr> + * <tr> + * <td>1.8.11</td> + * <td>Fortran subroutine introduced in this release.</td> + * </tr> + * <tr> + * <td>1.8.10</td> + * <td>Added \ref H5O_type_t structure to the Description section.</td> + * </tr> + * <tr> + * <td></td> + * <td>Separated \ref H5O_hdr_info_t structure from \ref H5O_info_t + * in the Description section.</td> + * </tr> + * <tr> + * <td></td> + * <td>Clarified the definition and implementation of the time fields.</td> + * </tr> + * <tr> + * <td>1.8.0</td> + * <td>Function introduced in this release.</td> + * </tr> + * </table> + * + * + */ diff --git a/doxygen/dox/H5Oget_info_by_idx.dox b/doxygen/dox/H5Oget_info_by_idx.dox new file mode 100644 index 0000000..2598374 --- /dev/null +++ b/doxygen/dox/H5Oget_info_by_idx.dox @@ -0,0 +1,92 @@ +/** + * \ingroup H5O + * \def H5Oget_info_by_idx() + * + * #H5Oget_info_by_idx is a macro that is mapped to: + * \li H5Oget_info_by_idx3() + * \li H5Oget_info_by_idx1() + * + * \details Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in + * API Compatibility Macros in HDF5; we urge you to read that + * document closely. + * + * In HDF5 versions 1.12 and after, #H5Oget_info_by_idx is mapped to + * \ref H5Oget_info_by_idx3() and \ref H5Oget_info_by_idx1() is deprecated. + * In version 1.10 #H5Oget_info_by_idx is identical to \ref H5Oget_info_by_idx1(). + * + * Specific compile-time compatibility flags and the resulting + * mappings are as follows: + * + * \par + * <table> + * <tr> + * <th>Compatibility setting</th> + * <th>H5Oget_info_by_idx</th> + * </tr> + * <tr> + * <td>No compatibility flag</td> + * <td>\ref H5Oget_info_by_idx3() for 1.12</td> + * </tr> + * <tr> + <td></td> + * <td>\ref H5Oget_info_by_idx1() for 1.8/1.10</td> + * </tr> + * <tr> + * <td>Emulate Release 1.12</td> + * <td>\ref H5Oget_info_by_idx3()</td> + * </tr> + * <tr> + * <td>Emulate Release 1.10/1.8 interface</td> + * <td>\ref H5Oget_info_by_idx1()</td> + * </tr> + * </table> + * + * \todo Fix reference to the document + * + * \par Version + * <table> + * <tr> + * <th>Release</th> + * <th>Change</th> + * </tr> + * <tr> + * <td>1.12.0</td> + * <td>The macro #H5Oget_info_by_idx and function \ref H5Oget_info_by_idx3() were added, + * and \ref H5Oget_info_by_idx1() was deprecated.</td> + * </tr> + * <tr> + * <td>1.10.5</td> + * <td>The macro #H5Oget_info_by_idx was removed.</td> + * </tr> + * <tr> + * <td></td> + * <td>The functions \ref H5Oget_info_by_idx() and + * H5Oget_info_by_idx1() are identical in this release.</td> + * </tr> + * <tr> + * <td></td> + * <td>This change was added to restore the broken API compatibility + * introduced in HDF5-1.10.3.</td> + * </tr> + * <tr> + * <td>1.10.3</td> + * <td>The function \ref H5Oget_info_by_idx() was renamed \ref H5Oget_info_by_idx1.</td> + * </tr> + * <tr> + * <td></td> + * <td>The macro #H5Oget_info_by_idx and the function \ref H5Oget_info_by_idx2() were + * introduced in this release.</td> + * </tr> + * <tr> + * <td>1.8.11</td> + * <td>Fortran subroutine introduced in this release.</td> + * </tr> + * <tr> + * <td>1.8.0</td> + * <td>Function introduced in this release.</td> + * </tr> + * </table> + * + * + */ diff --git a/doxygen/dox/H5Oget_info_by_name.dox b/doxygen/dox/H5Oget_info_by_name.dox new file mode 100644 index 0000000..b1b9540 --- /dev/null +++ b/doxygen/dox/H5Oget_info_by_name.dox @@ -0,0 +1,99 @@ +/** + * \ingroup H5O + * \def H5Oget_info_by_name() + * + * #H5Oget_info_by_name is a macro that is mapped to: + * \li H5Oget_info_by_name3() + * \li H5Oget_info_by_name1() + * + * \details Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in + * API Compatibility Macros in HDF5; we urge you to read that + * document closely. + * + * In HDF5 versions 1.12 and after, #H5Oget_info_by_name is mapped to + * \ref H5Oget_info_by_name3(). In version 1.10 #H5Oget_info_by_name is + * identical to \ref H5Oget_info_by_name1(). + * + * Specific compile-time compatibility flags and the resulting + * mappings are as follows: + * + * \par + * <table> + * <tr> + * <th>Compatibility setting</th> + * <th>H5Oget_info_by_name</th> + * </tr> + * <tr> + * <td>No compatibility flag</td> + * <td>\ref H5Oget_info_by_name3() for 1.12 and above</td> + * </tr> + * <tr> + <td></td> + * <td>\ref H5Oget_info_by_name1() for 1.8 or 1.10</td> + * </tr> + * <tr> + * <td>Emulate Release 1.12</td> + * <td>\ref H5Oget_info_by_name3()</td> + * </tr> + * <tr> + * <td>Emulate Release 1.10 or 1.8 interface</td> + * <td>\ref H5Oget_info_by_name1()</td> + * </tr> + * </table> + * + * \todo Fix reference to the document; exchange 1.8.8 and 1.8.0 + * + * \par Version + * <table> + * <tr> + * <th>Release</th> + * <th>Change</th> + * </tr> + * <tr> + * <td>1.12.0</td> + * <td>The macro #H5Oget_info_by_name and function \ref H5Oget_info_by_name3() were added + * and \ref H5Oget_info_by_name1() was deprecated.</td> + * </tr> + * <tr> + * <td>1.10.5</td> + * <td>The macro #H5Oget_info_by_name was removed.</td> + * </tr> + * <tr> + * <td></td> + * <td>The functions \ref H5Oget_info_by_name() and + * H5Oget_info_by_name1() are identical in this release.</td> + * </tr> + * <tr> + * <td></td> + * <td>This change was added to restore the broken API compatibility + * introduced in HDF5-1.10.3.</td> + * </tr> + * <tr> + * <td>1.10.3</td> + * <td>The function \ref H5Oget_info_by_name() was renamed + * to \ref H5Oget_info_by_name1.</td> + * </tr> + * <tr> + * <td></td> + * <td>The macro #H5Oget_info_by_name was renamed to + * \ref H5Oget_info_by_name1().</td> + * </tr> + * <tr> + * <td></td> + * <td>The macro #H5Oget_info_by_name and the function \ref H5Oget_info_by_name2() + * were introduced in this release.</td> + * </tr> + * <tr> + * <td>1.8.8</td> + * <td>Fortran 2003 subroutine and \ref H5O_info_t derived + * type introduced in this release.</td> + * </tr> + * <tr> + * <td>1.8.0</td> + * <td>C function introduced in this release.</td> + * </tr> + * </table> + * + * + */ diff --git a/doxygen/dox/H5Ovisit.dox b/doxygen/dox/H5Ovisit.dox new file mode 100644 index 0000000..5030a13 --- /dev/null +++ b/doxygen/dox/H5Ovisit.dox @@ -0,0 +1,92 @@ +/** + * \ingroup H5O + * \def H5Ovisit() + * + * #H5Ovisit is a macro that is mapped to one of the following: + * \li H5Ovisit3() + * \li H5Ovisit1() + * + * \details Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in + * API Compatibility Macros in HDF5; we urge you to read that + * document closely. + * + * In HDF5 versions 1.12 and after, \ref H5Ovisit() is mapped to + * \ref H5Ovisit3(). In version 1.10, \ref H5Ovisit() is identical + * to \ref H5Ovisit1(). + * + * Specific compile-time compatibility flags and the resulting + * mappings are as follows: + * + * \par + * <table> + * <tr> + * <th>Compatibility settings</th> + * <th>H5Ovisit</th> + * </tr> + * <tr> + * <td>No compatibility flag</td> + * <td>\ref H5Ovisit3() in 1.12 or after</td> + * </tr> + * <tr> + <td></td> + * <td>\ref H5Ovisit1() for 1.8 and 1.10</td> + * </tr> + * <tr> + * <td>Emulate Release 1.12</td> + * <td>\ref H5Ovisit3()</td> + * </tr> + * <tr> + * <td>Emulate Release 1.10 or 1.8 interface</td> + * <td>\ref H5Ovisit1()</td> + * </tr> + * </table> + * + * \todo Fix reference to the document + * + * \par Version + * <table> + * <tr> + * <th>Release</th> + * <th>Change</th> + * </tr> + * <tr> + * <td>1.12.0</td> + * <td>The macro #H5Ovisit and function \ref H5Ovisit3() were added, + * and \ref H5Ovisit1() was deprecated.</td> + * </tr> + * <tr> + * <td>1.10.5</td> + * <td>The macro #H5Ovisit was removed.</td> + * </tr> + * <tr> + * <td></td> + * <td>The functions \ref H5Ovisit() and + * H5Ovisit1() are identical in this release.</td> + * </tr> + * <tr> + * <td></td> + * <td>This change was added to restore the broken API compatibility + * introduced in HDF5-1.10.3.</td> + * </tr> + * <tr> + * <td>1.10.3</td> + * <td>The function \ref H5Ovisit() was renamed to \ref H5Ovisit1.</td> + * </tr> + * <tr> + * <td></td> + * <td>The macro #H5Ovisit and the function \ref H5Ovisit2() were + * introduced in this release.</td> + * </tr> + * <tr> + * <td>1.8.8</td> + * <td>Fortran subroutine and data structure added.</td> + * </tr> + * <tr> + * <td>1.8.0</td> + * <td>C function introduced.</td> + * </tr> + * </table> + * + * + */ diff --git a/doxygen/dox/H5Ovisit_by_name.dox b/doxygen/dox/H5Ovisit_by_name.dox new file mode 100644 index 0000000..5c6e51a --- /dev/null +++ b/doxygen/dox/H5Ovisit_by_name.dox @@ -0,0 +1,92 @@ +/** + * \ingroup H5O + * \def H5Ovisit_by_name() + * + * #H5Ovisit_by_name is a macro that is mapped to one of the following: + * \li H5Ovisit_by_name3() + * \li H5Ovisit_by_name1() + * + * \details Such macros are provided to facilitate application + * compatibility. Their use and mappings are fully described in + * API Compatibility Macros in HDF5; we urge you to read that + * document closely. + * + * In HDF5 versions 1.12 and after, \ref H5Ovisit_by_name() is mapped to + * \ref H5Ovisit_by_name3(). In version 1.10, \ref H5Ovisit_by_name() + * is identical to \ref H5Ovisit_by_name1(). + * + * Specific compile-time compatibility flags and the resulting + * mappings are as follows: + * + * \par + * <table> + * <tr> + * <th>Compatibility settings</th> + * <th>H5Ovisit_by_name</th> + * </tr> + * <tr> + * <td>No compatibility flag</td> + * <td>\ref H5Ovisit_by_name3() for 1.12 and above</td> + * </tr> + * <tr> + <td></td> + * <td>\ref H5Ovisit_by_name1() for 1.10 or 1.8</td> + * </tr> + * <tr> + * <td>Emulate Release 1.12 interface</td> + * <td>\ref H5Ovisit_by_name3()</td> + * </tr> + * <tr> + * <td>Emulate Release 1.10 or 1.8 interface</td> + * <td>\ref H5Ovisit_by_name1()</td> + * </tr> + * </table> + * + * \todo Fix reference to the document + * + * \par Version + * <table> + * <tr> + * <th>Release</th> + * <th>Change</th> + * </tr> + * <tr> + * <td>1.12.0</td> + * <td>The macro #H5Ovisit_by_name and function \ref H5Ovisit_by_name3() were added. + * </tr> + * <tr> + * <td>1.10.5</td> + * <td>The macro #H5Ovisit_by_name was removed.</td> + * </tr> + * <tr> + * <td></td> + * <td>The functions \ref H5Ovisit_by_name() and + * H5Ovisit_by_name1() are identical in this release.</td> + * </tr> + * <tr> + * <td></td> + * <td>This change was added to restore the broken API compatibility + * introduced in HDF5-1.10.3.</td> + * </tr> + * <tr> + * <td>1.10.3</td> + * <td>The function \ref H5Ovisit_by_name() was renamed + * to \ref H5Ovisit_by_name1.</td> + * </tr> + * <tr> + * <td></td> + * <td>The macro #H5Ovisit_by_name and the function \ref H5Ovisit_by_name2() + * were introduced in this release.</td> + * </tr> + * <tr> + * <td>1.8.8</td> + * <td>Fortran subroutine introduced in this release.</td> + * </tr> + * <tr> + * <td>1.8.0</td> + * <td>Function introduced in this release.</td> + * </tr> + * </table> + * + * + */ diff --git a/doxygen/dox/H5Sencode.dox b/doxygen/dox/H5Sencode.dox new file mode 100644 index 0000000..fe0995c --- /dev/null +++ b/doxygen/dox/H5Sencode.dox @@ -0,0 +1,5 @@ +/** + * \ingroup H5S + * \def H5Sencode() + * H5Sencode() is a macro that is mapped to either H5Sencode1() or H5Sencode2(). +*/ diff --git a/doxygen/dox/api-compat-macros.dox b/doxygen/dox/api-compat-macros.dox new file mode 100644 index 0000000..6b85ccb --- /dev/null +++ b/doxygen/dox/api-compat-macros.dox @@ -0,0 +1,899 @@ +/** \page api-compat-macros API Compatibility Macros + \tableofcontents + + \section audience Audience + The target audience for this document has existing applications that use the + HDF5 library, and is considering moving to the latest HDF5 release to take + advantage of the latest library features and enhancements. + + \section compat-issues Compatibility Issues + With each major release of HDF5, such as 1.12 or 1.10, certain compatibility + issues must be considered when migrating applications from an earlier major + release. + + This document describes the approach taken by The HDF Group to help existing + users of HDF5 address compatibility issues in the HDF5 API. + + \section summary Summary and Motivation + In response to new and evolving requirements for the library and data format, + several basic functions have changed since HDF5 was first released. To allow + existing applications to continue to compile and run properly, all versions + of these functions have been retained in the later releases of the HDF5 library. + + Given the scope of changes available with each major release of HDF5, and + recognizing the potentially time-consuming task of editing all the affected + calls in user applications, The HDF Group has created a set of macros that + can be used to flexibly and easily map existing API calls to previous release + functions. We refer to these as the \Emph{API compatibility macros}. + + The HDF Group generally encourages users to update applications to work with + the latest HDF5 library release so that all new features and enhancements are + available to them. At the same time, The HDF Group understands that, under + some circumstances, updating applications may not be feasible or necessary. + The API compatibility macros, described in this document, provide a bridge + from old APIs to new and can be particularly helpful in situations such as these: + <ul> + <li>Source code is not available - only binaries are available; updating the + application is not feasible.</li> + <li>Source code is available, but there are no resources to update it.</li> + <li>Source code is available, as are resources to update it, but the old + version works quite well so updates are not a priority. At the same time, + it is desirable to take advantage of certain efficiencies in the newer HDF5 + release that do not require code changes.</li> + <li>Source code is available, as are resources to update it, but the applications + are large or complex, and must continue to run while the code updates are + carried out.</li> + </ul> + + \section using Understanding and Using the Macros + As part of latest HDF5 release, several functions that existed in previous + versions of the library were updated with new calling parameters and given + new names. The updated versions of the functions have a number (for, e.g., '2') + at the end of the original function name. The original versions of these + functions were retained and renamed to have an earlier number (for, e.g., '1') + at the end of the original function name. + + For example, consider the function \Code{H5Lvisit} in HDF5 release 1.10 + as compared with 1.12: + + <table> + <tr> + <th>Original function name and signature in 1.10.0</th> + <td colspan="1"> + \Code{herr_t H5Lvisit(hid_t grp_id, H5_index_t idx_type, H5_iter_order_t order, H5L_iterate_t op, void *op_data)} + </td> + </tr> + <tr> + <th>Updated function and signature, introduced in release 1.12.0</th> + <td colspan="1"> + \Code{herr_t H5Lvisit2(hid_t group_id, H5_index_t idx_type, H5_iter_order_t order, H5L_iterate2_t op, void *op_data)} + </td> + </tr> + <tr><th>Original function and signature, renamed in release 1.12.0</th> + <td colspan="1"> + \Code{herr_t H5Lvisit1(hid_t group_id, H5_index_t idx_type, H5_iter_order_t order, H5L_iterate1_t op, void *op_data)} + </td> + </tr> + <tr><th>API compatibility macro, introduced in release 1.12.0</th> + <td colspan="1"> + \Code{H5Lvisit} + <p>The macro, \Code{H5Lvisit}, will be mapped to either \Code{H5Lvisit1} or + \Code{H5Lvisit2}. The mapping is determined by a combination of the + configuration options use to build the HDF5 library and compile-time + options used to build the application. The calling parameters used with the + \Code{H5Lvisit} compatibility macro should match the number and type of the + function the macros will be mapped to (\Code{H5Lvisit1} or \Code{H5Lvisit2}). + </p> + <p>The function names ending in '1' or '2' are referred to as \Emph{versioned names}, + and the corresponding functions are referred to as \Emph{versioned functions}. + For new code development, The HDF Group recommends use of the compatibility macro + mapped to the latest version of the function. The original version of the function + should be considered deprecated and, in general, should not be used when developing + new code. + </p> + </td> + </tr> + </table> + + \section options Compatibility Macro Mapping Options + To determine the mapping for a given API compatibility macro in a given application, + a combination of user-controlled selections, collectively referred to as the + \Emph{compatibility macro mapping options}, is considered in the following sequence: + + <table border="0" style="width: 100.0%;"> + <tr> + <td valign="top" width="50%"> + <ol> + <li>What compatibility macro configuration option was used to build the HDF5 library? + We refer to this selection as the \Emph{library mapping}.</li> + <li>Was a compatibility macro global compile-time option specified when the application + was built? We refer to this (optional) selection as the \Emph{application mapping}. + If an application mapping exists, it overrides the library mapping. + \Emph{(See adjacent notes.)}</li> + <li>Were any compatibility macro function-level compile-time options specified when the + application was built? We refer to these (optional) selections as \Emph{function mappings}. + If function mappings exist, they override library and application mappings for the + relevant API compatibility macros. \Emph{(See adjacent notes.)}</li> + </ol> + </td> + <td valign="top" width="50%"> + <table border="1" cellpadding="10" style="width: 100.0%;"> + <tr><td> + \Bold{Notes:} An application mapping can map APIs to the same version or to a version + older than the configured library mapping. When the application attempts to map APIs + to a newer version of the API than the library was configured with, it will fail to + "upgrade" the mapping (and may fail silently). + + When it is necessary to "upgrade" the macro mappings from those set in the library mapping, + it must be done at the per-function level, using the function-level mappings. As long as + one does not try to map a function to a version that was compiled out in the library mapping, + individual functions can be upgraded or downgraded freely. + </td> + </tr> + </table> + </td> + </tr> + </table> + + \subsection lib-options Library Mapping Options + When the HDF5 library is built, \Code{configure} flags can be used to control the API + compatibility macro mapping behavior exhibited by the library. This behavior can be + overridden by application and function mappings. One configure flag excludes deprecated + functions from the HDF5 library, making them unavailable to applications linked with the + library. + + <div align="center">Table 1: Library Mapping Options + <table border="1" cellpadding="3"> + <tr> + <th>\Code{configure} flag</th> + <th>Macros map to release <br/> (versioned function; \Code{H5Lvisit} shown)</th> + <th>Deprecated functions available? <br/> (\Code{H5Lvisit1})</th> + </tr> + <tr align="center"> + <td>\Code{--with-default-api-version=v112} <br/> (the default in 1.12)</td> + <td>1.12.x (\Code{H5Lvisit2})</td> + <td>yes</td> + </tr> + <tr align="center"> + <td align="left">\Code{--with-default-api-version=v110}</td> + <td>1.10.x (\Code{H5Lvisit1})</td> + <td>yes</td> + </tr> + <tr align="center"> + <td align="left">\Code{--with-default-api-version=v18}</td> + <td>1.8.x (\Code{H5Lvisit1})</td> + <td>yes</td> + </tr> + <tr align="center"> + <td align="left">\Code{--with-default-api-version=v16}</td> + <td>1.6.x (\Code{H5Lvisit1})</td> + <td>yes</td> + </tr> + <tr align="center"> + <td align="left">\Code{--disable-deprecated-symbols}</td> + <td>1.12.x (\Code{H5Lvisit2})</td> + <td>no</td> + </tr> + </table> + </div> + Refer to the file \Code{libhdf5.settings} in the directory where the HDF5 library is + installed to determine the \Code{configure} flags used to build the library. In particular, + look for the two lines shown here under \Emph{Features}: + + \Code{Default API mapping: v112} + + \Code{With deprecated public symbols: yes} + + \subsection app-options Application Mapping Options + When an application using HDF5 APIs is built and linked with the HDF5 library, + compile-time options to \Code{h5cc} can be used to control the API compatibility + macro mapping behavior exhibited by the application. The application mapping + overrides the behavior specified by the library mapping, and can be overridden + on a function-by-function basis by the function mappings. + + If the HDF5 library was configured with the \Code{--disable-deprecated-symbols} flag, then + the deprecated functions will not be available, regardless of the application mapping options. + + <div align="center">Table 2: Application Mapping Options + <table border="1" cellpadding="3"> + <tr> + <th>\Code{h5cc} option</th> + <th>Macros map to release <br/>(versioned function; \Code{H5Lvisit} shown)</th> + <th>Deprecated functions available? <br/>(\Code{H5Lvisit1})</th> + </tr> + <tr align="center"> + <td align="left">\Code{-DH5_USE_112_API} <br/> \Emph{(Default behavior if no option specified.)}</td> + <td>1.12.x (\Code{HLvisit2})</td> + <td>yes* <br/> \Emph{*if available in library}</td> + </tr> + <tr align="center"> + <td align="left">\Code{-DH5_USE_110_API}</td> + <td>1.10.x (\Code{HLvisit1})</td> + <td>yes* <br/> \Emph{*if available in library}</td> + </tr> + <tr align="center"> + <td align="left">\Code{-DH5_USE_18_API}</td> + <td>1.8.x (\Code{H5Lvisit1})</td> + <td>yes* <br/> \Emph{*if available in library}</td> + </tr> + <tr align="center"> + <td align="left">\Code{-DH5_USE_16_API}</td> + <td>1.6.x (\Code{H5Lvisit1})</td> + <td>yes* <br/> \Emph{*if available in library}</td> + </tr> + <tr align="center"> + <td align="left">\Code{-DH5_NO_DEPRECATED_SYMBOLS}</td> + <td>1.10.x (\Code{H5Lvisit1})</td> + <td>no</td> + </tr> + </table> + </div> + + \subsection fun-options Function Mapping Options + Function mappings are specified when the application is built. These mappings + can be used to control the mapping of the API compatibility macros to + underlying functions on a function-by-function basis. The function mappings + override the library and application mappings discussed earlier. + + If the HDF5 library was configured with the \Code{--disable-deprecated-symbols} + flag, or \Code{-DH5_NO_DEPRECATED_SYMBOLS} is used to compile the application, + then the deprecated functions will not be available, regardless of the function + mapping options. + + For every function with multiple available versions, a compile-time version flag + can be defined to selectively map the function macro to the desired versioned + function. The function mapping consists of the function name followed by + "\Code{_vers}" which is mapped by number to a specific function or + struct: + <table> + <tr> + <th>Macro</th> + <th>Function Mapping</th> + <th>Mapped to function or struct</th> + </tr> + <tr><td>\Code{H5xxx}</td> + <td>\Code{H5xxx_vers=1}</td> + <td>\Code{H5xxx1}</td> + </tr> + <tr> + <td> </td> + <td>\Code{H5xxx_vers=2}</td> + <td>\Code{H5xxx2}</td> + </tr> + </table> + + For example, in version 1.10 the \Code{H5Rreference} macro can be mapped to + either \Code{H5Rreference1} or \Code{H5Rreference2}. When used, the value of + the \Code{H5Rreference_vers} compile-time version flag determines which + function will be called: + + <ul> + <li>When \Code{H5Rreference_vers} is set to \Code{1}, the macro \Code{H5Rreference} + will be mapped to \Code{H5Rreference1}. <br/> + \Code{H5cc ... -DH5Rreference_vers=1 ...}</li> + <li>When \Code{H5Rdereference_vers} is set to \Code{2}, the macro \Code{H5Rdereference} + will be mapped to \Code{H5Rdereference2}. <br/> + \Code{h5cc ... -DH5Rreference_vers=2 ...}</li> + <li>When \Code{H5Rreference_vers} is not set, the macro \Code{H5Rreference} will be + mapped to either \Code{H5Rreference1} or \Code{H5Rreference2}, based on the + application mapping, if one was specified, or on the library mapping. <br/> + \Code{h5cc ... }</li> + </ul> + + \warning Please be aware that some function mappings use mapped structures, as + well. If compiling an application with a function mapping that uses + a mapped structure, you must include each function and mapped structure + plus EVERY function that uses the mapped structure, whether or not that + function is used in the application. \Emph{In 1.12, mappings of structures + are used by the H5L and H5O function mappings.}\n\n + For example, an application \Code{application.c} only calls \Code{H5Lvisit}, + \Code{H5Ovisit}, and \Code{H5Oget_info_by_name}. To compile this application + with 1.10 APIs in 1.12 with the function specific mappings, then not only must + \Code{H5Lvisit_vers}, \Code{H5Ovisit_vers}, and \Code{H5Oget_info_by_name_vers} + be specified on the command line, but the mapped structures and every + function that uses the mapped structures must be included, as well. + The full compile line is shown below: + \code{.sh} + h5cc -DH5Lvisit_vers=1 -DH5Ovisit_vers=1 -DH5Oget_info_by_name_vers=1 \ + -DH5Lvisit_by_name_vers=1 -DH5Literate_vers=1 \ + -DH5Literate_by_name_vers= -DH5O_info_t_vers=1 -DH5L_info_t_vers=1 \ + -DH5L_iterate_t_vers=1 -DH5Lget_info_by_idx_vers=1 \ + -DH5Lget_info_vers=1 application.c + \endcode + + \subsubsection fun-options-112 Function Mapping Options in Releases 1.12.x + <table> + <tr> + <th style="text-align: left;">Macro <br/> (\Code{H5xxx})</th> + <th>Default function used if no macro specified + <ul><li>Function/struct mapping:\Code{H5xxx_vers=N}</li></ul> + </th> + <th>Function used if specifying 1.10 + <ul><li>Function/struct mapping: \Code{H5xxx_vers=1}</li></ul> + </th> + </tr> + <tr> + <td>H5Lget_info()</td> + <td>H5Lget_info2() + <ul> + <li>Function mapping:\Code{H5Lget_info_vers=2}</li> + <li>Struct mapping:\Code{H5L_info_t_vers=2}</li> + </ul> + </td> + <td>H5Lget_info1() + <ul> + <li>Function mapping \Code{H5Lget_info_vers=1}</li> + <li>Struct mapping: \Code{H5L_info_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Lget_info_by_idx()</td> + <td>H5Lget_info_by_idx2() + <ul> + <li>Function mapping: \Code{H5Lget_info_by_idx_vers=2}</li> + <li>Struct mapping: \Code{H5L_info_t_vers=2}</li> + </ul> + </td> + <td>H5Lget_info_by_idx1() + <ul> + <li>Function mapping: \Code{H5Lget_info_by_idx_vers=1}</li> + <li>Struct mapping: \Code{H5L_info_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Literate()</td> + <td>H5Literate2() + <ul> + <li>Function mapping: \Code{H5Literate_vers=2}</li> + <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li> + </ul> + </td> + <td>H5Literate1() + <ul> + <li>Function mapping: \Code{H5Literate_vers=1}</li> + <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Literate_by_name()</td> + <td>H5Literate_by_name2() + <ul> + <li>Function mapping: \Code{H5Literate_by_name_vers=2}</li> + <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li> + </ul> + </td> + <td>H5Literate_by_name1() + <ul> + <li>Function mapping: \Code{H5Literate_by_name_vers=1}</li> + <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Lvisit()</td> + <td>H5Lvisit2() + <ul> + <li>Function mapping: \Code{H5Lvisit_vers=2}</li> + <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li> + </ul> + </td> + <td>H5Lvisit1() + <ul> + <li>Function mapping: \Code{H5Lvisit_vers=1}</li> + <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Lvisit_by_name()</td> + <td>H5Lvisit_by_name2() + <ul> + <li>Function mapping: \Code{H5Lvisit_by_name_vers=2}</li> + <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li> + </ul> + </td> + <td>H5Lvisit_by_name1() + <ul> + <li>Function mapping: \Code{H5Lvisit_by_name_vers=1}</li> + <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Oget_info()</td> + <td>H5Oget_info3() + <ul> + <li>Function mapping: \Code{H5Oget_info_vers=3}</li> + <li>Struct mapping: \Code{H5O_info_t_vers=2}</li> + </ul> + </td> + <td>H5Oget_info1() + <ul> + <li>Function mapping: \Code{H5Oget_info_vers=1}</li> + <li>Struct mapping: \Code{H5O_info_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Oget_info_by_idx()</td> + <td>H5Oget_info_by_idx3() + <ul><li>Function mapping: \Code{H5Oget_info_by_idx_vers=3}</li> + <li>Struct mapping: \Code{H5O_info_t_vers=2}</li> + </ul> + </td> + <td>H5Oget_info_by_idx1() + <ul> + <li>Function mapping: \Code{H5Oget_info_by_idx_vers=1}</li> + <li>Struct mapping: \Code{H5O_info_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Oget_info_by_name()</td> + <td>H5Oget_info_by_name3() + <ul> + <li>Function mapping: \Code{H5O_get_info_by_name_vers=3}</li> + <li>Struct mapping: \Code{H5O_info_t_vers=2}</li> + </ul> + </td> + <td>H5Oget_info_by_name1() + <ul> + <li>Function mapping: \Code{H5O_get_info_by_name_vers=1}</li> + <li>Struct mapping: \Code{H5O_info_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Ovisit()</td> + <td>H5Ovisit3() + <ul> + <li>Function mapping: \Code{H5Ovisit_vers=3}</li> + <li>Struct mapping: \Code{H5O_iterate_t_vers=2}</li> + </ul> + </td> + <td>H5Ovisit1() + <ul><li>Function mapping: \Code{H5Ovisit_vers=1}</li> + <li>Struct mapping: \Code{H5O_iterate_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Ovisit_by_name()</td> + <td>H5Ovisit_by_name3() + <ul> + <li>Function mapping: \Code{H5Ovisit_by_name_vers=3}</li> + <li>Struct mapping: \Code{H5O_iterate_t_vers=2}</li> + </ul> + </td> + <td>H5Ovisit_by_name1() + <ul> + <li>Function mapping: \Code{H5Ovisit_by_name_vers=1}</li> + <li>Struct mapping: \Code{H5O_iterate_t_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Pencode()</td> + <td>H5Pencode2() + <ul> + <li>Function mapping: \Code{H5Pencode_vers=2}</li> + </ul> + </td> + <td>H5Pencode1() + <ul> + <li>Function mapping: \Code{H5Pencode_vers=1}</li> + </ul> + </td> + </tr> + <tr> + <td>H5Sencode()</td> + <td>H5Sencode2() + <ul> + <li>Function mapping: \Code{H5Sencode_vers=2}</li> + </ul> + </td> + <td>H5Sencode1() + <ul> + <li>Function mapping: \Code{H5Sencode_vers=1}</li> + </ul> + </td> + </tr> + </table> + + \subsubsection fun-options-110 Function Mapping Options in Releases 1.10.x + <table> + <tr> + <th>Macro</th> + <th>Default function used <br/> <sub>(if no macro specified)</sub></th> + <th>Introduced in</th> + <th>\Code{h5cc} version flag and value</th> + <th>Mapped to function or struct</th> + </tr> + <tr> + <td rowspan="2">H5Rdereference()</td> + <td rowspan="2">H5Rdereference2()</td> + <td rowspan="2">HDF5-1.10.0</td> + <td>\Code{-DH5Rdereference_vers=1}</td> + <td>H5Rdereference1()</td> + </tr> + <tr> + <td>\Code{-DH5Rdereference_vers=2}</td> + <td>H5Rdereference2()</td> + </tr> + <tr> + <td rowspan="2">H5Fget_info()</td> + <td rowspan="2">H5Fget_info2()</td> + <td rowspan="2">HDF5-1.10.0</td> + <td>\Code{-DH5Fget_info_vers=1}</td> + <td>H5Fget_info1() with struct \ref H5F_info1_t</td> + </tr> + <tr> + <td>\Code{-DH5Fget_info_vers=2}</td> + <td>H5Fget_info2() with struct \ref H5F_info2_t</td> + </tr> + <tr> + <td rowspan="2">H5Oget_info()</td> + <td rowspan="2">H5Oget_info1()</td> + <td rowspan="2">HDF5-1.10.3</td> + <td>\Code{-DH5Oget_info_vers=1}</td> + <td>H5Oget_info1()</td> + </tr> + <tr> + <td>\Code{-DH5Oget_info_vers=2}</td> + <td>H5Oget_info2()</td> + </tr> + <tr> + <td rowspan="2">H5Oget_info_by_idx()</td> + <td rowspan="2">H5Oget_info_by_idx1()</td> + <td rowspan="2">HDF5-1.10.3</td> + <td>\Code{-DH5Oget_info_by_idx_vers=1}</td> + <td>H5Oget_info_by_idx1()</td> + </tr> + <tr> + <td>\Code{-DH5Oget_info_by_idx_vers=2}</td> + <td>H5Oget_info_by_idx2()</td> + </tr> + <tr> + <td rowspan="2">H5Oget_info_by_name()</td> + <td rowspan="2">H5Oget_info_by_name1()</td> + <td rowspan="2">HDF5-1.10.3</td> + <td>\Code{-DH5Oget_info_by_name_vers=1}</td> + <td>H5Oget_info_by_name1()</td> + </tr> + <tr> + <td>\Code{-DH5Oget_info_by_name_vers=2}</td> + <td>H5Oget_info_by_name2()</td> + </tr> + <tr> + <td rowspan="2">H5Ovisit()</td> + <td rowspan="2">H5Ovisit1()</td> + <td rowspan="2">HDF5-1.10.3</td> + <td>\Code{-DH5Ovisit_vers=1}</td> + <td>H5Ovisit1()</td> + </tr> + <tr> + <td>\Code{-DH5Ovisit_vers=2}</td> + <td>H5Ovisit2()</td> + </tr> + <tr> + <td rowspan="2">H5Ovisit_by_name()</td> + <td rowspan="2">H5Ovisit_by_name1()</td> + <td rowspan="2">HDF5-1.10.3</td> + <td>\Code{-DH5Ovisit_by_name_vers=1}</td> + <td>H5Ovisit_by_name1()</td> + </tr> + <tr> + <td>\Code{-DH5Ovisit_by_name_vers=2}</td> + <td>H5Ovisit_by_name2()</td> + </tr> + </table> + + \subsubsection fun-options-18 Function Mapping Options in Releases 1.8.x + At release 1.8.0, the API compatibility macros, function mapping compile-time + version flags and values, and corresponding versioned functions listed in the + following table were introduced. If the application being compiled to run with + any 1.10.x release was written to use any 1.6.x release of HDF5, you must also + consider these macros and mapping options. + + <div align="center">Table 5: Function Mapping Options in Releases 1.8.x + <table border="1" cellpadding="3" style="width: 90.0%;"> + <tr> + <th>Macro</th> + <th><code>h5cc</code> version flag and value</th> + <th>Mapped to function <br/> or struct</th> + </tr> + <tr> + <td