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Merge remote-tracking branch 'origin/develop' into pause_errors_5
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@qkoziol
qkoziol committed Jul 16, 2024
2 parents a94b0b8 + 69dda03 commit 03a3f5c
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6 changes: 3 additions & 3 deletions .../TUTR/H5_CreateGroupAbsoluteRelative.java → ...TUTR/HDF5GroupAbsoluteRelativeCreate.java
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Expand Up @@ -17,8 +17,8 @@
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;

public class H5_CreateGroupAbsoluteRelative {
private static String FILENAME = "H5_CreateGroupAbsoluteRelative.h5";
public class HDF5GroupAbsoluteRelativeCreate {
private static String FILENAME = "HDF5GroupAbsoluteRelativeCreate.h5";
private static String GROUPNAME = "MyGroup";
private static String GROUPNAME_A = "GroupA";
private static String GROUPNAME_B = "GroupB";
Expand Down Expand Up @@ -109,6 +109,6 @@ private static void CreateGroupAbsoluteAndRelative()

public static void main(String[] args)
{
H5_CreateGroupAbsoluteRelative.CreateGroupAbsoluteAndRelative();
HDF5GroupAbsoluteRelativeCreate.CreateGroupAbsoluteAndRelative();
}
}
1 change: 1 addition & 0 deletions HDF5Examples/JAVA/TUTR/Java_sourcefiles.cmake
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Expand Up @@ -9,6 +9,7 @@ set (HDF_JAVA_EXAMPLES
HDF5DatasetRead.java
HDF5GroupDatasetCreate.java
HDF5SubsetSelect.java
HDF5GroupAbsoluteRelativeCreate.java
)
if (H5_LIBVER_DIR EQUAL 110)
set (HDF_JAVA_EXAMPLES ${HDF_JAVA_EXAMPLES}
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Empty file added HDF5Examples/JAVA/TUTR/tfiles/110/HDF5GroupAbsoluteRelativeCreate.txt
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Empty file.
12 changes: 3 additions & 9 deletions config/cmake/HDF5PluginMacros.cmake
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Expand Up @@ -24,15 +24,9 @@ macro (EXTERNAL_PLUGIN_LIBRARY compress_type)
URL_HASH ""
)
endif ()
FetchContent_GetProperties(PLUGIN)
message (VERBOSE "HDF5_INCLUDE_DIR=${HDF5_INCLUDE_DIR}")
if(NOT PLUGIN_POPULATED)
FetchContent_Populate(PLUGIN)
include (${HDF_RESOURCES_DIR}/HDF5PluginCache.cmake)
set(CMAKE_POLICY_DEFAULT_CMP0077 NEW)
add_subdirectory(${plugin_SOURCE_DIR} ${plugin_BINARY_DIR})
endif ()
message (VERBOSE "HDF5_INCLUDE_DIR=${HDF5_INCLUDE_DIR}")
include (${HDF_RESOURCES_DIR}/HDF5PluginCache.cmake)
set(CMAKE_POLICY_DEFAULT_CMP0077 NEW)
FetchContent_MakeAvailable(PLUGIN)
set (PLUGIN_BINARY_DIR "${plugin_BINARY_DIR}")
set (PLUGIN_SOURCE_DIR "${plugin_SOURCE_DIR}")
set (PLUGIN_LIBRARY "PLUGIN")
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40 changes: 19 additions & 21 deletions config/cmake/HDFLibMacros.cmake
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Expand Up @@ -11,31 +11,31 @@
#
#-------------------------------------------------------------------------------
macro (EXTERNAL_ZLIB_LIBRARY compress_type)
if (HDF5_USE_ZLIB_NG)
set (zlib_folder "ZLIBNG")
else ()
set (zlib_folder "ZLIB")
endif ()
if (${compress_type} MATCHES "GIT")
FetchContent_Declare (HDF5_ZLIB
GIT_REPOSITORY ${ZLIB_URL}
GIT_TAG ${ZLIB_BRANCH}
PATCH_COMMAND ${CMAKE_COMMAND} -E copy
${HDF_RESOURCES_DIR}/${zlib_folder}/CMakeLists.txt
<SOURCE_DIR>/CMakeLists.txt
)
elseif (${compress_type} MATCHES "TGZ")
message (VERBOSE "Filter ZLIB file ${ZLIB_URL}")
FetchContent_Declare (HDF5_ZLIB
URL ${ZLIB_URL}
URL_HASH ""
PATCH_COMMAND ${CMAKE_COMMAND} -E copy
${HDF_RESOURCES_DIR}/${zlib_folder}/CMakeLists.txt
<SOURCE_DIR>/CMakeLists.txt
)
endif ()
FetchContent_GetProperties(HDF5_ZLIB)
if(NOT hdf5_zlib_POPULATED)
FetchContent_Populate(HDF5_ZLIB)

