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c1e44d3 Fix doxygen warnings and remove javadocs (HDFGroup#2324)
149b8e9 Disable hl tools by default (HDFGroup#2313)
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derobins committed Dec 20, 2022
1 parent e6df527 commit 7854ee8
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17 changes: 17 additions & 0 deletions configure.ac
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Expand Up @@ -833,6 +833,7 @@ AC_LANG_POP(C++)
## library is disabled.
AC_SUBST([HDF5_HL])
AC_SUBST([HDF5_HL_TOOLS])
AC_SUBST([HDF5_HL_GIF_TOOLS])

## The high-level library and high-level tools are enabled unless the build mode
## is clean.
Expand Down Expand Up @@ -888,6 +889,21 @@ else
AC_MSG_RESULT([no])
fi

AC_MSG_CHECKING([if the high-level GIF tools are enabled])
AC_ARG_ENABLE([hltools],
[AS_HELP_STRING([--enable-hlgiftools],
[Enable the high-level GIF tools.
[default=no]
])],
[HDF5_HL_GIF_TOOLS=$enableval])

if test "X${HDF5_GIF_HL}" = "Xyes" -a "X-$HDF5_HL_TOOLS" = "X-yes" -a "X-$HDF5_HL_GIF_TOOLS" = "X-yes"; then
AC_MSG_RESULT([yes])
HL_GIF_TOOLS="tools"
else
AC_MSG_RESULT([no])
fi


## ----------------------------------------------------------------------
## Enable new references for dimension scales
Expand Down Expand Up @@ -3907,6 +3923,7 @@ AM_CONDITIONAL([BUILD_TESTS_CONDITIONAL], [test "X$HDF5_TESTS" = "Xyes"])
AM_CONDITIONAL([BUILD_TESTS_PARALLEL_CONDITIONAL], [test -n "$TESTPARALLEL"])
AM_CONDITIONAL([BUILD_TOOLS_CONDITIONAL], [test "X$HDF5_TOOLS" = "Xyes"])
AM_CONDITIONAL([BUILD_TOOLS_HL_CONDITIONAL], [test "X$HDF5_HL_TOOLS" = "Xyes"])
AM_CONDITIONAL([BUILD_TOOLS_HL_GIF_CONDITIONAL], [test "X$HDF5_HL_GIF_TOOLS" = "Xyes"])
AM_CONDITIONAL([BUILD_DOXYGEN_CONDITIONAL], [test "X$HDF5_DOXYGEN" = "Xyes"])

## ----------------------------------------------------------------------
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2 changes: 1 addition & 1 deletion doxygen/Doxyfile.in
Original file line number Diff line number Diff line change
Expand Up @@ -854,7 +854,7 @@ INPUT_ENCODING = UTF-8
# *.vhdl, *.ucf, *.qsf and *.ice.

FILE_PATTERNS = H5*public.h H5*module.h H5*develop.h H5FD*.h \
H5VLconnector.h H5VLconnector_passthru.h H5VLnative.h \
H5VLconnector.h H5VLconnector_passthru.h H5VLnative.h H5PLextern.h \
H5Zdevelop.h \
H5version.h \
H5*.java \
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8 changes: 3 additions & 5 deletions doxygen/dox/ViewTools.dox
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Expand Up @@ -829,6 +829,7 @@ by simply viewing the specified dataset with the <code style="background-color:w
\code
h5dump -d "HDFEOS/GRIDS/OMI Column Amount O3/Data Fields/SolarZenithAngle" OMI-Aura.he5
\endcode

Subsetting narrows down the output that is displayed. In the following example, the first
15x10 elements (-c "15,10") are specified, beginning with position (0,0) (-s "0,0"):
\code
Expand All @@ -840,11 +841,8 @@ If using the shorthand method, specify:
h5dump -A 0 -d "HDFEOS/GRIDS/OMI Column Amount O3/Data Fields/SolarZenithAngle[0,0;;15,10;]" -w 0 OMI-Aura.he5
\endcode

Where,
\par The <code style="background-color:whitesmoke;">-d</code> option must be specified

before
\par subsetting options (if not using the shorthand method).
Where, the <code style="background-color:whitesmoke;">-d</code> option must be specified
before subsetting options (if not using the shorthand method).

The <code style="background-color:whitesmoke;">-A 0</code> option suppresses the printing of attributes.

