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doygen adjustments (#614)
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* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* correct window os name

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* HDFFV-11113 long double in tools

* HDFFV-11113 add note

* Disable long double tests for now

* HDFFV-11228 remove arbitrary CMake warning groups.

* Make each flag a string

* Some Javadoc warning fixes

* Updated javadoc fixes

* # WARNING: head commit changed in the meantime

HDFFV-11229 Fix long double usage in tools and java

Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.

* Committing clang-format changes

* HDFFV-11229 Add release note

* HDFFV-11229 windows testfile needed

* fix typo

* Remove non supported message text

* HDFFV-11229 - change ldouble test to check both native and general

* HDFFV-11229 add second file compare

* HDFFV-11229 fix reference file

* HDFFV-11229 autotools check two refs

* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output

* Committing clang-format changes

* Update release note

* Update attribute type of ref file

* Change source of ninja for macs

* try port instead of brew

* Recommended is to use brew.

* Undo non long double changes

* remove unneeded file

* Fix perl and doxygen CMake code

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

* Add stamp files to BYPRODUCTS

* Only one copy of file exists

* Fix custom cmmand depends targets

* Fix fortran custom command DEPENDS

* Add LD_LIBRARY_PATH to tests

* Add custom target for DEPENDS

* Add h5detect conditionaly to generated target DEPENDS

* Correct DEPENDS targets

* Parallel builds need the mpi compiler for pkgconfig scripts.

* install only if MPI build

* Fortran target depends

* Remove incorrect source attribute

* doxygen adjustments

* doxygen build updates

* Correct version

* Correct function version - function has been merged to 1.12

* Correct version string for map functions

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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@byrnHDF @github-actions
byrnHDF and github-actions[bot] authored May 4, 2021
1 parent dc639bd commit 2f79e3f
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Showing 11 changed files with 112 additions and 100 deletions.
16 changes: 7 additions & 9 deletions Makefile.am
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,9 @@

include $(top_srcdir)/config/commence.am

# include Doxygen rules (requires autoconf-archive >2016-03-20)
@DX_RULES@

# Define subdirectories to build.
## Automake understands that `make distclean' should recurse into
## conditional subdirectories even if `make all' does not.
Expand Down Expand Up @@ -187,15 +190,10 @@ 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
# doxygen support
if BUILD_DOXYGEN_CONDITIONAL
doxygen: doxygen-doc
endif

# Run tests with different Virtual File Drivers.
# Currently, only invoke check-vfd in the test directory.
Expand Down
5 changes: 3 additions & 2 deletions configure.ac
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Original file line number Diff line number Diff line change
Expand Up @@ -1126,6 +1126,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
AC_SUBST([DOXYGEN_EXTERNAL_SEARCH])
AC_SUBST([DOXYGEN_SEARCHENGINE_URL])

# SRCDIR Environment variables used inside doxygen macro for the source location:
DOXYGEN_PACKAGE=${PACKAGE_NAME}
DOXYGEN_VERSION_STRING=${PACKAGE_VERSION}
DOXYGEN_INCLUDE_ALIASES='$(SRCDIR)/doxygen/aliases'
Expand All @@ -1135,7 +1136,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES
DOXYGEN_MACRO_EXPANSION=YES
DOXYGEN_OUTPUT_DIRECTORY=hdf5lib_docs
DOXYGEN_EXAMPLES_DIRECTORY='$(SRCDIR)/doxygen/examples'
DOXYGEN_EXAMPLES_DIRECTORY='$(SRCDIR)/doxygen/examples $(SRCDIR)/src $(SRCDIR)/examples $(SRCDIR)/test'
DOXYGEN_LAYOUT_FILE='$(SRCDIR)/doxygen/hdf5doxy_layout.xml'
DOXYGEN_HTML_HEADER='$(SRCDIR)/doxygen/hdf5_header.html'
DOXYGEN_HTML_FOOTER='$(SRCDIR)/doxygen/hdf5_footer.html'
Expand All @@ -1145,7 +1146,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
DOXYGEN_EXTERNAL_SEARCH=NO
DOXYGEN_SEARCHENGINE_URL=

DX_INIT_DOXYGEN([HDF5], [../doxygen/Doxyfile], [hdf5lib_docs])
DX_INIT_DOXYGEN([HDF5], [./doxygen/Doxyfile], [hdf5lib_docs])

else
AC_MSG_RESULT([no])
Expand Down
2 changes: 1 addition & 1 deletion doxygen/Doxyfile.in
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Original file line number Diff line number Diff line change
Expand Up @@ -917,7 +917,7 @@ EXCLUDE_SYMBOLS =
# that contain example code fragments that are included (see the \include
# command).