# Copy an additional/replacement files into the populated source
if (HDF5_USE_ZLIB_NG)
file(COPY ${HDF_RESOURCES_DIR}/ZLIBNG/CMakeLists.txt DESTINATION ${hdf5_zlib_SOURCE_DIR})
else ()
file(COPY ${HDF_RESOURCES_DIR}/ZLIB/CMakeLists.txt DESTINATION ${hdf5_zlib_SOURCE_DIR})
endif ()

add_subdirectory(${hdf5_zlib_SOURCE_DIR} ${hdf5_zlib_BINARY_DIR})
endif()
FetchContent_MakeAvailable(HDF5_ZLIB)

add_library(${HDF_PACKAGE_NAMESPACE}zlib-static ALIAS zlib-static)
set (H5_ZLIB_STATIC_LIBRARY "${HDF_PACKAGE_NAMESPACE}zlib-static")
Expand All @@ -54,23 +54,21 @@ macro (EXTERNAL_SZIP_LIBRARY compress_type encoding)
FetchContent_Declare (SZIP
GIT_REPOSITORY ${SZIP_URL}
GIT_TAG ${SZIP_BRANCH}
PATCH_COMMAND ${CMAKE_COMMAND} -E copy
${HDF_RESOURCES_DIR}/LIBAEC/CMakeLists.txt
<SOURCE_DIR>/CMakeLists.txt
)
elseif (${compress_type} MATCHES "TGZ")
message (VERBOSE "Filter SZIP file ${SZIP_URL}")
FetchContent_Declare (SZIP
URL ${SZIP_URL}
URL_HASH ""
PATCH_COMMAND ${CMAKE_COMMAND} -E copy
${HDF_RESOURCES_DIR}/LIBAEC/CMakeLists.txt
<SOURCE_DIR>/CMakeLists.txt
)
endif ()
FetchContent_GetProperties(SZIP)
if(NOT szip_POPULATED)
FetchContent_Populate(SZIP)

# Copy an additional/replacement files into the populated source
file(COPY ${HDF_RESOURCES_DIR}/LIBAEC/CMakeLists.txt DESTINATION ${szip_SOURCE_DIR})

add_subdirectory(${szip_SOURCE_DIR} ${szip_BINARY_DIR})
endif()
FetchContent_MakeAvailable(SZIP)

add_library (${HDF_PACKAGE_NAMESPACE}szaec-static ALIAS szaec-static)
add_library (${HDF_PACKAGE_NAMESPACE}aec-static ALIAS aec-static)
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10 changes: 9 additions & 1 deletion doxygen/aliases
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Expand Up @@ -3,18 +3,26 @@ ALIASES += THG="The HDF Group"
################################################################################
# Default URLs (Note that md files do not use any aliases)
################################################################################
# Default URL for HDF Group Files
ALIASES += HDFURL="docs.hdfgroup.org/hdf5"
# URL for archived files
ALIASES += ARCURL="docs.hdfgroup.org/archive/support/HDF5/doc"
# URL for RFCs
ALIASES += RFCURL="docs.hdfgroup.org/hdf5/rfc"
# URL for documentation
ALIASES += DSPURL="portal.hdfgroup.org/display/HDF5"
ALIASES += DOCURL="portal.hdfgroup.org/documentation/hdf5-docs"
# URL for downloads
ALIASES += DWNURL="portal.hdfgroup.org/downloads"
ALIASES += AEXURL="support.hdfgroup.org/ftp/HDF5/examples"
# doxygen subdir (develop, v1_14)
ALIASES += DOXURL="hdfgroup.github.io/hdf5/develop"
#branch name (develop, hdf5_1_14)
ALIASES += SRCURL="github.com/HDFGroup/hdf5/blob/develop"