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2 changes: 1 addition & 1 deletion doxygen/dox/cookbook/Accessibility.dox
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@@ -1,6 +1,6 @@
/** \page Accessibility

\section Accessibility
\section secAccessibility Accessibility

\subsection CB_MaintainCompat Maintaining Compatibility with other HDF5 Library Versions

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2 changes: 1 addition & 1 deletion doxygen/dox/cookbook/Attributes.dox
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
/** \page Attributes

\section Attributes
\section secAttributes Attributes

\subsection CB_LargeAttributes Creating "Large" HDF5 Attributes

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2 changes: 1 addition & 1 deletion doxygen/dox/cookbook/Files.dox
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@@ -1,6 +1,6 @@
/** \page Files

\section Files
\section secFiles Files

\subsection CB_FreeSpace Tracking Free Space in HDF5 Files

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2 changes: 1 addition & 1 deletion doxygen/dox/cookbook/Performance.dox
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
/** \page Performance

\section Performance
\section secPerformance Performance

\subsection CB_MDCPerf Assessing HDF5 Metadata Cache Performance

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8 changes: 4 additions & 4 deletions doxygen/hdf5doxy_layout.xml
Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,13 @@
<navindex>
<tab type="user" url="index.html" title="Overview" />
<tab type="user" url="@ref GettingStarted" title="Getting started" />
<tab type="user" url="@ref Cookbook" title="Cookbook" />
<tab type="user" url="@ref UG" title="User Guide" />
<tab type="user" url="https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide" title="Application Developer's Guide" />
<tab type="user" url="@ref GLS" title="Glossary" />
<tab type="user" url="@ref RM" title="Reference Manual" />
<tab type="user" url="@ref TN" title="Technical Notes" />
<tab type="user" url="@ref GLS" title="Glossary" />
<tab type="user" url="https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide" title="Application Developer's Guide" />
<tab type="user" url="@ref SPEC" title="Specifications" />
<tab type="user" url="@ref Cookbook" title="Cookbook" />
<tab type="user" url="@ref TN" title="Technical Notes" />
<tab type="user" url="@ref RFC" title="RFCs" />
<tab type="user" url="@ref FTS" title="Full-Text Search" />
<tab type="user" url="@ref About" title="About" />
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25 changes: 0 additions & 25 deletions fortran/src/H5Pff.F90
Original file line number Diff line number Diff line change
Expand Up @@ -4305,31 +4305,6 @@ SUBROUTINE h5pset_f(prp_id, name, value, hdferr)
CHARACTER(LEN=*), INTENT(IN) :: name
INTEGER , INTENT(IN) :: value
INTEGER , INTENT(OUT) :: hdferr
END SUBROUTINE h5pset

!>
!! \ingroup FH5P
!!
!! \brief Sets a property list value.
!!
!! \attention \fortran_obsolete
!!
!! \param prp_id Property list identifier to modify.
!! \param name Name of property to modify.
!! \param value Property value, supported types are:
!! \li INTEGER
!! \li REAL
!! \li DOUBLE PRECISION
!! \li CHARACTER(LEN=*)
!! \param hdferr \fortran_error
!!
!! See C API: @ref H5Pset()
!!
SUBROUTINE h5pset_f(prp_id, name, value, hdferr)
INTEGER(HID_T), INTENT(IN) :: prp_id
CHARACTER(LEN=*), INTENT(IN) :: name
INTEGER, INTENT(IN) :: value
INTEGER, INTENT(OUT) :: hdferr
END SUBROUTINE h5pset_f
!>
!! \ingroup FH5P
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10 changes: 9 additions & 1 deletion hl/tools/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,14 @@
cmake_minimum_required (VERSION 3.18)
project (HDF5_HL_TOOLS C)

add_subdirectory (gif2h5)
#-----------------------------------------------------------------------------
#-- Option to build the High level GIF Tools
#-----------------------------------------------------------------------------
if (EXISTS "${HDF5_HL_SOURCE_DIR}/gif2h5" AND IS_DIRECTORY "${HDF5_HL_SOURCE_DIR}/gif2h5")
option (HDF5_BUILD_HL_GIF_TOOLS "Build HDF5 HL GIF Tools" OFF)
if (HDF5_BUILD_HL_GIF_TOOLS)
add_subdirectory (gif2h5)
endif ()
endif ()

add_subdirectory (h5watch)
8 changes: 7 additions & 1 deletion hl/tools/Makefile.am
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,13 @@

include $(top_srcdir)/config/commence.am

if BUILD_TOOLS_HL_GIF_CONDITIONAL
TOOLS_GIF_DIR = gif2h5
else
TOOLS_GIF_DIR =
endif