rowspan="2">H5Acreate()</td> + <td>\Code{DH5Acreate_vers=1}</td> + <td>H5Acreate1()</td> + </tr> + <tr> + <td>\Code{DH5Acreate_vers=2}</td> + <td>H5Acreate2()</td> + </tr> + <tr> + <td rowspan="2">H5Aiterate()</td> + <td>\Code{DH5Aiterate_vers=1}</td> + <td>H5Aiterate1() <br/> with struct \ref H5A_operator1_t</td> + </tr> + <tr> + <td>\Code{DH5Aiterate_vers=2}</td> + <td>H5Aiterate2() <br/> with struct \ref H5A_operator2_t</td> + </tr> + <tr> + <td rowspan="2">H5Dcreate()</td> + <td>\Code{DH5Dcreate_vers=1}</td> + <td>H5Dcreate1()</td> + </tr> + <tr> + <td>\Code{DH5Dcreate_vers=2}</td> + <td>H5Dcreate2()</td> + </tr> + <tr><td rowspan="2">H5Dopen()</td> + <td>\Code{DH5Dopen_vers=1}</td> + <td>H5Dopen1()</td> + </tr> + <tr> + <td>\Code{DH5Dopen_vers=2}</td> + <td>H5Dopen2()</td> + </tr> + <tr> + <td rowspan="2">H5Eclear()</td> + <td>\Code{DH5Eclear_vers=1}</td> + <td>H5Eclear1()</td> + </tr> + <tr> + <td>\Code{DH5Eclear_vers=2}</td> + <td>H5Eclear2()</td> + </tr> + <tr> + <td rowspan="2">H5Eprint()</td> + <td>\Code{DH5Eprint_vers=1}</td> + <td>H5Eprint1()</td> + </tr> + <tr> + <td>\Code{DH5Eprint_vers=2}</td> + <td>H5Eprint2()</td> + </tr> + <tr> + <td rowspan="2">H5Epush()</td> + <td>\Code{DH5Epush_vers=1}</td> + <td>H5Epush1()</td> + </tr> + <tr> + <td>\Code{DH5Epush_vers=2}</td> + <td>H5Epush2()</td> + </tr> + <tr> + <td rowspan="2">H5Eset_auto()</td> + <td>\Code{DH5Eset_auto_vers=1}</td> + <td>H5Eset_auto1()</td> + </tr> + <tr> + <td>\Code{DH5Eset_auto_vers=2}</td> + <td>H5Eset_auto2()</td> + </tr> + <tr> + <td rowspan="2">H5Eget_auto()</td> + <td>\Code{DH5Eget_auto_vers=1}</td> + <td>H5Eget_auto1()</td> + </tr> + <tr> + <td>\Code{DH5Eget_auto_vers=2}</td> + <td>H5Eget_auto2()</td> + </tr> + <tr> + <td rowspan="2">\ref H5E_auto_t <br/> struct for H5Eset_auto() <br/> and H5Eget_auto()</td> + <td>\Code{DH5E_auto_t_vers=1}</td> + <td>\ref H5E_auto1_t</td> + </tr> + <tr> + <td>\Code{DH5E_auto_t_vers=2}</td> + <td>\ref H5E_auto2_t</td> + </tr> + <tr> + <td rowspan="2">H5Ewalk()</td> + <td>\Code{DH5Ewalk_vers=1}</td> + <td>H5Ewalk1() <br/> with callback \ref H5E_walk1_t <br/> and struct \ref H5E_error1_t</td> + </tr> + <tr> + <td>\Code{DH5Ewalk_vers=2}</td> + <td>H5Ewalk2() <br/> with callback \ref H5E_walk2_t <br/> and struct \ref H5E_error2_t</td> + </tr> + <tr> + <td rowspan="2">H5Gcreate()</td> + <td>\Code{DH5Gcreate_vers=1}</td> + <td>H5Gcreate1()</td> + </tr> + <tr> + <td>\Code{DH5Gcreate_vers=2}</td> + <td>H5Gcreate2()</td> + </tr> + <tr> + <td rowspan="2">H5Gopen()</td> + <td>\Code{DH5Gopen_vers=1}</td> + <td>H5Gopen1()</td> + </tr> + <tr> + <td>\Code{DH5Gopen_vers=2}</td> + <td>H5Gopen2()</td> + </tr> + <tr> + <td rowspan="2">H5Pget_filter()</td> + <td>\Code{DH5Pget_filter_vers=1}</td> + <td>H5Pget_filter1()</td> + </tr> + <tr> + <td>\Code{DH5Pget_filter_vers=2}</td> + <td>H5Pget_filter2()</td> + </tr> + <tr> + <td rowspan="2">H5Pget_filter_by_id()</td> + <td>\Code{DH5Pget_filter_by_id_vers=1}</td> + <td>H5Pget_filter_by_id1()</td> + </tr> + <tr> + <td>\Code{DH5Pget_filter_by_id_vers=2}</td> + <td>H5Pget_filter_by_id2()</td> + </tr> + <tr> + <td rowspan="2">H5Pinsert()</td> + <td>\Code{DH5Pinsert_vers=1}</td> + <td>H5Pinsert1()</td> + </tr> + <tr> + <td>\Code{DH5Pinsert_vers=2}</td> + <td>H5Pinsert2()</td> + </tr> + <tr> + <td rowspan="2">H5Pregister()</td> + <td>\Code{DH5Pregister_vers=1}</td> + <td>H5Pregister1()</td> + </tr> + <tr> + <td>\Code{DH5Pregister_vers=2}</td> + <td>H5Pregister2()</td> + </tr> + <tr> + <td rowspan="2">H5Rget_obj_type()</td> + <td>\Code{DH5Rget_obj_typevers=1}</td> + <td>H5Rget_obj_type1()</td> + </tr> + <tr> + <td>\Code{DH5Rget_obj_type_vers=2}</td> + <td>H5Rget_obj_type2()</td> + </tr> + <tr> + <td rowspan="2">H5Tarray_create()</td> + <td>\Code{DH5Tarray_create_vers=1}</td> + <td>H5Tarray_create1()</td> + </tr> + <tr> + <td>\Code{DH5Tarray_create_vers=2}</td> + <td>H5Tarray_create2()</td> + </tr> + <tr> + <td rowspan="2">H5Tcommit()</td> + <td>\Code{DH5Tcommit_vers=1}</td> + <td>H5Tcommit1()</td> + </tr> + <tr> + <td>\Code{DH5Tcommit_vers=2}</td> + <td>H5Tcommit2()</td> + </tr> + <tr> + <td rowspan="2">H5Tget_array_dims()</td> + <td>\Code{DH5Tget_array_dims_vers=1}</td> + <td>H5Tget_array_dims1()</td> + </tr> + <tr> + <td>\Code{DH5Tget_array_dims_vers=2}</td> + <td>H5Tget_array_dims2()</td> + </tr> + <tr> + <td rowspan="2">H5Topen()</td> + <td>\Code{DH5Topen_vers=1}</td> + <td>H5Topen1()</td> + </tr> + <tr> + <td>\Code{DH5Topen_vers=2}</td> + <td>H5Topen2()</td> + </tr> + <tr> + <td rowspan="2">\ref H5Z_class_t struct for H5Zregister()</td> + <td>\Code{DH5Z_class_t_vers=1}</td> + <td>\ref H5Z_class1_t</td> + </tr> + <tr> + <td>\Code{DH5Z_class_t_vers=2}</td> + <td>\ref H5Z_class2_t</td> + </tr> + </table> + </div> + + \subsubsection further Further Information + It is possible to specify multiple function mappings for a single application build: + \code{.sh} + h5cc ... -DH5Rdereference_vers=1 -DH5Fget_info_vers=2 ... + \endcode + As a result of the function and struct mappings in this compile example, all + occurrences of the macro \Code{H5Rdereference} will be mapped to \Code{H5Rdereference1} + and all occurrences of the macro \Code{H5Fget_info} will be mapped to \Code{H5Fget_info2} + for the application being built. + + The function and struct mappings can be used to guarantee that a given API compatibility + macro will be mapped to the desired underlying function or struct version regardless of + the library or application mappings. In cases where an application may benefit greatly + from features offered by some of the later APIs, or must continue to use some earlier + API versions for compatibility reasons, this fine-grained control may be very important. + + As noted earlier, the function mappings can only reference versioned functions that are + included in the HDF5 library, as determined by the configure flag used to build the + library. For example, if the HDF5 library being linked with the application was built + with the \Code{--disable-deprecated-symbols} option, version 1 of the underlying functions + would not be available, and the example above that defined \Code{H5Rdereference_vers=1} + would not be supported. + + The function mappings do not negate any available functions. If \Code{H5Rdereference1} + is available in the installed version of the HDF5 library, and the application was not + compiled with the \Code{-DH5_NO_DEPRECATED_SYMBOLS} flag, the function \Code{H5Rdereference1} + will remain available to the application through its versioned name. Similarly, + \Code{H5Rdereference2} will remain available to the application as \Code{H5Rdereference2}. + The function mapping version flag \Code{H5Rdereference_vers} only controls the mapping of + the API compatibility macro \Code{H5Rdereference} to one of the two available functions. + + This can be especially useful in any case where the programmer does not have direct control + over global macro definitions, such as when writing code meant to be copied to multiple + applications or when writing code in a header file. + + \section macros Compatibility Macros in HDF5 1.6.8 and Later + A series of similar compatibility macros were introduced into the release 1.6 + series of the library, starting with release 1.6.8. These macros simply alias the + '1' version functions, callbacks, and typedefs listed above to their original + non-numbered names. + + These macros were strictly a forward-looking feature at that time; they were not + necessary for compatibility in 1.6.x. These macros were created at that time to + enable writing code that could be used with any version of the library after 1.6.8 + and any library compilation options except \Code{H5_NO_DEPRECATED_SYMBOLS}, by always + using the '1' version of versioned functions and types. For example, \Code{H5Dopen1} + will always be interpreted in exactly the same manner by any version of the library + since 1.6.8. + + \section use-case Common Use Case + A common scenario where the API compatibility macros may be helpful is the migration + of an existing application to a new HDF5 release. An incremental migration plan is + outlined here: + <ol> + <li>Build the HDF5 library without specifying any library mapping \Code{configure} + flag. In this default mode, the 1.6.x, 1.8.x, and 1.10.x versions of the + underlying functions are available, and the API compatibility macros will + be mapped to the current HDF5 versioned functions.</li> + <li>Compile the application with the \Code{-DH5_USE_NN_API} application mapping + option if it was written for use with an earlier HDF5 library. Because the + application mapping overrides the library mapping, the macros will all be + mapped to the earlier versions of the functions.</li> + <li>Remap one API compatibility macro at a time (or sets of macros), to use the + current HDF5 versions. At each stage, use the function mappings to map the macros + being worked on to the current versions. For example, use the + \Code{-DH5Rdereference_vers=2} version flag setting to remap the \Code{H5Rdereference} + macro to \Code{H5Rdereference2}, the 1.10.x version. + + During this step, the application code will need to be modified to change the calling + parameters used with the API compatibility macros to match the number and type + of the 1.10.x versioned functions. The macro name, for example \Code{H5Rdereference}, + should continue to be used in the code, to allow for possible re-mappings to later + versioned functions in a future release.</li> + <li>After all macros have been migrated to the latest versioned functions in step 3, + compile the application without any application or function mappings. This build + uses the library mappings set in step 1, and maps API compatibility macros to the + latest versions.</li> + <li>Finally, compile the application with the application mapping + \Code{-DH5_NO_DEPRECATED_SYMBOLS}, and address any failures to complete + the application migration process.</li> + </ol> + + */
\ No newline at end of file diff --git a/doxygen/dox/mainpage.dox b/doxygen/dox/mainpage.dox new file mode 100644 index 0000000..83fc323 --- /dev/null +++ b/doxygen/dox/mainpage.dox @@ -0,0 +1,36 @@ +/*! \mainpage API Documentation for HDF5 Version 1.13 (Draft) + * + * \todo Fix the search form for server deployments. + * \todo Make it mobile-friendly + * + * \section intro_sec Introduction + * + * \todo Write an introduction. + * + * \section quick_links Quick Links + * + * <ul> + * <li>\ref PDT "Predefined Datatypes"</li> + * <li>\ref api-compat-macros "API Compatibility Macros"</li> + * <li><a href="https://hdf5.wiki/">HDF5 Wiki</a></li> + * </ul> + * + * \section using_locations The Use of Locations (Identifier + Name) in the HDF5 API + * + * \todo Make this crystal clear! + * + * \section cpp_note Programming Note for C++ Developers Using C Functions + * + * If a C routine that takes a function pointer as an argument is called from + * within C++ code, the C routine should be returned from normally. + * + * Examples of this kind of routine include callbacks such as H5Pset_elink_cb() + * and H5Pset_type_conv_cb() and functions such as H5Tconvert() and H5Ewalk2(). + * + * Exiting the routine in its normal fashion allows the HDF5 C library to clean + * up its work properly. In other words, if the C++ application jumps out of + * the routine back to the C++ \c catch statement, the library is not given the + * opportunity to close any temporary data structures that were set up when the + * routine was called. The C++ application should save some state as the + * routine is started so that any problem that occurs might be diagnosed. + */
\ No newline at end of file diff --git a/doxygen/dox/rm-template.dox b/doxygen/dox/rm-template.dox new file mode 100644 index 0000000..64e4770 --- /dev/null +++ b/doxygen/dox/rm-template.dox @@ -0,0 +1,72 @@ +/**\ingroup H5XYZ + * + * \brief A synopsis of what H5XYZgreat_function does + * + * \param[in] name1 Description of IN parameter \p name1 + * \param[out] name2 Description of OUT parameter \p name2 + * \param[in,out] name3 Description of INOUT parameter \p name3 + * + * \return Returns what you always wanted + * + * \pre Describe preconditions for an entity. Can be repreated. + * + * \invariant Describe invariants for an entity. Can be repeated. + * + * \post Describe postconditions for an entity. Can be repreated. + * + * \deprecated This was my favorite function while it lasted. + * + * \details Describe the normal behavior flow of the function here. Try to be + * helpful! + * + * Make reference to other functions like this: H5Fopen(). + * + * Make reference to formal parameters like this: \p name1 + * + * Make reference to macros like this: #H5P_DEFAULT. + * + * Make reference to enumeration constants like this: #H5F_CLOSE_WEAK. + * + * Include code snippets like this: + * \snippet H5Zpublic.h H5Z_class2_t_snip + * + * Lists are supported: + * - mouse events + * -# mouse move event + * -# mouse click event\n + * More info about the click event. + * -# mouse double click event + * - keyboard events + * 1. key down event + * 2. key up event + * + * The distance between \f$(x_1,y_1)\f$ and \f$(x_2,y_2)\f$ is + * \f$\sqrt{(x_2-x_1)^2+(y_2-y_1)^2}\f$.\n + * For tables, see + * <a href="https://www.doxygen.nl/manual/tables.html">this example</a>. + * + * This is an example of how to use the H5XYZgreat_function().\n + * The contents of the file hello_hdf5.c will be included. + * \include hello_hdf5.c + * + * \note Dear reader, ... + * + * \attention Colorless green ideas sleep furiously. + * + * \warning Don't do this at home! + * + * \author This function was written by an esteemed author. Repeat this + * command for multiple authors. + * + * \date Record the function's birthdate! + * + * \since 1.MAJOR.MINOR The 'since' command can also be used to record a + * function's introduction (via its initial release + * version). + * + * \version 1.MAJOR.MINOR An important event in the version history of this + * function. There can be multiple such events. + * + * \see H5XYZanother_great_function(), H5XYZnot_so_great_a_function() + * + */ diff --git a/doxygen/examples/H5Fclose.c b/doxygen/examples/H5Fclose.c new file mode 100644 index 0000000..6bb1d9f --- /dev/null +++ b/doxygen/examples/H5Fclose.c @@ -0,0 +1,12 @@ +#include "hdf5.h" + +int main() +{ + hid_t file; + if ((file = H5Fcreate("foo.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) + return -1; + /* Do something good with this file. */ + if(H5Fclose(file) < 0) + return -2; + return 0; +} diff --git a/doxygen/examples/H5Fcreate.c b/doxygen/examples/H5Fcreate.c new file mode 100644 index 0000000..6bb1d9f --- /dev/null +++ b/doxygen/examples/H5Fcreate.c @@ -0,0 +1,12 @@ +#include "hdf5.h" + +int main() +{ + hid_t file; + if ((file = H5Fcreate("foo.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) + return -1; + /* Do something good with this file. */ + if(H5Fclose(file) < 0) + return -2; + return 0; +} diff --git a/doxygen/examples/hello_hdf5.c b/doxygen/examples/hello_hdf5.c new file mode 100644 index 0000000..56a179c --- /dev/null +++ b/doxygen/examples/hello_hdf5.c @@ -0,0 +1,12 @@ +#include "hdf5.h" + +int main() +{ + herr_t retval; + unsigned majnum, minnum, relnum; + + if ((retval = H5get_libversion(&majnum, &minnum, &relnum)) >= 0) { + printf("Hello, HDF5 %d.%d.%d!\n", majnum, minnum, relnum); + } + return retval; +} diff --git a/doxygen/img/HDFG-logo.png b/doxygen/img/HDFG-logo.png Binary files differnew file mode 100644 index 0000000..a2d52a9 --- /dev/null +++ b/doxygen/img/HDFG-logo.png diff --git a/java/examples/datasets/CMakeLists.txt b/java/examples/datasets/CMakeLists.txt index fc4acc4..8198135 100644 --- a/java/examples/datasets/CMakeLists.txt +++ b/java/examples/datasets/CMakeLists.txt @@ -39,7 +39,7 @@ set (HDF_JAVA_SZIP_EXAMPLES set (${HDF_JAVA_EXAMPLES} ${HDF_JAVA_EXAMPLES} ${HDF_JAVA_SZIP_EXAMPLES}) endif (H5_HAVE_FILTER_SZIP) -if (WIN32 OR MINGW) +if (WIN32) set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";") else () set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") diff --git a/java/examples/datatypes/CMakeLists.txt b/java/examples/datatypes/CMakeLists.txt index bd4f483..6997b2e 100644 --- a/java/examples/datatypes/CMakeLists.txt +++ b/java/examples/datatypes/CMakeLists.txt @@ -24,7 +24,7 @@ set (HDF_JAVA_EXAMPLES H5Ex_T_VLString ) -if (WIN32 OR MINGW) +if (WIN32) set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";") else () set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") diff --git a/java/examples/groups/CMakeLists.txt b/java/examples/groups/CMakeLists.txt index c2c7d0f..6483f91 100644 --- a/java/examples/groups/CMakeLists.txt +++ b/java/examples/groups/CMakeLists.txt @@ -13,7 +13,7 @@ set (HDF_JAVA_EXAMPLES H5Ex_G_Visit ) -if (WIN32 OR MINGW) +if (WIN32) set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";") else () set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") diff --git a/java/examples/intro/CMakeLists.txt b/java/examples/intro/CMakeLists.txt index 6cb1e16..867740b 100644 --- a/java/examples/intro/CMakeLists.txt +++ b/java/examples/intro/CMakeLists.txt @@ -13,7 +13,7 @@ set (HDF_JAVA_EXAMPLES H5_ReadWrite ) -if (WIN32 OR MINGW) +if (WIN32) set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";") else () set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index f7d8dc4..1f6d0dc 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -5370,7 +5370,6 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native long H5Iget_file_id(long obj_id) throws HDF5LibraryException; - /** * H5Iget_name_long retrieves the name of an object specified by the identifier, obj_id. * @deprecated @@ -5387,6 +5386,7 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ + @Deprecated public synchronized static native long H5Iget_name_long(long obj_id, String[] name, long size) throws HDF5LibraryException, NullPointerException; /** @@ -10047,7 +10047,7 @@ public class H5 implements java.io.Serializable { throws HDF5LibraryException, NullPointerException; /** - * H5Pget_fapl_direct queries properties set by the H5Pset_fapl_core. + * H5Pget_fapl_direct queries properties set by the H5Pset_fapl_direct. * * @param fapl_id * IN: File access property list identifier @@ -11028,50 +11028,7 @@ public class H5 implements java.io.Serializable { // // // //////////////////////////////////////////////////////////// - /** - * H5Sclose releases a dataspace. - * - * @param space_id - * Identifier of dataspace to release. - * - * @return a non-negative value if successful - * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. - **/ - public static int H5Sclose(long space_id) throws HDF5LibraryException { - if (space_id < 0) - return 0; // throw new HDF5LibraryException("Negative ID");; - - log.trace("OPEN_IDS: H5Sclose remove {}", space_id); - OPEN_IDS.remove(space_id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - return _H5Sclose(space_id); - } - - private synchronized static native int _H5Sclose(long space_id) throws HDF5LibraryException; - - /** - * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by space_id. - * - * @param space_id - * Identifier of dataspace to copy. - * @return a dataspace identifier if successful - * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. - **/ - public static long H5Scopy(long space_id) throws HDF5LibraryException { - long id = _H5Scopy(space_id); - if (id > 0) { - log.trace("OPEN_IDS: H5Scopy add {}", id); - OPEN_IDS.add(id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - } - return id; - } - - private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException; + /**************** Operations on dataspaces ********************/ /** * H5Screate creates a new dataspace of a particular type. @@ -11128,19 +11085,96 @@ public class H5 implements java.io.Serializable { throws HDF5Exception, NullPointerException; /** - * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it. + * H5Sset_extent_simple sets or resets the size of an existing dataspace. * - * @param buf - * IN: Buffer for the data space object to be decoded. + * @param space_id + * Dataspace identifier. + * @param rank + * Rank, or dimensionality, of the dataspace. + * @param current_size + * Array containing current size of dataspace. + * @param maximum_size + * Array containing maximum size of dataspace. * - * @return a new object handle + * @return a dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - * @exception NullPointerException - * - buf is null. **/ - public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; + public synchronized static native long H5Sset_extent_simple(long space_id, int rank, long[] current_size, + long[] maximum_size) throws HDF5LibraryException, NullPointerException; + + /** + * H5Sset_extent_simple sets or resets the size of an existing dataspace. + * + * @param space_id + * Dataspace identifier. + * @param rank + * Rank, or dimensionality, of the dataspace. + * @param current_size + * Array containing current size of dataspace. + * @param maximum_size + * Array containing maximum size of dataspace. + * + * @return a dataspace identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static long H5Sset_extent_simple(long space_id, int rank, byte[] current_size, + byte[] maximum_size) throws HDF5LibraryException, NullPointerException { + ByteBuffer csbb = ByteBuffer.wrap(current_size); + long[] lacs = (csbb.asLongBuffer()).array(); + ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size); + long[] lamaxs = (maxsbb.asLongBuffer()).array(); + + return H5Sset_extent_simple(space_id, rank, lacs, lamaxs); + } + + /** + * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by space_id. + * + * @param space_id + * Identifier of dataspace to copy. + * @return a dataspace identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static long H5Scopy(long space_id) throws HDF5LibraryException { + long id = _H5Scopy(space_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Scopy add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException; + + /** + * H5Sclose releases a dataspace. + * + * @param space_id + * Identifier of dataspace to release. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static int H5Sclose(long space_id) throws HDF5LibraryException { + if (space_id < 0) + return 0; // throw new HDF5LibraryException("Negative ID");; + + log.trace("OPEN_IDS: H5Sclose remove {}", space_id); + OPEN_IDS.remove(space_id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + return _H5Sclose(space_id); + } + + private synchronized static native int _H5Sclose(long space_id) throws HDF5LibraryException; /** * H5Sencode converts a data space description into binary form in a buffer. @@ -11156,154 +11190,139 @@ public class H5 implements java.io.Serializable { public synchronized static native byte[] H5Sencode(long obj_id) throws HDF5LibraryException, NullPointerException; /** - * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the - * dataspace. + * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it. * - * @param dest_space_id - * IN: The identifier for the dataspace from which the extent is copied. - * @param source_space_id - * IN: The identifier for the dataspace to which the extent is copied. + * @param buf + * IN: Buffer for the data space object to be decoded. * - * @return a non-negative value if successful + * @return a new object handle * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. **/ - public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id) - throws HDF5LibraryException; + public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; /** - * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal. + * H5Sget_simple_extent_npoints determines the number of elements in a dataspace. * - * @param first_space_id - * IN: The identifier for the first dataspace. - * @param second_space_id - * IN: The identifier for the seconddataspace. + * @param space_id + * ID of the dataspace object to query + * @return the number of elements in the dataspace if successful * - * @return true if successful, else false + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException; + + /** + * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace. + * + * @param space_id + * IN: Identifier of the dataspace + * + * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id) - throws HDF5LibraryException; + public synchronized static native int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException; /** - * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current selection and places - * them into user-supplied buffers. - * <P> - * The start and end buffers must be large enough to hold the dataspace rank number of coordinates. + * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through the dims + * and maxdims parameters. * - * @param spaceid - * Identifier of dataspace to release. - * @param start - * coordinates of lowest corner of bounding box. - * @param end - * coordinates of highest corner of bounding box. + * @param space_id + * IN: Identifier of the dataspace object to query + * @param dims + * OUT: Pointer to array to store the size of each dimension. + * @param maxdims + * OUT: Pointer to array to store the maximum size of each dimension. * - * @return a non-negative value if successful,with start and end initialized. + * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - start or end is null. + * - dims or maxdims is null. **/ - public synchronized static native int H5Sget_select_bounds(long spaceid, long[] start, long[] end) + public synchronized static native int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims) throws HDF5LibraryException, NullPointerException; /** - * H5Sget_select_elem_npoints returns the number of element points in the current dataspace selection. + * H5Sis_simple determines whether a dataspace is a simple dataspace. * - * @param spaceid - * Identifier of dataspace to release. + * @param space_id + * Identifier of the dataspace to query * - * @return a non-negative value if successful + * @return true if is a simple dataspace * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException; + public synchronized static native boolean H5Sis_simple(long space_id) throws HDF5LibraryException; /** - * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace selection. The point - * coordinates have the same dimensionality (rank) as the dataspace they are located within, one coordinate per - * point. + * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace. * - * @param spaceid - * Identifier of dataspace to release. - * @param startpoint - * first point to retrieve - * @param numpoints - * number of points to retrieve - * @param buf - * returns points startblock to startblock+num-1, each points is <i>rank</i> longs. + * @param space_id + * Dataspace identifier. * - * @return a non-negative value if successful + * @return a dataspace class name if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - * @exception NullPointerException - * - buf is null. **/ - public synchronized static native int H5Sget_select_elem_pointlist(long spaceid, long startpoint, long numpoints, - long[] buf) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException; /** - * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates have the same - * dimensionality (rank) as the dataspace they are located within. The list of blocks is formatted as follows: - * - * <pre> - * <"start" coordinate>, immediately followed by - * <"opposite" corner coordinate>, followed by - * the next "start" and "opposite" coordinates, - * etc. - * until all of the selected blocks have been listed. - * </pre> + * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE. * - * @param spaceid - * Identifier of dataspace to release. - * @param startblock - * first block to retrieve - * @param numblocks - * number of blocks to retrieve - * @param buf - * returns blocks startblock to startblock+num-1, each block is <i>rank</i> * 2 (corners) longs. + * @param space_id + * The identifier for the dataspace from which the extent is to be removed. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - * @exception NullPointerException - * - buf is null. **/ - public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid, long startblock, long numblocks, - long[] buf) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Sset_extent_none(long space_id) throws HDF5LibraryException; /** - * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace selection. + * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the + * dataspace. * - * @param spaceid - * Identifier of dataspace to release. + * @param dest_space_id + * IN: The identifier for the dataspace from which the extent is copied. + * @param source_space_id + * IN: The identifier for the dataspace to which the extent is copied. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException; + public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id) + throws HDF5LibraryException; /** - * H5Sget_select_npoints determines the number of elements in the current selection of a dataspace. + * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal. * - * @param space_id - * IN: Identifier of the dataspace object to query + * @param first_space_id + * IN: The identifier for the first dataspace. + * @param second_space_id + * IN: The identifier for the seconddataspace. * - * @return the number of elements in the selection if successful + * @return true if successful, else false * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5Sget_select_npoints(long space_id) throws HDF5LibraryException; + public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id) + throws HDF5LibraryException; + + /***************** Operations on dataspace selections *****************/ /** * H5Sget_select_type retrieves the type of selection currently defined for the dataspace space_id. @@ -11319,76 +11338,118 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Sget_select_type(long space_id) throws HDF5LibraryException; /** - * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through the dims - * and maxdims parameters. + * H5Sget_select_npoints determines the number of elements in the current selection of a dataspace. * * @param space_id * IN: Identifier of the dataspace object to query - * @param dims - * OUT: Pointer to array to store the size of each dimension. - * @param maxdims - * OUT: Pointer to array to store the maximum size of each dimension. * - * @return the number of dimensions in the dataspace if successful + * @return the number of elements in the selection if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - * @exception NullPointerException - * - dims or maxdims is null. **/ - public synchronized static native int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims) - throws HDF5LibraryException, NullPointerException; + public synchronized static native long H5Sget_select_npoints(long space_id) throws HDF5LibraryException; /** - * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace. + * H5Sselect_copy copies all the selection information (including offset) from the source + * dataspace to the destination dataspace. + * @param dst_id ID of the destination dataspace + * @param src_id ID of the source dataspace + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native void H5Sselect_copy(long dst_id, long src_id) throws HDF5LibraryException; + + /** + * H5Sselect_valid verifies that the selection for the dataspace. * * @param space_id - * IN: Identifier of the dataspace + * The identifier for the dataspace in which the selection is being reset. * - * @return the number of dimensions in the dataspace if successful + * @return true if the selection is contained within the extent and FALSE if it is not or is an error. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException; + public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException; /** - * H5Sget_simple_extent_npoints determines the number of elements in a dataspace. + * H5Sselect_adjust moves a selection by subtracting an offset from it. * * @param space_id - * ID of the dataspace object to query - * @return the number of elements in the dataspace if successful + * ID of dataspace to adjust + * @param offset + * Offset to subtract * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - offset is null. **/ - public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException; + public synchronized static native void H5Sselect_adjust(long space_id, long[][] offset) + throws HDF5LibraryException, NullPointerException; /** - * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace. + * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current selection and places + * them into user-supplied buffers. + * <P> + * The start and end buffers must be large enough to hold the dataspace rank number of coordinates. * * @param space_id - * Dataspace identifier. + * Identifier of dataspace to release. + * @param start + * coordinates of lowest corner of bounding box. + * @param end + * coordinates of highest corner of bounding box. * - * @return a dataspace class name if successful + * @return a non-negative value if successful,with start and end initialized. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - start or end is null. **/ - public synchronized static native int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException; + public synchronized static native int H5Sget_select_bounds(long space_id, long[] start, long[] end) + throws HDF5LibraryException, NullPointerException; /** - * H5Sis_simple determines whether a dataspace is a simple dataspace. + * H5Sselect_shape_same checks to see if the current selection in the dataspaces are the same + * dimensionality and shape. + * This is primarily used for reading the entire selection in one swoop. + * + * @param space1_id ID of 1st Dataspace pointer to compare + * @param space2_id ID of 2nd Dataspace pointer to compare + * + * @return true if the selection is the same dimensionality and shape; + * false otherwise + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native boolean H5Sselect_shape_same(long space1_id, long space2_id) throws HDF5LibraryException; + + /** + * H5Sselect_intersect_block checks to see if the current selection in the + * dataspace intersects with the block given. * * @param space_id - * Identifier of the dataspace to query + * ID of dataspace pointer to compare + * @param start + * Starting coordinate of block + * @param end + * Opposite ("ending") coordinate of block * - * @return true if is a simple dataspace + * @return a TRUE if the current selection in the dataspace intersects with the block given + * FALSE otherwise * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - offset is null. **/ - public synchronized static native boolean H5Sis_simple(long space_id) throws HDF5LibraryException; + public synchronized static native boolean H5Sselect_intersect_block(long space_id, long[] start, long[] end) + throws HDF5LibraryException, NullPointerException; /** * H5Soffset_simple sets the offset of a simple dataspace space_id. @@ -11453,6 +11514,18 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Sselect_all(long space_id) throws HDF5LibraryException; /** + * H5Sselect_none resets the selection region for the dataspace space_id to include no elements. + * + * @param space_id + * IN: The identifier of the dataspace to be reset. + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native int H5Sselect_none(long space_id) throws HDF5LibraryException; + + /** * H5Sselect_elements selects array elements to be included in the selection for the space_id dataspace. * * @param space_id @@ -11510,6 +11583,43 @@ public class H5 implements java.io.Serializable { } /** + * H5Sget_select_elem_npoints returns the number of element points in the current dataspace selection. + * + * @param spaceid + * Identifier of dataspace to release. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException; + + /** + * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace selection. The point + * coordinates have the same dimensionality (rank) as the dataspace they are located within, one coordinate per + * point. + * + * @param spaceid + * Identifier of dataspace to release. + * @param startpoint + * first point to retrieve + * @param numpoints + * number of points to retrieve + * @param buf + * returns points startblock to startblock+num-1, each points is <i>rank</i> longs. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. + **/ + public synchronized static native int H5Sget_select_elem_pointlist(long spaceid, long startpoint, long numpoints, + long[] buf) throws HDF5LibraryException, NullPointerException; + + /** * H5Sselect_hyperslab selects a hyperslab region to add to the current selected region for the dataspace specified * by space_id. The start, stride, count, and block arrays must be the same size as the rank of the dataspace. * @@ -11578,90 +11688,89 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; - /** - * H5Sselect_none resets the selection region for the dataspace space_id to include no elements. - * - * @param space_id - * IN: The identifier of the dataspace to be reset. - * @return a non-negative value if successful - * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. - **/ - public synchronized static native int H5Sselect_none(long space_id) throws HDF5LibraryException; /** - * H5Sselect_valid verifies that the selection for the dataspace. + * H5Scombine_hyperslab combines a hyperslab selection with the current selection for a dataspace, + * creating a new dataspace to return the generated selection. + * If the current selection is not a hyperslab, it is freed and the hyperslab + * parameters passed in are combined with the H5S_SEL_ALL hyperslab (ie. a + * selection composing the entire current extent). If STRIDE or BLOCK is + * NULL, they are assumed to be set to all '1'. * * @param space_id - * The identifier for the dataspace in which the selection is being reset. + * IN: Dataspace ID of selection to use + * @param op + * IN: Operation to perform on current selection. + * @param start + * IN: Offset of start of hyperslab + * @param stride + * IN: Hyperslab stride. + * @param count + * IN: Number of blocks included in hyperslab. + * @param block + * IN: Size of block in hyperslab. * - * @return true if the selection is contained within the extent and FALSE if it is not or is an error. + * @return a dataspace ID on success / H5I_INVALID_HID on failure * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - an input array is null. + * @exception IllegalArgumentException + * - an input array is invalid. **/ - public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException; + public synchronized static native long H5Scombine_hyperslab(long space_id, int op, long[] start, long[] stride, + long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** - * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE. - * - * @param space_id - * The identifier for the dataspace from which the extent is to be removed. + * H5Smodify_select refine an existing hyperslab selection with an operation, using a second + * hyperslab. The first selection is modified to contain the result of + * space1 operated on by space2. * - * @return a non-negative value if successful + * @param space1_id + * ID of the destination dataspace + * @param op + * Operation to perform on current selection. + * @param space2_id + * ID of the source dataspace * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native int H5Sset_extent_none(long space_id) throws HDF5LibraryException; + public synchronized static native void H5Smodify_select(long space1_id, int op, long space2_id) throws HDF5LibraryException; /** - * H5Sset_extent_simple sets or resets the size of an existing dataspace. + * H5Scombine_select combines two existing hyperslab selections with an operation, returning + * a new dataspace with the resulting selection. The dataspace extent from + * space1 is copied for the dataspace extent of the newly created dataspace. * - * @param space_id - * Dataspace identifier. - * @param rank - * Rank, or dimensionality, of the dataspace. - * @param current_size - * Array containing current size of dataspace. - * @param maximum_size - * Array containing maximum size of dataspace. + * @param space1_id + * ID of the first dataspace + * @param op + * Operation to perform on current selection. + * @param space2_id + * ID of the second dataspace * - * @return a dataspace identifier if successful + * @return a dataspace ID on success / H5I_INVALID_HID on failure * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5Sset_extent_simple(long space_id, int rank, long[] current_size, - long[] maximum_size) throws HDF5LibraryException, NullPointerException; + public synchronized static native long H5Scombine_select(long space1_id, int op, long space2_id) throws HDF5LibraryException; /** - * H5Sset_extent_simple sets or resets the size of an existing dataspace. + * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified + * by space_id. * * @param space_id - * Dataspace identifier. - * @param rank - * Rank, or dimensionality, of the dataspace. - * @param current_size - * Array containing current size of dataspace. - * @param maximum_size - * Array containing maximum size of dataspace. + * IN: Identifier of dataspace selection to query * - * @return a dataspace identifier if successful + * @return a TRUE/FALSE for hyperslab selection if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static long H5Sset_extent_simple(long space_id, int rank, byte[] current_size, - byte[] maximum_size) throws HDF5LibraryException, NullPointerException { - ByteBuffer csbb = ByteBuffer.wrap(current_size); - long[] lacs = (csbb.asLongBuffer()).array(); - ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size); - long[] lamaxs = (maxsbb.asLongBuffer()).array(); - - return H5Sset_extent_simple(space_id, rank, lacs, lamaxs); - } + public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException; /** * H5Sget_regular_hyperslab determines if a hyperslab selection is regular for the dataspace specified @@ -11687,33 +11796,82 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native void H5Sget_regular_hyperslab(long space_id, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + /** + * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace selection. + * + * @param spaceid + * Identifier of dataspace to release. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException; + /** - * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified - * by space_id. + * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates have the same + * dimensionality (rank) as the dataspace they are located within. The list of blocks is formatted as follows: * - * @param space_id - * IN: Identifier of dataspace selection to query + * <pre> + * <"start" coordinate>, immediately followed by + * <"opposite" corner coordinate>, followed by + * the next "start" and "opposite" coordinates, + * etc. + * until all of the selected blocks have been listed. + * </pre> * - * @return a TRUE/FALSE for hyperslab selection if successful + * @param spaceid + * Identifier of dataspace to release. + * @param startblock + * first block to retrieve + * @param numblocks + * number of blocks to retrieve + * @param buf + * returns blocks startblock to startblock+num-1, each block is <i>rank</i> * 2 (corners) longs. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. + **/ + public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid, long startblock, long numblocks, + long[] buf) throws HDF5LibraryException, NullPointerException; + + /** + * H5Sselect_project_intersection projects the intersection of the selections of src_space_id and + * src_intersect_space_id within the selection of src_space_id as a + * selection within the selection of dst_space_id. + * + * @param src_space_id + * Selection that is mapped to dst_space_id, and intersected with src_intersect_space_id + * @param dst_space_id + * Selection that is mapped to src_space_id + * @param src_intersect_space_id + * Selection whose intersection with src_space_id is projected to dst_space_id to obtain the result + * + * @return a dataspace with a selection equal to the intersection of + * src_intersect_space_id and src_space_id projected from src_space to dst_space on success * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException; + public synchronized static native long H5Sselect_project_intersection(long src_space_id, long dst_space_id, + long src_intersect_space_id) throws HDF5LibraryException; - // /////// unimplemented //////// - // #ifdef NEW_HYPERSLAB_API - // hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op, - // const hsize_t start[], - // const hsize_t _stride[], - // const hsize_t count[], - // const hsize_t _block[]); - // herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op, - // hid_t space2_id); - // hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op, - // hid_t space2_id); - // #endif /* NEW_HYPERSLAB_API */ - // herr_t H5Sselect_copy(hid_t dst_id, hid_t src_id); + + // /////// unimplemented //////// + ///// Operations on dataspace selections ///// + + // + ///// Operations on dataspace selection iterators ///// + //public synchronized static native H5Ssel_iter_create(hid_t spaceid, size_t elmt_size, unsigned flags); + //public synchronized static native H5Ssel_iter_get_seq_list(hid_t sel_iter_id, size_t maxseq, size_t maxbytes, size_t *nseq, + // size_t *nbytes, hsize_t *off, size_t *len); + //public synchronized static native H5Ssel_iter_reset(hid_t sel_iter_id, hid_t space_id); + //public synchronized static native H5Ssel_iter_close(hid_t sel_iter_id); diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java index beba1d1..7ecfe95 100644 --- a/java/src/hdf/hdf5lib/HDF5Constants.java +++ b/java/src/hdf/hdf5lib/HDF5Constants.java @@ -35,12 +35,17 @@ public class HDF5Constants { // Get the HDF5 constants from the library // // ///////////////////////////////////////////////////////////////////////// - public static final long H5_QUARTER_HADDR_MAX = H5_QUARTER_HADDR_MAX(); + //public static final long H5_QUARTER_HADDR_MAX = H5_QUARTER_HADDR_MAX(); + /** Special parameters for szip compression */ public static final int H5_SZIP_MAX_PIXELS_PER_BLOCK = H5_SZIP_MAX_PIXELS_PER_BLOCK(); + /** Special parameters for szip compression */ public static final int H5_SZIP_NN_OPTION_MASK = H5_SZIP_NN_OPTION_MASK(); + /** Special parameters for szip compression */ public static final int H5_SZIP_EC_OPTION_MASK = H5_SZIP_EC_OPTION_MASK(); + /** Special parameters for szip compression */ public static final int H5_SZIP_ALLOW_K13_OPTION_MASK = H5_SZIP_ALLOW_K13_OPTION_MASK(); + /** Special parameters for szip compression */ public static final int H5_SZIP_CHIP_OPTION_MASK = H5_SZIP_CHIP_OPTION_MASK(); public static final int H5_INDEX_UNKNOWN = H5_INDEX_UNKNOWN(); public static final int H5_INDEX_NAME = H5_INDEX_NAME(); @@ -92,110 +97,359 @@ public class HDF5Constants { public static final int H5D_VDS_LAST_AVAILABLE = H5D_VDS_LAST_AVAILABLE(); public static final int H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS = H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS(); + /** Different kinds of error information - H5E_type_t */ public static final int H5E_MAJOR = H5E_MAJOR(); + /** Different kinds of error information - H5E_type_t */ public static final int H5E_MINOR = H5E_MINOR(); + /** Minor error codes - Object header related errors - Alignment error */ public static final long H5E_ALIGNMENT = H5E_ALIGNMENT(); + /** Minor error codes - Resource errors - Object already exists */ public static final long H5E_ALREADYEXISTS = H5E_ALREADYEXISTS(); + /** Minor error codes - Function entry/exit interface - Object already initialized */ public static final long H5E_ALREADYINIT = H5E_ALREADYINIT(); + /** Major error codes - Invalid arguments to routine */ public static final long H5E_ARGS = H5E_ARGS(); + /** Major error codes - Object atom */ public static final long H5E_ATOM = H5E_ATOM(); + /** Major error codes - Attribute */ public static final long H5E_ATTR = H5E_ATTR(); + /** Minor error codes - Object atom related errors - Unable to find atom information (already closed?) */ public static final long H5E_BADATOM = H5E_BADATOM(); + /** Minor error codes - File accessibility errors - Bad file ID accessed */ public static final long H5E_BADFILE = H5E_BADFILE(); + /** Minor error codes - Object atom related errors - Unable to find ID group information */ public static final long H5E_BADGROUP = H5E_BADGROUP(); + /** Minor error codes - Object header related errors - Iteration failed */ + public static final long H5E_BADITER = H5E_BADITER(); + /** Minor error codes - Object header related errors - Unrecognized message */ public static final long H5E_BADMESG = H5E_BADMESG(); + /** Minor error codes - Argument errors - Out of range */ public static final long H5E_BADRANGE = H5E_BADRANGE(); + /** Minor error codes - Dataspace errors - Invalid selection */ public static final long H5E_BADSELECT = H5E_BADSELECT(); + /** Datatype conversion errors - Bad size for object */ public static final long H5E_BADSIZE = H5E_BADSIZE(); + /** Minor error codes - Argument errors - Inappropriate type */ public static final long H5E_BADTYPE = H5E_BADTYPE(); + /** Minor error codes - Argument errors - Bad value */ public static final long H5E_BADVALUE = H5E_BADVALUE(); + /** Major error codes - B-Tree node */ public static final long H5E_BTREE = H5E_BTREE(); + /** Major error codes - Object cache */ public static final long H5E_CACHE = H5E_CACHE(); + /** I/O pipeline errors - Callback failed */ public static final long H5E_CALLBACK = H5E_CALLBACK(); + /** I/O pipeline errors - Error from filter 'can apply' callback */ public static final long H5E_CANAPPLY = H5E_CANAPPLY(); - // public static final long H5E_CANTALLOC = H5E_CANTALLOC(); + /** Minor error codes - Resource errors - Can't allocate space */ + public static final long H5E_CANTALLOC = H5E_CANTALLOC(); + /** Minor error codes - Dataspace errors - Can't append object */ + public static final long H5E_CANTAPPEND = H5E_CANTAPPEND(); + /** Minor error codes - Heap errors - Can't attach object */ + public static final long H5E_CANTATTACH = H5E_CANTATTACH(); + /** Minor error codes - Cache related errors - Unable to mark metadata as clean */ + public static final long H5E_CANTCLEAN = H5E_CANTCLEAN(); + /** Minor error codes - Dataspace errors - Can't clip hyperslab region */ public static final long H5E_CANTCLIP = H5E_CANTCLIP(); + /** Minor error codes - File accessibility errors - Unable to close file */ public static final long H5E_CANTCLOSEFILE = H5E_CANTCLOSEFILE(); + /** Minor error codes - Group related errors - Can't close object */ + public static final long H5E_CANTCLOSEOBJ = H5E_CANTCLOSEOBJ(); + /** Minor error codes - Dataspace errors - Can't compare objects */ + public static final long H5E_CANTCOMPARE = H5E_CANTCOMPARE(); + /** Minor error codes - Heap errors - Can't compute value */ + public static final long H5E_CANTCOMPUTE = H5E_CANTCOMPUTE(); + /** Datatype conversion errors - Can't convert datatypes */ public static final long H5E_CANTCONVERT = H5E_CANTCONVERT(); + /** Minor error codes - Resource errors - Unable to copy object */ public static final long H5E_CANTCOPY = H5E_CANTCOPY(); + /** Minor error codes - Cache related errors - Unable to cork an object */ + public static final long H5E_CANTCORK = H5E_CANTCORK(); + /** Minor error codes - Dataspace errors - Can't count elements */ public static final long H5E_CANTCOUNT = H5E_CANTCOUNT(); + /** Minor error codes - File accessibility errors - Unable to create file */ public static final long H5E_CANTCREATE = H5E_CANTCREATE(); + /** Minor error codes - Object atom related errors - Unable to decrement reference count */ public static final long H5E_CANTDEC = H5E_CANTDEC(); + /** Minor error codes - B-tree related errors - Unable to decode value */ public static final long H5E_CANTDECODE = H5E_CANTDECODE(); + /** Minor error codes - Object header related errors - Can't delete message */ public static final long H5E_CANTDELETE = H5E_CANTDELETE(); + /** Minor error codes - File accessibility errors - Unable to delete file */ public static final long H5E_CANTDELETEFILE = H5E_CANTDELETEFILE(); + /** Minor error codes - Cache related errors - Unable to create a flush dependency */ + public static final long H5E_CANTDEPEND = H5E_CANTDEPEND(); + /** Minor error codes - Cache related errors - Unable to mark metadata as dirty */ + public static final long H5E_CANTDIRTY = H5E_CANTDIRTY(); + /** Minor error codes - B-tree related errors - Unable to encode value */ public static final long H5E_CANTENCODE = H5E_CANTENCODE(); + /** Minor error codes - Cache related errors - Unable to expunge a metadata cache entry */ + public static final long H5E_CANTEXPUNGE = H5E_CANTEXPUNGE(); + /** Minor error codes - Heap errors - Can't extend heap's space */ + public static final long H5E_CANTEXTEND = H5E_CANTEXTEND(); + /** I/O pipeline errors - Filter operation failed */ + public static final long H5E_CANTFILTER = H5E_CANTFILTER(); + /** Minor error codes - Cache related errors - Unable to flush data from cache */ public static final long H5E_CANTFLUSH = H5E_CANTFLUSH(); + /** Minor error codes - Resource errors - Unable to free object */ public static final long H5E_CANTFREE = H5E_CANTFREE(); + /** Minor error codes - Parallel MPI - Can't gather data */ + public static final long H5E_CANTGATHER = H5E_CANTGATHER(); + /** Minor error codes - Resource errors - Unable to garbage collect */ + public static final long H5E_CANTGC = H5E_CANTGC(); + /** Minor error codes - Property list errors - Can't get value */ public static final long H5E_CANTGET = H5E_CANTGET(); + /** Minor error codes - Resource errors - Unable to compute size */ + public static final long H5E_CANTGETSIZE = H5E_CANTGETSIZE(); + /** Minor error codes - Object atom related errors - Unable to increment reference count */ public static final long H5E_CANTINC = H5E_CANTINC(); + /** Minor error codes - Function entry/exit interface - Unable to initialize object */ public static final long H5E_CANTINIT = H5E_CANTINIT(); + /** Minor error codes - Cache related errors - Unable to insert metadata into cache */ + public static final long H5E_CANTINS = H5E_CANTINS(); + /** Minor error codes - B-tree related errors - Unable to insert object */ public static final long H5E_CANTINSERT = H5E_CANTINSERT(); + /** Minor error codes - B-tree related errors - Unable to list node */ public static final long H5E_CANTLIST = H5E_CANTLIST(); + /** Minor error codes - Cache related errors - Unable to load metadata into cache */ public static final long H5E_CANTLOAD = H5E_CANTLOAD(); + /** Minor error codes - Resource errors - Unable to lock object */ public static final long H5E_CANTLOCK = H5E_CANTLOCK(); + /** Minor error codes - File accessibility errors Unable to lock file */ + public static final long H5E_CANTLOCKFILE = H5E_CANTLOCKFILE(); + /** Minor error codes - Cache related errors - Unable to mark a pinned entry as clean */ + public static final long H5E_CANTMARKCLEAN = H5E_CANTMARKCLEAN(); + /** Minor error codes - Cache related errors - Unable to mark a pinned entry as dirty */ + public static final long H5E_CANTMARKDIRTY = H5E_CANTMARKDIRTY(); + /** Minor error codes - Cache related errors - Unable to mark an entry as unserialized */ + public static final long H5E_CANTMARKSERIALIZED = H5E_CANTMARKSERIALIZED(); + /** Minor error codes - Cache related errors - Unable to mark an entry as serialized */ + public static final long H5E_CANTMARKUNSERIALIZED = H5E_CANTMARKUNSERIALIZED(); + /** Minor error codes - Free space errors - Can't merge objects */ + public static final long H5E_CANTMERGE = H5E_CANTMERGE(); + /** Minor error codes - B-tree related errors - Unable to modify record */ + public static final long H5E_CANTMODIFY = H5E_CANTMODIFY(); + /** Minor error codes - Link related errors - Can't move object */ + public static final long H5E_CANTMOVE = H5E_CANTMOVE(); + /** Minor error codes - Dataspace errors - Can't move to next iterator location */ public static final long H5E_CANTNEXT = H5E_CANTNEXT(); + /** Minor error codes - Cache related errors - Unable to notify object about action */ + public static final long H5E_CANTNOTIFY = H5E_CANTNOTIFY(); + /** Minor error codes - File accessibility errors - Unable to open file */ public static final long H5E_CANTOPENFILE = H5E_CANTOPENFILE(); + /** Minor error codes - Group related errors - Can't open object */ public static final long H5E_CANTOPENOBJ = H5E_CANTOPENOBJ(); - // public static final long H5E_CANTRECV = H5E_CANTRECV(); + /** Minor error codes - Heap errors - Can't operate on object */ + public static final long H5E_CANTOPERATE = H5E_CANTOPERATE(); + /** Minor error codes - Object header related errors - Can't pack messages */ + public static final long H5E_CANTPACK = H5E_CANTPACK(); + /** Minor error codes - Cache related errors - Unable to pin cache entry */ + public static final long H5E_CANTPIN = H5E_CANTPIN(); + /** Minor error codes - Cache related errors - Unable to protect metadata */ + public static final long H5E_CANTPROTECT = H5E_CANTPROTECT(); + /** Minor error codes - Parallel MPI - Can't receive data */ + public static final long H5E_CANTRECV = H5E_CANTRECV(); + /** Minor error codes - B-tree related errors - Unable to redistribute records */ + public static final long H5E_CANTREDISTRIBUTE = H5E_CANTREDISTRIBUTE(); + /** Minor error codes - Object atom related errors - Unable to register new atom */ public static final long H5E_CANTREGISTER = H5E_CANTREGISTER(); + /** Minor error codes - Function entry/exit interface - Unable to release object */ public static final long H5E_CANTRELEASE = H5E_CANTRELEASE(); + /** Minor error codes - B-tree related errors - Unable to remove object */ + public static final long H5E_CANTREMOVE = H5E_CANTREMOVE(); + /** Minor error codes - Object header related errors - Unable to rename object */ + public static final long H5E_CANTRENAME = H5E_CANTRENAME(); + /** Minor error codes - Object header related errors - Can't reset object */ + public static final long H5E_CANTRESET = H5E_CANTRESET(); + /** Minor error codes - Cache related errors - Unable to resize a metadata cache entry */ + public static final long H5E_CANTRESIZE = H5E_CANTRESIZE(); + /** Minor error codes - Heap errors - Can't restore condition */ + public static final long H5E_CANTRESTORE = H5E_CANTRESTORE(); + /** Minor error codes - Free space errors - Can't revive object */ + public static final long H5E_CANTREVIVE = H5E_CANTREVIVE(); + /** Minor error codes - Free space errors - Can't shrink container */ + public static final long H5E_CANTSHRINK = H5E_CANTSHRINK(); + /** Minor error codes - Dataspace errors - Can't select hyperslab */ public static final long H5E_CANTSELECT = H5E_CANTSELECT(); + /** Minor error codes - Cache related errors - Unable to serialize data from cache */ + public static final long H5E_CANTSERIALIZE = H5E_CANTSERIALIZE(); + /** Minor error codes - Property list errors - Can't set value */ public static final long H5E_CANTSET = H5E_CANTSET(); + /** Minor error codes - Link related errors - Can't sort objects */ + public static final long H5E_CANTSORT = H5E_CANTSORT(); + /** Minor error codes - B-tree related errors - Unable to split node */ public static final long H5E_CANTSPLIT = H5E_CANTSPLIT(); + /** Minor error codes - B-tree related errors - Unable to swap records */ + public static final long H5E_CANTSWAP = H5E_CANTSWAP(); + /** Minor error codes - Cache related errors - Unable to tag metadata in the cache */ + public static final long H5E_CANTTAG = H5E_CANTTAG(); + /** Minor error codes - Cache related errors - Unable to uncork an object */ + public static final long H5E_CANTUNCORK = H5E_CANTUNCORK(); + /** Minor error codes - Cache related errors - Unable to destroy a flush dependency */ + public static final long H5E_CANTUNDEPEND = H5E_CANTUNDEPEND(); + /** Minor error codes - Resource errors - Unable to unlock object */ public static final long H5E_CANTUNLOCK = H5E_CANTUNLOCK(); + /** Minor error codes - File accessibility errors Unable to unlock file */ + public static final long H5E_CANTUNLOCKFILE = H5E_CANTUNLOCKFILE(); + /** Minor error codes - Cache related errors - Unable to un-pin cache entry */ + public static final long H5E_CANTUNPIN = H5E_CANTUNPIN(); + /** Minor error codes - Cache related errors - Unable to unprotect metadata */ + public static final long H5E_CANTUNPROTECT = H5E_CANTUNPROTECT(); + /** Minor error codes - Cache related errors - Unable to mark metadata as unserialized */ + public static final long H5E_CANTUNSERIALIZE = H5E_CANTUNSERIALIZE(); + /** Minor error codes - Heap errors - Can't update object */ + public static final long H5E_CANTUPDATE = H5E_CANTUPDATE(); + /** Generic low-level file I/O errors - Close failed */ public static final long H5E_CLOSEERROR = H5E_CLOSEERROR(); + /** Minor error codes - Group related errors - Name component is too long */ public static final long H5E_COMPLEN = H5E_COMPLEN(); + /** Major error codes - API Context */ + public static final long H5E_CONTEXT = H5E_CONTEXT(); + /** Major error codes - Dataset */ public static final long H5E_DATASET = H5E_DATASET(); + /** Major error codes - Dataspace */ public static final long H5E_DATASPACE = H5E_DATASPACE(); + /** Major error codes - Datatype */ public static final long H5E_DATATYPE = H5E_DATATYPE(); + /** Value for the default error stack */ public static final long H5E_DEFAULT = H5E_DEFAULT(); + /** Minor error codes - Property list errors - Duplicate class name in parent class */ public static final long H5E_DUPCLASS = H5E_DUPCLASS(); + /** Major error codes - Extensible Array */ + public static final long H5E_EARRAY = H5E_EARRAY(); + /** Major error codes - External file list */ public static final long H5E_EFL = H5E_EFL(); + /** Major error codes - Error API */ + public static final long H5E_ERROR = H5E_ERROR(); + /** Minor error codes - B-tree related errors - Object already exists */ public static final long H5E_EXISTS = H5E_EXISTS(); + /** Major error codes - Fixed Array */ + public static final long H5E_FARRAY = H5E_FARRAY(); + /** Generic low-level file I/O errors - File control (fcntl) failed */ public static final long H5E_FCNTL = H5E_FCNTL(); + /** Major error codes - File accessibility */ public static final long H5E_FILE = H5E_FILE(); + /** Minor error codes - File accessibility errors - File already exists */ public static final long H5E_FILEEXISTS = H5E_FILEEXISTS(); + /** Minor error codes - File accessibility errors - File already open */ public static final long H5E_FILEOPEN = H5E_FILEOPEN(); + /** Major error codes - Free Space Manager */ + public static final long H5E_FSPACE = H5E_FSPACE(); + /** Major error codes - Function entry/exit */ public static final long H5E_FUNC = H5E_FUNC(); + /** Major error codes - Heap */ public static final long H5E_HEAP = H5E_HEAP(); + /** Minor error codes - Dataspace errors - Internal states are inconsistent */ + public static final long H5E_INCONSISTENTSTATE = H5E_INCONSISTENTSTATE(); + /** Major error codes - Internal error (too specific to document in detail) */ public static final long H5E_INTERNAL = H5E_INTERNAL(); + /** Major error codes - Low-level I/O */ public static final long H5E_IO = H5E_IO(); + /** Major error codes - Links */ public static final long H5E_LINK = H5E_LINK(); + /** Minor error codes - Object header related errors - Bad object header link count */ public static final long H5E_LINKCOUNT = H5E_LINKCOUNT(); + /** Minor error codes - Cache related errors - Failure in the cache logging framework */ + public static final long H5E_LOGGING = H5E_LOGGING(); + /** Major error codes - Map */ + public static final long H5E_MAP = H5E_MAP(); + /** Minor error codes - File accessibility errors - File mount error */ public static final long H5E_MOUNT = H5E_MOUNT(); + /** Minor error codes - Parallel MPI - Some MPI function failed */ public static final long H5E_MPI = H5E_MPI(); + /** Minor error codes - Parallel MPI - MPI Error String */ public static final long H5E_MPIERRSTR = H5E_MPIERRSTR(); + /** Minor error codes - Link related errors - Too many soft links in path */ + public static final long H5E_NLINKS = H5E_NLINKS(); + /** Minor error codes - Parallel MPI - Can't perform independent IO */ + public static final long H5E_NO_INDEPENDENT = H5E_NO_INDEPENDENT(); + /** I/O pipeline errors - Filter present but encoding disabled */ + public static final long H5E_NOENCODER = H5E_NOENCODER(); + /** I/O pipeline errors - Requested filter is not available */ public static final long H5E_NOFILTER = H5E_NOFILTER(); + /** Minor error codes - Object atom related errors - Out of IDs for group */ public static final long H5E_NOIDS = H5E_NOIDS(); + /** Major error codes - No error */ public static final long H5E_NONE_MAJOR = H5E_NONE_MAJOR(); + /** No error */ public static final long H5E_NONE_MINOR = H5E_NONE_MINOR(); + /** Minor error codes - Resource errors - No space available for allocation */ public static final long H5E_NOSPACE = H5E_NOSPACE(); + /** Minor error codes - Cache related errors - Metadata not currently cached */ public static final long H5E_NOTCACHED = H5E_NOTCACHED(); + /** Minor error codes - B-tree related errors - Object not found */ public static final long H5E_NOTFOUND = H5E_NOTFOUND(); + /** Minor error codes - File accessibility errors - Not an HDF5 file */ public static final long H5E_NOTHDF5 = H5E_NOTHDF5(); + /** Minor error codes - Link related errors - Link class not registered */ + public static final long H5E_NOTREGISTERED = H5E_NOTREGISTERED(); + /** Minor error codes - Resource errors - Object is already open */ + public static final long