mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-11-21 01:04:10 +08:00
Fix various warnings and issues in doxygen doc generation (#994)
* Fix various warnings and issues in doxygen doc generation * Add new file to list
This commit is contained in:
Allen Byrne
GitHub
parent
8e06298ecf
commit
b58f8540ac
@ -571,20 +571,6 @@ endif ()
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# set (H5_HAVE_DMALLOC DMALLOC_FOUND)
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# endif ()
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#-----------------------------------------------------------------------------
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# Option to build documentation
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#-----------------------------------------------------------------------------
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option (HDF5_BUILD_DOC "Build documentation" OFF)
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if (HDF5_BUILD_DOC AND EXISTS "${HDF5_DOXYGEN_DIR}" AND IS_DIRECTORY "${HDF5_DOXYGEN_DIR}")
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# check if Doxygen is installed
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find_package(Doxygen)
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if (DOXYGEN_FOUND)
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message(STATUS "Doxygen version: ${DOXYGEN_VERSION}")
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else ()
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message(STATUS "Doxygen needs to be installed to generate the doxygen documentation")
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endif ()
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endif ()
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#-----------------------------------------------------------------------------
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# Option to indicate using a memory checker
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#-----------------------------------------------------------------------------
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@ -925,6 +911,21 @@ if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MAT
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endif ()
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endif ()
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#-----------------------------------------------------------------------------
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# Option to build documentation
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#-----------------------------------------------------------------------------
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option (HDF5_BUILD_DOC "Build documentation" OFF)
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if (HDF5_BUILD_DOC AND EXISTS "${HDF5_DOXYGEN_DIR}" AND IS_DIRECTORY "${HDF5_DOXYGEN_DIR}")
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# check if Doxygen is installed
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find_package(Doxygen)
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if (DOXYGEN_FOUND)
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message(STATUS "Doxygen version: ${DOXYGEN_VERSION}")
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add_subdirectory (doxygen)
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else ()
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message(STATUS "Doxygen needs to be installed to generate the doxygen documentation")
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endif ()
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endif ()
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#-----------------------------------------------------------------------------
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# Dashboard and Testing Settings
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#-----------------------------------------------------------------------------
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1
MANIFEST
1
MANIFEST
@ -212,6 +212,7 @@
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./doc/code-conventions.md
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./doc/contributing.md
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./doxygen/aliases
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./doxygen/CMakeLists.txt
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./doxygen/Doxyfile.in
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./doxygen/dox/APIVersions.dox
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./doxygen/dox/About.dox
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@ -1106,6 +1106,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
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AC_SUBST([DOXYGEN_SERVER_BASED_SEARCH])
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AC_SUBST([DOXYGEN_EXTERNAL_SEARCH])
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AC_SUBST([DOXYGEN_SEARCHENGINE_URL])
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AC_SUBST([DOXYGEN_STRIP_FROM_PATH])
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AC_SUBST([DOXYGEN_PREDEFINED])
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# SRCDIR Environment variables used inside doxygen macro for the source location:
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@ -1113,7 +1114,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
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DOXYGEN_VERSION_STRING=${PACKAGE_VERSION}
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DOXYGEN_INCLUDE_ALIASES='$(SRCDIR)/doxygen/aliases'
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DOXYGEN_PROJECT_LOGO='$(SRCDIR)/doxygen/img/HDFG-logo.png'
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DOXYGEN_PROJECT_BRIEF=