# All subdirectories
SUBDIRS=gif2h5 h5watch
SUBDIRS=$(TOOLS_DIR) h5watch

include $(top_srcdir)/config/conclude.am
8 changes: 2 additions & 6 deletions java/src/Makefile.am
Original file line number Diff line number Diff line change
Expand Up @@ -111,26 +111,22 @@ hdf5_java_JAVA = \
${pkgpath}/HDFArray.java \
${pkgpath}/HDFNativeData.java

$(jarfile): classhdf5_java.stamp classes docs
$(jarfile): classhdf5_java.stamp classes
$(JAR) cvf $@ -C $(JAVAROOT)/ $(pkgpath)

hdf5_java_DATA = $(jarfile)

.PHONY: docs classes
.PHONY: classes

WINDOWTITLE = 'HDF5 Java'
DOCTITLE = '<h1>HDF5 Java Wrapper</h1>'
SRCDIR = '$(pkgpath)'

docs:
$(JAVADOC) -sourcepath $(srcdir) -d javadoc -Xdoclint:none -use -splitIndex -windowtitle $(WINDOWTITLE) -doctitle $(DOCTITLE) -J-Xmx180m -verbose -overview $(top_srcdir)/java/src/hdf/overview.html -classpath $(CLASSPATH_ENV) hdf.hdf5lib

CLEANFILES = classhdf5_java.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/callbacks/*.class $(JAVAROOT)/$(pkgpath)/exceptions/*.class $(JAVAROOT)/$(pkgpath)/structs/*.class $(JAVAROOT)/$(pkgpath)/*.class

clean:
rm -rf $(JAVAROOT)/*
rm -f $(jarfile)
rm -rf javadoc
rm -f classhdf5_java.stamp


Expand Down
12 changes: 0 additions & 12 deletions java/src/hdf/hdf5lib/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -134,15 +134,3 @@ set_target_properties (${HDF5_JAVA_HDF5_LIB_TARGET} PROPERTIES FOLDER libraries/
if (HDF5_ENABLE_FORMATTERS)
clang_format (HDF5_JAVA_SRC_FORMAT ${HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES} ${HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES} ${HDF5_JAVA_HDF_HDF5_STRUCTS_SOURCES} ${HDF5_JAVA_HDF_HDF5_SOURCES})
endif ()

create_javadoc(hdf5_java_doc
FILES ${HDF5_JAVADOC_HDF_HDF5_CALLBACKS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_EXCEPTIONS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_STRUCTS_SOURCES} ${HDF5_JAVADOC_HDF_HDF5_SOURCES}
OVERVIEW ${HDF5_JAVA_HDF5_SRC_DIR}/overview.html
CLASSPATH ${CMAKE_JAVA_INCLUDE_PATH}
WINDOWTITLE "HDF5 Java"
DOCTITLE "<h1>HDF5 Java Wrapper</h1>"
INSTALLPATH ${HDF5_INSTALL_DOC_DIR}
AUTHOR TRUE
USE TRUE
VERSION TRUE
)
1 change: 1 addition & 0 deletions release_docs/INSTALL_CMake.txt
Original file line number Diff line number Diff line change
Expand Up @@ -741,6 +741,7 @@ HDF5_BUILD_JAVA "Build JAVA support" OFF
HDF5_BUILD_HL_LIB "Build HIGH Level HDF5 Library" ON
HDF5_BUILD_TOOLS "Build HDF5 Tools" ON
HDF5_BUILD_HL_TOOLS "Build HIGH Level HDF5 Tools" ON
HDF5_BUILD_HL_GIF_TOOLS "Build HIGH Level HDF5 GIF Tools" OFF

---------------- HDF5 Folder Build Options ---------------------
Defaults relative to $<INSTALL_PREFIX>
Expand Down
26 changes: 22 additions & 4 deletions release_docs/RELEASE.txt
Original file line number Diff line number Diff line change
Expand Up @@ -301,6 +301,24 @@ Bug Fixes since HDF5-1.13.3 release

Configuration
-------------
- Remove Javadoc generation

The use of doxygen now supersedes the requirement to build javadocs. We do not
have the resources to continue to support two documentation methods and have
chosen doxygen as our standard.