EXAMPLE_PATH = ../src ../examples ../test @DOXYGEN_EXAMPLES_DIRECTORY@
EXAMPLE_PATH = @DOXYGEN_EXAMPLES_DIRECTORY@

# 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
Expand Down
13 changes: 13 additions & 0 deletions release_docs/INSTALL
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Original file line number Diff line number Diff line change
Expand Up @@ -450,6 +450,19 @@ CONTENTS

$ make -j -l6

4.4. Building doxygen
One can optionally build the doxygen files for the HDF5 C library.
By default, this option is disabled. To build the html files, specify
'--enable-doxygen'.

$ ./configure --enable-doxygen

Configuration will halt if the required applications are not available.
To build:

$ make doxygen


4.5. Testing
HDF5 comes with various test suites, all of which can be run by
specifying:
Expand Down
14 changes: 11 additions & 3 deletions src/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -1390,8 +1390,8 @@ endif ()
# Option to build documentation
#-----------------------------------------------------------------------------
if (DOXYGEN_FOUND)
set (DOXYGEN_PACKAGE ${HDF5_PACKAGE})
set (DOXYGEN_VERSION_STRING ${HDF5_VERSION_STRING})
set (DOXYGEN_PACKAGE ${HDF5_PACKAGE_NAME})
set (DOXYGEN_VERSION_STRING ${HDF5_PACKAGE_VERSION_STRING})
set (DOXYGEN_INCLUDE_ALIASES_PATH ${HDF5_DOXYGEN_DIR})
set (DOXYGEN_INCLUDE_ALIASES aliases)
set (DOXYGEN_VERBATIM_VARS DOXYGEN_INCLUDE_ALIASES)
Expand All @@ -1401,7 +1401,15 @@ if (DOXYGEN_FOUND)
set (DOXYGEN_OPTIMIZE_OUTPUT_FOR_C YES)
set (DOXYGEN_MACRO_EXPANSION YES)
set (DOXYGEN_OUTPUT_DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs)
set (DOXYGEN_EXAMPLES_DIRECTORY ${HDF5_DOXYGEN_DIR}/examples)
set (DOXYGEN_EXAMPLES_DIRECTORY "${HDF5_DOXYGEN_DIR}/examples ${HDF5_SRC_DIR} ${HDF5_SOURCE_DIR}/examples ${HDF5_TEST_SRC_DIR}")
set (DOXYGEN_LAYOUT_FILE ${HDF5_DOXYGEN_DIR}/hdf5doxy_layout.xml)
set (DOXYGEN_HTML_HEADER ${HDF5_DOXYGEN_DIR}/hdf5_header.html)
set (DOXYGEN_HTML_FOOTER ${HDF5_DOXYGEN_DIR}/hdf5_footer.html)
set (DOXYGEN_HTML_EXTRA_STYLESHEET ${HDF5_DOXYGEN_DIR}/hdf5doxy.css)
set (DOXYGEN_HTML_EXTRA_FILES "${HDF5_DOXYGEN_DIR}/hdf5_navtree_hacks.js ${HDF5_DOXYGEN_DIR}/img/ftv2node.png ${HDF5_DOXYGEN_DIR}/img/ftv2pnode.png")
set (DOXYGEN_SERVER_BASED_SEARCH NO)
set (DOXYGEN_EXTERNAL_SEARCH NO)
set (DOXYGEN_SEARCHENGINE_URL)