#Other projects that contribute to HDF5
ALIASES += PRJURL="\HDFURL/projects"
ALIASES += HVURL="github.com/HDFGroup/hdfview/blob/master"
ALIASES += PLURL="github.com/HDFGroup/hdf5_plugins/blob/master"
################################################################################
# Styling
################################################################################
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24 changes: 16 additions & 8 deletions doxygen/dox/IntroHDF5.dox
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Expand Up @@ -298,19 +298,27 @@ hsize_t is used for dimensions
Language specific files must be included in applications:
<ul>
<li>
Python: Add <code>"import h5py / import numpy"</code>
<strong>Python</strong>:<br />
<code>
import h5py<br />
import numpy
</code>
</li>
<li>
C: Add <code>"#include hdf5.h"</code>
<strong>C</strong>:<br />
<code>"#include hdf5.h"</code>
</li>
<li>
FORTRAN: Add <code>"USE HDF5"</code> and call h5open_f and h5close_f to initialize and close the HDF5 FORTRAN interface
<strong>FORTRAN</strong>:<br />
<code>USE HDF5</code><br />
and call h5open_f and h5close_f to initialize and close the HDF5 FORTRAN interface
</li>
<li>
Java: Add <code>"import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;"</code>
</li>
</ul>
<strong>Java</strong>:<br />
<code>
import hdf.hdf5lib.H5;<br />
import hdf.hdf5lib.HDF5Constants;
</code>
</li>
</ul>

Expand Down Expand Up @@ -608,7 +616,7 @@ on the <a href="http://hdfeos.org/">HDF-EOS Tools and Information Center</a> pag
\section secHDF5Examples Examples
\li \ref LBExamples
\li \ref ExAPI
\li <a href="https://github.com/HDFGroup/hdf5/tree/develop/examples">Examples in the Source Code</a>
\li <a href="https://github.com/HDFGroup/hdf5/tree/develop/HDF5Examples">Examples in the Source Code</a>
\li <a href="https://\DSPURL/Other+Examples">Other Examples</a>

\section secHDF5ExamplesCompile How To Compile
Expand Down
18 changes: 9 additions & 9 deletions doxygen/dox/LearnBasics.dox
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Expand Up @@ -41,7 +41,7 @@ Navigate back: \ref index "Main" / \ref GettingStarted
Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
<hr>

\section secLBExamples
\section secLBExamples HDF5 Examples
These examples are used in the \ref LearnBasics topic. See \ref LBCompiling for details on compiling them.
PLEASE NOTE that the example programs are listed in the order they are expected to be run. Some example
programs use files created in earlier examples.
Expand All @@ -59,63 +59,63 @@ These examples (C, C++, Fortran, Java, Python) are provided in the HDF5 source c
<tr>
<td>Create a file
</td>
<td>C Fortran C++ <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5FileCreateFile.java">Java</a> Python
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtgrp.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtgrp.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtgrp.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5FileCreate.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtgrp.py">Python</a>
</td>
<td>
</td>
</tr>
<tr>
<td>Create a dataset
</td>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtdat.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtdat.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtdat.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/H5_CreateDataset.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtdat.py">Python</a>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtdat.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtdat.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtdat.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5DatasetCreate.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtdat.py">Python</a>
</td>
<td>
</td>
</tr>
<tr>
<td>Read and write to a dataset
</td>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_rdwt.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_rdwt.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_rdwt.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/H5_ReadWrite.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_rdwt.py">Python</a>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_rdwt.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_rdwt.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_rdwt.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5DatasetRead.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_rdwt.py">Python</a>
</td>
<td>
</td>
</tr>
<tr>
<td>Create an attribute
</td>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtatt.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtatt.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtatt.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/H5_CreateAttribute.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtatt.py">Python</a>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtatt.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtatt.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtatt.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5AttributeCreate.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtatt.py">Python</a>
</td>
<td>
</td>
</tr>
<tr>
<td>Create a group
</td>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtgrp.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtgrp.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtgrp.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/H5_CreateGroup.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtgrp.py">Python</a>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtgrp.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtgrp.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtgrp.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5GroupCreate.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtgrp.py">Python</a>
</td>
<td>
</td>
</tr>
<tr>
<td>Create groups in a file using absolute and relative paths
</td>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtgrpar.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtgrpar.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtgrpar.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/H5_CreateGroupAbsoluteRelative.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtgrpar.py">Python</a>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtgrpar.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtgrpar.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtgrpar.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5GroupAbsoluteRelativeCreate.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtgrpar.py">Python</a>
</td>
<td>
</td>
</tr>
<tr>
<td>Create datasets in a group
</td>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtgrpd.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtgrpd.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtgrpd.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/H5_CreateGroupDataset.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtgrpd.py">Python</a>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtgrpd.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtgrpd.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtgrpd.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5GroupDatasetCreate.java">Java</a> <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtgrpd.py">Python</a>
</td>
<td>
</td>
</tr>
<tr>
<td>Create a file and dataset and select/read a subset from the dataset
</td>
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_subset.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_subset.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_subset.cpp">C++</a> Java Python
<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_subset.c">C</a> <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_subset.f90">Fortran</a> <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_subset.cpp">C++</a> <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5SubsetSelect.java">Java</a> Python
</td>
<td>Also see examples to Write by row (and column) below.
</td>
Expand Down
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