(ADB - 2022/12/19)

- Change the default for building the high-level tools

The gif2hdf5 and hdf2gif high-level tools are deprecated and will be removed
in a future release. The default build setting for them have been changed from enabled
to disabled. A user can enable the build of these tools if needed.
autotools: --enable-hlgiftools
cmake: HDF5_BUILD_HL_GIF_TOOLS=ON

(ADB - 2022/12/16)

- Change the settings of the *pc files to use the correct format

The pkg-config files generated by CMake uses incorrect syntax for the 'Requires'
Expand Down Expand Up @@ -583,7 +601,7 @@ The issues with the gif tool are:
HDFFV-10592 CVE-2018-17433
HDFFV-10593 CVE-2018-17436
HDFFV-11048 CVE-2020-10809
These CVE issues have not yet been addressed and can be avoided by not building
the gif tool. Disable building the High-Level tools with these options:
autotools: --disable-hltools
cmake: HDF5_BUILD_HL_TOOLS=OFF
These CVE issues have not yet been addressed and are avoided by not building
the gif tool by default. Enable building the High-Level tools with these options:
autotools: --enable-hltools
cmake: HDF5_BUILD_HL_TOOLS=ON
2 changes: 1 addition & 1 deletion src/H5Amodule.h
Original file line number Diff line number Diff line change
Expand Up @@ -363,7 +363,7 @@
* will be ignored by HDF5.
*
* The use of ASCII or UTF-8 characters is determined by the character encoding property. See
* #H5Pset_char_encoding in the \ref RM.
* #H5Pset_char_encoding in the \ref RM.
*
* <h4>No Special I/O or Storage</h4>
*
Expand Down
2 changes: 1 addition & 1 deletion src/H5Gmodule.h
Original file line number Diff line number Diff line change
Expand Up @@ -923,7 +923,7 @@
* containing thousands to millions of members. Links are stored in
* a fractal heap and indexed with an improved B-tree.
* \li The new implementation also enables the use of link names consisting of
* non-ASCII character sets (see H5Pset_char_encoding()) and is
* non-ASCII character sets (see #H5Pset_char_encoding) and is
* required for all link types other than hard or soft links, e.g.,
* external and user-defined links (see the \ref H5L APIs).
*
Expand Down
4 changes: 2 additions & 2 deletions src/H5Lpublic.h
Original file line number Diff line number Diff line change
Expand Up @@ -729,7 +729,7 @@ H5_DLL herr_t H5Lexists_async(hid_t loc_id, const char *name, hbool_t *exists, h
* \p cset specifies the character set in which the link name is
* encoded. Valid values include the following:
* \csets
* This value is set with H5Pset_char_encoding().
* This value is set with #H5Pset_char_encoding.
*
* \c token is the location that a hard link points to, and
* \c val_size is the size of a soft link or user defined link value.
Expand Down Expand Up @@ -1525,7 +1525,7 @@ typedef herr_t (*H5L_iterate1_t)(hid_t group, const char *name, const H5L_info1_
* \c cset specifies the character set in which the link name is
* encoded. Valid values include the following:
* \csets
* This value is set with H5Pset_char_encoding().
* This value is set with #H5Pset_char_encoding.
*
* \c address and \c val_size are returned for hard and symbolic
* links, respectively. Symbolic links include soft and external links
Expand Down
2 changes: 1 addition & 1 deletion src/H5Tpublic.h
Original file line number Diff line number Diff line change
Expand Up @@ -1035,7 +1035,7 @@ H5_DLLVAR hid_t H5T_NATIVE_UINT_FAST64_g;
* When creating a fixed-length string datatype, \p size will
* be the length of the string in bytes. The length of the
* string in characters will depend on i the encoding used; see
* H5Pset_char_encoding().
* #H5Pset_char_encoding.
*
* ENUMs created with this function have a signed native integer
* base datatype. Use H5Tenum_create() if a different integer base
Expand Down
2 changes: 1 addition & 1 deletion src/H5VLconnector_passthru.h
Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ H5_DLL herr_t H5VLcmp_connector_cls(int *cmp, hid_t connector_id1, hid_t connect
* - #H5I_MAP
* - #H5I_ATTR
*
* \return \hid_t
* \return \hid_t{VOL connector}
*
* \note This routine is mainly targeted toward wrapping objects for
* iteration routine callbacks (i.e. the callbacks from H5Aiterate*,
Expand Down

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