H5E_OBJOPEN = H5E_OBJOPEN(); + /** Major error codes - Object header */ public static final long H5E_OHDR = H5E_OHDR(); + /** Minor error codes - Plugin errors - Can't open directory or file */ + public static final long H5E_OPENERROR = H5E_OPENERROR(); + /** Generic low-level file I/O errors - Address overflowed */ public static final long H5E_OVERFLOW = H5E_OVERFLOW(); + /** Major error codes - Page Buffering */ + public static final long H5E_PAGEBUF = H5E_PAGEBUF(); + /** Minor error codes - Group related errors - Problem with path to object */ + public static final long H5E_PATH = H5E_PATH(); + /** Major error codes - Data filters */ public static final long H5E_PLINE = H5E_PLINE(); + /** Major error codes - Property lists */ public static final long H5E_PLIST = H5E_PLIST(); + /** Major error codes - Plugin for dynamically loaded library */ + public static final long H5E_PLUGIN = H5E_PLUGIN(); + /** Minor error codes - Cache related errors - Protected metadata error */ public static final long H5E_PROTECT = H5E_PROTECT(); + /** Generic low-level file I/O errors - Read failed */ public static final long H5E_READERROR = H5E_READERROR(); + /** Major error codes - References */ public static final long H5E_REFERENCE = H5E_REFERENCE(); + /** Major error codes - Resource unavailable */ public static final long H5E_RESOURCE = H5E_RESOURCE(); + /** Major error codes - Reference Counted Strings */ public static final long H5E_RS = H5E_RS(); + /** Generic low-level file I/O errors - Seek failed */ public static final long H5E_SEEKERROR = H5E_SEEKERROR(); + /** Minor error codes - Property list errors - Disallowed operation */ + public static final long H5E_SETDISALLOWED = H5E_SETDISALLOWED(); + /** I/O pipeline errors - Error from filter 'set local' callback */ public static final long H5E_SETLOCAL = H5E_SETLOCAL(); + /** Major error codes - Skip Lists */ + public static final long H5E_SLIST = H5E_SLIST(); + /** Major error codes - Shared Object Header Messages */ + public static final long H5E_SOHM = H5E_SOHM(); + /** Major error codes - Data storage */ public static final long H5E_STORAGE = H5E_STORAGE(); + /** Major error codes - Symbol table */ public static final long H5E_SYM = H5E_SYM(); + /** Minor error codes - System level errors - System error message */ + public static final long H5E_SYSERRSTR = H5E_SYSERRSTR(); + /** Minor error codes - Cache related errors - Internal error detected */ + public static final long H5E_SYSTEM = H5E_SYSTEM(); + /** Minor error codes - Link related errors - Link traversal failure */ + public static final long H5E_TRAVERSE = H5E_TRAVERSE(); + /** Minor error codes - File accessibility errors - File has been truncated */ public static final long H5E_TRUNCATED = H5E_TRUNCATED(); + /** Major error codes - Ternary Search Trees */ public static final long H5E_TST = H5E_TST(); + /** Minor error codes - Argument errors - Information is uinitialized */ public static final long H5E_UNINITIALIZED = H5E_UNINITIALIZED(); + /** Minor error codes - Argument errors - Feature is unsupported */ public static final long H5E_UNSUPPORTED = H5E_UNSUPPORTED(); + /** Minor error codes - Object header related errors - Wrong version number */ public static final long H5E_VERSION = H5E_VERSION(); + /** Major error codes - Virtual File Layer */ public static final long H5E_VFL = H5E_VFL(); + /** Major error codes - Virtual Object Layer */ public static final long H5E_VOL = H5E_VOL(); + /** Error stack traversal direction - begin at API function, end deep */ public static final long H5E_WALK_DOWNWARD = H5E_WALK_DOWNWARD(); + /** Error stack traversal direction - begin deep, end at API function */ public static final long H5E_WALK_UPWARD = H5E_WALK_UPWARD(); + /** Generic low-level file I/O errors - Write failed */ public static final long H5E_WRITEERROR = H5E_WRITEERROR(); private static final int H5ES_STATUS_IN_PROGRESS = H5ES_STATUS_IN_PROGRESS(); @@ -424,29 +678,53 @@ public class HDF5Constants { public static final int H5R_OBJECT1 = H5R_OBJECT1(); public static final int H5R_OBJECT2 = H5R_OBJECT2(); + /** Define atomic datatypes */ public static final int H5S_ALL = H5S_ALL(); + /** Define user-level maximum number of dimensions */ public static final int H5S_MAX_RANK = H5S_MAX_RANK(); + /** Different types of dataspaces - error */ public static final int H5S_NO_CLASS = H5S_NO_CLASS(); + /** Different types of dataspaces - null dataspace */ public static final int H5S_NULL = H5S_NULL(); + /** Different types of dataspaces - scalar variable */ public static final int H5S_SCALAR = H5S_SCALAR(); + /** Enumerated type for the type of selection - Entire extent selected */ public static final int H5S_SEL_ALL = H5S_SEL_ALL(); + /** Enumerated type for the type of selection - Error */ public static final int H5S_SEL_ERROR = H5S_SEL_ERROR(); + /** Enumerated type for the type of selection - Hyperslab selected */ public static final int H5S_SEL_HYPERSLABS = H5S_SEL_HYPERSLABS(); + /** Enumerated type for the type of selection - LAST */ public static final int H5S_SEL_N = H5S_SEL_N(); + /** Enumerated type for the type of selection - Nothing selected */ public static final int H5S_SEL_NONE = H5S_SEL_NONE(); + /** Enumerated type for the type of selection - Points / elements selected */ public static final int H5S_SEL_POINTS = H5S_SEL_POINTS(); + /** Different ways of combining selections - Binary "and" operation for hyperslabs */ public static final int H5S_SELECT_AND = H5S_SELECT_AND(); + /** Different ways of combining selections - Append elements to end of point selection */ public static final int H5S_SELECT_APPEND = H5S_SELECT_APPEND(); + /** Different ways of combining selections - Invalid upper bound on selection operations */ public static final int H5S_SELECT_INVALID = H5S_SELECT_INVALID(); + /** Different ways of combining selections - error */ public static final int H5S_SELECT_NOOP = H5S_SELECT_NOOP(); + /** Different ways of combining selections - Binary "not" operation for hyperslabs */ public static final int H5S_SELECT_NOTA = H5S_SELECT_NOTA(); + /** Different ways of combining selections - Binary "not" operation for hyperslabs */ public static final int H5S_SELECT_NOTB = H5S_SELECT_NOTB(); + /** Different ways of combining selections - Binary "or" operation for hyperslabs */ public static final int H5S_SELECT_OR = H5S_SELECT_OR(); + /** Different ways of combining selections - Prepend elements to beginning of point selection */ public static final int H5S_SELECT_PREPEND = H5S_SELECT_PREPEND(); + /** Different ways of combining selections - Select "set" operation */ public static final int H5S_SELECT_SET = H5S_SELECT_SET(); + /** Different ways of combining selections - Binary "xor" operation for hyperslabs */ public static final int H5S_SELECT_XOR = H5S_SELECT_XOR(); + /** Different types of dataspaces - simple dataspace */ public static final int H5S_SIMPLE = H5S_SIMPLE(); + /** Define atomic datatypes */ public static final int H5S_UNLIMITED = H5S_UNLIMITED(); + public static final long H5T_ALPHA_B16 = H5T_ALPHA_B16(); public static final long H5T_ALPHA_B32 = H5T_ALPHA_B32(); public static final long H5T_ALPHA_B64 = H5T_ALPHA_B64(); @@ -665,48 +943,96 @@ public class HDF5Constants { public static final int H5_VOL_RESERVED = H5_VOL_RESERVED(); public static final int H5_VOL_MAX = H5_VOL_MAX(); + /** Return values for filter callback function */ public static final int H5Z_CB_CONT = H5Z_CB_CONT(); + /** Return values for filter callback function */ public static final int H5Z_CB_ERROR = H5Z_CB_ERROR(); + /** Return values for filter callback function */ public static final int H5Z_CB_FAIL = H5Z_CB_FAIL(); + /** Return values for filter callback function */ public static final int H5Z_CB_NO = H5Z_CB_NO(); + /** Values to decide if EDC is enabled for reading data */ public static final int H5Z_DISABLE_EDC = H5Z_DISABLE_EDC(); + /** Values to decide if EDC is enabled for reading data */ public static final int H5Z_ENABLE_EDC = H5Z_ENABLE_EDC(); + /** Values to decide if EDC is enabled for reading data */ public static final int H5Z_ERROR_EDC = H5Z_ERROR_EDC(); + /** Filter IDs - deflation like gzip */ public static final int H5Z_FILTER_DEFLATE = H5Z_FILTER_DEFLATE(); + /** Filter IDs - no filter */ public static final int H5Z_FILTER_ERROR = H5Z_FILTER_ERROR(); + /** Filter IDs - fletcher32 checksum of EDC */ public static final int H5Z_FILTER_FLETCHER32 = H5Z_FILTER_FLETCHER32(); + /** Filter IDs - maximum filter id */ public static final int H5Z_FILTER_MAX = H5Z_FILTER_MAX(); + /** Filter IDs - nbit compression */ public static final int H5Z_FILTER_NBIT = H5Z_FILTER_NBIT(); + /** Filter IDs - reserved indefinitely */ public static final int H5Z_FILTER_NONE = H5Z_FILTER_NONE(); + /** Filter IDs - filter ids below this value are reserved for library use */ public static final int H5Z_FILTER_RESERVED = H5Z_FILTER_RESERVED(); + /** Filter IDs - scale+offset compression */ public static final int H5Z_FILTER_SCALEOFFSET = H5Z_FILTER_SCALEOFFSET(); + /** Filter IDs - shuffle the data */ public static final int H5Z_FILTER_SHUFFLE = H5Z_FILTER_SHUFFLE(); + /** Filter IDs - szip compression */ public static final int H5Z_FILTER_SZIP = H5Z_FILTER_SZIP(); + /** Flags for filter definition (stored) + * definition flag mask */ public static final int H5Z_FLAG_DEFMASK = H5Z_FLAG_DEFMASK(); + /** Additional flags for filter invocation (not stored) + * invocation flag mask */ public static final int H5Z_FLAG_INVMASK = H5Z_FLAG_INVMASK(); + /** Flags for filter definition (stored) + * filter is mandatory */ public static final int H5Z_FLAG_MANDATORY = H5Z_FLAG_MANDATORY(); + /** Flags for filter definition (stored) + * filter is optional */ public static final int H5Z_FLAG_OPTIONAL = H5Z_FLAG_OPTIONAL(); + /** Additional flags for filter invocation (not stored) + * reverse direction; read */ public static final int H5Z_FLAG_REVERSE = H5Z_FLAG_REVERSE(); + /** Additional flags for filter invocation (not stored) + * skip EDC filters for read */ public static final int H5Z_FLAG_SKIP_EDC = H5Z_FLAG_SKIP_EDC(); + /** Symbol to remove all filters in H5Premove_filter */ + public static final int H5Z_FILTER_ALL = H5Z_FILTER_ALL(); + /** Maximum number of filters allowed in a pipeline */ public static final int H5Z_MAX_NFILTERS = H5Z_MAX_NFILTERS(); + /** Values to decide if EDC is enabled for reading data */ public static final int H5Z_NO_EDC = H5Z_NO_EDC(); + /** Bit flags for H5Zget_filter_info */ public static final int H5Z_FILTER_CONFIG_ENCODE_ENABLED = H5Z_FILTER_CONFIG_ENCODE_ENABLED(); + /** Bit flags for H5Zget_filter_info */ public static final int H5Z_FILTER_CONFIG_DECODE_ENABLED = H5Z_FILTER_CONFIG_DECODE_ENABLED(); + /** Special parameters for ScaleOffset filter*/ public static final int H5Z_SO_INT_MINBITS_DEFAULT = H5Z_SO_INT_MINBITS_DEFAULT(); + /** Special parameters for ScaleOffset filter*/ public static final int H5Z_SO_FLOAT_DSCALE = H5Z_SO_FLOAT_DSCALE(); + /** Special parameters for ScaleOffset filter*/ public static final int H5Z_SO_FLOAT_ESCALE = H5Z_SO_FLOAT_ESCALE(); + /** Special parameters for ScaleOffset filter*/ public static final int H5Z_SO_INT = H5Z_SO_INT(); + /** shuffle filter - Number of parameters that users can set */ public static final int H5Z_SHUFFLE_USER_NPARMS = H5Z_SHUFFLE_USER_NPARMS(); + /** shuffle filter - Total number of parameters for filter */ public static final int H5Z_SHUFFLE_TOTAL_NPARMS = H5Z_SHUFFLE_TOTAL_NPARMS(); + /** szip filter - Number of parameters that users can set */ public static final int H5Z_SZIP_USER_NPARMS = H5Z_SZIP_USER_NPARMS(); + /** szip filter - Total number of parameters for filter */ public static final int H5Z_SZIP_TOTAL_NPARMS = H5Z_SZIP_TOTAL_NPARMS(); + /** szip filter - "User" parameter for option mask */ public static final int H5Z_SZIP_PARM_MASK = H5Z_SZIP_PARM_MASK(); + /** szip filter - "User" parameter for pixels-per-block */ public static final int H5Z_SZIP_PARM_PPB = H5Z_SZIP_PARM_PPB(); + /** szip filter - "Local" parameter for bits-per-pixel */ public static final int H5Z_SZIP_PARM_BPP = H5Z_SZIP_PARM_BPP(); + /** szip filter - "Local" parameter for pixels-per-scanline */ public static final int H5Z_SZIP_PARM_PPS = H5Z_SZIP_PARM_PPS(); + /** nbit filter - Number of parameters that users can set */ public static final int H5Z_NBIT_USER_NPARMS = H5Z_NBIT_USER_NPARMS(); + /** scale offset filter - Number of parameters that users can set */ public static final int H5Z_SCALEOFFSET_USER_NPARMS = H5Z_SCALEOFFSET_USER_NPARMS(); - public static final int H5Z_FILTER_ALL = H5Z_FILTER_ALL(); // ///////////////////////////////////////////////////////////////////////// // List of private native variables to get constant values from C // @@ -841,6 +1167,8 @@ public class HDF5Constants { private static native final long H5E_BADGROUP(); + private static native final long H5E_BADITER(); + private static native final long H5E_BADMESG(); private static native final long H5E_BADRANGE(); @@ -861,15 +1189,30 @@ public class HDF5Constants { private static native final long H5E_CANAPPLY(); - // private static native final long H5E_CANTALLOC(); + private static native final long H5E_CANTALLOC(); + + private static native final long H5E_CANTAPPEND(); + + private static native final long H5E_CANTATTACH(); + + private static native final long H5E_CANTCLEAN(); + private static native final long H5E_CANTCLIP(); private static native final long H5E_CANTCLOSEFILE(); + private static native final long H5E_CANTCLOSEOBJ(); + + private static native final long H5E_CANTCOMPARE(); + + private static native final long H5E_CANTCOMPUTE(); + private static native final long H5E_CANTCONVERT(); private static native final long H5E_CANTCOPY(); + private static native final long H5E_CANTCORK(); + private static native final long H5E_CANTCOUNT(); private static native final long H5E_CANTCREATE(); @@ -882,18 +1225,36 @@ public class HDF5Constants { private static native final long H5E_CANTDELETEFILE(); + private static native final long H5E_CANTDEPEND(); + + private static native final long H5E_CANTDIRTY(); + private static native final long H5E_CANTENCODE(); + private static native final long H5E_CANTEXPUNGE(); + + private static native final long H5E_CANTEXTEND(); + + private static native final long H5E_CANTFILTER(); + private static native final long H5E_CANTFLUSH(); private static native final long H5E_CANTFREE(); + private static native final long H5E_CANTGATHER(); + + private static native final long H5E_CANTGC(); + private static native final long H5E_CANTGET(); + private static native final long H5E_CANTGETSIZE(); + private static native final long H5E_CANTINC(); private static native final long H5E_CANTINIT(); + private static native final long H5E_CANTINS(); + private static native final long H5E_CANTINSERT(); private static native final long H5E_CANTLIST(); @@ -902,29 +1263,96 @@ public class HDF5Constants { private static native final long H5E_CANTLOCK(); + private static native final long H5E_CANTLOCKFILE(); + + private static native final long H5E_CANTMARKCLEAN(); + + private static native final long H5E_CANTMARKDIRTY(); + + private static native final long H5E_CANTMARKSERIALIZED(); + + private static native final long H5E_CANTMARKUNSERIALIZED(); + + private static native final long H5E_CANTMERGE(); + + private static native final long H5E_CANTMOVE(); + + private static native final long H5E_CANTMODIFY(); + private static native final long H5E_CANTNEXT(); + private static native final long H5E_CANTNOTIFY(); + private static native final long H5E_CANTOPENFILE(); private static native final long H5E_CANTOPENOBJ(); - // private static native final long H5E_CANTRECV(); + private static native final long H5E_CANTOPERATE(); + + private static native final long H5E_CANTPACK(); + + private static native final long H5E_CANTPIN(); + + private static native final long H5E_CANTPROTECT(); + + private static native final long H5E_CANTRECV(); + + private static native final long H5E_CANTREDISTRIBUTE(); + private static native final long H5E_CANTREGISTER(); private static native final long H5E_CANTRELEASE(); + private static native final long H5E_CANTREMOVE(); + + private static native final long H5E_CANTRENAME(); + + private static native final long H5E_CANTRESET(); + + private static native final long H5E_CANTRESIZE(); + + private static native final long H5E_CANTRESTORE(); + + private static native final long H5E_CANTREVIVE(); + + private static native final long H5E_CANTSHRINK(); + private static native final long H5E_CANTSELECT(); private static native final long H5E_CANTSET(); + private static native final long H5E_CANTSERIALIZE(); + + private static native final long H5E_CANTSORT(); + private static native final long H5E_CANTSPLIT(); + private static native final long H5E_CANTSWAP(); + + private static native final long H5E_CANTTAG(); + + private static native final long H5E_CANTUNCORK(); + + private static native final long H5E_CANTUNDEPEND(); + private static native final long H5E_CANTUNLOCK(); + private static native final long H5E_CANTUNLOCKFILE(); + + private static native final long H5E_CANTUNPIN(); + + private static native final long H5E_CANTUNPROTECT(); + + private static native final long H5E_CANTUNSERIALIZE(); + + private static native final long H5E_CANTUPDATE(); + private static native final long H5E_CLOSEERROR(); private static native final long H5E_COMPLEN(); + private static native final long H5E_CONTEXT(); + private static native final long H5E_DATASET(); private static native final long H5E_DATASPACE(); @@ -935,10 +1363,16 @@ public class HDF5Constants { private static native final long H5E_DUPCLASS(); + private static native final long H5E_EARRAY(); + private static native final long H5E_EFL(); + private static native final long H5E_ERROR(); + private static native final long H5E_EXISTS(); + private static native final long H5E_FARRAY(); + private static native final long H5E_FCNTL(); private static native final long H5E_FILE(); @@ -947,10 +1381,14 @@ public class HDF5Constants { private static native final long H5E_FILEOPEN(); + private static native final long H5E_FSPACE(); + private static native final long H5E_FUNC(); private static native final long H5E_HEAP(); + private static native final long H5E_INCONSISTENTSTATE(); + private static native final long H5E_INTERNAL(); private static native final long H5E_IO(); @@ -959,8 +1397,12 @@ public class HDF5Constants { private static native final long H5E_LINKCOUNT(); + private static native final long H5E_LOGGING(); + private static native final int H5E_MAJOR(); + private static native final long H5E_MAP(); + private static native final int H5E_MINOR(); private static native final long H5E_MOUNT(); @@ -969,6 +1411,12 @@ public class HDF5Constants { private static native final long H5E_MPIERRSTR(); + private static native final long H5E_NLINKS(); + + private static native final long H5E_NO_INDEPENDENT(); + + private static native final long H5E_NOENCODER(); + private static native final long H5E_NOFILTER(); private static native final long H5E_NOIDS(); @@ -985,14 +1433,26 @@ public class HDF5Constants { private static native final long H5E_NOTHDF5(); + private static native final long H5E_NOTREGISTERED(); + + private static native final long H5E_OBJOPEN(); + private static native final long H5E_OHDR(); + private static native final long H5E_OPENERROR(); + private static native final long H5E_OVERFLOW(); + private static native final long H5E_PAGEBUF(); + + private static native final long H5E_PATH(); + private static native final long H5E_PLINE(); private static native final long H5E_PLIST(); + private static native final long H5E_PLUGIN(); + private static native final long H5E_PROTECT(); private static native final long H5E_READERROR(); @@ -1005,12 +1465,24 @@ public class HDF5Constants { private static native final long H5E_SEEKERROR(); + private static native final long H5E_SETDISALLOWED(); + private static native final long H5E_SETLOCAL(); + private static native final long H5E_SLIST(); + + private static native final long H5E_SOHM(); + private static native final long H5E_STORAGE(); private static native final long H5E_SYM(); + private static native final long H5E_SYSERRSTR(); + + private static native final long H5E_SYSTEM(); + + private static native final long H5E_TRAVERSE(); + private static native final long H5E_TRUNCATED(); private static native final long H5E_TST(); diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c index 38f0883..94d5b19 100644 --- a/java/src/jni/h5Constants.c +++ b/java/src/jni/h5Constants.c @@ -355,6 +355,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1BADGROUP(JNIEnv *env, jclass cls) return H5E_BADGROUP; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1BADITER(JNIEnv *env, jclass cls) +{ + return H5E_BADITER; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1BADMESG(JNIEnv *env, jclass cls) { return H5E_BADMESG; @@ -404,8 +409,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANAPPLY(JNIEnv *env, jclass cls) { return H5E_CANAPPLY; } -/*JNIEXPORT jlong JNICALL -Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTALLOC(JNIEnv *env, jclass cls) { return H5E_CANTALLOC; }*/ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTALLOC(JNIEnv *env, jclass cls) +{ + return H5E_CANTALLOC; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTAPPEND(JNIEnv *env, jclass cls) +{ + return H5E_CANTAPPEND; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTATTACH(JNIEnv *env, jclass cls) +{ + return H5E_CANTATTACH; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLEAN(JNIEnv *env, jclass cls) +{ + return H5E_CANTCLEAN; +} JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLIP(JNIEnv *env, jclass cls) { @@ -417,6 +440,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLOSEFILE(JNIEnv *env, jclass cls) return H5E_CANTCLOSEFILE; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLOSEOBJ(JNIEnv *env, jclass cls) +{ + return H5E_CANTCLOSEOBJ; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOMPARE(JNIEnv *env, jclass cls) +{ + return H5E_CANTCOMPARE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOMPUTE(JNIEnv *env, jclass cls) +{ + return H5E_CANTCOMPUTE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCONVERT(JNIEnv *env, jclass cls) { return H5E_CANTCONVERT; @@ -427,6 +465,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOPY(JNIEnv *env, jclass cls) return H5E_CANTCOPY; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCORK(JNIEnv *env, jclass cls) +{ + return H5E_CANTCORK; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOUNT(JNIEnv *env, jclass cls) { return H5E_CANTCOUNT; @@ -457,11 +500,36 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDELETEFILE(JNIEnv *env, jclass cls) return H5E_CANTDELETEFILE; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDEPEND(JNIEnv *env, jclass cls) +{ + return H5E_CANTDEPEND; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDIRTY(JNIEnv *env, jclass cls) +{ + return H5E_CANTDIRTY; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFILTER(JNIEnv *env, jclass cls) +{ + return H5E_CANTFILTER; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTENCODE(JNIEnv *env, jclass cls) { return H5E_CANTENCODE; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTEXPUNGE(JNIEnv *env, jclass cls) +{ + return H5E_CANTEXPUNGE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTEXTEND(JNIEnv *env, jclass cls) +{ + return H5E_CANTEXTEND; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFLUSH(JNIEnv *env, jclass cls) { return H5E_CANTFLUSH; @@ -472,11 +540,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFREE(JNIEnv *env, jclass cls) return H5E_CANTFREE; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGATHER(JNIEnv *env, jclass cls) +{ + return H5E_CANTGATHER; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGC(JNIEnv *env, jclass cls) +{ + return H5E_CANTGC; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGET(JNIEnv *env, jclass cls) { return H5E_CANTGET; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGETSIZE(JNIEnv *env, jclass cls) +{ + return H5E_CANTGETSIZE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINC(JNIEnv *env, jclass cls) { return H5E_CANTINC; @@ -487,6 +570,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINIT(JNIEnv *env, jclass cls) return H5E_CANTINIT; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINS(JNIEnv *env, jclass cls) +{ + return H5E_CANTINS; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINSERT(JNIEnv *env, jclass cls) { return H5E_CANTINSERT; @@ -507,11 +595,56 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCK(JNIEnv *env, jclass cls) return H5E_CANTLOCK; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCKFILE(JNIEnv *env, jclass cls) +{ + return H5E_CANTLOCKFILE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKCLEAN(JNIEnv *env, jclass cls) +{ + return H5E_CANTMARKCLEAN; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKDIRTY(JNIEnv *env, jclass cls) +{ + return H5E_CANTMARKDIRTY; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKSERIALIZED(JNIEnv *env, jclass cls) +{ + return H5E_CANTMARKSERIALIZED; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKUNSERIALIZED(JNIEnv *env, jclass cls) +{ + return H5E_CANTMARKUNSERIALIZED; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMERGE(JNIEnv *env, jclass cls) +{ + return H5E_CANTMERGE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMODIFY(JNIEnv *env, jclass cls) +{ + return H5E_CANTMODIFY; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMOVE(JNIEnv *env, jclass cls) +{ + return H5E_CANTMOVE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTNEXT(JNIEnv *env, jclass cls) { return H5E_CANTNEXT; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTNOTIFY(JNIEnv *env, jclass cls) +{ + return H5E_CANTNOTIFY; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPENFILE(JNIEnv *env, jclass cls) { return H5E_CANTOPENFILE; @@ -521,8 +654,36 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPENOBJ(JNIEnv *env, jclass cls) { return H5E_CANTOPENOBJ; } -/*JNIEXPORT jlong JNICALL -Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRECV(JNIEnv *env, jclass cls) { return H5E_CANTRECV; }*/ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPERATE(JNIEnv *env, jclass cls) +{ + return H5E_CANTOPERATE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPACK(JNIEnv *env, jclass cls) +{ + return H5E_CANTPACK; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPIN(JNIEnv *env, jclass cls) +{ + return H5E_CANTPIN; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPROTECT(JNIEnv *env, jclass cls) +{ + return H5E_CANTPROTECT; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRECV(JNIEnv *env, jclass cls) +{ + return H5E_CANTRECV; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREDISTRIBUTE(JNIEnv *env, jclass cls) +{ + return H5E_CANTREDISTRIBUTE; +} JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREGISTER(JNIEnv *env, jclass cls) { @@ -534,6 +695,41 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRELEASE(JNIEnv *env, jclass cls) return H5E_CANTRELEASE; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREMOVE(JNIEnv *env, jclass cls) +{ + return H5E_CANTREMOVE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRENAME(JNIEnv *env, jclass cls) +{ + return H5E_CANTRENAME; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESET(JNIEnv *env, jclass cls) +{ + return H5E_CANTRESET; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESIZE(JNIEnv *env, jclass cls) +{ + return H5E_CANTRESIZE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESTORE(JNIEnv *env, jclass cls) +{ + return H5E_CANTRESTORE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREVIVE(JNIEnv *env, jclass cls) +{ + return H5E_CANTREVIVE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSHRINK(JNIEnv *env, jclass cls) +{ + return H5E_CANTSHRINK; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSELECT(JNIEnv *env, jclass cls) { return H5E_CANTSELECT; @@ -544,16 +740,71 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSET(JNIEnv *env, jclass cls) return H5E_CANTSET; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSERIALIZE(JNIEnv *env, jclass cls) +{ + return H5E_CANTSERIALIZE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSORT(JNIEnv *env, jclass cls) +{ + return H5E_CANTSORT; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSPLIT(JNIEnv *env, jclass cls) { return H5E_CANTSPLIT; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSWAP(JNIEnv *env, jclass cls) +{ + return H5E_CANTSWAP; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTTAG(JNIEnv *env, jclass cls) +{ + return H5E_CANTTAG; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNCORK(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNCORK; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNDEPEND(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNDEPEND; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCK(JNIEnv *env, jclass cls) { return H5E_CANTUNLOCK; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCKFILE(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNLOCKFILE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNPIN(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNPIN; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNPROTECT(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNPROTECT; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNSERIALIZE(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNSERIALIZE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUPDATE(JNIEnv *env, jclass cls) +{ + return H5E_CANTUPDATE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CLOSEERROR(JNIEnv *env, jclass cls) { return H5E_CLOSEERROR; @@ -564,6 +815,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1COMPLEN(JNIEnv *env, jclass cls) return H5E_COMPLEN; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CONTEXT(JNIEnv *env, jclass cls) +{ + return H5E_CONTEXT; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1DATASET(JNIEnv *env, jclass cls) { return H5E_DATASET; @@ -589,16 +845,31 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1DUPCLASS(JNIEnv *env, jclass cls) return H5E_DUPCLASS; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1EARRAY(JNIEnv *env, jclass cls) +{ + return H5E_EARRAY; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1EFL(JNIEnv *env, jclass cls) { return H5E_EFL; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1ERROR(JNIEnv *env, jclass cls) +{ + return H5E_ERROR; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1EXISTS(JNIEnv *env, jclass cls) { return H5E_EXISTS; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1FARRAY(JNIEnv *env, jclass cls) +{ + return H5E_FARRAY; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1FCNTL(JNIEnv *env, jclass cls) { return H5E_FCNTL; @@ -619,6 +890,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1FILEOPEN(JNIEnv *env, jclass cls) return H5E_FILEOPEN; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1FSPACE(JNIEnv *env, jclass cls) +{ + return H5E_FSPACE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1FUNC(JNIEnv *env, jclass cls) { return H5E_FUNC; @@ -629,6 +905,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1HEAP(JNIEnv *env, jclass cls) return H5E_HEAP; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1INCONSISTENTSTATE(JNIEnv *env, jclass cls) +{ + return H5E_INCONSISTENTSTATE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1INTERNAL(JNIEnv *env, jclass cls) { return H5E_INTERNAL; @@ -648,11 +929,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1LINKCOUNT(JNIEnv *env, jclass cls) { return H5E_LINKCOUNT; } +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1LOGGING(JNIEnv *env, jclass cls) +{ + return H5E_LOGGING; +} JNIEXPORT jint JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1MAJOR(JNIEnv *env, jclass cls) { return H5E_MAJOR; } +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1MAP(JNIEnv *env, jclass cls) +{ + return H5E_MAP; +} JNIEXPORT jint JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1MINOR(JNIEnv *env, jclass cls) { @@ -674,6 +965,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1MPIERRSTR(JNIEnv *env, jclass cls) return H5E_MPIERRSTR; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1NLINKS(JNIEnv *env, jclass cls) +{ + return H5E_NLINKS; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1NO_1INDEPENDENT(JNIEnv *env, jclass cls) +{ + return H5E_NO_INDEPENDENT; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1NOENCODER(JNIEnv *env, jclass cls) +{ + return H5E_NOENCODER; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1NOFILTER(JNIEnv *env, jclass cls) { return H5E_NOFILTER; @@ -714,16 +1020,41 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1NOTHDF5(JNIEnv *env, jclass cls) return H5E_NOTHDF5; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1NOTREGISTERED(JNIEnv *env, jclass cls) +{ + return