Merge branch 'HDFGroup:develop' into develop-doxy-debugging

CMakePresets.json

@@ -68,7 +68,7 @@
         "LZF_PACKAGE_NAME": {"type": "STRING", "value": "lzf"},
         "SZ_TGZ_NAME": {"type": "STRING", "value": "SZ-2.1.12.5.tar.gz"},
         "SZ_PACKAGE_NAME": {"type": "STRING", "value": "SZ"},
-        "ZFP_TGZ_NAME": {"type": "STRING", "value": "zfp-1.0.0.tar.gz"},
+        "ZFP_TGZ_NAME": {"type": "STRING", "value": "zfp-1.0.1.tar.gz"},
         "ZFP_PACKAGE_NAME": {"type": "STRING", "value": "zfp"},
         "ZSTD_TGZ_NAME": {"type": "STRING", "value": "zstd-1.5.6.tar.gz"},
         "ZSTD_PACKAGE_NAME": {"type": "STRING", "value": "zstd"}

HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.ddl

@@ -10,7 +10,7 @@ GROUP "/" {
       FILTERS {
          USER_DEFINED_FILTER {
             FILTER_ID 32013
-            COMMENT H5Z-ZFP-1.1.1 (ZFP-1.0.0) github.com/LLNL/H5Z-ZFP
+            COMMENT H5Z-ZFP-1.1.1 (ZFP-1.0.1) github.com/LLNL/H5Z-ZFP
             PARAMS { XXXX }
          }
       }

HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.tst

@@ -5,7 +5,7 @@ zfp filter is available for encoding and decoding.
 Filter info is available from the dataset creation property
    Filter identifier is 32013
    Number of parameters is 6 with the value 268456209
-   To find more about the filter check H5Z-ZFP-1.1.1 (ZFP-1.0.0) github.com/LLNL/H5Z-ZFP
+   To find more about the filter check H5Z-ZFP-1.1.1 (ZFP-1.0.1) github.com/LLNL/H5Z-ZFP
 ....Reading zfp compressed data ................
 Maximum value in DS1 is 1890.0000
 zfp filter is available now since H5Dread triggered loading of the filter.

config/cmake/cacheinit.cmake

@@ -229,7 +229,7 @@ set (ZFP_GIT_URL "https://github.com/LLNL/zfp.git" CACHE STRING "Use ZFP from  G
 set (ZFP_GIT_BRANCH "develop" CACHE STRING "" FORCE)
 
 set (ZFP_TGZ_ORIGPATH "https://github.com/LLNL/zfp/releases/download/1.0.0" CACHE STRING "Use PLUGINS from original location" FORCE)
-set (ZFP_TGZ_NAME "zfp-1.0.0.tar.gz" CACHE STRING "Use ZFP from compressed file" FORCE)
+set (ZFP_TGZ_NAME "zfp-1.0.1.tar.gz" CACHE STRING "Use ZFP from compressed file" FORCE)
 
 set (ZFP_PACKAGE_NAME "zfp" CACHE STRING "Name of ZFP package" FORCE)
 

doxygen/aliases

@@ -260,7 +260,6 @@ ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_co
 ################################################################################
 
 ALIASES += ref_cons_semantics="<a href=\"https://\RFCURL/RFC%20PHDF5%20Consistency%20Semantics%20MC%20120328.docx.pdf\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>"
-ALIASES += ref_file_image_ops="<a href=\"https://\RFCURL/HDF5FileImageOperations.pdf\">HDF5 File Image Operations</a>"
 ALIASES += ref_filter_pipe="<a href=\"https://\DOCURL/advanced_topics/data_flow_pline_H5Dread.md\">Data Flow Pipeline for H5Dread()</a>"
 ALIASES += ref_group_impls="<a href=\"https://\DOXURL/group___h5_g.html\">Group implementations in HDF5</a>"
 ALIASES += ref_h5lib_relver="<a href=\"https://\ARCURL/TechNotes/Version.html\">HDF5 Library Release Version Numbers</a>"
@@ -327,7 +326,6 @@ ALIASES += ref_rfc20121114="<a href=\"https://\RFCURL/DECTRIS%20Integration%20RF
 ALIASES += ref_rfc20121024="<a href=\"https://\RFCURL/FileSpaceManagement.pdf\">HDF5 File Space Management</a>"
 ALIASES += ref_rfc20120828="<a href=\"https://\RFCURL/H5HPC_MultiDset_RW_IO_RFC.pdf\">New HDF5 API Routines for HPC Applications - Read/Write Multiple Datasets in an HDF5 file</a>"
 ALIASES += ref_rfc20120523="<a href=\"https://\RFCURL/paged_aggregation.pdf\">HDF5 File Space Management: Paged Aggregation</a>"
-ALIASES += ref_rfc20120501="<a href=\"https://\RFCURL/HDF5FileImageOperations.pdf\">HDF5 File Image Operations</a>"
 ALIASES += ref_rfc20120305="<a href=\"https://\RFCURL/RFC%20PHDF5%20Consistency%20Semantics%20MC%20120328.docx.pdf\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>"
 ALIASES += ref_rfc20120220="<a href=\"https://\RFCURL/h5repack_improve_hyperslab_over_chunked_dataset_v1.pdf\"><tt>h5repack</tt>: Improved Hyperslab selections for Large Chunked Datasets</a>"
 ALIASES += ref_rfc20120120="<a href=\"https://\RFCURL/2012-1-25-Maintainers-guide-for-datatype.docx.pdf\">A Maintainer's Guide for the Datatype Module in HDF5 Library</a>"