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DOXYGEN_PROJECT_BRIEF='C-API Reference'
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DOXYGEN_INPUT_DIRECTORY='$(SRCDIR) $(SRCDIR)/doxygen/dox'
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DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES
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DOXYGEN_MACRO_EXPANSION=YES
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@ -1128,6 +1129,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
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DOXYGEN_SERVER_BASED_SEARCH=NO
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DOXYGEN_EXTERNAL_SEARCH=NO
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DOXYGEN_SEARCHENGINE_URL=
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DOXYGEN_STRIP_FROM_PATH='$(SRCDIR)'
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DOXYGEN_PREDEFINED='H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD'
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DX_INIT_DOXYGEN([HDF5], [./doxygen/Doxyfile], [hdf5lib_docs])
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46
doxygen/CMakeLists.txt
Normal file
46
doxygen/CMakeLists.txt
Normal file
@ -0,0 +1,46 @@
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cmake_minimum_required (VERSION 3.12)
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project (HDF5_DOXYGEN C)
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#-----------------------------------------------------------------------------
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# Option to build documentation
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#-----------------------------------------------------------------------------
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if (DOXYGEN_FOUND)
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set (DOXYGEN_PACKAGE ${HDF5_PACKAGE_NAME})
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set (DOXYGEN_VERSION_STRING ${HDF5_PACKAGE_VERSION_STRING})
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set (DOXYGEN_INCLUDE_ALIASES_PATH ${HDF5_DOXYGEN_DIR})
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set (DOXYGEN_INCLUDE_ALIASES aliases)
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set (DOXYGEN_VERBATIM_VARS DOXYGEN_INCLUDE_ALIASES)
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set (DOXYGEN_PROJECT_LOGO ${HDF5_DOXYGEN_DIR}/img/HDFG-logo.png)
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set (DOXYGEN_PROJECT_BRIEF "C-API Reference")
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set (DOXYGEN_INPUT_DIRECTORY "${HDF5_SOURCE_DIR} ${HDF5_DOXYGEN_DIR}/dox ${HDF5_GENERATED_SOURCE_DIR}")
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set (DOXYGEN_OPTIMIZE_OUTPUT_FOR_C YES)
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set (DOXYGEN_MACRO_EXPANSION YES)
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set (DOXYGEN_OUTPUT_DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs)
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set (DOXYGEN_EXAMPLES_DIRECTORY "${HDF5_DOXYGEN_DIR}/dox/cookbook ${HDF5_DOXYGEN_DIR}/examples ${HDF5_SRC_DIR} ${HDF5_SOURCE_DIR}/examples ${HDF5_TEST_SRC_DIR}")
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set (DOXYGEN_LAYOUT_FILE ${HDF5_DOXYGEN_DIR}/hdf5doxy_layout.xml)
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set (DOXYGEN_HTML_HEADER ${HDF5_DOXYGEN_DIR}/hdf5_header.html)
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set (DOXYGEN_HTML_FOOTER ${HDF5_DOXYGEN_DIR}/hdf5_footer.html)
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set (DOXYGEN_HTML_EXTRA_STYLESHEET ${HDF5_DOXYGEN_DIR}/hdf5doxy.css)
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set (DOXYGEN_HTML_EXTRA_FILES "${HDF5_DOXYGEN_DIR}/hdf5_navtree_hacks.js ${HDF5_DOXYGEN_DIR}/img/ftv2node.png ${HDF5_DOXYGEN_DIR}/img/ftv2pnode.png")
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set (DOXYGEN_TAG_FILE ${HDF5_BINARY_DIR}/hdf5.tag)
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set (DOXYGEN_SERVER_BASED_SEARCH NO)
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set (DOXYGEN_EXTERNAL_SEARCH NO)
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set (DOXYGEN_SEARCHENGINE_URL)
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set (DOXYGEN_STRIP_FROM_PATH ${HDF5_SOURCE_DIR})
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set (DOXYGEN_PREDEFINED "H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD")
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# This configure and individual custom targets work together
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# Replace variables inside @@ with the current values
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configure_file (${HDF5_DOXYGEN_DIR}/Doxyfile.in ${HDF5_BINARY_DIR}/Doxyfile @ONLY)
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install (
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DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs/html
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DESTINATION ${HDF5_INSTALL_DATA_DIR}
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COMPONENT Documents
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)
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if (NOT TARGET doxygen)
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add_custom_target (doxygen)
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endif ()
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endif ()
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@ -170,7 +170,7 @@ FULL_PATH_NAMES = YES
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# will be relative from the directory where doxygen is started.
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# This tag requires that the tag FULL_PATH_NAMES is set to YES.