H5E_NOTREGISTERED; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1OBJOPEN(JNIEnv *env, jclass cls) +{ + return H5E_OBJOPEN; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1OHDR(JNIEnv *env, jclass cls) { return H5E_OHDR; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1OPENERROR(JNIEnv *env, jclass cls) +{ + return H5E_OPENERROR; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1OVERFLOW(JNIEnv *env, jclass cls) { return H5E_OVERFLOW; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1PAGEBUF(JNIEnv *env, jclass cls) +{ + return H5E_PAGEBUF; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1PATH(JNIEnv *env, jclass cls) +{ + return H5E_PATH; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1PLINE(JNIEnv *env, jclass cls) { return H5E_PLINE; @@ -734,6 +1065,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1PLIST(JNIEnv *env, jclass cls) return H5E_PLIST; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1PLUGIN(JNIEnv *env, jclass cls) +{ + return H5E_PLUGIN; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1PROTECT(JNIEnv *env, jclass cls) { return H5E_PROTECT; @@ -764,11 +1100,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1SEEKERROR(JNIEnv *env, jclass cls) return H5E_SEEKERROR; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1SETDISALLOWED(JNIEnv *env, jclass cls) +{ + return H5E_SETDISALLOWED; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1SETLOCAL(JNIEnv *env, jclass cls) { return H5E_SETLOCAL; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1SLIST(JNIEnv *env, jclass cls) +{ + return H5E_SLIST; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1SOHM(JNIEnv *env, jclass cls) +{ + return H5E_SOHM; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1STORAGE(JNIEnv *env, jclass cls) { return H5E_STORAGE; @@ -779,6 +1130,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1SYM(JNIEnv *env, jclass cls) return H5E_SYM; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1SYSERRSTR(JNIEnv *env, jclass cls) +{ + return H5E_SYSERRSTR; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1SYSTEM(JNIEnv *env, jclass cls) +{ + return H5E_SYSTEM; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1TRAVERSE(JNIEnv *env, jclass cls) +{ + return H5E_TRAVERSE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1TRUNCATED(JNIEnv *env, jclass cls) { return H5E_TRUNCATED; diff --git a/java/src/jni/h5sImp.c b/java/src/jni/h5sImp.c index 2a9cff5..f7b65d9 100644 --- a/java/src/jni/h5sImp.c +++ b/java/src/jni/h5sImp.c @@ -1340,6 +1340,389 @@ done: return; } /* end Java_hdf_hdf5lib_H5_H5Sget_1regular_1hyperslab */ +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_copy + * Signature: (JJ)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5Sselect_1copy(JNIEnv *env, jclass clss, jlong dst_id, jlong src_id) +{ + herr_t status = FAIL; + + UNUSED(clss); + + if ((status = H5Sselect_copy((hid_t)dst_id, (hid_t)src_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + return; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1copy */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_shape_same + * Signature: (JJ)Z + */ +JNIEXPORT jboolean JNICALL +Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same(JNIEnv *env, jclass clss, jlong space1_id, jlong space2_id) +{ + htri_t bval = JNI_FALSE; + + UNUSED(clss); + + if ((bval = H5Sselect_shape_same((hid_t)space1_id, (hid_t)space2_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + bval = (bval > 0) ? JNI_TRUE : JNI_FALSE; + +done: + return (jboolean)bval; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_adjust + * Signature: (J[J)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5Sselect_1adjust(JNIEnv *env, jclass clss, jlong space_id, jlongArray offset) +{ + jboolean isCopy; + hssize_t *offst = NULL; + jlong * offsetP = NULL; + jsize offset_rank = -1; + int i, rank = -1; + herr_t status = FAIL; + + UNUSED(clss); + + if (space_id < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: invalid dataspace ID"); + + if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (NULL == offset) { + offsetP = NULL; + offst = (hssize_t *)offsetP; + } + else { + if ((offset_rank = ENVPTR->GetArrayLength(ENVONLY, offset)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: offset length < 0"); + } + + if (offset_rank != rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: offset rank doesn't match dataspace rank!"); + + PIN_LONG_ARRAY(ENVONLY, offset, offsetP, &isCopy, "H5Sselect_adjust: offset not pinned"); + + if (NULL == (offst = (hssize_t *)HDmalloc((size_t)offset_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_adjust: failed to allocate offset buffer"); + } + + if ((status = H5Sselect_adjust(space_id, (hssize_t *)offst)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + for (i = 0; i < offset_rank; i++) { + offsetP[i] = (jlong)offst[i]; + } /* end for */ + +done: + if (offst) + HDfree(offst); + if (offsetP) + UNPIN_LONG_ARRAY(ENVONLY, offset, offsetP, (status < 0) ? JNI_ABORT : 0); + + return; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1adjust */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_intersect_block + * Signature: (J[J[J)Z + */ +JNIEXPORT jboolean JNICALL +Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block(JNIEnv *env, jclass clss, jlong space_id, jlongArray start, + jlongArray end) +{ + htri_t bval = JNI_FALSE; + jboolean isCopy; + hsize_t *strt = NULL, *nd = NULL; + jlong * startP = NULL, *endP = NULL; + jsize start_rank = -1, end_rank = -1; + int i, rank = -1; + + UNUSED(clss); + + if (space_id < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: invalid dataspace ID"); + + if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (NULL == start) { + startP = NULL; + strt = (hsize_t *)startP; + } + else { + if ((start_rank = ENVPTR->GetArrayLength(ENVONLY, start)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: start length < 0"); + } + + if (start_rank != rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, + "H5Sselect_intersect_block: start rank doesn't match dataspace rank!"); + + PIN_LONG_ARRAY(ENVONLY, start, startP, &isCopy, "H5Sselect_intersect_block: start not pinned"); + + if (NULL == (strt = (hsize_t *)HDmalloc((size_t)start_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_intersect_block: failed to allocate start buffer"); + } + + if (NULL == end) { + endP = NULL; + nd = (hsize_t *)endP; + } + else { + if ((end_rank = ENVPTR->GetArrayLength(ENVONLY, end)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: end array length < 0"); + } + + if (end_rank != rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, + "H5Sselect_intersect_block: end rank doesn't match dataspace rank!"); + + PIN_LONG_ARRAY(ENVONLY, end, endP, &isCopy, "H5Sselect_intersect_block: end not pinned"); + + if (NULL == (nd = (hsize_t *)HDmalloc((size_t)end_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_intersect_block: failed to allocate end buffer"); + } + + if ((bval = H5Sselect_intersect_block(space_id, (hsize_t *)strt, (hsize_t *)nd)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + bval = (bval > 0) ? JNI_TRUE : JNI_FALSE; + + for (i = 0; i < start_rank; i++) { + startP[i] = (jlong)strt[i]; + endP[i] = (jlong)nd[i]; + } /* end for */ + +done: + if (strt) + HDfree(strt); + if (startP) + UNPIN_LONG_ARRAY(ENVONLY, start, startP, (bval < 0) ? JNI_ABORT : 0); + if (nd) + HDfree(nd); + if (endP) + UNPIN_LONG_ARRAY(ENVONLY, end, endP, (bval < 0) ? JNI_ABORT : 0); + + return (jboolean)bval; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_project_intersection + * Signature: (JJJ)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection(JNIEnv *env, jclass clss, jlong src_space_id, + jlong dst_space_id, jlong src_intersect_space_id) +{ + hid_t sid = H5I_INVALID_HID; + + UNUSED(clss); + + if ((sid = H5Sselect_project_intersection(src_space_id, dst_space_id, src_intersect_space_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + + return (jlong)sid; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Scombine_hyperslab + * Signature: (JI[J[J[J[J)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *env, jclass clss, jlong space_id, jint op, jlongArray start, + jlongArray stride, jlongArray count, jlongArray block) +{ + jboolean isCopy; + hsize_t *strt = NULL, *strd = NULL, *cnt = NULL, *blk = NULL; + hsize_t *lp = NULL; + jlong * startP = NULL, *strideP = NULL, *countP = NULL, *blockP = NULL; + jlong * jlp = NULL; + jsize start_rank, stride_rank, count_rank, block_rank; + int i; + hid_t sid = H5I_INVALID_HID; + + UNUSED(clss); + + if (NULL == start) + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: start is NULL"); + if (NULL == count) + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count is NULL"); + + if ((start_rank = ENVPTR->GetArrayLength(ENVONLY, start)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: start array length < 0"); + } + if ((count_rank = ENVPTR->GetArrayLength(ENVONLY, count)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count array length < 0"); + } + + if (start_rank != count_rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count and start have different rank!"); + + PIN_LONG_ARRAY(ENVONLY, start, startP, &isCopy, "H5Scombine_hyperslab: start not pinned"); + + if (NULL == (strt = lp = (hsize_t *)HDmalloc((size_t)start_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate start buffer"); + + jlp = (jlong *)startP; + for (i = 0; i < start_rank; i++) { + *lp = (hsize_t)*jlp; + lp++; + jlp++; + } /* end if */ + + PIN_LONG_ARRAY(ENVONLY, count, countP, &isCopy, "H5Scombine_hyperslab: count not pinned"); + + if (NULL == (cnt = lp = (hsize_t *)HDmalloc((size_t)count_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate count buffer"); + + jlp = (jlong *)countP; + for (i = 0; i < count_rank; i++) { + *lp = (hsize_t)*jlp; + lp++; + jlp++; + } /* end if */ + + if (NULL == stride) { + strideP = NULL; + strd = (hsize_t *)strideP; + } + else { + if ((stride_rank = ENVPTR->GetArrayLength(ENVONLY, stride)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: stride array length < 0"); + } + + if (stride_rank != start_rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: stride and start have different rank!"); + + PIN_LONG_ARRAY(ENVONLY, stride, strideP, &isCopy, "H5Scombine_hyperslab: stride not pinned"); + + if (NULL == (strd = lp = (hsize_t *)HDmalloc((size_t)stride_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate stride buffer"); + + jlp = (jlong *)strideP; + for (i = 0; i < stride_rank; i++) { + *lp = (hsize_t)*jlp; + lp++; + jlp++; + } /* end if */ + } + + if (NULL == block) { + blockP = NULL; + blk = (hsize_t *)blockP; + } + else { + if ((block_rank = ENVPTR->GetArrayLength(ENVONLY, block)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: block array length < 0"); + } + + if (block_rank != start_rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: block and start have different rank!"); + + PIN_LONG_ARRAY(ENVONLY, block, blockP, &isCopy, "H5Scombine_hyperslab: block not pinned"); + + if (NULL == (blk = lp = (hsize_t *)HDmalloc((size_t)block_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate block buffer"); + + jlp = (jlong *)blockP; + for (i = 0; i < block_rank; i++) { + *lp = (hsize_t)*jlp; + lp++; + jlp++; + } /* end for */ + } + + if ((sid = H5Scombine_hyperslab(space_id, (H5S_seloper_t)op, (const hsize_t *)strt, (const hsize_t *)strd, + (const hsize_t *)cnt, (const hsize_t *)blk)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + if (blk) + HDfree(blk); + if (blockP) + UNPIN_LONG_ARRAY(ENVONLY, block, blockP, JNI_ABORT); + if (strd) + HDfree(strd); + if (strideP) + UNPIN_LONG_ARRAY(ENVONLY, stride, strideP, JNI_ABORT); + if (cnt) + HDfree(cnt); + if (countP) + UNPIN_LONG_ARRAY(ENVONLY, count, countP, JNI_ABORT); + if (strt) + HDfree(strt); + if (startP) + UNPIN_LONG_ARRAY(ENVONLY, start, startP, JNI_ABORT); + + return (jlong)sid; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1hyperslab */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Smodify_select + * Signature: (JIJ)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5Smodify_1select(JNIEnv *env, jclass clss, jlong space1_id, jint op, jlong space2_id) +{ + herr_t status = FAIL; + + UNUSED(clss); + + if ((status = H5Smodify_select((hid_t)space1_id, (H5S_seloper_t)op, (hid_t)space2_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + return; +} /* end Java_hdf_hdf5lib_H5_H5Smodify_1select */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Scombine_select + * Signature: (JIJ)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5_H5Scombine_1select(JNIEnv *env, jclass clss, jlong space1_id, jint op, jlong space2_id) +{ + hid_t sid = H5I_INVALID_HID; + + UNUSED(clss); + + if ((sid = H5Scombine_select((hid_t)space1_id, (H5S_seloper_t)op, (hid_t)space2_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + + return (jlong)sid; +} /* end Java_hdf_hdf5lib_H5_H5Scombine_1select */ + #ifdef __cplusplus } /* end extern "C" */ #endif /* __cplusplus */ diff --git a/java/src/jni/h5sImp.h b/java/src/jni/h5sImp.h index ee28b39..83255c1 100644 --- a/java/src/jni/h5sImp.h +++ b/java/src/jni/h5sImp.h @@ -259,6 +259,65 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sis_1regular_1hyperslab(JNIEnv JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sget_1regular_1hyperslab(JNIEnv *, jclass, jlong, jlongArray, jlongArray, jlongArray, jlongArray); +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_copy + * Signature: (JJ)V + */ +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1copy(JNIEnv *, jclass, jlong, jlong); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_shape_same + * Signature: (JJ)Z + */ +JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same(JNIEnv *, jclass, jlong, jlong); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_adjust + * Signature: (J[J)V + */ +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1adjust(JNIEnv *, jclass, jlong, jlongArray); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_intersect_block + * Signature: (J[J[J)Z + */ +JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block(JNIEnv *, jclass, jlong, + jlongArray, jlongArray); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_project_intersection + * Signature: (JJJ)J + */ +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection(JNIEnv *, jclass, jlong, jlong, + jlong); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Scombine_hyperslab + * Signature: (JI[J[J[J[J)J + */ +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *, jclass, jlong, jint, jlongArray, + jlongArray, jlongArray, jlongArray); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Smodify_select + * Signature: (JIJ)V + */ +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Smodify_1select(JNIEnv *, jclass, jlong, jint, jlong); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Scombine_select + * Signature: (JIJ)J + */ +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Scombine_1select(JNIEnv *, jclass, jlong, jint, jlong); + #ifdef __cplusplus } /* end extern "C" */ #endif /* __cplusplus */ diff --git a/java/test/CMakeLists.txt b/java/test/CMakeLists.txt index b97ad26..b0a0d53 100644 --- a/java/test/CMakeLists.txt +++ b/java/test/CMakeLists.txt @@ -96,7 +96,7 @@ HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/h5ex_g_iterate.orig" "${PROJECT_BINARY_ add_custom_target(${HDF5_JAVA_TEST_LIB_TARGET}_files ALL COMMENT "Copying files needed by ${HDF5_JAVA_TEST_LIB_TARGET} tests" DEPENDS ${${HDF5_JAVA_TEST_LIB_TARGET}_files_list}) -if (WIN32 OR MINGW) +if (WIN32) set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";") else () set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") diff --git a/java/test/TestH5Sbasic.java b/java/test/TestH5Sbasic.java index 2173647..9874584 100644 --- a/java/test/TestH5Sbasic.java +++ b/java/test/TestH5Sbasic.java @@ -242,4 +242,142 @@ public class TestH5Sbasic { H5.H5Sdecode(null); } + @Test(expected = IllegalArgumentException.class) + public void testH5Sget_regular_hyperslab_invalid() throws Throwable { + long q_start[] = new long[2]; + long q_stride[] = new long[2]; + long q_count[] = new long[2]; + long q_block[] = new long[2]; + + H5.H5Sget_regular_hyperslab(-1, q_start, q_stride, q_count, q_block); + } + + @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class) + public void testH5Sselect_copy_invalid() throws Throwable { + H5.H5Sselect_copy(-1, -1); + } + + @Test(expected = hdf.hdf5lib.exceptions.HDF5DataspaceInterfaceException.class) + public void testH5Sselect_shape_same_invalid() throws Throwable { + H5.H5Sselect_shape_same(-1, -1); + } + + @Test(expected = IllegalArgumentException.class) + public void testH5Sselect_adjust_invalid() throws Throwable { + long offset[][] = {{0,1},{2,4},{5,6}}; + H5.H5Sselect_adjust(-1, offset); + } + + @Test(expected = IllegalArgumentException.class) + public void testH5Sselect_adjust_rank_offset() throws Throwable { + long sid = -1; + long offset[][] = {{0,1},{2,4},{5,6}}; + + try { + sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE); + assertTrue("H5.H5Screate_simple_extent",sid > 0); + H5.H5Sselect_adjust(sid, offset); + } + finally { + try {H5.H5Sclose(sid);} catch (Exception ex) {} + } + } + + @Test(expected = IllegalArgumentException.class) + public void testH5Sselect_intersect_block_invalid() throws Throwable { + long start[] = new long[2]; + long end[] = new long[2]; + H5.H5Sselect_intersect_block(-1, start, end); + } + + @Test(expected = IllegalArgumentException.class) + public void testH5Sselect_intersect_block_rank_start() throws Throwable { + long sid = -1; + long start[] = new long[2]; + long end[] = null; + + try { + sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE); + assertTrue("H5.H5Screate_simple_extent",sid > 0); + H5.H5Sselect_intersect_block(sid, start, end); + } + finally { + try {H5.H5Sclose(sid);} catch (Exception ex) {} + } + } + + @Test(expected = IllegalArgumentException.class) + public void testH5Sselect_intersect_block_rank_end() throws Throwable { + long sid = -1; + long start[] = null; + long end[] = new long[2]; + + try { + sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE); + assertTrue("H5.H5Screate_simple_extent",sid > 0); + H5.H5Sselect_intersect_block(sid, start, end); + } + finally { + try {H5.H5Sclose(sid);} catch (Exception ex) {} + } + } + + @Test(expected = hdf.hdf5lib.exceptions.HDF5DataspaceInterfaceException.class) + public void testH5Sselect_project_intersection_invalid() throws Throwable { + H5.H5Sselect_project_intersection(-1, -1, -1); + } + + @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class) + public void testH5Scombine_hyperslab_invalid() throws Throwable { + long start[] = new long[2]; + long count[] = new long[2]; + H5.H5Scombine_hyperslab(-1, 0, start, null, count, null); + } + + @Test(expected = NullPointerException.class) + public void testH5Scombine_hyperslab_null_start() throws Throwable { + long sid = -1; + long start[] = null; + long stride[] = null; + long count[] = new long[2]; + long block[] = null; + + try { + sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE); + assertTrue("H5.H5Screate_simple_extent",sid > 0); + H5.H5Scombine_hyperslab(sid, 0, start, stride, count, block); + } + finally { + try {H5.H5Sclose(sid);} catch (Exception ex) {} + } + } + + @Test(expected = NullPointerException.class) + public void testH5Scombine_hyperslab_null_count() throws Throwable { + long sid = -1; + long start[] = new long[2]; + long stride[] = null; + long count[] = null; + long block[] = null; + + try { + sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE); + assertTrue("H5.H5Screate_simple_extent",sid > 0); + H5.H5Scombine_hyperslab(sid, 0, start, stride, count, block); + } + finally { + try {H5.H5Sclose(sid);} catch (Exception ex) {} + } + } + + @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class) + public void testH5Smodify_select_invalid() throws Throwable { + H5.H5Smodify_select(-1, 0, -1); + } + + @Test(expected = hdf.hdf5lib.exceptions.HDF5FunctionArgumentException.class) + public void testH5Scombine_select_invalid() throws Throwable { + H5.H5Scombine_select(-1, 0, -1); + } + } diff --git a/java/test/testfiles/JUnit-TestH5Sbasic.txt b/java/test/testfiles/JUnit-TestH5Sbasic.txt index 707878e..3422442 100644 --- a/java/test/testfiles/JUnit-TestH5Sbasic.txt +++ b/java/test/testfiles/JUnit-TestH5Sbasic.txt @@ -5,18 +5,32 @@ JUnit version 4.11 .testH5Sdecode_null .testH5Screate_simple_dims_exceed .testH5Screate_simple_unlimted_1d +.testH5Sselect_intersect_block_rank_start +.testH5Sget_regular_hyperslab_invalid +.testH5Sselect_adjust_rank_offset .testH5Screate_simple_dims_invalid .testH5Screate_scalar .testH5Screate_simple +.testH5Sselect_project_intersection_invalid .testH5Screate_simple_rank_invalid .testH5Sget_simple_extent_type_invalid +.testH5Scombine_hyperslab_invalid +.testH5Scombine_hyperslab_null_count +.testH5Scombine_hyperslab_null_start .testH5Sencode_invalid .testH5Screate_null .testH5Screate_simple_extent .testH5Screate_invalid +.testH5Sselect_intersect_block_invalid +.testH5Sselect_adjust_invalid .testH5Screate_simple_unlimted +.testH5Sselect_shape_same_invalid +.testH5Smodify_select_invalid +.testH5Scombine_select_invalid +.testH5Sselect_copy_invalid +.testH5Sselect_intersect_block_rank_end Time: XXXX -OK (16 tests) +OK (30 tests) diff --git a/m4/ax_prog_doxygen.m4 b/m4/ax_prog_doxygen.m4 new file mode 100644 index 0000000..3af4956 --- /dev/null +++ b/m4/ax_prog_doxygen.m4 @@ -0,0 +1,586 @@ +# =========================================================================== +# https://www.gnu.org/software/autoconf-archive/ax_prog_doxygen.html +# =========================================================================== +# +# SYNOPSIS +# +# DX_INIT_DOXYGEN(PROJECT-NAME, [DOXYFILE-PATH], [OUTPUT-DIR], ...) +# DX_DOXYGEN_FEATURE(ON|OFF) +# DX_DOT_FEATURE(ON|OFF) +# DX_HTML_FEATURE(ON|OFF) +# DX_CHM_FEATURE(ON|OFF) +# DX_CHI_FEATURE(ON|OFF) +# DX_MAN_FEATURE(ON|OFF) +# DX_RTF_FEATURE(ON|OFF) +# DX_XML_FEATURE(ON|OFF) +# DX_PDF_FEATURE(ON|OFF) +# DX_PS_FEATURE(ON|OFF) +# +# DESCRIPTION +# +# The DX_*_FEATURE macros control the default setting for the given +# Doxygen feature. Supported features are 'DOXYGEN' itself, 'DOT' for +# generating graphics, 'HTML' for plain HTML, 'CHM' for compressed HTML +# help (for MS users), 'CHI' for generating a separate .chi file by the +# .chm file, and 'MAN', 'RTF', 'XML', 'PDF' and 'PS' for the appropriate +# output formats. The environment variable DOXYGEN_PAPER_SIZE may be +# specified to override the default 'a4wide' paper size. +# +# By default, HTML, PDF and PS documentation is generated as this seems to +# be the most popular and portable combination. MAN pages created by +# Doxygen are usually problematic, though by picking an appropriate subset +# and doing some massaging they might be better than nothing. CHM and RTF +# are specific for MS (note that you can't generate both HTML and CHM at +# the same time). The XML is rather useless unless you apply specialized +# post-processing to it. +# +# The macros mainly control the default state of the feature. The use can +# override the default by specifying --enable or --disable. The macros +# ensure that contradictory flags are not given (e.g., +# --enable-doxygen-html and --enable-doxygen-chm, +# --enable-doxygen-anything with --disable-doxygen, etc.) Finally, each +# feature will be automatically disabled (with a warning) if the required +# programs are missing. +# +# Once all the feature defaults have been specified, call DX_INIT_DOXYGEN +# with the following parameters: a one-word name for the project for use +# as a filename base etc., an optional configuration file name (the +# default is '$(srcdir)/Doxyfile', the same as Doxygen's default), and an +# optional output directory name (the default is 'doxygen-doc'). To run +# doxygen multiple times for different configuration files and output +# directories provide more parameters: the second, forth, sixth, etc +# parameter are configuration file names and the third, fifth, seventh, +# etc parameter are output directories. No checking is done to catch +# duplicates. +# +# Automake Support +# +# The DX_RULES substitution can be used to add all needed rules to the +# Makefile. Note that this is a substitution without being a variable: +# only the @DX_RULES@ syntax will work. +# +# The provided targets are: +# +# doxygen-doc: Generate all doxygen documentation. +# +# doxygen-run: Run doxygen, which will generate some of the +# documentation (HTML, CHM, CHI, MAN, RTF, XML) +# but will not do the post processing required +# for the rest of it (PS, PDF). +# +# doxygen-ps: Generate doxygen PostScript documentation. +# +# doxygen-pdf: Generate doxygen PDF documentation. +# +# Note that by default these are not integrated into the automake targets. +# If doxygen is used to generate man pages, you can achieve this +# integration by setting man3_MANS to the list of man pages generated and +# then adding the dependency: +# +# $(man3_MANS): doxygen-doc +# +# This will cause make to run doxygen and generate all the documentation. +# +# The following variable is intended for use in Makefile.am: +# +# DX_CLEANFILES = everything to clean. +# +# Then add this variable to MOSTLYCLEANFILES. +# +# LICENSE +# +# Copyright (c) 2009 Oren Ben-Kiki <oren@ben-kiki.org> +# Copyright (c) 2015 Olaf Mandel <olaf@mandel.name> +# +# Copying and distribution of this file, with or without modification, are +# permitted in any medium without royalty provided the copyright notice +# and this notice are preserved. This file is offered as-is, without any +# warranty. + +#serial 24 + +## ----------## +## Defaults. ## +## ----------## + +DX_ENV="" +AC_DEFUN([DX_FEATURE_doc], ON) +AC_DEFUN([DX_FEATURE_dot], OFF) +AC_DEFUN([DX_FEATURE_man], OFF) +AC_DEFUN([DX_FEATURE_html], ON) +AC_DEFUN([DX_FEATURE_chm], OFF) +AC_DEFUN([DX_FEATURE_chi], OFF) +AC_DEFUN([DX_FEATURE_rtf], OFF) +AC_DEFUN([DX_FEATURE_xml], OFF) +AC_DEFUN([DX_FEATURE_pdf], ON) +AC_DEFUN([DX_FEATURE_ps], ON) + +## --------------- ## +## Private macros. ## +## --------------- ## + +# DX_ENV_APPEND(VARIABLE, VALUE) +# ------------------------------ +# Append VARIABLE="VALUE" to DX_ENV for invoking doxygen and add it +# as a substitution (but not a Makefile variable). The substitution +# is skipped if the variable name is VERSION. +AC_DEFUN([DX_ENV_APPEND], +[AC_SUBST([DX_ENV], ["$DX_ENV $1='$2'"])dnl +m4_if([$1], [VERSION], [], [AC_SUBST([$1], [$2])dnl +AM_SUBST_NOTMAKE([$1])])dnl +]) + +# DX_DIRNAME_EXPR +# --------------- +# Expand into a shell expression prints the directory part of a path. +AC_DEFUN([DX_DIRNAME_EXPR], + [[expr ".$1" : '\(\.\)[^/]*$' \| "x$1" : 'x\(.*\)/[^/]*$']]) + +# DX_IF_FEATURE(FEATURE, IF-ON, IF-OFF) +# ------------------------------------- +# Expands according to the M4 (static) status of the feature. +AC_DEFUN([DX_IF_FEATURE], [ifelse(DX_FEATURE_$1, ON, [$2], [$3])]) + +# DX_REQUIRE_PROG(VARIABLE, PROGRAM) +# ---------------------------------- +# Require the specified program to be found for the DX_CURRENT_FEATURE to work. +AC_DEFUN([DX_REQUIRE_PROG], [ +AC_PATH_TOOL([$1], [$2]) +if test "$DX_FLAG_[]DX_CURRENT_FEATURE$$1" = 1; then + AC_MSG_WARN([$2 not found - will not DX_CURRENT_DESCRIPTION]) + AC_SUBST(DX_FLAG_[]DX_CURRENT_FEATURE, 0) +fi +]) + +# DX_TEST_FEATURE(FEATURE) +# ------------------------ +# Expand to a shell expression testing whether the feature is active. +AC_DEFUN([DX_TEST_FEATURE], [test "$DX_FLAG_$1" = 1]) + +# DX_CHECK_DEPEND(REQUIRED_FEATURE, REQUIRED_STATE) +# ------------------------------------------------- +# Verify that a required features has the right state before trying to turn on +# the DX_CURRENT_FEATURE. +AC_DEFUN([DX_CHECK_DEPEND], [ +test "$DX_FLAG_$1" = "$2" \ +|| AC_MSG_ERROR([doxygen-DX_CURRENT_FEATURE ifelse([$2], 1, + requires, contradicts) doxygen-$1]) +]) + +# DX_CLEAR_DEPEND(FEATURE, REQUIRED_FEATURE, REQUIRED_STATE) +# ---------------------------------------------------------- +# Turn off the DX_CURRENT_FEATURE if the required feature is off. +AC_DEFUN([DX_CLEAR_DEPEND], [ +test "$DX_FLAG_$1" = "$2" || AC_SUBST(DX_FLAG_[]DX_CURRENT_FEATURE, 0) +]) + +# DX_FEATURE_ARG(FEATURE, DESCRIPTION, +# CHECK_DEPEND, CLEAR_DEPEND, +# REQUIRE, DO-IF-ON, DO-IF-OFF) +# -------------------------------------------- +# Parse the command-line option controlling a feature. CHECK_DEPEND is called +# if the user explicitly turns the feature on (and invokes DX_CHECK_DEPEND), +# otherwise CLEAR_DEPEND is called to turn off the default state if a required +# feature is disabled (using DX_CLEAR_DEPEND). REQUIRE performs additional +# requirement tests (DX_REQUIRE_PROG). Finally, an automake flag is set and +# DO-IF-ON or DO-IF-OFF are called according to the final state of the feature. +AC_DEFUN([DX_ARG_ABLE], [ + AC_DEFUN([DX_CURRENT_FEATURE], [$1]) + AC_DEFUN([DX_CURRENT_DESCRIPTION], [$2]) + AC_ARG_ENABLE(doxygen-$1, + [AS_HELP_STRING(DX_IF_FEATURE([$1], [--disable-doxygen-$1], + [--enable-doxygen-$1]), + DX_IF_FEATURE([$1], [don't $2], [$2]))], + [ +case "$enableval" in +#( +y|Y|yes|Yes|YES) + AC_SUBST([DX_FLAG_$1], 1) + $3 +;; #( +n|N|no|No|NO) + AC_SUBST([DX_FLAG_$1], 0) +;; #( +*) + AC_MSG_ERROR([invalid value '$enableval' given to doxygen-$1]) +;; +esac +], [ +AC_SUBST([DX_FLAG_$1], [DX_IF_FEATURE([$1], 1, 0)]) +$4 +]) +if DX_TEST_FEATURE([$1]); then + $5 + : +fi +if DX_TEST_FEATURE([$1]); then + $6 + : +else + $7 + : +fi +]) + +## -------------- ## +## Public macros. ## +## -------------- ## + +# DX_XXX_FEATURE(DEFAULT_STATE) +# ----------------------------- +AC_DEFUN([DX_DOXYGEN_FEATURE], [AC_DEFUN([DX_FEATURE_doc], [$1])]) +AC_DEFUN([DX_DOT_FEATURE], [AC_DEFUN([DX_FEATURE_dot], [$1])]) +AC_DEFUN([DX_MAN_FEATURE], [AC_DEFUN([DX_FEATURE_man], [$1])]) +AC_DEFUN([DX_HTML_FEATURE], [AC_DEFUN([DX_FEATURE_html], [$1])]) +AC_DEFUN([DX_CHM_FEATURE], [AC_DEFUN([DX_FEATURE_chm], [$1])]) +AC_DEFUN([DX_CHI_FEATURE], [AC_DEFUN([DX_FEATURE_chi], [$1])]) +AC_DEFUN([DX_RTF_FEATURE], [AC_DEFUN([DX_FEATURE_rtf], [$1])]) +AC_DEFUN([DX_XML_FEATURE], [AC_DEFUN([DX_FEATURE_xml], [$1])]) +AC_DEFUN([DX_XML_FEATURE], [AC_DEFUN([DX_FEATURE_xml], [$1])]) +AC_DEFUN([DX_PDF_FEATURE], [AC_DEFUN([DX_FEATURE_pdf], [$1])]) +AC_DEFUN([DX_PS_FEATURE], [AC_DEFUN([DX_FEATURE_ps], [$1])]) + +# DX_INIT_DOXYGEN(PROJECT, [CONFIG-FILE], [OUTPUT-DOC-DIR], ...) +# -------------------------------------------------------------- +# PROJECT also serves as the base name for the documentation files. +# The default CONFIG-FILE is "$(srcdir)/Doxyfile" and OUTPUT-DOC-DIR is +# "doxygen-doc". +# More arguments are interpreted as interleaved CONFIG-FILE and +# OUTPUT-DOC-DIR values. +AC_DEFUN([DX_INIT_DOXYGEN], [ + +# Files: +AC_SUBST([DX_PROJECT], [$1]) +AC_SUBST([DX_CONFIG], ['ifelse([$2], [], [$(srcdir)/Doxyfile], [$2])']) +AC_SUBST([DX_DOCDIR], ['ifelse([$3], [], [doxygen-doc], [$3])']) +m4_if(m4_eval(3 < m4_count($@)), 1, [m4_for([DX_i], 4, m4_count($@), 2, + [AC_SUBST([DX_CONFIG]m4_eval(DX_i[/2]), + 'm4_default_nblank_quoted(m4_argn(DX_i, $@), + [$(srcdir)/Doxyfile])')])])dnl +m4_if(m4_eval(3 < m4_count($@)), 1, [m4_for([DX_i], 5, m4_count($@,), 2, + [AC_SUBST([DX_DOCDIR]m4_eval([(]DX_i[-1)/2]), + 'm4_default_nblank_quoted(m4_argn(DX_i, $@), + [doxygen-doc])')])])dnl +m4_define([DX_loop], m4_dquote(m4_if(m4_eval(3 < m4_count($@)), 1, + [m4_for([DX_i], 4, m4_count($@), 2, [, m4_eval(DX_i[/2])])], + [])))dnl + +# Environment variables used inside doxygen.cfg: +DX_ENV_APPEND(SRCDIR, $srcdir) +DX_ENV_APPEND(PROJECT, $DX_PROJECT) +DX_ENV_APPEND(VERSION, $PACKAGE_VERSION) + +# Doxygen itself: +DX_ARG_ABLE(doc, [generate any doxygen documentation], + [], + [], + [DX_REQUIRE_PROG([DX_DOXYGEN], doxygen) + DX_REQUIRE_PROG([DX_PERL], perl)], + [DX_ENV_APPEND(PERL_PATH, $DX_PERL)]) + +# Dot for graphics: +DX_ARG_ABLE(dot, [generate graphics for doxygen documentation], + [DX_CHECK_DEPEND(doc, 1)], + [DX_CLEAR_DEPEND(doc, 1)], + [DX_REQUIRE_PROG([DX_DOT], dot)], + [DX_ENV_APPEND(HAVE_DOT, YES) + DX_ENV_APPEND(DOT_PATH, [`DX_DIRNAME_EXPR($DX_DOT)`])], + [DX_ENV_APPEND(HAVE_DOT, NO)]) + +# Man pages generation: +DX_ARG_ABLE(man, [generate doxygen manual pages], + [DX_CHECK_DEPEND(doc, 1)], + [DX_CLEAR_DEPEND(doc, 1)], + [], + [DX_ENV_APPEND(GENERATE_MAN, YES)], + [DX_ENV_APPEND(GENERATE_MAN, NO)]) + +# RTF file generation: +DX_ARG_ABLE(rtf, [generate doxygen RTF documentation], + [DX_CHECK_DEPEND(doc, 1)], + [DX_CLEAR_DEPEND(doc, 1)], + [], + [DX_ENV_APPEND(GENERATE_RTF, YES)], + [DX_ENV_APPEND(GENERATE_RTF, NO)]) + +# XML file generation: +DX_ARG_ABLE(xml, [generate doxygen XML documentation], + [DX_CHECK_DEPEND(doc, 1)], + [DX_CLEAR_DEPEND(doc, 1)], + [], + [DX_ENV_APPEND(GENERATE_XML, YES)], + [DX_ENV_APPEND(GENERATE_XML, NO)]) + +# (Compressed) HTML help generation: +DX_ARG_ABLE(chm, [generate doxygen compressed HTML help documentation], + [DX_CHECK_DEPEND(doc, 1)], + [DX_CLEAR_DEPEND(doc, 