doxygen/dox/RFC.dox

@@ -53,7 +53,6 @@
 <tr> <td>2012-10-24</td> <td>\ref_rfc20121024</td></tr>
 <tr> <td>2012-08-28</td> <td>\ref_rfc20120828</td></tr>
 <tr> <td>2012-05-23</td> <td>\ref_rfc20120523</td></tr>
-<tr> <td>2012-05-01</td> <td>\ref_rfc20120501</td></tr>
 <tr> <td>2012-03-05</td> <td>\ref_rfc20120305</td></tr>
 <tr> <td>2012-02-20</td> <td>\ref_rfc20120220</td></tr>
 <tr> <td>2012-01-20</td> <td>\ref_rfc20120120</td></tr>

doxygen/dox/UsersGuide.dox

@@ -304,12 +304,54 @@
         <li> \ref subsubsec_vol_compat_opt
     </ul>
 
+\ref sec_file_image
+\li \ref subsec_file_image_intro
+\li \ref subsec_file_image_api
+    <ul>
+        <li> \ref subsubsec_file_image_api_low
+        <li> \ref subsubsec_file_image_api_high
+    </ul>
+\li \ref subsec_file_image_semantics
+    <ul>
+        <li> \ref subsubsec_file_image_semantics_cbk
+        <li> \ref subsubsec_file_image_semantics_init
+    </ul>
+\li \ref subsec_file_image_example
+    <ul>
+        <li> \ref subsubsec_file_image_example_read
+        <li> \ref subsubsec_file_image_example_const
+        <li> \ref subsubsec_file_image_example_dp
+        <li> \ref subsubsec_file_image_example_template
+    </ul>
+\li \ref subsec_file_image_java
+\li \ref subsec_file_image_fort
+    <ul>
+        <li> \ref subsubsec_file_image_fort_low
+        <li> \ref subsubsec_file_image_fort_high
+    </ul>
+
 \ref sec_async
 \li \ref subsec_async_intro
 
 \ref sec_map
 
 \ref sec_cltools
+\li \ref H5TOOL_CP_UG
+\li \ref H5TOOL_DF_UG
+\li \ref H5TOOL_DP_UG
+\li \ref H5TOOL_FC_UG
+\li \ref H5TOOL_IM_UG
+\li \ref H5TOOL_JAM_UG
+\li \ref H5TOOL_LS_UG
+\li \ref H5TOOL_RP_UG
+\li \ref H5TOOL_ST_UG
+\li \ref H5TOOL_CR_UG
+\li \ref H5TOOL_DG_UG
+\li \ref H5TOOL_DT_UG
+\li \ref H5TOOL_MG_UG
+\li \ref H5TOOL_RT_UG
+\li \ref H5TOOL_WH_UG
+
 
 \ref sec_addition
 
@@ -345,7 +387,7 @@ These documents provide additional information for the use and tuning of specifi
 </tr>
   <tr style="height: 36.00pt;">
   <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
-  <p style="font-style: italic; color: #0000ff;"><span class="FM_LT_LinkText"><a href="http://\ARCURL/Advanced/DirectChunkWrite/UsingDirectChunkWrite.pdf">Using the Direct Chunk Write Function</a></span></p>
+  <p style="font-style: italic; color: #0000ff;"><span class="FM_LT_LinkText">@ref H5DO_UG</span></p>
 </td>
   <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
   <p>Describes another way that chunks can be written to datasets.</p>
@@ -377,7 +419,7 @@ These documents provide additional information for the use and tuning of specifi
 </tr>
   <tr style="height: 62.00pt;">
   <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
-  <p style="font-style: italic; color: #0000ff;"><span><a href="https://\RFCURL/HDF5FileImageOperations.pdf">HDF5 File Image Operations</a></span></p>
+  <p style="font-style: italic; color: #0000ff;"><span>\ref H5FIM_UG</span></p>
 </td>
   <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
   <p>Describes how to work with HDF5 files in memory. Disk I/O is not required when file images are opened, created, read from, or written to.</p>

doxygen/dox/ViewTools.dox

@@ -303,6 +303,8 @@ GROUP "/" {
 }
 \endcode
 
+\see H5TOOL_DP_UG for more information.
+
 \subsection subsecViewToolsViewContent_h5ls h5ls
 The h5ls tool by default just displays the objects in the root group. It will not display
 items in groups beneath the root group unless specified. Useful h5ls options for viewing
@@ -355,6 +357,8 @@ The output is shown below:
 /HDFEOS\ INFORMATION/StructMetadata.0 Dataset {SCALAR}
 \endcode
 
+\see H5TOOL_LS_UG for more information.
+
 \section secViewToolsViewDset Datasets and Dataset Properties
 Both h5dump and h5ls can be used to view specific datasets.
 <ul>