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STRIP_FROM_PATH =
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STRIP_FROM_PATH = @DOXYGEN_STRIP_FROM_PATH@
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# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
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# path mentioned in the documentation of a class, which tells the reader which
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@ -1126,13 +1126,6 @@ CLANG_DATABASE_PATH =
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ALPHABETICAL_INDEX = YES
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# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
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# which the alphabetical index list will be split.
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# Minimum value: 1, maximum value: 20, default value: 5.
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# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
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COLS_IN_ALPHA_INDEX = 5
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# In case all classes in a project start with a common prefix, all classes will
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# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
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# can be used to specify a prefix (or a list of prefixes) that should be ignored
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@ -298,7 +298,7 @@ ALIASES += ref_rfc20120305="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC%20P
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ALIASES += ref_rfc20120220="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/h5repack_improve_hyperslab_over_chunked_dataset_v1.pdf\"><tt>h5repack</tt>: Improved Hyperslab selections for Large Chunked Datasets</a>"
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ALIASES += ref_rfc20120120="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/2012-1-25-Maintainers-guide-for-datatype.docx.pdf\">A Maintainer’s Guide for the Datatype Module in HDF5 Library</a>"
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ALIASES += ref_rfc20120104="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_actual_io_v4-1_done.docx.pdf\">Actual I/O Mode</a>"
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ALIASES += ref_rfc20111119="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-H5Ocompare-review_v6.pdf\">New public functions to handle comparison</a>"
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ALIASES += ref_rfc20111119="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-H5Ocompare-review_v6.pdf\">New public functions to handle comparison</a>"
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ALIASES += ref_rfc20110825="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/2011-08-31-RFC_H5Ocopy_Named_DT_v2.docx.pdf\">Merging Named Datatypes in H5Ocopy()</a>"
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ALIASES += ref_rfc20110811="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_Enhancement_Hyperslab_Selection-1.4.docx.pdf\">Expanding the HDF5 Hyperslab Selection Interface</a>"
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ALIASES += ref_rfc20110726="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/metadata_aggregation_RFC_v03.docx.pdf\">HDF5 File Space Allocation and Aggregation</a>"
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@ -327,7 +327,7 @@ ALIASES += ref_rfc20071111="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/AURA-co
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ALIASES += ref_rfc20071018="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_NaNsHDF5.pdf\"><tt>NaN</tt> detection in HDF5</a>"
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ALIASES += ref_rfc20070801="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/Metadata_Journaling_RFC.pdf\">Metadata Journaling to Improve Crash Survivability</a>"
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ALIASES += ref_rfc20070413="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/API_Compatibility_RFC.txt.pdf\">API Compatibility Strategies for HDF5</a>"
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ALIASES += ref_rfc20070115="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/PrivateHeap.pdf\">A "Private" Heap for HDF5</a>"
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ALIASES += ref_rfc20070115="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/PrivateHeap.pdf\">A 'Private' Heap for HDF5</a>"
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ALIASES += ref_rfc20060623="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/coll_ind_dd6.pdf\">Performance Comparison of Collective I/O and Independent I/O with Derived Datatypes</a>"
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ALIASES += ref_rfc20060604="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/h5stat_spec_v3_2006-06-04.pdf\"><tt>h5stat</tt> tool</a>"
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ALIASES += ref_rfc20060505="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/Simple%20Performance%20Test%20on%20Fletcher32%20Filter.pdf\">Simple Performance Test on Fletcher32 Filter</a>"
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@ -668,7 +668,7 @@ reduction.
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With the hit rate threshold cache size decrement algorithm, the remaining fields
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in the section are ignored.
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\subsubsection acsr Ageout Cache Size Reduction
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\subsubsection dacsr Ageout Cache Size Reduction
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If \ref H5AC_cache_config_t.decr_mode "decr_mode" is #H5C_decr__age_out the
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cache size is decreased by the ageout algorithm, and the remaining fields of the
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@ -692,7 +692,7 @@ The \ref H5AC_cache_config_t.decrement "decrement" and \ref
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H5AC_cache_config_t.upper_hr_threshold "upper_hr_threshold" fields are ignored
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in this case.