1)], + [DX_REQUIRE_PROG([DX_HHC], hhc)], + [DX_ENV_APPEND(HHC_PATH, $DX_HHC) + DX_ENV_APPEND(GENERATE_HTML, YES) + DX_ENV_APPEND(GENERATE_HTMLHELP, YES)], + [DX_ENV_APPEND(GENERATE_HTMLHELP, NO)]) + +# Separate CHI file generation. +DX_ARG_ABLE(chi, [generate doxygen separate compressed HTML help index file], + [DX_CHECK_DEPEND(chm, 1)], + [DX_CLEAR_DEPEND(chm, 1)], + [], + [DX_ENV_APPEND(GENERATE_CHI, YES)], + [DX_ENV_APPEND(GENERATE_CHI, NO)]) + +# Plain HTML pages generation: +DX_ARG_ABLE(html, [generate doxygen plain HTML documentation], + [DX_CHECK_DEPEND(doc, 1) DX_CHECK_DEPEND(chm, 0)], + [DX_CLEAR_DEPEND(doc, 1) DX_CLEAR_DEPEND(chm, 0)], + [], + [DX_ENV_APPEND(GENERATE_HTML, YES)], + [DX_TEST_FEATURE(chm) || DX_ENV_APPEND(GENERATE_HTML, NO)]) + +# PostScript file generation: +DX_ARG_ABLE(ps, [generate doxygen PostScript documentation], + [DX_CHECK_DEPEND(doc, 1)], + [DX_CLEAR_DEPEND(doc, 1)], + [DX_REQUIRE_PROG([DX_LATEX], latex) + DX_REQUIRE_PROG([DX_MAKEINDEX], makeindex) + DX_REQUIRE_PROG([DX_DVIPS], dvips) + DX_REQUIRE_PROG([DX_EGREP], egrep)]) + +# PDF file generation: +DX_ARG_ABLE(pdf, [generate doxygen PDF documentation], + [DX_CHECK_DEPEND(doc, 1)], + [DX_CLEAR_DEPEND(doc, 1)], + [DX_REQUIRE_PROG([DX_PDFLATEX], pdflatex) + DX_REQUIRE_PROG([DX_MAKEINDEX], makeindex) + DX_REQUIRE_PROG([DX_EGREP], egrep)]) + +# LaTeX generation for PS and/or PDF: +if DX_TEST_FEATURE(ps) || DX_TEST_FEATURE(pdf); then + DX_ENV_APPEND(GENERATE_LATEX, YES) +else + DX_ENV_APPEND(GENERATE_LATEX, NO) +fi + +# Paper size for PS and/or PDF: +AC_ARG_VAR(DOXYGEN_PAPER_SIZE, + [a4wide (default), a4, letter, legal or executive]) +case "$DOXYGEN_PAPER_SIZE" in +#( +"") + AC_SUBST(DOXYGEN_PAPER_SIZE, "") +;; #( +a4wide|a4|letter|legal|executive) + DX_ENV_APPEND(PAPER_SIZE, $DOXYGEN_PAPER_SIZE) +;; #( +*) + AC_MSG_ERROR([unknown DOXYGEN_PAPER_SIZE='$DOXYGEN_PAPER_SIZE']) +;; +esac + +# Rules: +AS_IF([[test $DX_FLAG_html -eq 1]], +[[DX_SNIPPET_html="## ------------------------------- ## +## Rules specific for HTML output. ## +## ------------------------------- ## + +DX_CLEAN_HTML = \$(DX_DOCDIR)/html]dnl +m4_foreach([DX_i], [m4_shift(DX_loop)], [[\\ + \$(DX_DOCDIR]DX_i[)/html]])[ + +"]], +[[DX_SNIPPET_html=""]]) +AS_IF([[test $DX_FLAG_chi -eq 1]], +[[DX_SNIPPET_chi=" +DX_CLEAN_CHI = \$(DX_DOCDIR)/\$(PACKAGE).chi]dnl +m4_foreach([DX_i], [m4_shift(DX_loop)], [[\\ + \$(DX_DOCDIR]DX_i[)/\$(PACKAGE).chi]])["]], +[[DX_SNIPPET_chi=""]]) +AS_IF([[test $DX_FLAG_chm -eq 1]], +[[DX_SNIPPET_chm="## ------------------------------ ## +## Rules specific for CHM output. ## +## ------------------------------ ## + +DX_CLEAN_CHM = \$(DX_DOCDIR)/chm]dnl +m4_foreach([DX_i], [m4_shift(DX_loop)], [[\\ + \$(DX_DOCDIR]DX_i[)/chm]])[\ +${DX_SNIPPET_chi} + +"]], +[[DX_SNIPPET_chm=""]]) +AS_IF([[test $DX_FLAG_man -eq 1]], +[[DX_SNIPPET_man="## ------------------------------ ## +## Rules specific for MAN output. ## +## ------------------------------ ## + +DX_CLEAN_MAN = \$(DX_DOCDIR)/man]dnl +m4_foreach([DX_i], [m4_shift(DX_loop)], [[\\ + \$(DX_DOCDIR]DX_i[)/man]])[ + +"]], +[[DX_SNIPPET_man=""]]) +AS_IF([[test $DX_FLAG_rtf -eq 1]], +[[DX_SNIPPET_rtf="## ------------------------------ ## +## Rules specific for RTF output. ## +## ------------------------------ ## + +DX_CLEAN_RTF = \$(DX_DOCDIR)/rtf]dnl +m4_foreach([DX_i], [m4_shift(DX_loop)], [[\\ + \$(DX_DOCDIR]DX_i[)/rtf]])[ + +"]], +[[DX_SNIPPET_rtf=""]]) +AS_IF([[test $DX_FLAG_xml -eq 1]], +[[DX_SNIPPET_xml="## ------------------------------ ## +## Rules specific for XML output. ## +## ------------------------------ ## + +DX_CLEAN_XML = \$(DX_DOCDIR)/xml]dnl +m4_foreach([DX_i], [m4_shift(DX_loop)], [[\\ + \$(DX_DOCDIR]DX_i[)/xml]])[ + +"]], +[[DX_SNIPPET_xml=""]]) +AS_IF([[test $DX_FLAG_ps -eq 1]], +[[DX_SNIPPET_ps="## ----------------------------- ## +## Rules specific for PS output. ## +## ----------------------------- ## + +DX_CLEAN_PS = \$(DX_DOCDIR)/\$(PACKAGE).ps]dnl +m4_foreach([DX_i], [m4_shift(DX_loop)], [[\\ + \$(DX_DOCDIR]DX_i[)/\$(PACKAGE).ps]])[ + +DX_PS_GOAL = doxygen-ps + +doxygen-ps: \$(DX_CLEAN_PS) + +]m4_foreach([DX_i], [DX_loop], +[[\$(DX_DOCDIR]DX_i[)/\$(PACKAGE).ps: \$(DX_DOCDIR]DX_i[)/\$(PACKAGE).tag + \$(DX_V_LATEX)cd \$(DX_DOCDIR]DX_i[)/latex; \\ + rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \\ + \$(DX_LATEX) refman.tex; \\ + \$(DX_MAKEINDEX) refman.idx; \\ + \$(DX_LATEX) refman.tex; \\ + countdown=5; \\ + while \$(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \\ + refman.log > /dev/null 2>&1 \\ + && test \$\$countdown -gt 0; do \\ + \$(DX_LATEX) refman.tex; \\ + countdown=\`expr \$\$countdown - 1\`; \\ + done; \\ + \$(DX_DVIPS) -o ../\$(PACKAGE).ps refman.dvi + +]])["]], +[[DX_SNIPPET_ps=""]]) +AS_IF([[test $DX_FLAG_pdf -eq 1]], +[[DX_SNIPPET_pdf="## ------------------------------ ## +## Rules specific for PDF output. ## +## ------------------------------ ## + +DX_CLEAN_PDF = \$(DX_DOCDIR)/\$(PACKAGE).pdf]dnl +m4_foreach([DX_i], [m4_shift(DX_loop)], [[\\ + \$(DX_DOCDIR]DX_i[)/\$(PACKAGE).pdf]])[ + +DX_PDF_GOAL = doxygen-pdf + +doxygen-pdf: \$(DX_CLEAN_PDF) + +]m4_foreach([DX_i], [DX_loop], +[[\$(DX_DOCDIR]DX_i[)/\$(PACKAGE).pdf: \$(DX_DOCDIR]DX_i[)/\$(PACKAGE).tag + \$(DX_V_LATEX)cd \$(DX_DOCDIR]DX_i[)/latex; \\ + rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \\ + \$(DX_PDFLATEX) refman.tex; \\ + \$(DX_MAKEINDEX) refman.idx; \\ + \$(DX_PDFLATEX) refman.tex; \\ + countdown=5; \\ + while \$(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \\ + refman.log > /dev/null 2>&1 \\ + && test \$\$countdown -gt 0; do \\ + \$(DX_PDFLATEX) refman.tex; \\ + countdown=\`expr \$\$countdown - 1\`; \\ + done; \\ + mv refman.pdf ../\$(PACKAGE).pdf + +]])["]], +[[DX_SNIPPET_pdf=""]]) +AS_IF([[test $DX_FLAG_ps -eq 1 -o $DX_FLAG_pdf -eq 1]], +[[DX_SNIPPET_latex="## ------------------------------------------------- ## +## Rules specific for LaTeX (shared for PS and PDF). ## +## ------------------------------------------------- ## + +DX_V_LATEX = \$(_DX_v_LATEX_\$(V)) +_DX_v_LATEX_ = \$(_DX_v_LATEX_\$(AM_DEFAULT_VERBOSITY)) +_DX_v_LATEX_0 = @echo \" LATEX \" \$][@; + +DX_CLEAN_LATEX = \$(DX_DOCDIR)/latex]dnl +m4_foreach([DX_i], [m4_shift(DX_loop)], [[\\ + \$(DX_DOCDIR]DX_i[)/latex]])[ + +"]], +[[DX_SNIPPET_latex=""]]) + +AS_IF([[test $DX_FLAG_doc -eq 1]], +[[DX_SNIPPET_doc="## --------------------------------- ## +## Format-independent Doxygen rules. ## +## --------------------------------- ## + +${DX_SNIPPET_html}\ +${DX_SNIPPET_chm}\ +${DX_SNIPPET_man}\ +${DX_SNIPPET_rtf}\ +${DX_SNIPPET_xml}\ +${DX_SNIPPET_ps}\ +${DX_SNIPPET_pdf}\ +${DX_SNIPPET_latex}\ +DX_V_DXGEN = \$(_DX_v_DXGEN_\$(V)) +_DX_v_DXGEN_ = \$(_DX_v_DXGEN_\$(AM_DEFAULT_VERBOSITY)) +_DX_v_DXGEN_0 = @echo \" DXGEN \" \$<; + +.PHONY: doxygen-run doxygen-doc \$(DX_PS_GOAL) \$(DX_PDF_GOAL) + +.INTERMEDIATE: doxygen-run \$(DX_PS_GOAL) \$(DX_PDF_GOAL) + +doxygen-run:]m4_foreach([DX_i], [DX_loop], + [[ \$(DX_DOCDIR]DX_i[)/\$(PACKAGE).tag]])[ + +doxygen-doc: doxygen-run \$(DX_PS_GOAL) \$(DX_PDF_GOAL) + +]m4_foreach([DX_i], [DX_loop], +[[\$(DX_DOCDIR]DX_i[)/\$(PACKAGE).tag: \$(DX_CONFIG]DX_i[) \$(pkginclude_HEADERS) + \$(A""M_V_at)rm -rf \$(DX_DOCDIR]DX_i[) + \$(DX_V_DXGEN)\$(DX_ENV) DOCDIR=\$(DX_DOCDIR]DX_i[) \$(DX_DOXYGEN) \$(DX_CONFIG]DX_i[) + \$(A""M_V_at)echo Timestamp >\$][@ + +]])dnl +[DX_CLEANFILES = \\] +m4_foreach([DX_i], [DX_loop], +[[ \$(DX_DOCDIR]DX_i[)/doxygen_sqlite3.db \\ + \$(DX_DOCDIR]DX_i[)/\$(PACKAGE).tag \\ +]])dnl +[ -r \\ + \$(DX_CLEAN_HTML) \\ + \$(DX_CLEAN_CHM) \\ + \$(DX_CLEAN_CHI) \\ + \$(DX_CLEAN_MAN) \\ + \$(DX_CLEAN_RTF) \\ + \$(DX_CLEAN_XML) \\ + \$(DX_CLEAN_PS) \\ + \$(DX_CLEAN_PDF) \\ + \$(DX_CLEAN_LATEX)"]], +[[DX_SNIPPET_doc=""]]) +AC_SUBST([DX_RULES], +["${DX_SNIPPET_doc}"])dnl +AM_SUBST_NOTMAKE([DX_RULES]) + +#For debugging: +#echo DX_FLAG_doc=$DX_FLAG_doc +#echo DX_FLAG_dot=$DX_FLAG_dot +#echo DX_FLAG_man=$DX_FLAG_man +#echo DX_FLAG_html=$DX_FLAG_html +#echo DX_FLAG_chm=$DX_FLAG_chm +#echo DX_FLAG_chi=$DX_FLAG_chi +#echo DX_FLAG_rtf=$DX_FLAG_rtf +#echo DX_FLAG_xml=$DX_FLAG_xml +#echo DX_FLAG_pdf=$DX_FLAG_pdf +#echo DX_FLAG_ps=$DX_FLAG_ps +#echo DX_ENV=$DX_ENV +])
\ No newline at end of file diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt index 0d35b3f..f42f780 100644 --- a/release_docs/INSTALL_CMake.txt +++ b/release_docs/INSTALL_CMake.txt @@ -777,6 +777,8 @@ HDF5_USE_FOLDERS "Enable folder grouping of projects in IDEs." HDF5_WANT_DATA_ACCURACY "IF data accuracy is guaranteed during data conversions" ON HDF5_WANT_DCONV_EXCEPTION "exception handling functions is checked during data conversions" ON HDF5_ENABLE_THREADSAFE "Enable Threadsafety" OFF +HDF5_MSVC_NAMING_CONVENTION "Use MSVC Naming conventions for Shared Libraries" OFF +HDF5_MINGW_STATIC_GCC_LIBS "Statically link libgcc/libstdc++" OFF if (APPLE) HDF5_BUILD_WITH_INSTALL_NAME "Build with library install_name set to the installation path" OFF if (CMAKE_BUILD_TYPE MATCHES Debug) @@ -789,6 +791,10 @@ if (HDF5_BUILD_FORTRAN) if (BUILD_SHARED_LIBS AND NOT BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is SHARED if (NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is STATIC if (NOT BUILD_SHARED_LIBS AND NOT BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is SHARED +HDF5_BUILD_DOC "Build documentation" OFF +HDF5_ENABLE_ANALYZER_TOOLS "enable the use of Clang tools" OFF +HDF5_ENABLE_SANITIZERS "execute the Clang sanitizer" OFF +HDF5_ENABLE_FORMATTERS "format source files" OFF ---------------- External Library Options --------------------- HDF5_ALLOW_EXTERNAL_SUPPORT "Allow External Library Building (NO GIT TGZ)" "NO" diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 1c5d96d..639dbe7 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -48,6 +48,31 @@ New Features Configuration: ------------- + - Autotools and CMake target added to produce doxygen generated documentation + + The default is OFF or disabled. + Autoconf option is '--enable-doxygen' + autotools make target is 'doxygen' and will build all doxygen targets + CMake configure option is 'HDF5_BUILD_DOC'. + CMake target is 'doxygen' for all available doxygen targets + CMake target is 'hdf5lib_doc' for the src subdirectory + + (ADB - 2020/11/03) + + - CMake option to use MSVC naming conventions with MinGW + + HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions + when using a MinGW toolchain + + (xan - 2020/10/30) + + - CMake option to statically link gcc libs with MinGW + + HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++ + with the MinGW toolchain + + (xan - 2020/10/30) + - CMake option to build the HDF filter plugins project as an external project The HDF filter plugins project is a collection of registered compression @@ -717,6 +742,15 @@ New Features Java Library: ---------------- + - Added new H5S functions. + + H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust, + H5Sselect_intersect_block, H5Sselect_project_intersection, + H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select + wrapper functions added. + + (ADB - 2020/10/27, HDFFV-10868) + - Added ability to test java library with VOLs. Created new CMake script that combines the java and vol test scripts. diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 597f620..38225e9 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1356,3 +1356,41 @@ if (NOT WIN32) COMPONENT libraries ) endif () + +#----------------------------------------------------------------------------- +# Option to build documentation +#----------------------------------------------------------------------------- +if (DOXYGEN_FOUND) + set (DOXYGEN_PACKAGE ${HDF5_PACKAGE}) + set (DOXYGEN_VERSION_STRING ${HDF5_VERSION_STRING}) + set (DOXYGEN_INCLUDE_ALIASES ${HDF5_DOXYGEN_DIR}/aliases) + set (DOXYGEN_PROJECT_LOGO ${HDF5_DOXYGEN_DIR}/img/HDFG-logo.png) + set (DOXYGEN_PROJECT_BRIEF "C-API Reference") + set (DOXYGEN_INPUT_DIRECTORY ${HDF5_SRC_DIR} ${HDF5_DOXYGEN_DIR}/dox ${HDF5_GENERATED_SOURCE_DIR}/shared) + set (DOXYGEN_OPTIMIZE_OUTPUT_FOR_C YES) + set (DOXYGEN_MACRO_EXPANSION YES) + set (DOXYGEN_OUTPUT_DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs) + + # Replace variables inside @@ with the current values + configure_file(${HDF5_DOXYGEN_DIR}/Doxyfile.in Doxyfile @ONLY) + + doxygen_add_docs(hdf5lib_doc +# ${common_SRCS} ${shared_gen_SRCS} ${H5_PUBLIC_HEADERS} ${H5_PRIVATE_HEADERS} ${H5_GENERATED_HEADERS} ${HDF5_DOXYGEN_DIR}/dox + ${DOXYGEN_INPUT_DIRECTORY} + ALL + WORKING_DIRECTORY ${HDF5_SRC_DIR} + COMMENT "Generating HDF5 library Source Documentation" + ) + install( + DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs/html + DESTINATION ${HDF5_INSTALL_DATA_DIR} + COMPONENT Documents + ) + + if(NOT TARGET doxygen) + add_custom_target(doxygen) + endif() + + add_dependencies(doxygen hdf5lib_doc) + +endif () diff --git a/src/H5FDdirect.c b/src/H5FDdirect.c index ac7720f..4c2d251 100644 --- a/src/H5FDdirect.c +++ b/src/H5FDdirect.c @@ -384,14 +384,13 @@ static void * H5FD__direct_fapl_get(H5FD_t *_file) { H5FD_direct_t *file = (H5FD_direct_t *)_file; - void * ret_value; /* Return value */ + void *ret_value = NULL; /* Return value */ - FUNC_ENTER_STATIC + FUNC_ENTER_STATIC_NOERR /* Set return value */ ret_value = H5FD__direct_fapl_copy(&(file->fa)); -done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5FD__direct_fapl_get() */ @@ -447,7 +446,7 @@ H5FD__direct_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxad int o_flags; int fd = (-1); H5FD_direct_t * file = NULL; - H5FD_direct_fapl_t *fa; + const H5FD_direct_fapl_t *fa; #ifdef H5_HAVE_WIN32_API HFILE filehandle; struct _BY_HANDLE_FILE_INFORMATION fileinfo; @@ -496,7 +495,7 @@ H5FD__direct_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxad /* Get the driver specific information */ if (NULL == (plist = H5P_object_verify(fapl_id, H5P_FILE_ACCESS))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a file access property list") - if (NULL == (fa = (H5FD_direct_fapl_t *)H5P_peek_driver_info(plist))) + if (NULL == (fa = (const H5FD_direct_fapl_t *)H5P_peek_driver_info(plist))) HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, NULL, "bad VFL driver info") file->fd = fd; @@ -546,7 +545,8 @@ H5FD__direct_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxad } else { file->fa.must_align = FALSE; - HDftruncate(file->fd, (HDoff_t)0); + if (-1 == HDftruncate(file->fd, (HDoff_t)0)) + HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, NULL, "unable to truncate file") } } else { @@ -793,7 +793,7 @@ H5FD__direct_get_eof(const H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type) { const H5FD_direct_t *file = (const H5FD_direct_t *)_file; - FUNC_ENTER_STATIC + FUNC_ENTER_STATIC_NOERR FUNC_LEAVE_NOAPI(file->eof) } diff --git a/src/H5FDdirect.h b/src/H5FDdirect.h index 2d88a69..ea2b3f2 100644 --- a/src/H5FDdirect.h +++ b/src/H5FDdirect.h @@ -23,7 +23,7 @@ #ifdef H5_HAVE_DIRECT #define H5FD_DIRECT (H5FD_direct_init()) #else -#define H5FD_DIRECT (-1) +#define H5FD_DIRECT (H5I_INVALID_HID) #endif /* H5_HAVE_DIRECT */ #ifdef H5_HAVE_DIRECT diff --git a/src/H5FDhdfs.c b/src/H5FDhdfs.c index a7c6aae..38145d0 100644 --- a/src/H5FDhdfs.c +++ b/src/H5FDhdfs.c @@ -20,6 +20,9 @@ * File System (HDFS). */ +/* This source code file is part of the H5FD driver module */ +#include "H5FDdrvr_module.h" + #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5FDprivate.h" /* File drivers */ @@ -30,9 +33,6 @@ #ifdef H5_HAVE_LIBHDFS -/* This source code file is part of the H5FD driver module */ -#include "H5FDdrvr_module.h" - /* HDFS routines */ #include "hdfs.h" @@ -356,7 +356,7 @@ done: hid_t H5FD_hdfs_init(void) { - hid_t ret_value = H5I_INVALID_HID; /* Return value */ + hid_t ret_value = H5I_INVALID_HID; #if HDFS_STATS unsigned int bin_i; #endif @@ -674,7 +674,7 @@ H5Pget_fapl_hdfs(hid_t fapl_id, H5FD_hdfs_fapl_t *fa_out) HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "bad VFL driver info") /* Copy the hdfs fapl data out */ - HDmemcpy(fa_out, fa, sizeof(H5FD_hdfs_fapl_t)); + H5MM_memcpy(fa_out, fa, sizeof(H5FD_hdfs_fapl_t)); done: FUNC_LEAVE_API(ret_value) @@ -709,7 +709,7 @@ H5FD__hdfs_fapl_get(H5FD_t *_file) HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "memory allocation failed") /* Copy the fields of the structure */ - HDmemcpy(fa, &(file->fa), sizeof(H5FD_hdfs_fapl_t)); + H5MM_memcpy(fa, &(file->fa), sizeof(H5FD_hdfs_fapl_t)); ret_value = fa; @@ -747,7 +747,7 @@ H5FD__hdfs_fapl_copy(const void *_old_fa) if (new_fa == NULL) HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "memory allocation failed") - HDmemcpy(new_fa, old_fa, sizeof(H5FD_hdfs_fapl_t)); + H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_hdfs_fapl_t)); ret_value = new_fa; done: @@ -904,7 +904,7 @@ H5FD__hdfs_open(const char *path, unsigned flags, hid_t fapl_id, haddr_t maxaddr if (file == NULL) HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "unable to allocate file struct") file->hdfs_handle = handle; - HDmemcpy(&(file->fa), &fa, sizeof(H5FD_hdfs_fapl_t)); + H5MM_memcpy(&(file->fa), &fa, sizeof(H5FD_hdfs_fapl_t)); #if HDFS_STATS if (FAIL == hdfs__reset_stats(file)) diff --git a/src/H5FDhdfs.h b/src/H5FDhdfs.h index 9d14e9a..abe7682 100644 --- a/src/H5FDhdfs.h +++ b/src/H5FDhdfs.h @@ -25,7 +25,7 @@ #ifdef H5_HAVE_LIBHDFS #define H5FD_HDFS (H5FD_hdfs_init()) #else /* H5_HAVE_LIBHDFS */ -#define H5FD_HDFS (-1) +#define H5FD_HDFS (H5I_INVALID_HID) #endif /* H5_HAVE_LIBHDFS */ #ifdef H5_HAVE_LIBHDFS diff --git a/src/H5FDmirror.c b/src/H5FDmirror.c index 3895b42..7ea9609 100644 --- a/src/H5FDmirror.c +++ b/src/H5FDmirror.c @@ -242,7 +242,7 @@ H5FD_mirror_init(void) { hid_t ret_value = H5I_INVALID_HID; - FUNC_ENTER_NOAPI(FAIL) + FUNC_ENTER_NOAPI(H5I_INVALID_HID) LOG_OP_CALL(FUNC); @@ -298,7 +298,7 @@ H5FD__mirror_xmit_decode_uint16(uint16_t *out, const unsigned char *_buf) HDassert(_buf && out); - HDmemcpy(&n, _buf, sizeof(n)); + H5MM_memcpy(&n, _buf, sizeof(n)); *out = (uint16_t)HDntohs(n); return 2; /* number of bytes eaten */ @@ -326,7 +326,7 @@ H5FD__mirror_xmit_decode_uint32(uint32_t *out, const unsigned char *_buf) HDassert(_buf && out); - HDmemcpy(&n, _buf, sizeof(n)); + H5MM_memcpy(&n, _buf, sizeof(n)); *out = (uint32_t)HDntohl(n); return 4; /* number of bytes eaten */ @@ -385,7 +385,7 @@ H5FD__mirror_xmit_decode_uint64(uint64_t *out, const unsigned char *_buf) HDassert(_buf && out); - HDmemcpy(&n, _buf, sizeof(n)); + H5MM_memcpy(&n, _buf, sizeof(n)); if (TRUE == is_host_little_endian()) *out = BSWAP_64(n); else @@ -412,7 +412,7 @@ H5FD__mirror_xmit_decode_uint8(uint8_t *out, const unsigned char *_buf) HDassert(_buf && out); - HDmemcpy(out, _buf, sizeof(uint8_t)); + H5MM_memcpy(out, _buf, sizeof(uint8_t)); return 1; /* number of bytes eaten */ } /* end H5FD__mirror_xmit_decode_uint8() */ @@ -439,7 +439,7 @@ H5FD__mirror_xmit_encode_uint16(unsigned char *_dest, uint16_t v) HDassert(_dest); n = (uint16_t)HDhtons(v); - HDmemcpy(_dest, &n, sizeof(n)); + H5MM_memcpy(_dest, &n, sizeof(n)); return 2; } /* end H5FD__mirror_xmit_encode_uint16() */ @@ -466,7 +466,7 @@ H5FD__mirror_xmit_encode_uint32(unsigned char *_dest, uint32_t v) HDassert(_dest); n = (uint32_t)HDhtonl(v); - HDmemcpy(_dest, &n, sizeof(n)); + H5MM_memcpy(_dest, &n, sizeof(n)); return 4; } /* end H5FD__mirror_xmit_encode_uint32() */ @@ -494,7 +494,7 @@ H5FD__mirror_xmit_encode_uint64(unsigned char *_dest, uint64_t v) if (TRUE == is_host_little_endian()) n = BSWAP_64(v); - HDmemcpy(_dest, &n, sizeof(n)); + H5MM_memcpy(_dest, &n, sizeof(n)); return 8; } /* H5FD__mirror_xmit_encode_uint64() */ @@ -519,7 +519,7 @@ H5FD__mirror_xmit_encode_uint8(unsigned char *dest, uint8_t v) HDassert(dest); - HDmemcpy(dest, &v, sizeof(v)); + H5MM_memcpy(dest, &v, sizeof(v)); return 1; } /* end H5FD__mirror_xmit_encode_uint8() */ @@ -1188,7 +1188,7 @@ H5FD__mirror_fapl_get(H5FD_t *_file) if (NULL == fa) HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "calloc failed"); - HDmemcpy(fa, &(file->fa), sizeof(H5FD_mirror_fapl_t)); + H5MM_memcpy(fa, &(file->fa), sizeof(H5FD_mirror_fapl_t)); ret_value = fa; @@ -1224,7 +1224,7 @@ H5FD__mirror_fapl_copy(const void *_old_fa) if (new_fa == NULL) HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "memory allocation failed"); - HDmemcpy(new_fa, old_fa, sizeof(H5FD_mirror_fapl_t)); + H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_mirror_fapl_t)); ret_value = new_fa; done: @@ -1298,7 +1298,7 @@ H5Pget_fapl_mirror(hid_t fapl_id, H5FD_mirror_fapl_t *fa_out) HDassert(fa->magic == H5FD_MIRROR_FAPL_MAGIC); /* sanity check */ - HDmemcpy(fa_out, fa, sizeof(H5FD_mirror_fapl_t)); + H5MM_memcpy(fa_out, fa, sizeof(H5FD_mirror_fapl_t)); done: FUNC_LEAVE_API(ret_value); diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index 6042776..c16e01e 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -1746,33 +1746,4 @@ H5FD__mpio_communicator(const H5FD_t *_file) FUNC_LEAVE_NOAPI(file->comm) } /* end H5FD__mpio_communicator() */ -/*------------------------------------------------------------------------- - * Function: H5FD__mpio_get_info - * - * Purpose: Returns the file info of MPIO file driver. - * - * Returns: Non-negative if succeed or negative if fails. - * - * Programmer: John Mainzer - * April 4, 2017 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD__mpio_get_info(H5FD_t *_file, void **mpi_info) -{ - H5FD_mpio_t *file = (H5FD_mpio_t *)_file; - herr_t ret_value = SUCCEED; - - FUNC_ENTER_STATIC - - if (!mpi_info) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "mpi info not valid") - - *mpi_info = &(file->info); - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* H5FD__mpio_get_info() */ - #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5FDmpio.h b/src/H5FDmpio.h index c9280c7..0773d9e 100644 --- a/src/H5FDmpio.h +++ b/src/H5FDmpio.h @@ -25,7 +25,7 @@ #ifdef H5_HAVE_PARALLEL #define H5FD_MPIO (H5FD_mpio_init()) #else -#define H5FD_MPIO (-1) +#define H5FD_MPIO (H5I_INVALID_HID) #endif /* H5_HAVE_PARALLEL */ #ifdef H5_HAVE_PARALLEL diff --git a/src/H5FDros3.c b/src/H5FDros3.c index fa41b6f..a557f1d 100644 --- a/src/H5FDros3.c +++ b/src/H5FDros3.c @@ -320,7 +320,7 @@ H5FD_ros3_init(void) unsigned int bin_i; #endif - FUNC_ENTER_NOAPI(FAIL) + FUNC_ENTER_NOAPI(H5I_INVALID_HID) #if ROS3_DEBUG HDfprintf(stdout, "H5FD_ros3_init() called.\n"); @@ -340,7 +340,6 @@ H5FD_ros3_init(void) } #endif - /* Set return value */ ret_value = H5FD_ROS3_g; done: @@ -501,7 +500,7 @@ H5Pget_fapl_ros3(hid_t fapl_id, H5FD_ros3_fapl_t *fa_out) HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "bad VFL driver info") /* Copy the ros3 fapl data out */ - HDmemcpy(fa_out, fa, sizeof(H5FD_ros3_fapl_t)); + H5MM_memcpy(fa_out, fa, sizeof(H5FD_ros3_fapl_t)); done: FUNC_LEAVE_API(ret_value) @@ -536,7 +535,7 @@ H5FD__ros3_fapl_get(H5FD_t *_file) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy the fields of the structure */ - HDmemcpy(fa, &(file->fa), sizeof(H5FD_ros3_fapl_t)); + H5MM_memcpy(fa, &(file->fa), sizeof(H5FD_ros3_fapl_t)); /* Set return value */ ret_value = fa; @@ -576,7 +575,7 @@ H5FD__ros3_fapl_copy(const void *_old_fa) if (new_fa == NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); - HDmemcpy(new_fa, old_fa, sizeof(H5FD_ros3_fapl_t)); + H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_ros3_fapl_t)); ret_value = new_fa; done: @@ -769,7 +768,7 @@ H5FD__ros3_open(const char *url, unsigned flags, hid_t fapl_id, haddr_t maxaddr) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "unable to allocate file struct") file->s3r_handle = handle; - HDmemcpy(&(file->fa), &fa, sizeof(H5FD_ros3_fapl_t)); + H5MM_memcpy(&(file->fa), &fa, sizeof(H5FD_ros3_fapl_t)); #if ROS3_STATS if (FAIL == ros3_reset_stats(file)) diff --git a/src/H5FDs3comms.c b/src/H5FDs3comms.c index 92921ad..ac58f67 100644 --- a/src/H5FDs3comms.c +++ b/src/H5FDs3comms.c @@ -144,7 +144,7 @@ curlwritecallback(char *ptr, size_t size, size_t nmemb, void *userdata) return written; if (size > 0) { - HDmemcpy(&(sds->data[sds->size]), ptr, product); + H5MM_memcpy(&(sds->data[sds->size]), ptr, product); sds->size += product; written = product; } @@ -263,12 +263,12 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value) namecpy = (char *)H5MM_malloc(sizeof(char) * (namelen + 1)); if (namecpy == NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "cannot make space for name copy."); - HDmemcpy(namecpy, name, (namelen + 1)); + H5MM_memcpy(namecpy, name, (namelen + 1)); valuecpy = (char *)H5MM_malloc(sizeof(char) * (valuelen + 1)); if (valuecpy == NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "cannot make space for value copy."); - HDmemcpy(valuecpy, value, (valuelen + 1)); + H5MM_memcpy(valuecpy, value, (valuelen + 1)); nvcat = (char *)H5MM_malloc(sizeof(char) * catwrite); if (nvcat == NULL) @@ -701,14 +701,14 @@ H5FD_s3comms_hrb_init_request(const char *_verb, const char *_resource, const ch res = (char *)H5MM_malloc(sizeof(char) * (reslen + 1)); if (res == NULL) HGOTO_ERROR(H5E_ARGS, H5E_CANTALLOC, NULL, "no space for resource string"); - HDmemcpy(res, _resource, (reslen + 1)); + H5MM_memcpy(res, _resource, (reslen + 1)); } else { res = (char *)H5MM_malloc(sizeof(char) * (reslen + 2)); if (res == NULL) HGOTO_ERROR(H5E_ARGS, H5E_CANTALLOC, NULL, "no space for resource string"); *res = '/'; - HDmemcpy((&res[1]), _resource, (reslen + 1)); + H5MM_memcpy((&res[1]), _resource, (reslen + 1)); HDassert((reslen + 1) == HDstrlen(res)); } /* end if (else resource string not starting with '/') */ @@ -910,7 +910,7 @@ H5FD_s3comms_s3r_getsize(s3r_t *handle) handle->httpverb = (char *)H5MM_malloc(sizeof(char) * 16); if (handle->httpverb == NULL) HGOTO_ERROR(H5E_ARGS, H5E_CANTALLOC, FAIL, "unable to allocate space for S3 request HTTP verb"); - HDmemcpy(handle->httpverb, "HEAD", 5); + H5MM_memcpy(handle->httpverb, "HEAD", 5); headerresponse = (char *)H5MM_malloc(sizeof(char) * CURL_MAX_HTTP_HEADER); if (headerresponse == NULL) @@ -1078,19 +1078,19 @@ H5FD_s3comms_s3r_open(const char *url, const char *region, const char *id, const handle->region = (char *)H5MM_malloc(sizeof(char) * tmplen); if (handle->region == NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "could not malloc space for handle region copy."); - HDmemcpy(handle->region, region, tmplen); + H5MM_memcpy(handle->region, region, tmplen); tmplen = HDstrlen(id) + 1; handle->secret_id = (char *)H5MM_malloc(sizeof(char) * tmplen); if (handle->secret_id == NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "could not malloc space for handle ID copy."); - HDmemcpy(handle->secret_id, id, tmplen); + H5MM_memcpy(handle->secret_id, id, tmplen); tmplen = SHA256_DIGEST_LENGTH; handle->signing_key = (unsigned char *)H5MM_malloc(sizeof(unsigned char) * tmplen); if (handle->signing_key == NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "could not malloc space for handle key copy."); - HDmemcpy(handle->signing_key, signing_key, tmplen); + H5MM_memcpy(handle->signing_key, signing_key, tmplen); } /* if authentication information provided */ /************************ @@ -1138,7 +1138,7 @@ H5FD_s3comms_s3r_open(const char *url, const char *region, const char *id, const *********************/ HDassert(handle->httpverb != NULL); - HDmemcpy(handle->httpverb, "GET", 4); + H5MM_memcpy(handle->httpverb, "GET", 4); ret_value = handle; @@ -2150,7 +2150,7 @@ H5FD_s3comms_nlowercase(char *dest, const char *s, size_t len) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "destination cannot be null."); if (len > 0) { - HDmemcpy(dest, s, len); + H5MM_memcpy(dest, s, len); do { len--; dest[len] = (char)HDtolower((int)dest[len]); @@ -2686,14 +2686,14 @@ H5FD_s3comms_tostringtosign(char *dest, const char *req, const char *now, const if (ret <= 0 || ret >= 127) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "problem adding day and region to string") - HDmemcpy((dest + d), "AWS4-HMAC-SHA256\n", 17); + H5MM_memcpy((dest + d), "AWS4-HMAC-SHA256\n", 17); d = 17; - HDmemcpy((dest + d), now, HDstrlen(now)); + H5MM_memcpy((dest + d), now, HDstrlen(now)); d += HDstrlen(now); dest[d++] = '\n'; - HDmemcpy((dest + d), tmp, HDstrlen(tmp)); + H5MM_memcpy((dest + d), tmp, HDstrlen(tmp)); d += HDstrlen(tmp); dest[d++] = '\n'; @@ -2777,7 +2777,7 @@ H5FD_s3comms_trim(char *dest, char *s, size_t s_len, size_t *n_written) s_len++; /* write output into dest */ - HDmemcpy(dest, s, s_len); + H5MM_memcpy(dest, s, s_len); } } diff --git a/src/H5FDsplitter.c b/src/H5FDsplitter.c index 5ba1a27..6ecafe0 100644 --- a/src/H5FDsplitter.c +++ b/src/H5FDsplitter.c @@ -210,7 +210,7 @@ H5FD_splitter_init(void) { hid_t ret_value = H5I_INVALID_HID; - FUNC_ENTER_NOAPI(FAIL) + FUNC_ENTER_NOAPI(H5I_INVALID_HID) H5FD_SPLITTER_LOG_CALL(FUNC); @@ -585,7 +585,7 @@ H5FD__splitter_fapl_copy(const void *_old_fa) if (NULL == new_fa_ptr) HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, NULL, "unable to allocate log file FAPL") - HDmemcpy(new_fa_ptr, old_fa_ptr, sizeof(H5FD_splitter_fapl_t)); + H5MM_memcpy(new_fa_ptr, old_fa_ptr, sizeof(H5FD_splitter_fapl_t)); HDstrncpy(new_fa_ptr->wo_path, old_fa_ptr->wo_path, H5FD_SPLITTER_PATH_MAX); HDstrncpy(new_fa_ptr->log_file_path, old_fa_ptr->log_file_path, H5FD_SPLITTER_PATH_MAX); @@ -1300,14 +1300,14 @@ H5FD__splitter_log_error(const H5FD_splitter_t *file, const char *atfunc, const char * s; size = HDstrlen(atfunc) + HDstrlen(msg) + 3; /* ':', ' ', '\n' */ - s = (char *)HDmalloc(sizeof(char) * (size + 1)); + s = (char *)H5MM_malloc(sizeof(char) * (size + 1)); if (NULL == s) ret_value = FAIL; else if (size < (size_t)HDsnprintf(s, size + 1, "%s: %s\n", atfunc, msg)) ret_value = FAIL; else if (size != HDfwrite(s, 1, size, file->logfp)) ret_value = FAIL; - HDfree(s); + H5MM_free(s); } FUNC_LEAVE_NOAPI(ret_value) diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h index 953b4da..d57926f 100644 --- a/src/H5Fmodule.h +++ b/src/H5Fmodule.h @@ -29,4 +29,17 @@ #define H5_MY_PKG_ERR H5E_FILE #define H5_MY_PKG_INIT YES +/** + * \defgroup H5F H5F + * \brief File Interface + * \todo Describe concisely what the functions in this module are about. + * + * \defgroup MDC Metadata Cache + * \ingroup H5F + * \defgroup PH5F Parallel + * \ingroup H5F + * \defgroup SWMR Single Writer Multiple Readers + * \ingroup H5F + */ + #endif /* _H5Fmodule_H */ diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h index b84cff6..be8eced 100644 --- a/src/H5Fpublic.h +++ b/src/H5Fpublic.h @@ -47,24 +47,20 @@ * We're assuming that these constants are used rather early in the hdf5 * session. */ -#define H5F_ACC_RDONLY (H5CHECK H5OPEN 0x0000u) /*absence of rdwr => rd-only */ -#define H5F_ACC_RDWR (H5CHECK H5OPEN 0x0001u) /*open for read and write */ -#define H5F_ACC_TRUNC (H5CHECK H5OPEN 0x0002u) /*overwrite existing files */ -#define H5F_ACC_EXCL (H5CHECK H5OPEN 0x0004u) /*fail if file already exists*/ +#define H5F_ACC_RDONLY (H5CHECK H5OPEN 0x0000u) /**< absence of rdwr => rd-only */ +#define H5F_ACC_RDWR (H5CHECK H5OPEN 0x0001u) /**< open for read and write */ +#define H5F_ACC_TRUNC (H5CHECK H5OPEN 0x0002u) /**< overwrite existing files */ +#define H5F_ACC_EXCL (H5CHECK H5OPEN 0x0004u) /**< fail if file already exists*/ /* NOTE: 0x0008u was H5F_ACC_DEBUG, now deprecated */ -#define H5F_ACC_CREAT (H5CHECK H5OPEN 0x0010u) /*create non-existing files */ +#define H5F_ACC_CREAT (H5CHECK H5OPEN 0x0010u) /**< create non-existing files */ #define H5F_ACC_SWMR_WRITE \ - (H5CHECK 0x0020u) /*indicate that this file is \ - * open for writing in a \ - * single-writer/multi-reader (SWMR) \ - * scenario. Note that the \ - * process(es) opening the file \ - * for reading must open the file \ - * with RDONLY access, and use \ - * the special "SWMR_READ" access \ - * flag. */ + (H5CHECK 0x0020u) /**< indicate that this file is open for writing in a \ + single-writer/multi-reader (SWMR) scenario. \ + Note that the process(es) opening the file for reading must \ + open the file with RDONLY access, and use the special "SWMR_READ" \ + access flag. */ #define H5F_ACC_SWMR_READ \ - (H5CHECK 0x0040u) /*indicate that this file is \ + (H5CHECK 0x0040u) /**< indicate that this file is \ * open for reading in a \ * single-writer/multi-reader (SWMR) \ * scenario. Note that the \ @@ -73,19 +69,23 @@ * open the file with the RDONLY \ * flag. */ -/* Value passed to H5Pset_elink_acc_flags to cause flags to be taken from the - * parent file. */ -#define H5F_ACC_DEFAULT (H5CHECK H5OPEN 0xffffu) /*ignore setting on lapl */ +/** + * Default property list identifier + * + * \internal Value passed to H5Pset_elink_acc_flags to cause flags to be taken from the parent file. + * \internal ignore setting on lapl + */ +#define H5F_ACC_DEFAULT (H5CHECK H5OPEN 0xffffu) /* Flags for H5Fget_obj_count() & H5Fget_obj_ids() calls */ -#define H5F_OBJ_FILE (0x0001u) /* File objects */ -#define H5F_OBJ_DATASET (0x0002u) /* Dataset objects */ -#define H5F_OBJ_GROUP (0x0004u) /* Group objects */ -#define H5F_OBJ_DATATYPE (0x0008u) /* Named datatype objects */ -#define H5F_OBJ_ATTR (0x0010u) /* Attribute objects */ +#define H5F_OBJ_FILE (0x0001u) /**< File objects */ +#define H5F_OBJ_DATASET (0x0002u) /**< Dataset objects */ +#define H5F_OBJ_GROUP (0x0004u) /**< Group objects */ +#define H5F_OBJ_DATATYPE (0x0008u) /**< Named datatype objects */ +#define H5F_OBJ_ATTR (0x0010u) /**< Attribute objects */ #define H5F_OBJ_ALL (H5F_OBJ_FILE | H5F_OBJ_DATASET | H5F_OBJ_GROUP | H5F_OBJ_DATATYPE | H5F_OBJ_ATTR) -#define H5F_OBJ_LOCAL (0x0020u) /* Restrict search to objects opened through current file ID */ -/* (as opposed to objects opened through any file ID accessing this file) */ +#define H5F_OBJ_LOCAL (0x0020u) /**< Restrict search to objects opened through current file ID + (as opposed to objects opened through any file ID accessing this file) */ #define H5F_FAMILY_DEFAULT (hsize_t)0 @@ -99,128 +99,147 @@ #define H5F_MPIO_DEBUG_KEY "H5F_mpio_debug_key" #endif /* H5_HAVE_PARALLEL */ -/* The difference between a single file and a set of mounted files */ +/** + * The difference between a single file and a set of mounted files + */ typedef enum H5F_scope_t { - H5F_SCOPE_LOCAL = 0, /*specified file handle only */ - H5F_SCOPE_GLOBAL = 1 /*entire virtual file */ + H5F_SCOPE_LOCAL = 0, /**< specified file handle only */ + H5F_SCOPE_GLOBAL = 1 /**< entire virtual file */ } H5F_scope_t; -/* Unlimited file size for H5Pset_external() */ +/** + * Unlimited file size for H5Pset_external() + */ #define H5F_UNLIMITED ((hsize_t)(-1L)) -/* How does file close behave? - * H5F_CLOSE_DEFAULT - Use the degree pre-defined by underlining VFL - * H5F_CLOSE_WEAK - file closes only after all opened objects are closed - * H5F_CLOSE_SEMI - if no opened objects, file is close; otherwise, file - close fails - * H5F_CLOSE_STRONG - if there are opened objects, close them first, then - close file +/** + * How does file close behave? */ typedef enum H5F_close_degree_t { - H5F_CLOSE_DEFAULT = 0, - H5F_CLOSE_WEAK = 1, - H5F_CLOSE_SEMI = 2, - H5F_CLOSE_STRONG = 3 + H5F_CLOSE_DEFAULT = 0, /**< Use the degree pre-defined by underlining VFL */ + H5F_CLOSE_WEAK = 1, /**< File closes only after all opened objects are closed */ + H5F_CLOSE_SEMI = 2, /**< If no opened objects, file is close; otherwise, file close fails */ + H5F_CLOSE_STRONG = 3 /**< If there are opened objects, close them first, then close file */ } H5F_close_degree_t; -/* Current "global" information about file */ +/** + * Current "global" information about file + */ +//! [H5F_info2_t_snip] typedef struct H5F_info2_t { struct { - unsigned version; /* Superblock version # */ - hsize_t super_size; /* Superblock size */ - hsize_t super_ext_size; /* Superblock extension size */ + unsigned version; /**< Superblock version # */ + hsize_t super_size; /**< Superblock size */ + hsize_t super_ext_size; /**< Superblock extension size */ } super; struct { - unsigned version; /* Version # of file free space management */ - hsize_t meta_size; /* Free space manager metadata size */ - hsize_t tot_space; /* Amount of free space in the file */ + unsigned version; /**< Version # of file free space management */ + hsize_t meta_size; /**< Free space manager metadata size */ + hsize_t tot_space; /**< Amount of free space in the file */ } free; struct { - unsigned version; /* Version # of shared object header info */ - hsize_t hdr_size; /* Shared object header message header size */ - H5_ih_info_t msgs_info; /* Shared object header message index & heap size */ + unsigned version; /**< Version # of shared object header info */ + hsize_t hdr_size; /**< Shared object header message header size */ + H5_ih_info_t msgs_info; /**< Shared object header message index & heap size */ } sohm; } H5F_info2_t; +//! [H5F_info2_t_snip] -/* - * Types of allocation requests. The values larger than H5FD_MEM_DEFAULT +/** + * Types of allocation requests. The values larger than #H5FD_MEM_DEFAULT * should not change other than adding new types to the end. These numbers * might appear in files. * - * Note: please change the log VFD flavors array if you change this - * enumeration. + * \internal Please change the log VFD flavors array if you change this + * enumeration. */ typedef enum H5F_mem_t { - H5FD_MEM_NOLIST = -1, /* Data should not appear in the free list. + H5FD_MEM_NOLIST = -1, /**< Data should not appear in the free list. * Must be negative. */ - H5FD_MEM_DEFAULT = 0, /* Value not yet set. Can also be the + H5FD_MEM_DEFAULT = 0, /**< Value not yet set. Can also be the * datatype set in a larger allocation * that will be suballocated by the library. * Must be zero. */ - H5FD_MEM_SUPER = 1, /* Superblock data */ - H5FD_MEM_BTREE = 2, /* B-tree data */ - H5FD_MEM_DRAW = 3, /* Raw data (content of datasets, etc.) */ - H5FD_MEM_GHEAP = 4, /* Global heap data */ - H5FD_MEM_LHEAP = 5, /* Local heap data */ - H5FD_MEM_OHDR = 6, /* Object header data */ - - H5FD_MEM_NTYPES /* Sentinel value - must be last */ + H5FD_MEM_SUPER = 1, /**< Superblock data */ + H5FD_MEM_BTREE = 2, /**< B-tree data */ + H5FD_MEM_DRAW = 3, /**< Raw data (content of datasets, etc.) */ + H5FD_MEM_GHEAP = 4, /**< Global heap data */ + H5FD_MEM_LHEAP = 5, /**< Local heap data */ + H5FD_MEM_OHDR = 6, /**< Object header data */ + + H5FD_MEM_NTYPES /**< Sentinel value - must be last */ } H5F_mem_t; -/* Free space section information */ +/** + * Free space section information + */ +//! [H5F_sect_info_t_snip] typedef struct H5F_sect_info_t { - haddr_t addr; /* Address of free space section */ - hsize_t size; /* Size of free space section */ + haddr_t addr; /**< Address of free space section */ + hsize_t size; /**< Size of free space section */ } H5F_sect_info_t; +//! [H5F_sect_info_t_snip] -/* Library's format versions */ +/** + * Library's format versions + */ typedef enum H5F_libver_t { H5F_LIBVER_ERROR = -1, - H5F_LIBVER_EARLIEST = 0, /* Use the earliest possible format for storing objects */ - H5F_LIBVER_V18 = 1, /* Use the latest v18 format for storing objects */ - H5F_LIBVER_V110 = 2, /* Use the latest v110 format for storing objects */ - H5F_LIBVER_V112 = 3, /* Use the latest v112 format for storing objects */ - H5F_LIBVER_V114 = 4, /* Use the latest v114 format for storing objects */ + H5F_LIBVER_EARLIEST = 0, /**< Use the earliest possible format for storing objects */ + H5F_LIBVER_V18 = 1, /**< Use the latest v18 format for storing objects */ + H5F_LIBVER_V110 = 2, /**< Use the latest v110 format for storing objects */ + H5F_LIBVER_V112 = 3, /**< Use the latest v112 format for storing objects */ + H5F_LIBVER_V114 = 4, /**< Use the latest v114 format for storing objects */ H5F_LIBVER_NBOUNDS } H5F_libver_t; #define H5F_LIBVER_LATEST H5F_LIBVER_V114 -/* File space handling strategy */ +/** + * File space handling strategy + */ typedef enum H5F_fspace_strategy_t { H5F_FSPACE_STRATEGY_FSM_AGGR = - 0, /* Mechanisms: free-space managers, aggregators, and virtual file drivers */ - /* This is the library default when not set */ + 0, /**< Mechanisms: free-space managers, aggregators, and virtual file drivers + This is the library default when not set */ H5F_FSPACE_STRATEGY_PAGE = - 1, /* Mechanisms: free-space managers with embedded paged aggregation and virtual file drivers */ - H5F_FSPACE_STRATEGY_AGGR = 2, /* Mechanisms: aggregators and virtual file drivers */ - H5F_FSPACE_STRATEGY_NONE = 3, /* Mechanisms: virtual file drivers */ - H5F_FSPACE_STRATEGY_NTYPES /* must be last */ + 1, /**< Mechanisms: free-space managers with embedded paged aggregation and virtual file drivers */ + H5F_FSPACE_STRATEGY_AGGR = 2, /**< Mechanisms: aggregators and virtual file drivers */ + H5F_FSPACE_STRATEGY_NONE = 3, /**< Mechanisms: virtual file drivers */ + H5F_FSPACE_STRATEGY_NTYPES /**< Sentinel */ } H5F_fspace_strategy_t; -/* Deprecated: File space handling strategy for release 1.10.0 */ -/* They are mapped to H5F_fspace_strategy_t as defined above from release 1.10.1 onwards */ +/** + * File space handling strategy for release 1.10.0 + * + * \deprecated 1.10.1 + */ typedef enum H5F_file_space_type_t { - H5F_FILE_SPACE_DEFAULT = 0, /* Default (or current) free space strategy setting */ - H5F_FILE_SPACE_ALL_PERSIST = 1, /* Persistent free space managers, aggregators, virtual file driver */ - H5F_FILE_SPACE_ALL = 2, /* Non-persistent free space managers, aggregators, virtual file driver */ - /* This is the library default */ - H5F_FILE_SPACE_AGGR_VFD = 3, /* Aggregators, Virtual file driver */ - H5F_FILE_SPACE_VFD = 4, /* Virtual file driver */ - H5F_FILE_SPACE_NTYPES /* must be last */ + H5F_FILE_SPACE_DEFAULT = 0, /**< Default (or current) free space strategy setting */ + H5F_FILE_SPACE_ALL_PERSIST = 1, /**< Persistent free space managers, aggregators, virtual file driver */ + H5F_FILE_SPACE_ALL = 2, /**< Non-persistent free space managers, aggregators, virtual file driver + This is the library default */ + H5F_FILE_SPACE_AGGR_VFD = 3, /**< Aggregators, Virtual file driver */ + H5F_FILE_SPACE_VFD = 4, /**< Virtual file driver */ + H5F_FILE_SPACE_NTYPES /**< Sentinel */ } H5F_file_space_type_t; -/* Data structure to report the collection of read retries for metadata items with checksum */ -/* Used by public routine H5Fget_metadata_read_retry_info() */ #define H5F_NUM_METADATA_READ_RETRY_TYPES 21 + +/** + * Data structure to report the collection of read retries for metadata items with checksum as + * used by H5Fget_metadata_read_retry_info() + */ typedef struct H5F_retry_info_t { unsigned nbins; uint32_t *retries[H5F_NUM_METADATA_READ_RETRY_TYPES]; } H5F_retry_info_t; -/* Callback for H5Pset_object_flush_cb() in a file access property list */ +/** + * Callback for H5Pset_object_flush_cb() in a file access property list + */ typedef herr_t (*H5F_flush_cb_t)(hid_t object_id, void *udata); /*********************/ @@ -230,56 +249,1073 @@ typedef herr_t (*H5F_flush_cb_t)(hid_t object_id, void *udata); extern "C" { #endif +/** + * \ingroup H5F + * + * \brief Checks if a file can be opened with a given file access property + * list + * + * \param[in] container_name Name of a file + * \fapl_id + * + * \return \htri_t + * + * \details H5Fis_accessible() checks if the file specified by \p + * container_name can be opened with the file access property list + * \p fapl_id. + * + * \note The H5Fis_accessible() function enables files to be checked with a + * given file access property list, unlike H5Fis_hdf5(), which only uses + * the default file driver when opening a file. + * + * \since 1.12.0 + * + */ H5_DLL htri_t H5Fis_accessible(const char *container_name, hid_t fapl_id); -H5_DLL hid_t H5Fcreate(const char *filename, unsigned flags, hid_t create_plist, hid_t access_plist); -H5_DLL hid_t H5Fopen(const char *filename, unsigned flags, hid_t access_plist); +/** + * \example H5Fcreate.c + * After creating an HDF5 file with H5Fcreate(), we close it with + * H5Fclose(). + */ +/** + * \ingroup H5F + * + * \brief Creates an HDF5 file + * + * \param[in] filename Name of the file to create + * \param[in] flags File access flags. Allowable values are: + * - #H5F_ACC_TRUNC: Truncate file, if it already exists, + * erasing all data previously stored in the file + * - #H5F_ACC_EXCL: Fail if file already exists + * \fcpl_id + * \fapl_id + * \return \hid_t{file} + * + * \details H5Fcreate() is the primary function for creating HDF5 files; it + * creates a new HDF5 file with the specified name and property lists. + * + * The \p filename parameter specifies the name of the new file. + * + * The \p flags parameter specifies whether an existing file is to be + * overwritten. It should be set to either #H5F_ACC_TRUNC to overwrite + * an existing file or #H5F_ACC_EXCL, instructing the function to fail + * if the file already exists. + * + * New files are always created in read-write mode, so the read-write + * and read-only flags, #H5F_ACC_RDWR and #H5F_ACC_RDONLY, + * respectively, are not relevant in this function. Further note that + * a specification of #H5F_ACC_RDONLY will be ignored; the file will + * be created in read-write mode, regardless. + * + * More complex behaviors of file creation and access are controlled + * through the file creation and file access property lists, + * \p fcpl_id and \p fapl_id, respectively. The value of #H5P_DEFAULT + * for any property list value indicates that the library should use + * the default values for that appropriate property list. + * + * The return value is a file identifier for the newly-created file; + * this file identifier should be closed by calling H5Fclose() when + * it is no longer needed. + * + * \include H5Fcreate.c + * + * \note #H5F_ACC_TRUNC and #H5F_ACC_EXCL are mutually exclusive; use + * exactly one. + * + * \note An additional flag, #H5F_ACC_DEBUG, prints debug information. This + * flag can be combined with one of the above values using the bit-wise + * OR operator (\c |), but it is used only by HDF5 library developers; + * \Emph{it is neither tested nor supported for use in applications}. + * + * \attention \Bold{Special case — File creation in the case of an already-open file:} + * If a file being created is already opened, by either a previous + * H5Fopen() or H5Fcreate() call, the HDF5 library may or may not + * detect that the open file and the new file are the same physical + * file. (See H5Fopen() regarding the limitations in detecting the + * re-opening of an already-open file.)\n + * If the library detects that the file is already opened, + * H5Fcreate() will return a failure, regardless of the use of + * #H5F_ACC_TRUNC.\n + * If the library does not detect that the file is already opened + * and #H5F_ACC_TRUNC is not used, H5Fcreate() will return a failure + * because the file already exists. Note that this is correct + * behavior.\n + * But if the library does not detect that the file is already + * opened and #H5F_ACC_TRUNC is used, H5Fcreate() will truncate the + * existing file and return a valid file identifier. Such a + * truncation of a currently-opened file will almost certainly + * result in errors. While unlikely, the HDF5 library may not be + * able to detect, and thus report, such errors.\n + * Applications should avoid calling H5Fcreate() with an already + * opened file. + * + * \since 1.0.0 + * + * \see H5Fopen(), H5Fclose() + * + */ +H5_DLL hid_t H5Fcreate(const char *filename, unsigned flags, hid_t fcpl_id, hid_t fapl_id); +/** + * \ingroup H5F + * + * \brief Opens an existing HDF5 file + * + * \param[in] filename Name of the file to be opened + * \param[in] flags File access flags. Allowable values are: + * - #H5F_ACC_RDWR: Allows read and write access to file + * - #H5F_ACC_RDONLY: Allows read-only access to file + * - #H5F_ACC_RDWR \c | #H5F_ACC_SWMR_WRITE: Indicates that + * the file is open for writing in a + * single-writer/multi-writer (SWMR) scenario. + * - #H5F_ACC_RDONLY \c | #H5F_ACC_SWMR_READ: Indicates + * that the file is open for reading in a + * single-writer/multi-reader (SWMR) scenario. + * - An additional flag, #H5F_ACC_DEBUG, prints debug + * information. This flag can be combined with one of the + * above values using the bit-wise OR operator (\c |), but + * it is used only by HDF5 library developers; + * \Emph{it is neither tested nor supported} for use in + * applications. + * \fapl_id + * \return \hid_t{file} + * + * \details H5Fopen() is the primary function for accessing existing HDF5 files. + * This function opens the named file in the specified access mode and + * with the specified access property list. + * + * Note that H5Fopen() does not create a file if it does not already + * exist; see H5Fcreate(). + * + * The \p filename parameter specifies the name of the file to be + * opened. + * + * The \p fapl_id parameter specifies the file access property list. + * Use of #H5P_DEFAULT specifies that default I/O access properties + * are to be used. + * + * The \p flags parameter specifies whether the file will be opened in + * read-write or read-only mode, #H5F_ACC_RDWR or #H5F_ACC_RDONLY, + * respectively. More complex behaviors of file access are controlled + * through the file-access property list. + * + * The return value is a file identifier for the open file; this file + * identifier should be closed by calling H5Fclose() when it is no + * longer needed. + * + * \note #H5F_ACC_RDWR and #H5F_ACC_RDONLY are mutually exclusive; use + * exactly one. + * + * \attention \Bold{Special cases — Multiple opens:} A file can often be opened + * with a new H5Fopen() call without closing an already-open + * identifier established in a previous H5Fopen() or H5Fcreate() + * call. Each such H5Fopen() call will return a unique identifier + * and the file can be accessed through any of these identifiers as + * long as the identifier remains valid. In such multiply-opened + * cases, the open calls must use the same flags argument and the + * file access property lists must use the same file close degree + * property setting (see the external link discussion below and + * H5Pset_fclose_degree()).\n + * In some cases, such as files on a local Unix file system, the + * HDF5 library can detect that a file is multiply opened and will + * maintain coherent access among the file identifiers.\n + * But in many other cases, such as parallel file systems or + * networked file systems, it is not always possible to detect + * multiple opens of the same physical file. In such cases, HDF5 + * will treat the file identifiers as though they are accessing + * different files and will be unable to maintain coherent access. + * Errors are likely to result in these cases. While unlikely, the + * HDF5 library may not be able to detect, and thus report, + * such errors.\n + * It is generally recommended that applications avoid multiple + * opens of the same file. + * + * \attention \Bold{Special restriction on multiple opens of a file first + * opened by means of an external link:} When an external link is + * followed, the external file is always opened with the weak file + * close degree property setting, #H5F_CLOSE_WEAK (see + * H5Lcreate_external() and H5Pset_fclose_degree()). If the file is + * reopened with H5Fopen while it remains held open from such an + * external link call, the file access property list used in the + * open call must include the file close degree setting + * #H5F_CLOSE_WEAK or the open will fail. + * + * \version 1.10.0 The #H5F_ACC_SWMR_WRITE and #H5F_ACC_SWMR_READ flags were added. + * + * \see H5Fclose() + * + */ +H5_DLL hid_t H5Fopen(const char *filename, unsigned flags, hid_t fapl_id); +/** + * \ingroup H5F + * + * \brief Returns a new identifier for a previously-opened HDF5 file + * + * \param[in] file_id Identifier of a file for which an additional identifier + * is required + * + * \return \hid_t{file} + * + * \details H5Freopen() returns a new file identifier for an already-open HDF5 + * file, as specified by \p file_id. Both identifiers share caches and + * other information. The only difference between the identifiers is + * that the new identifier is not mounted anywhere and no files are + * mounted on it. + * + * The new file identifier should be closed by calling H5Fclose() when + * it is no longer needed. + * + * \note Note that there is no circumstance under which H5Freopen() can + * actually open a closed file; the file must already be open and have an + * active \p file_id. E.g., one cannot close a file with H5Fclose() on + * \p file_id then use H5Freopen() on \p file_id to reopen it. + * + */ H5_DLL hid_t H5Freopen(hid_t file_id); +/** + * \ingroup H5F + * + * \brief Flushes all buffers associated with a file to storage + * + * \loc_id{object_id} + * \param[in] scope The scope of the flush action + * + * \return \herr_t + * + * \details H5Fflush() causes all buffers associated with a file to be + * immediately flushed to storage without removing the data from the + * cache. + * + * \p object_id can be any object associated with the file, including + * the file itself, a dataset, a group, an attribute, or a named + * datatype. + * + * \p scope specifies whether the scope of the flush action is + * global or local. Valid values are as follows: + * \scopes + * + * \attention HDF5 does not possess full control over buffering. H5Fflush() + * flushes the internal HDF5 buffers then asks the operating system + * (the OS) to flush the system buffers for the open files. After + * that, the OS is responsible for ensuring that the data is + * actually flushed to disk. + * + */ H5_DLL herr_t H5Fflush(hid_t object_id, H5F_scope_t scope); +/** + * \example H5Fclose.c + * After creating an HDF5 file with H5Fcreate(), we close it with + * H5Fclose(). + */ +/** + * \ingroup H5F + * + * \brief Terminates access to an HDF5 file + * + * \file_id + * \return \herr_t + * + * \details H5Fclose() terminates access to an HDF5 file (specified by + * \p file_id) by flushing all data to storage. + * + * If this is the last file identifier open for the file and no other + * access identifier is open (e.g., a dataset identifier, group + * identifier, or shared datatype identifier), the file will be fully + * closed and access will end. + * + * Use H5Fclose() as shown in the following example: + * \include H5Fclose.c + * + * \note \Bold{Delayed close:} Note the following deviation from the + * above-described behavior. If H5Fclose() is called for a file but one + * or more objects within the file remain open, those objects will remain + * accessible until they are individually closed. Thus, if the dataset + * \c data_sample is open when H5Fclose() is called for the file + * containing it, \c data_sample will remain open and accessible + * (including writable) until it is explicitly closed. The file will be + * automatically closed once all objects in the file have been closed.\n + * Be warned, however, that there are circumstances where it is not + * possible to delay closing a file. For example, an MPI-IO file close is + * a collective call; all of the processes that opened the file must + * close it collectively. The file cannot be closed at some time in the + * future by each process in an independent fashion. Another example is + * that an application using an AFS token-based file access privilege may + * destroy its AFS token after H5Fclose() has returned successfully. This + * would make any future access to the file, or any object within it, + * illegal.\n + * In such situations, applications must close all open objects in a file + * before calling H5Fclose. It is generally recommended to do so in all + * cases. + * + * \see H5Fopen() + * + */ H5_DLL herr_t H5Fclose(hid_t file_id); +/** + * \ingroup H5F + * + * \brief Deletes an HDF5 file + * + * \param[in] filename Name of the file to delete + * \fapl_id + * + * \return \herr_t + * + * \details H5Fdelete() deletes an HDF5 file \p filename with a file access + * property list \p fapl_id. The \p fapl_id should be configured with + * the same VOL connector or VFD that was used to open the file. + * + * This API was introduced for use with the Virtual Object Layer + * (VOL). With the VOL, HDF5 "files" can map to arbitrary storage + * schemes such as object stores and relational database tables. The + * data created by these implementations may be inconvenient for a + * user to remove without a detailed knowledge of the storage scheme. + * H5Fdelete() gives VOL connector authors the ability to add + * connector-specific delete code to their connectors so that users + * can remove these "files" without detailed knowledge of the storage + * scheme. + * + * For a VOL connector, H5Fdelete() deletes the file in a way that + * makes sense for the specified VOL connector. + * + * For the native HDF5 connector, HDF5 files will be deleted via the + * VFDs, each of which will have to be modified to delete the files it + * creates. + * + * For all implementations, H5Fdelete() will first check if the file + * is an HDF5 file via H5Fis_accessible(). This is done to ensure that + * H5Fdelete() cannot be used as an arbitrary file deletion call. + * + * \since 1.12.0 + * + */ H5_DLL herr_t H5Fdelete(const char *filename, hid_t fapl_id); +/** + * \ingroup H5F + * + * \brief Returns a file creation property list identifier + * + * \file_id + * \return \hid_t{file creation property list} + * + * \details H5Fget_create_plist() returns the file creation property list + * identifier identifying the creation properties used to create this + * file. This function is useful for duplicating properties when + * creating another file. + * + * The creation property list identifier should be released with + * H5Pclose(). + * + */ H5_DLL hid_t H5Fget_create_plist(hid_t file_id); +/** + * \ingroup H5F + * + * \brief Returns a file access property list identifier + * + * \file_id + * \return \hid_t{file access property list} + * + * \details H5Fget_access_plist() returns the file access property list + * identifier of the specified file. + * + */ H5_DLL hid_t H5Fget_access_plist(hid_t file_id); +/** + * \ingroup H5F + * + * \brief Determines the read/write or read-only status of a file + * + * \file_id + * \param[out] intent Access mode flag as originally passed with H5Fopen() + * + * \return \herr_t + * + * \details Given the identifier of an open file, \p file_id, H5Fget_intent() + * retrieves the intended access mode" flag passed with H5Fopen() when + * the file was opened. + * + * The value of the flag is returned in \p intent. Valid values are as + * follows: + * \file_access + * + * \note The function will not return an error if intent is NULL; it will + * simply do nothing. + * + * \version 1.10.0 C function enhanced to work with SWMR functionality. + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Fget_intent(hid_t file_id, unsigned *intent); +/** + * \ingroup H5F + * + * \brief Retrieves a file's file number that uniquely identifies an open file + * + * \file_id + * \param[out] fileno A buffer to hold the file number + * + * \return \herr_t + * + * \details H5Fget_fileno() retrieves a file number for a file specified by the + * file identifier \p file_id and the pointer \p fnumber to the file + * number. + * + * \since 1.12.0 + * + */ H5_DLL herr_t H5Fget_fileno(hid_t file_id, unsigned long *fileno); +/** + * \ingroup H5F + * + * \brief Returns the number of open object identifiers for an open file + * + * \file_id or #H5F_OBJ_ALL for all currently-open HDF5 files + * \param[in] types Type of object for which identifiers are to be returned + * + * \return Returns the number of open objects if successful; otherwise returns + * a negative value. + * + * \details Given the identifier of an open file, file_id, and the desired + * object types, types, H5Fget_obj_count() returns the number of open + * object identifiers for the file. + * + * To retrieve a count of open identifiers for open objects in all + * HDF5 application files that are currently open, pass the value + * #H5F_OBJ_ALL in \p file_id. + * + * The types of objects to be counted are specified in types as + * follows: + * \obj_types + * + * Multiple object types can be combined with the + * logical \c OR operator (|). For example, the expression + * \c (#H5F_OBJ_DATASET|#H5F_OBJ_GROUP) would call for datasets and + * groups. + * + * \version 1.6.8, 1.8.2 C function return type changed to \c ssize_t. + * \version 1.6.5 #H5F_OBJ_LOCAL has been added as a qualifier on the types + * of objects to be counted. #H5F_OBJ_LOCAL restricts the + * search to objects opened through current file identifier. + * + */ H5_DLL ssize_t H5Fget_obj_count(hid_t file_id, unsigned types); +/** + *------------------------------------------------------------------------- + * \ingroup H5F + * + * \brief Returns a list of open object identifiers + * + * \file_id or #H5F_OBJ_ALL for all currently-open HDF5 files + * \param[in] types Type of object for which identifiers are to be returned + * \param[in] max_objs Maximum number of object identifiers to place into + * \p obj_id_list + * \param[out] obj_id_list Pointer to the returned buffer of open object + * identifiers + * + * \return Returns number of objects placed into \p obj_id_list if successful; + * otherwise returns a negative value. + * + * \details Given the file identifier \p file_id and the type of objects to be + * identified, types, H5Fget_obj_ids() returns the list of identifiers + * for all open HDF5 objects fitting the specified criteria. + * + * To retrieve identifiers for open objects in all HDF5 application + * files that are currently open, pass the value #H5F_OBJ_ALL in + * \p file_id. + * + * The types of object identifiers to be retrieved are specified in + * types using the codes listed for the same parameter in + * H5Fget_obj_count(). + * + * To retrieve a count of open objects, use the H5Fget_obj_count() + * function. This count can be used to set the \p max_objs parameter. + * + * \version 1.8.2 C function return type changed to \c ssize_t and \p + * max_objs parameter datatype changed to \c size_t. + * \version 1.6.8 C function return type changed to \c ssize_t and \p + * max_objs parameter datatype changed to \c size_t. + * \since 1.6.0 + * + */ H5_DLL ssize_t H5Fget_obj_ids(hid_t file_id, unsigned types, size_t max_objs, hid_t *obj_id_list); +/** + * \ingroup H5F + * + * \brief Returns pointer to the file handle from the virtual file driver + * + * \file_id + * \fapl_id{fapl} + * \param[out] file_handle Pointer to the file handle being used by the + * low-level virtual file driver + * + * \return \herr_t + * + * \details Given the file identifier \p file_id and the file access property + * list \p fapl_id, H5Fget_vfd_handle() returns a pointer to the file + * handle from the low-level file driver currently being used by the + * HDF5 library for file I/O. + * + * \note For most drivers, the value of \p fapl_id will be #H5P_DEFAULT. For + * the \c FAMILY or \c MULTI drivers, this value should be defined + * through the property list functions: H5Pset_family_offset() for the + * \c FAMILY driver and H5Pset_multi_type() for the \c MULTI driver + * + * \since 1.6.0 + * + */ H5_DLL herr_t H5Fget_vfd_handle(hid_t file_id, hid_t fapl, void **file_handle); +/** + * \ingroup H5F + * + * \brief Mounts an HDF5 file + * + * \loc_id{loc} + * \param[in] name Name of the group onto which the file specified by \p child + * is to be mounted + * \file_id{child} + * \param[in] plist File mount property list identifier. Pass #H5P_DEFAULT! + * + * \return \herr_t + * + * \details H5Fmount() mounts the file specified by \p child onto the object + * specified by \p loc and \p name using the mount properties \p plist + * If the object specified by \p loc is a dataset, named datatype or + * attribute, then the file will be mounted at the location where the + * attribute, dataset, or named datatype is attached. + * + * \note To date, no file mount properties have been defined in HDF5. The + * proper value to pass for \p plist is #H5P_DEFAULT, indicating the + * default file mount property list. + * + */ H5_DLL herr_t H5Fmount(hid_t loc, const char *name, hid_t child, hid_t plist); +/** + * \ingroup H5F + * + * \brief Unounts an HDF5 file + * + * \loc_id{loc} + * \param[in] name Name of the mount point + * + * \return \herr_t + * + * \details Given a mount point, H5Funmount() dissociates the mount point's + * file from the file mounted there. This function does not close + * either file. + * + * The mount point can be either the group in the parent or the root + * group of the mounted file (both groups have the same name). If the + * mount point was opened before the mount then it is the group in the + * parent; if it was opened after the mount then it is the root group + * of the child. + * + */ H5_DLL herr_t H5Funmount(hid_t loc, const char *name); +/** + * \ingroup H5F + * + * \brief Returns the amount of free space in a file (in bytes) + * + * \file_id + * + * \return Returns the amount of free space in the file if successful; + * otherwise returns a negative value. + * + * \details Given the identifier of an open file, \p file_id, + * H5Fget_freespace() returns the amount of space that is unused by + * any objects in the file. + * + * The interpretation of this number depends on the configured free space + * management strategy. For example, if the HDF5 library only tracks free + * space in a file from a file open or create until that file is closed, + * then this routine will report the free space that has been created + * during that interval. + * + * \since 1.6.1 + * + */ H5_DLL hssize_t H5Fget_freespace(hid_t file_id); +/** + * \ingroup H5F + * + * \brief Returns the size of an HDF5 file (in bytes) + * + * \file_id + * \param[out] size Size of the file, in bytes + * + * \return \herr_t + * + * \details H5Fget_filesize() returns the size of the HDF5 file specified by + * \p file_id. + * + * The returned size is that of the entire file, as opposed to only + * the HDF5 portion of the file. I.e., size includes the user block, + * if any, the HDF5 portion of the file, and any data that may have + * been appended beyond the data written through the HDF5 library. + * + * \version 1.6.3 Fortran subroutine introduced in this release. + * + * \since 1.6.3 + * + */ H5_DLL herr_t H5Fget_filesize(hid_t file_id, hsize_t *size); +/** + * \ingroup H5F + * + * \brief Retrieves the file's end-of-allocation (EOA) + * + * \file_id + * \param[out] eoa The file's EOA + * + * \return \herr_t + * + * \details H5Fget_eoa() retrieves the file's EOA and returns it in the + * parameter eoa. + * + * \since 1.10.2 + * + */ H5_DLL herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa); +/** + * \ingroup H5F + * + * \brief Sets the file' EOA to the maximum of (EOA, EOF) + increment + * + * \file_id + * \param[in] increment The number of bytes to be added to the maximum of + * (EOA, EOF) + * + * \return \herr_t + * + * \details H5Fincrement_filesize() sets the file's EOA to the maximum of (EOA, + * EOF) + \p increment. The EOA is the end-of-file address stored in + * the file's superblock while EOF is the file's actual end-of-file. + * + * \since 1.10.2 + * + */ H5_DLL herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment); +/** + * \ingroup H5F + * + * \brief Retrieves a copy of the image of an existing, open file + * + * \file_id + * \param[out] buf_ptr Pointer to the buffer into which the image of the + * HDF5 file is to be copied. If \p buf_ptr is NULL, + * no data will be copied but the function’s return value + * will still indicate the buffer size required (or a + * negative value on error). + * \param[out] buf_len Size of the supplied buffer + * + * \return ssize_t + * + * \details H5Fget_file_image() retrieves a copy of the image of an existing, + * open file. This routine can be used with files opened using the + * SEC2 (or POSIX), STDIO, and Core (or Memory) virtual file drivers + * (VFDs). + * + * If the return value of H5Fget_file_image() is a positive value, it + * will be the length in bytes of the buffer required to store the + * file image. So if the file size is unknown, it can be safely + * determined with an initial H5Fget_file_image() call with buf_ptr + * set to NULL. The file image can then be retrieved with a second + * H5Fget_file_image() call with \p buf_len set to the initial call’s + * return value. + * + * While the current file size can also be retrieved with + * H5Fget_filesize(), that call may produce a larger value than is + * needed. The value returned by H5Fget_filesize() includes the user + * block, if it exists, and any unallocated space at the end of the + * file. It is safe in all situations to get the file size with + * H5Fget_file_image() and it often produces a value that is more + * appropriate for the size of a file image buffer. + * + * \note \Bold{Recommended Reading:} This function is part of the file image + * operations feature set. It is highly recommended to study the guide + * "HDF5 File Image Operations" before using this feature set.