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\subsubsection awhrtcsr Ageout With Hit Rate Threshold Cache Size Reduction
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\subsubsection dawhrtcsr Ageout With Hit Rate Threshold Cache Size Reduction
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If \ref H5AC_cache_config_t.decr_mode "decr_mode" is
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#H5C_decr__age_out_with_threshold, the cache size is decreased by the ageout
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@ -169,3 +169,32 @@ if (NOT WIN32 AND NOT MINGW)
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COMPONENT hllibraries
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)
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endif ()
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#-----------------------------------------------------------------------------
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# Option to build documentation
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#-----------------------------------------------------------------------------
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if (DOXYGEN_FOUND)
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# This cmake function requires that the non-default doxyfile settings are provided with set (DOXYGEN_xxx) commands
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# In addition the doxyfile aliases @INCLUDE option is not supported and would need to be provided in a set (DOXYGEN_ALIASES) command.
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# doxygen_add_docs (hdf5lib_doc
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## ${HL_SOURCES} ${HL_HEADERS} ${HDF5_DOXYGEN_DIR}/dox
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# ${DOXYGEN_INPUT_DIRECTORY}
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# ALL
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# WORKING_DIRECTORY ${HDF5_HL_SRC_DIR}
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# COMMENT "Generating HDF5 HL library Source Documentation"
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# )
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# This custom target and doxygen/configure work together
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# Replace variables inside @@ with the current values
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add_custom_target (hdf5hllib_doc ALL
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COMMAND ${DOXYGEN_EXECUTABLE} ${HDF5_BINARY_DIR}/Doxyfile
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WORKING_DIRECTORY ${HDF5_HL_SRC_DIR}
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COMMENT "Generating HDF5 HL library Source API documentation with Doxygen"
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VERBATIM )
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if (NOT TARGET doxygen)
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add_custom_target (doxygen)
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endif ()
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add_dependencies (doxygen hdf5hllib_doc)
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endif ()
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@ -1399,38 +1399,6 @@ endif ()
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# Option to build documentation
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#-----------------------------------------------------------------------------
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if (DOXYGEN_FOUND)
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set (DOXYGEN_PACKAGE ${HDF5_PACKAGE_NAME})
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set (DOXYGEN_VERSION_STRING ${HDF5_PACKAGE_VERSION_STRING})
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set (DOXYGEN_INCLUDE_ALIASES_PATH ${HDF5_DOXYGEN_DIR})
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set (DOXYGEN_INCLUDE_ALIASES aliases)
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set (DOXYGEN_VERBATIM_VARS DOXYGEN_INCLUDE_ALIASES)
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set (DOXYGEN_PROJECT_LOGO ${HDF5_DOXYGEN_DIR}/img/HDFG-logo.png)
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set (DOXYGEN_PROJECT_BRIEF "C-API Reference")
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set (DOXYGEN_INPUT_DIRECTORY "${HDF5_SRC_DIR} ${HDF5_DOXYGEN_DIR}/dox ${HDF5_GENERATED_SOURCE_DIR}")
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set (DOXYGEN_OPTIMIZE_OUTPUT_FOR_C YES)
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set (DOXYGEN_MACRO_EXPANSION YES)
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set (DOXYGEN_OUTPUT_DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs)
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set (DOXYGEN_EXAMPLES_DIRECTORY "${HDF5_DOXYGEN_DIR}/dox/cookbook ${HDF5_DOXYGEN_DIR}/examples ${HDF5_SRC_DIR} ${HDF5_SOURCE_DIR}/examples ${HDF5_TEST_SRC_DIR}")
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set (DOXYGEN_LAYOUT_FILE ${HDF5_DOXYGEN_DIR}/hdf5doxy_layout.xml)
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set (DOXYGEN_HTML_HEADER ${HDF5_DOXYGEN_DIR}/hdf5_header.html)
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set (DOXYGEN_HTML_FOOTER ${HDF5_DOXYGEN_DIR}/hdf5_footer.html)
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set (DOXYGEN_HTML_EXTRA_STYLESHEET ${HDF5_DOXYGEN_DIR}/hdf5doxy.css)
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set (DOXYGEN_HTML_EXTRA_FILES "${HDF5_DOXYGEN_DIR}/hdf5_navtree_hacks.js ${HDF5_DOXYGEN_DIR}/img/ftv2node.png ${HDF5_DOXYGEN_DIR}/img/ftv2pnode.png")
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set (DOXYGEN_TAG_FILE ${HDF5_BINARY_DIR}/hdf5.tag)
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set (DOXYGEN_SERVER_BASED_SEARCH NO)
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set (DOXYGEN_EXTERNAL_SEARCH NO)
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set (DOXYGEN_SEARCHENGINE_URL)
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set (DOXYGEN_PREDEFINED H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD)
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# This configure and custom target work together
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# Replace variables inside @@ with the current values
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configure_file (${HDF5_DOXYGEN_DIR}/Doxyfile.in ${HDF5_BINARY_DIR}/Doxyfile @ONLY)
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add_custom_target (hdf5lib_doc ALL
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COMMAND ${DOXYGEN_EXECUTABLE} ${HDF5_BINARY_DIR}/Doxyfile
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DEPENDS ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c ${HDF5_SRC_BINARY_DIR}/H5lib_settings.c
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WORKING_DIRECTORY ${HDF5_SRC_DIR}
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COMMENT "Generating HDF5 library Source API documentation with Doxygen"
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VERBATIM )
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# This cmake function requires that the non-default doxyfile settings are provided with set (DOXYGEN_xxx) commands
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# In addition the doxyfile aliases @INCLUDE option is not supported and would need to be provided in a set (DOXYGEN_ALIASES) command.
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# doxygen_add_docs (hdf5lib_doc
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@ -1440,11 +1408,15 @@ if (DOXYGEN_FOUND)
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# WORKING_DIRECTORY ${HDF5_SRC_DIR}
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# COMMENT "Generating HDF5 library Source Documentation"
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# )
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install (
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DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs/html
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DESTINATION ${HDF5_INSTALL_DATA_DIR}
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COMPONENT Documents
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)
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# This custom target and doxygen/configure work together
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# Replace variables inside @@ with the current values
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add_custom_target (hdf5lib_doc ALL
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COMMAND ${DOXYGEN_EXECUTABLE} ${HDF5_BINARY_DIR}/Doxyfile
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DEPENDS ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c ${HDF5_SRC_BINARY_DIR}/H5lib_settings.c
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WORKING_DIRECTORY ${HDF5_SRC_DIR}
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COMMENT "Generating HDF5 library Source API documentation with Doxygen"
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VERBATIM )
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if (NOT TARGET doxygen)
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add_custom_target (doxygen)
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@ -152,7 +152,7 @@ typedef herr_t (*H5D_append_cb_t)(hid_t dataset_id, hsize_t *cur_dims, void *op_
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*
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* \param[in,out] elem Pointer to the memory buffer containing the current dataset
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* element
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* \param[in] type_id Datatype identifier of the elements stored in \pelem
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* \param[in] type_id Datatype identifier of the elements stored in \p elem
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* \param[in] ndim Number of dimensions for the \p point array
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* \param[in] point Array containing the location of the element within
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* the original dataspace
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@ -7486,10 +7486,6 @@ H5_DLL size_t H5Pget_buffer(hid_t plist_id, void **tconv /*out*/, void **bkg /*o
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* If an error occurs, the buffer pointed to by \p expression is
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* unchanged, and the function returns a negative value.
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*
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* \par Example
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* An example snippet from examples/h5_dtransform.c:
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* \snippet h5_dtransform.c H5Pget_data_transform_snip
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*
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* \since 1.8.0
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*
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*/
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@ -8092,7 +8088,7 @@ H5_DLL herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no
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* the size of the \p start, \p stride, \p count, and \p block arrays.
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* \p rank must be between 1 and #H5S_MAX_RANK, inclusive.
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*
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* The \op, \p start, \p stride, \p count, and \p block parameters
|
||||
* The \p op, \p start, \p stride, \p count, and \p block parameters
|
||||
* behave identically to their behavior for H5Sselect_hyperslab(),
|
||||
* please see the documentation for that routine for details about
|
||||
* their use.
|
||||
|
||||
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Reference in New Issue
Block a user