\n See the + * "See Also" section below for links to other elements of HDF5 file + * image operations. \todo Fix the references. + * + * \attention H5Pget_file_image() will fail, returning a negative value, if the + * file is too large for the supplied buffer. + * + * \see H5LTopen_file_image(), H5Pset_file_image(), H5Pget_file_image(), + * H5Pset_file_image_callbacks(), H5Pget_file_image_callbacks() + * + * \version 1.8.13 Fortran subroutine added in this release. + * + * \since 1.8.0 + * + */ H5_DLL ssize_t H5Fget_file_image(hid_t file_id, void *buf_ptr, size_t buf_len); +/** + * \ingroup MDC + * + * \todo Finish this! + */ H5_DLL herr_t H5Fget_mdc_config(hid_t file_id, H5AC_cache_config_t *config_ptr); +/** + * \ingroup MDC + * + * \todo Finish this! + */ H5_DLL herr_t H5Fset_mdc_config(hid_t file_id, H5AC_cache_config_t *config_ptr); +/** + * \ingroup MDC + * + * \todo Finish this! + */ H5_DLL herr_t H5Fget_mdc_hit_rate(hid_t file_id, double *hit_rate_ptr); +/** + * \ingroup MDC + * + * \todo Finish this! + */ H5_DLL herr_t H5Fget_mdc_size(hid_t file_id, size_t *max_size_ptr, size_t *min_clean_size_ptr, size_t *cur_size_ptr, int *cur_num_entries_ptr); +/** + * \ingroup MDC + * + * \todo Finish this! + */ H5_DLL herr_t H5Freset_mdc_hit_rate_stats(hid_t file_id); +/** + * \ingroup H5F + * + * \brief Retrieves name of file to which object belongs + * + * \obj_id + * \param[out] name Buffer for the file name + * \param[in] size Size, in bytes, of the \p name buffer + * + * \return Returns the length of the file name if successful; otherwise returns + * a negative value. + * + * \details H5Fget_name() retrieves the name of the file to which the object \p + * obj_id belongs. The object can be a file, group, dataset, + * attribute, or named datatype. + * + * Up to \p size characters of the file name are returned in \p name; + * additional characters, if any, are not returned to the user + * application. + * + * If the length of the name, which determines the required value of + * size, is unknown, a preliminary H5Fget_name() call can be made by + * setting \p name to NULL. The return value of this call will be the + * size of the file name; that value plus one (1) can then be assigned + * to size for a second H5Fget_name() call, which will retrieve the + * actual name. (The value passed in with the parameter \p size must + * be one greater than size in bytes of the actual name in order to + * accommodate the null terminator; if \p size is set to the exact + * size of the name, the last byte passed back will contain the null + * terminator and the last character will be missing from the name + * passed back to the calling application.) + * + * If an error occurs, the buffer pointed to by \p name is unchanged + * and the function returns a negative value. + * + * \since 1.6.3 + * + */ H5_DLL ssize_t H5Fget_name(hid_t obj_id, char *name, size_t size); -H5_DLL herr_t H5Fget_info2(hid_t obj_id, H5F_info2_t *finfo); +/** + * \ingroup H5F + * + * \brief Retrieves name of file to which object belongs + * + * \fgdta_obj_id + * \param[out] file_info Buffer for global file information + * + * \return \herr_t + * + * \details H5Fget_info2() returns global information for the file associated + * with the object identifier \p obj_id in the H5F_info2_t \c struct + * named \p file_info. + * + * \p obj_id is an identifier for any object in the file of interest. + * + * H5F_info2_t struct is defined in H5Fpublic.h as follows: + * \snippet this H5F_info2_t_snip + * + * The \c super sub-struct contains the following information: + * \li \c vers is the version number of the superblock. + * \li \c super_size is the size of the superblock. + * \li \c super_ext_size is the size of the superblock extension. + * + * The \c free sub-struct contains the following information: + * \li vers is the version number of the free-space manager. + * \li \c hdr_size is the size of the free-space manager header. + * \li \c tot_space is the total amount of free space in the file. + * + * The \c sohm sub-struct contains shared object header message + * information as follows: + * \li \c vers is the version number of the shared object header information. + * \li \c hdr_size is the size of the shared object header message. + * \li \c msgs_info is an H5_ih_info_t struct defined in H5public.h as + * follows: \snippet H5public.h H5_ih_info_t_snip + * \li \p index_size is the summed size of all the shared object + * header indexes. Each index might be either a B-tree or + * a list. + * \li \p heap_size is the size of the heap. + * + * + * \since 1.10.0 + * + */ +H5_DLL herr_t H5Fget_info2(hid_t obj_id, H5F_info2_t *file_info); +/** + * \ingroup SWMR + * + * \todo Finish this! + */ H5_DLL herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info); +/** + * \ingroup SWMR + * + * \todo Finish this! + */ H5_DLL herr_t H5Fstart_swmr_write(hid_t file_id); +/** + * \ingroup H5F + * + * \brief Retrieves free-space section information for a file + * + * \file_id + * \param[in] type The file memory allocation type + * \param[in] nsects The number of free-space sections + * \param[out] sect_info Array of instances of H5F_sect_info_t in which + * the free-space section information is to be returned + * + * \return Returns the number of free-space sections for the specified + * free-space manager in the file; otherwise returns a negative value. + * + * \details H5Fget_free_sections() retrieves free-space section information for + * the free-space manager with type that is associated with file + * \p file_id. If type is #H5FD_MEM_DEFAULT, this routine retrieves + * free-space section information for all the free-space managers in + * the file. + * + * Valid values for \p type are the following: + * \mem_types + * + * H5F_sect_info_t is defined as follows (in H5Fpublic.h): + * \snippet this H5F_sect_info_t_snip + * + * This routine retrieves free-space section information for \p nsects + * sections or at most the maximum number of sections in the specified + * free-space manager. If the number of sections is not known, a + * preliminary H5Fget_free_sections() call can be made by setting \p + * sect_info to NULL and the total number of free-space sections for + * the specified free-space manager will be returned. Users can then + * allocate space for entries in \p sect_info, each of which is + * defined as an H5F_sect_info_t \c struct. + * + * \attention \Bold{Failure Modes:} This routine will fail when the following + * is true: + * \li The library fails to retrieve the file creation property list + * associated with \p file_id. + * \li If the parameter \p sect_info is non-null, but the parameter + * \p nsects is equal to 0. + * \li The library fails to retrieve free-space section information + * for the file. + * + * \since 1.10.0 + * + */ H5_DLL ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type, size_t nsects, H5F_sect_info_t *sect_info /*out*/); +/** + * \ingroup H5F + * + * \brief Clears the external link open file cache + * + * \file_id + * \return \herr_t + * + * \details H5Fclear_elink_file_cache() evicts all the cached child files in + * the specified file’s external file cache, causing them to be closed + * if there is nothing else holding them open. + * + * H5Fclear_elink_file_cache() does not close the cache itself; + * subsequent external link traversals from the parent file will again + * cache the target file. See H5Pset_elink_file_cache_size() for + * information on closing the file cache. + * + * \see H5Pset_elink_file_cache_size(), H5Pget_elink_file_cache_size() + * + * \since 1.8.7 + * + */ H5_DLL herr_t H5Fclear_elink_file_cache(hid_t file_id); +/** + * \ingroup H5F + * + * \brief Enables the switch of version bounds setting for a file + * + * \file_id + * \param[in] low The earliest version of the library that will be used for + * writing objects + * \param[in] high The latest version of the library that will be used for + * writing objects + * + * \return \herr_t + * + * \details H5Fset_libver_bounds() enables the switch of version bounds setting + * for an open file associated with \p file_id. + * + * For the parameters \p low and \p high, see the description for + * H5Pset_libver_bounds(). + * + * \since 1.10.2 + * + */ H5_DLL herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver_t high); +/** + * \ingroup MDC + * + * \todo Finish this! + */ H5_DLL herr_t H5Fstart_mdc_logging(hid_t file_id); +/** + * \ingroup MDC + * + * \todo Finish this! + */ H5_DLL herr_t H5Fstop_mdc_logging(hid_t file_id); +/** + * \ingroup MDC + * + * \todo Finish this! + */ H5_DLL herr_t H5Fget_mdc_logging_status(hid_t file_id, /*OUT*/ hbool_t *is_enabled, /*OUT*/ hbool_t *is_currently_logging); +/** + * \ingroup SWMR + * + * \todo Finish this! + */ H5_DLL herr_t H5Fformat_convert(hid_t fid); +/** + * \ingroup H5F + * + * \brief Resets the page buffer statistics + * + * \file_id + * + * \return \herr_t + * + * \details H5Freset_page_buffering_stats() resets the page buffer statistics + * for a specified file identifier \p file_id. + * + * \since 1.10.1 + * + */ H5_DLL herr_t H5Freset_page_buffering_stats(hid_t file_id); +/** + * \ingroup H5F + * + * \brief Retrieves statistics about page access when it is enabled + * + * \file_id + * \param[out] accesses Two integer array for the number of metadata and raw + * data accesses to the page buffer + * \param[out] hits Two integer array for the number of metadata and raw data + * hits in the page buffer + * \param[out] misses Two integer array for the number of metadata and raw data + * misses in the page buffer + * \param[out] evictions Two integer array for the number of metadata and raw + * data evictions from the page buffer + * \param[out] bypasses Two integer array for the number of metadata and raw + * data accesses that bypass the page buffer + * + * \return \herr_t + * + * \details H5Fget_page_buffering_stats() retrieves page buffering statistics + * such as the number of metadata and raw data accesses (\p accesses), + * hits (\p hits), misses (\p misses), evictions (\p evictions), and + * accesses that bypass the page buffer (\p bypasses). + * + * \since 1.10.1 + * + */ H5_DLL herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2], unsigned hits[2], unsigned misses[2], unsigned evictions[2], unsigned bypasses[2]); +/** + * \ingroup MDC + * + * \todo Finish this! + */ H5_DLL herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t *image_size); +/** + * \ingroup H5F + * + * \brief Retrieves the setting for whether or not a file will create minimized + * dataset object headers + * + * \file_id + * \param[out] minimize Flag indicating whether the library will or will not + * create minimized dataset object headers + * + * \return \herr_t + * + * \details H5Fget_dset_no_attrs_hint() retrieves the no dataset attributes + * hint setting for the file specified by the file identifier \p + * file_id. This setting is used to inform the library to create + * minimized dataset object headers when \c TRUE. + * + * The setting's value is returned in the boolean pointer minimize. + * + * \since 1.10.5 + * + */ H5_DLL herr_t H5Fget_dset_no_attrs_hint(hid_t file_id, hbool_t *minimize); +/** + * \ingroup H5F + * + * \brief Sets the flag to create minimized dataset object headers + * + * \file_id + * \param[in] minimize Flag indicating whether the library will or will not + * create minimized dataset object headers + * + * \return \herr_t + * + * \details H5Fset_dset_no_attrs_hint() sets the no dataset attributes hint + * setting for the file specified by the file identifier \p file_id. + * If the boolean flag \p minimize is set to \c TRUE, then the library + * will create minimized dataset object headers in the file. + * \Bold{All} files that refer to the same file-on-disk will be + * affected by the most recent setting, regardless of the file + * identifier/handle (e.g., as returned by H5Fopen()). By setting the + * \p minimize flag to \c TRUE, the library expects that no attributes + * will be added to the dataset - attributes can be added, but they + * are appended with a continuation message, which can reduce + * performance. + * + * \attention This setting interacts with H5Pset_dset_no_attrs_hint(): if + * either is set to \c TRUE, then the created dataset's object header + * will be minimized. + * + * \since 1.10.5 + * + */ H5_DLL herr_t H5Fset_dset_no_attrs_hint(hid_t file_id, hbool_t minimize); #ifdef H5_HAVE_PARALLEL +/** + * \ingroup PH5F + * + * \todo Finish this! + */ H5_DLL herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag); +/** + * \ingroup PH5F + * + * \todo Finish this! + */ H5_DLL herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag); #endif /* H5_HAVE_PARALLEL */ @@ -294,19 +1330,95 @@ H5_DLL herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag); /* Typedefs */ -/* Current "global" information about file */ +/** + * Current "global" information about file + */ +//! [H5F_info1_t_snip] typedef struct H5F_info1_t { - hsize_t super_ext_size; /* Superblock extension size */ + hsize_t super_ext_size; /**< Superblock extension size */ struct { - hsize_t hdr_size; /* Shared object header message header size */ - H5_ih_info_t msgs_info; /* Shared object header message index & heap size */ + hsize_t hdr_size; /**< Shared object header message header size */ + H5_ih_info_t msgs_info; /**< Shared object header message index & heap size */ } sohm; } H5F_info1_t; +//! [H5F_info1_t_snip] /* Function prototypes */ -H5_DLL herr_t H5Fget_info1(hid_t obj_id, H5F_info1_t *finfo); +/** + * \ingroup H5F + * + * \brief Retrieves name of file to which object belongs + * + * \fgdta_obj_id + * \param[out] file_info Buffer for global file information + * + * \return \herr_t + * + * \deprecated This function has been renamed from H5Fget_info() and is + * deprecated in favor of the macro #H5Fget_info or the function + * H5Fget_info2(). + * + * \details H5Fget_info1() returns global information for the file associated + * with the object identifier \p obj_id in the H5F_info1_t \c struct + * named \p file_info. + * + * \p obj_id is an identifier for any object in the file of interest. + * + * H5F_info1_t struct is defined in H5Fpublic.h as follows: + * \snippet this H5F_info1_t_snip + * + * \c super_ext_size is the size of the superblock extension. + * + * The \c sohm sub-struct contains shared object header message + * information as follows: + * \li \c hdr_size is the size of the shared object header message. + * \li \c msgs_info is an H5_ih_info_t struct defined in H5public.h as + * follows: \snippet H5public.h H5_ih_info_t_snip + * + * \li \p index_size is the summed size of all the shared object + * header indexes. Each index might be either a B-tree or + * a list. + * + * \version 1.10.0 C function H5Fget_info() renamed to H5Fget_info1() and + * deprecated in this release. + * + * \since 1.8.0 + * + */ +H5_DLL herr_t H5Fget_info1(hid_t obj_id, H5F_info1_t *file_info); +/** + * \ingroup H5F + * + * \brief Sets thelatest version of the library to be used for writing objects + * + * \file_id + * \param[in] latest_format Latest format flag + * + * \return \herr_t + * + * \deprecated When? + * + * \todo In which version was this function deprecated? + * + */ H5_DLL herr_t H5Fset_latest_format(hid_t file_id, hbool_t latest_format); -H5_DLL htri_t H5Fis_hdf5(const char *filename); +/** + * \ingroup H5F + * + * \brief Determines whether a file is in the HDF5 format + * + * \param[in] file_name File name + * + * \return \htri_t + * + * \deprecated When? + * + * \details H5Fis_hdf5() determines whether a file is in the HDF5 format. + * + * \todo In which version was this function deprecated? + * + */ +H5_DLL htri_t H5Fis_hdf5(const char *file_name); #endif /* H5_NO_DEPRECATED_SYMBOLS */ diff --git a/src/H5Rint.c b/src/H5Rint.c index 8f3163a..60f8131 100644 --- a/src/H5Rint.c +++ b/src/H5Rint.c @@ -746,8 +746,10 @@ H5R__copy(const H5R_ref_priv_t *src_ref, H5R_ref_priv_t *dst_ref) dst_ref->info.obj.filename = NULL; /* Set location ID and hold reference to it */ - if (H5R__set_loc_id(dst_ref, src_ref->loc_id, TRUE, TRUE) < 0) - HGOTO_ERROR(H5E_REFERENCE, H5E_CANTSET, FAIL, "cannot set reference location ID") + dst_ref->loc_id = src_ref->loc_id; + if (H5I_inc_ref(dst_ref->loc_id, TRUE) < 0) + HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINC, FAIL, "incrementing location ID failed") + dst_ref->app_ref = TRUE; } done: diff --git a/src/H5Tref.c b/src/H5Tref.c index ccb5232..c71724f 100644 --- a/src/H5Tref.c +++ b/src/H5Tref.c @@ -513,7 +513,7 @@ H5T__ref_mem_read(H5VL_object_t H5_ATTR_UNUSED *src_file, const void *src_buf, s /* Memory-to-memory conversion to support vlen conversion */ if (NULL == dst_file) { - HDmemcpy(dst_buf, src_buf, dst_size); + H5MM_memcpy(dst_buf, src_buf, dst_size); HGOTO_DONE(ret_value); } @@ -602,7 +602,7 @@ H5T__ref_mem_write(H5VL_object_t *src_file, const void *src_buf, size_t src_size /* Memory-to-memory conversion to support vlen conversion */ if (NULL == src_file) { - HDmemcpy(dst_buf, src_buf, src_size); + H5MM_memcpy(dst_buf, src_buf, src_size); HGOTO_DONE(ret_value); } diff --git a/src/H5mpi.c b/src/H5mpi.c index c1f9132..613a4bf 100644 --- a/src/H5mpi.c +++ b/src/H5mpi.c @@ -25,7 +25,7 @@ /****************/ /* Local Macros */ /****************/ -#define TWO_GIG_LIMIT (1 << 31) +#define TWO_GIG_LIMIT INT32_MAX #ifndef H5_MAX_MPI_COUNT #define H5_MAX_MPI_COUNT (1 << 30) #endif @@ -33,7 +33,7 @@ /*******************/ /* Local Variables */ /*******************/ -static hsize_t bigio_count = H5_MAX_MPI_COUNT; +static hsize_t bigio_count_g = H5_MAX_MPI_COUNT; /*------------------------------------------------------------------------- * Function: H5_mpi_set_bigio_count @@ -42,7 +42,7 @@ static hsize_t bigio_count = H5_MAX_MPI_COUNT; * when we utilize derived datatypes. This is of * particular interest for allowing nightly testing * - * Return: The current/previous value of bigio_count. + * Return: The current/previous value of bigio_count_g. * * Programmer: Richard Warren, March 10, 2017 * @@ -51,10 +51,10 @@ static hsize_t bigio_count = H5_MAX_MPI_COUNT; hsize_t H5_mpi_set_bigio_count(hsize_t new_count) { - hsize_t orig_count = bigio_count; + hsize_t orig_count = bigio_count_g; if ((new_count > 0) && (new_count < (hsize_t)TWO_GIG_LIMIT)) { - bigio_count = new_count; + bigio_count_g = new_count; } return orig_count; } /* end H5_mpi_set_bigio_count() */ @@ -63,9 +63,9 @@ H5_mpi_set_bigio_count(hsize_t new_count) * Function: H5_mpi_get_bigio_count * * Purpose: Allow other HDF5 library functions to access - * the current value for bigio_count. + * the current value for bigio_count_g. * - * Return: The current/previous value of bigio_count. + * Return: The current/previous value of bigio_count_g. * * Programmer: Richard Warren, October 7, 2019 * @@ -74,7 +74,7 @@ H5_mpi_set_bigio_count(hsize_t new_count) hsize_t H5_mpi_get_bigio_count(void) { - return bigio_count; + return bigio_count_g; } /*------------------------------------------------------------------------- @@ -471,8 +471,8 @@ H5_mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, MPI_Datat FUNC_ENTER_NOAPI(FAIL) /* Calculate how many Big MPI datatypes are needed to represent the buffer */ - num_big_types = (int)(num_elements / bigio_count); - leftover = (hsize_t)num_elements - (hsize_t)num_big_types * bigio_count; + num_big_types = (int)(num_elements / bigio_count_g); + leftover = (hsize_t)num_elements - (hsize_t)num_big_types * bigio_count_g; H5_CHECKED_ASSIGN(remaining_bytes, int, leftover, hsize_t); /* Create a contiguous datatype of size equal to the largest @@ -481,11 +481,11 @@ H5_mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, MPI_Datat * use type_hvector to create the type with the displacement provided */ if (0 == stride_bytes) { - if (MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)bigio_count, old_type, &inner_type))) + if (MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)bigio_count_g, old_type, &inner_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) } /* end if */ else if (MPI_SUCCESS != - (mpi_code = MPI_Type_create_hvector((int)bigio_count, 1, stride_bytes, old_type, &inner_type))) + (mpi_code = MPI_Type_create_hvector((int)bigio_count_g, 1, stride_bytes, old_type, &inner_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code) /* Create a contiguous datatype of the buffer (minus the remaining < 2GB part) @@ -510,7 +510,7 @@ H5_mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, MPI_Datat HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) } /* end if */ else if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector( - (int)(num_elements - (hsize_t)num_big_types * bigio_count), 1, + (int)(num_elements - (hsize_t)num_big_types * bigio_count_g), 1, stride_bytes, old_type, &leftover_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code) @@ -529,7 +529,7 @@ H5_mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, MPI_Datat block_len[0] = 1; block_len[1] = 1; disp[0] = 0; - disp[1] = (old_extent + stride_bytes) * num_big_types * (MPI_Aint)bigio_count; + disp[1] = (old_extent + stride_bytes) * num_big_types * (MPI_Aint)bigio_count_g; if (MPI_SUCCESS != (mpi_code = MPI_Type_create_struct(2, block_len, disp, type, new_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) diff --git a/src/H5public.h b/src/H5public.h index 5b9a5fe..1784a11 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -333,13 +333,15 @@ typedef enum H5_index_t { H5_INDEX_N /* Number of indices defined */ } H5_index_t; -/* +/** * Storage info struct used by H5O_info_t and H5F_info_t */ +//! [H5_ih_info_t_snip] typedef struct H5_ih_info_t { - hsize_t index_size; /* btree and/or list */ + hsize_t index_size; /**< btree and/or list */ hsize_t heap_size; } H5_ih_info_t; +//! [H5_ih_info_t_snip] /* Tokens are unique and permanent identifiers that are * used to reference HDF5 objects in a container. */ diff --git a/src/Makefile.am b/src/Makefile.am index cbecccd..40e5233 100644 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -19,6 +19,8 @@ include $(top_srcdir)/config/commence.am include $(top_srcdir)/config/lt_vers.am +# include Doxygen rules (requires autoconf-archive >2016-03-20) +@DX_RULES@ # How to build H5detect for number format detection. # Use -g to force no optimization since many compilers (e.g., Intel) takes @@ -33,13 +35,13 @@ lib_LTLIBRARIES=libhdf5.la libhdf5_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS) # H5Tinit.c and H5lib_settings.c are generated files and should be cleaned. -MOSTLYCLEANFILES=H5Tinit.c H5lib_settings.c +MOSTLYCLEANFILES=H5Tinit.c H5lib_settings.c $(DX_CLEANFILES) # H5pubconf.h is generated by configure, and should be cleaned. DISTCLEANFILES=H5pubconf.h # library sources libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5lib_settings.c H5system.c \ - H5timer.c H5trace.c \ + H5timer.c H5trace.c \ H5A.c H5Abtree2.c H5Adense.c H5Adeprec.c H5Aint.c H5Atest.c \ H5AC.c H5ACdbg.c H5ACproxy_entry.c \ H5B.c H5Bcache.c H5Bdbg.c \ @@ -61,7 +63,7 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5lib_settings.c H5system.c \ H5Fsuper.c H5Fsuper_cache.c H5Ftest.c \ H5FA.c H5FAcache.c H5FAdbg.c H5FAdblock.c H5FAdblkpage.c H5FAhdr.c \ H5FAint.c H5FAstat.c H5FAtest.c \ - H5FD.c H5FDcore.c H5FDfamily.c H5FDhdfs.c H5FDint.c H5FDlog.c \ + H5FD.c H5FDcore.c H5FDfamily.c H5FDint.c H5FDlog.c \ H5FDmulti.c H5FDsec2.c H5FDspace.c \ H5FDsplitter.c H5FDstdio.c H5FDtest.c \ H5FL.c H5FO.c H5FS.c H5FScache.c H5FSdbg.c H5FSint.c H5FSsection.c \ @@ -126,6 +128,11 @@ if DIRECT_VFD_CONDITIONAL libhdf5_la_SOURCES += H5FDdirect.c endif +# Only compile the read-only HDFS VFD if necessary +if HDFS_VFD_CONDITIONAL + libhdf5_la_SOURCES += H5FDhdfs.c +endif + # Only compile the mirror VFD if necessary if MIRROR_VFD_CONDITIONAL libhdf5_la_SOURCES += H5FDmirror.c @@ -196,12 +203,20 @@ $(top_srcdir)/src/H5version.h: $(top_srcdir)/src/H5vers.txt $(top_srcdir)/src/H5overflow.h: $(top_srcdir)/src/H5overflow.txt perl $(top_srcdir)/bin/make_overflow $? +# doxygen support +doxygen: + rm -fr $(top_builddir)/hdf5lib_docs + env $(DX_ENV) \ + PROJECT_NAME="HDF5" \ + SRCDIR=$(top_srcdir) \ + OUTPUTDIR=$(top_builddir)/hdf5lib_docs \ + $(DX_DOXYGEN) $(top_builddir)/$(DX_CONFIG) + # Add TRACE macros to library source files. This is done via the trace script # in the hdf5/bin directory. If the file contains HDF5 API macros, a "clean" # version of the source file is saved with a tilde (~) after its name and # tracing information is inserted. trace should have no effect on files # without HDF5 macros. -.PHONY: trace trace: $(libhdf5_la_SOURCES) @for dep in $? dummy; do \ diff --git a/test/CMakeTests.cmake b/test/CMakeTests.cmake index 462e9d5..013189c 100644 --- a/test/CMakeTests.cmake +++ b/test/CMakeTests.cmake @@ -844,7 +844,7 @@ endif () ### F I L T E R P L U G I N T E S T S ############################################################################## if (BUILD_SHARED_LIBS) - if (WIN32 OR MINGW) + if (WIN32) set (CMAKE_SEP "\;") set (BIN_REL_PATH "../../") else () @@ -940,7 +940,7 @@ endif () ### V O L P L U G I N T E S T S ############################################################################## if (BUILD_SHARED_LIBS) - if (WIN32 OR MINGW) + if (WIN32) set (CMAKE_SEP "\;") set (BIN_REL_PATH "../../") else () diff --git a/test/flushrefreshTest.cmake b/test/flushrefreshTest.cmake index 6faf37b..e280b8b 100644 --- a/test/flushrefreshTest.cmake +++ b/test/flushrefreshTest.cmake @@ -41,7 +41,7 @@ endif () message (STATUS "COMMAND: ${TEST_PROGRAM} ${TEST_ARGS}") if (TEST_LIBRARY_DIRECTORY) - if (WIN32 OR MINGW) + if (WIN32) set (ENV{PATH} "$ENV{PATH};${TEST_LIBRARY_DIRECTORY}") else () set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}") diff --git a/test/hdfs.c b/test/hdfs.c index 701df47..a59cdb6 100644 --- a/test/hdfs.c +++ b/test/hdfs.c @@ -564,9 +564,9 @@ test_fapl_config_validation(void) JSVERIFY(config.version, fa_fetch.version, "version number mismatch") JSVERIFY(config.namenode_port, fa_fetch.namenode_port, "namenode port mismatch") JSVERIFY(config.stream_buffer_size, fa_fetch.stream_buffer_size, "streambuffer size mismatch") - JSVERIFY_STR(config.namenode_name, fa_fetch.namenode_name, NULL) - JSVERIFY_STR(config.user_name, fa_fetch.user_name, NULL) - JSVERIFY_STR(config.kerberos_ticket_cache, fa_fetch.kerberos_ticket_cache, NULL) + JSVERIFY_STR(config.namenode_name, fa_fetch.namenode_name, "node name mismatch") + JSVERIFY_STR(config.user_name, fa_fetch.user_name, "user name mismatch") + JSVERIFY_STR(config.kerberos_ticket_cache, fa_fetch.kerberos_ticket_cache, "kerberos ticket cache mismatch") } /*----------------------------- @@ -996,7 +996,7 @@ test_eof_eoa(void) /* verify as found */ - JSVERIFY(5458199, H5FDget_eof(fd_shakespeare, H5FD_MEM_DEFAULT), NULL) + JSVERIFY(5458199, H5FDget_eof(fd_shakespeare, H5FD_MEM_DEFAULT), "EOF mismatch") JSVERIFY(H5FDget_eof(fd_shakespeare, H5FD_MEM_DEFAULT), H5FDget_eof(fd_shakespeare, H5FD_MEM_DRAW), "mismatch between DEFAULT and RAW memory types") JSVERIFY(0, H5FDget_eoa(fd_shakespeare, H5FD_MEM_DEFAULT), "EoA should be unset by H5FDopen") @@ -1272,7 +1272,7 @@ test_read(void) HADDR_UNDEF); /* Demonstrate success with "automatic" value */ FAIL_IF(NULL == file_raven) - JSVERIFY(6464, H5FDget_eof(file_raven, H5FD_MEM_DEFAULT), NULL) + JSVERIFY(6464, H5FDget_eof(file_raven, H5FD_MEM_DEFAULT), "EOF mismatch") /********* * TESTS * @@ -1432,8 +1432,8 @@ test_noops_and_autofails(void) /* no-op calls to `lock()` and `unlock()` */ JSVERIFY(SUCCEED, H5FDlock(file, TRUE), "lock always succeeds; has no effect") - JSVERIFY(SUCCEED, H5FDlock(file, FALSE), NULL) - JSVERIFY(SUCCEED, H5FDunlock(file), NULL) + JSVERIFY(SUCCEED, H5FDlock(file, FALSE), "lock issue") + JSVERIFY(SUCCEED, H5FDunlock(file), "unlock issue") /* Lock/unlock with null file or similar error crashes tests. * HDassert in calling heirarchy, `H5FD[un]lock()` and `H5FD_[un]lock()` */ @@ -2168,8 +2168,6 @@ test_ros3(void) hid_t driver_id = -1; /* ID for this VFD */ unsigned long driver_flags = 0; /* VFD feature flags */ char filename[1024]; /* filename */ - void * os_file_handle = NULL; /* OS file handle */ - hsize_t file_size; /* file size */ H5FD_ros3_fapl_t test_ros3_fa; H5FD_ros3_fapl_t ros3_fa_0 = { /* version = */ H5FD_CURR_ROS3_FAPL_T_VERSION, diff --git a/testpar/t_mdset.c b/testpar/t_mdset.c index a4bc26d..bf4ce73 100644 --- a/testpar/t_mdset.c +++ b/testpar/t_mdset.c @@ -1456,10 +1456,8 @@ read_attribute(hid_t obj_id, int this_type, int num) if (this_type == is_group) { HDsprintf(attr_name, "Group Attribute %d", num); aid = H5Aopen(obj_id, attr_name, H5P_DEFAULT); - if (MAINPROCESS) { - H5Aread(aid, H5T_NATIVE_INT, &in_num); - vrfy_errors = dataset_vrfy(NULL, NULL, NULL, group_block, &in_num, &num); - } + H5Aread(aid, H5T_NATIVE_INT, &in_num); + vrfy_errors = dataset_vrfy(NULL, NULL, NULL, group_block, &in_num, &num); H5Aclose(aid); } else if (this_type == is_dset) { @@ -1467,10 +1465,8 @@ read_attribute(hid_t obj_id, int this_type, int num) for (i = 0; i < 8; i++) out_data[i] = i; aid = H5Aopen(obj_id, attr_name, H5P_DEFAULT); - if (MAINPROCESS) { - H5Aread(aid, H5T_NATIVE_INT, in_data); - vrfy_errors = dataset_vrfy(NULL, NULL, NULL, dset_block, in_data, out_data); - } + H5Aread(aid, H5T_NATIVE_INT, in_data); + vrfy_errors = dataset_vrfy(NULL, NULL, NULL, dset_block, in_data, out_data); H5Aclose(aid); } diff --git a/tools/test/h5dump/CMakeTests.cmake b/tools/test/h5dump/CMakeTests.cmake index 91d3ea9..a664e6f 100644 --- a/tools/test/h5dump/CMakeTests.cmake +++ b/tools/test/h5dump/CMakeTests.cmake @@ -405,7 +405,7 @@ # -------------------------------------------------------------------- HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tbin1.ddl" "${PROJECT_BINARY_DIR}/testfiles/std/tbin1LE.ddl" "h5dump_std_files") - if (WIN32 OR MINGW) + if (WIN32) configure_file(${HDF5_TOOLS_DIR}/testfiles/tbinregR.exp ${PROJECT_BINARY_DIR}/testfiles/std/tbinregR.exp NEWLINE_STYLE CRLF) #file (READ ${HDF5_TOOLS_DIR}/testfiles/tbinregR.exp TEST_STREAM) #file (WRITE ${PROJECT_BINARY_DIR}/testfiles/std/tbinregR.exp "${TEST_STREAM}") |