# This configure and custom target work together
# Replace variables inside @@ with the current values
Expand Down
98 changes: 49 additions & 49 deletions src/H5Apublic.h
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Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,13 @@ extern "C" {
* \see H5Acreate(), H5Aopen()
*/
H5_DLL herr_t H5Aclose(hid_t attr_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Aclose}
*/
H5_DLL herr_t H5Aclose_async(const char *app_file, const char *app_func, unsigned app_line, hid_t attr_id,
hid_t es_id);
/* --------------------------------------------------------------------------*/
/**
* \ingroup H5A
Expand Down Expand Up @@ -195,6 +202,15 @@ H5_DLL hid_t H5Acreate_async(const char *app_file, const char *app_func, unsigne
*/
H5_DLL hid_t H5Acreate_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, hid_t type_id,
hid_t space_id, hid_t acpl_id, hid_t aapl_id, hid_t lapl_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Acreate_by_name}
*/
H5_DLL hid_t H5Acreate_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
hid_t loc_id, const char *obj_name, const char *attr_name, hid_t type_id,
hid_t space_id, hid_t acpl_id, hid_t aapl_id, hid_t lapl_id,
hid_t es_id);
/*-------------------------------------------------------------------------*/
/**
* \ingroup H5A
Expand Down Expand Up @@ -316,6 +332,13 @@ H5_DLL herr_t H5Adelete_by_name(hid_t loc_id, const char *obj_name, const char *
*
*/
H5_DLL htri_t H5Aexists(hid_t obj_id, const char *attr_name);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Aexists}
*/
H5_DLL herr_t H5Aexists_async(const char *app_file, const char *app_func, unsigned app_line, hid_t obj_id,
const char *attr_name, hbool_t *exists, hid_t es_id);
/*-------------------------------------------------------------------------*/
/**
* \ingroup H5A
Expand Down Expand Up @@ -349,6 +372,14 @@ H5_DLL htri_t H5Aexists(hid_t obj_id, const char *attr_name);
*
*/
H5_DLL htri_t H5Aexists_by_name(hid_t obj_id, const char *obj_name, const char *attr_name, hid_t lapl_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Aexists_by_name}
*/
H5_DLL herr_t H5Aexists_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
hid_t loc_id, const char *obj_name, const char *attr_name,
hbool_t *exists, hid_t lapl_id, hid_t es_id);
/*-------------------------------------------------------------------------*/
/**
* \ingroup H5A
Expand Down Expand Up @@ -789,15 +820,6 @@ H5_DLL herr_t H5Aiterate_by_name(hid_t loc_id, const char *obj_name, H5_index_t
H5_iter_order_t order, hsize_t *idx, H5A_operator2_t op, void *op_data,
hid_t lapl_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Acreate_by_name}
*/
H5_DLL hid_t H5Acreate_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
hid_t loc_id, const char *obj_name, const char *attr_name, hid_t type_id,
hid_t space_id, hid_t acpl_id, hid_t aapl_id, hid_t lapl_id,
hid_t es_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup H5A
*
Expand Down Expand Up @@ -969,6 +991,13 @@ H5_DLL hid_t H5Aopen_by_name_async(const char *app_file, const char *app_func, u
*
*/
H5_DLL herr_t H5Aread(hid_t attr_id, hid_t type_id, void *buf);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Aread}
*/
H5_DLL herr_t H5Aread_async(const char *app_file, const char *app_func, unsigned app_line, hid_t attr_id,
hid_t dtype_id, void *buf, hid_t es_id);
/*-------------------------------------------------------------------------*/
/**
* \ingroup H5A
Expand All @@ -994,10 +1023,18 @@ H5_DLL herr_t H5Arename(hid_t loc_id, const char *old_name, const char *new_name
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Aread}
* \async_variant_of{H5Arename}
*/
H5_DLL herr_t H5Aread_async(const char *app_file, const char *app_func, unsigned app_line, hid_t attr_id,
hid_t dtype_id, void *buf, hid_t es_id);
H5_DLL herr_t H5Arename_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
const char *old_name, const char *new_name, hid_t es_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Arename_by_name}
*/
H5_DLL herr_t H5Arename_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
hid_t loc_id, const char *obj_name, const char *old_attr_name,
const char *new_attr_name, hid_t lapl_id, hid_t es_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup H5A
Expand Down Expand Up @@ -1037,36 +1074,6 @@ H5_DLL herr_t H5Awrite(hid_t attr_id, hid_t type_id, const void *buf);
*/
H5_DLL herr_t H5Awrite_async(const char *app_file, const char *app_func, unsigned app_line, hid_t attr_id,
hid_t type_id, const void *buf, hid_t es_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Arename}
*/
H5_DLL herr_t H5Arename_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
const char *old_name, const char *new_name, hid_t es_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Arename_by_name}
*/
H5_DLL herr_t H5Arename_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
hid_t loc_id, const char *obj_name, const char *old_attr_name,
const char *new_attr_name, hid_t lapl_id, hid_t es_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Aexists}
*/
H5_DLL herr_t H5Aexists_async(const char *app_file, const char *app_func, unsigned app_line, hid_t obj_id,
const char *attr_name, hbool_t *exists, hid_t es_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Aexists_by_name}
*/
H5_DLL herr_t H5Aexists_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
hid_t loc_id, const char *obj_name, const char *attr_name,
hbool_t *exists, hid_t lapl_id, hid_t es_id);
/*-------------------------------------------------------------------------*/
/**
* \ingroup H5A
Expand All @@ -1092,13 +1099,6 @@ H5_DLL herr_t H5Aexists_by_name_async(const char *app_file, const char *app_func
*/
H5_DLL herr_t H5Arename_by_name(hid_t loc_id, const char *obj_name, const char *old_attr_name,
const char *new_attr_name, hid_t lapl_id);
/*--------------------------------------------------------------------------*/
/**
* \ingroup ASYNC
* \async_variant_of{H5Aclose}
*/
H5_DLL herr_t H5Aclose_async(const char *app_file, const char *app_func, unsigned app_line, hid_t attr_id,
hid_t es_id);

/* API Wrappers for async routines */
/* (Must be defined _after_ the function prototype) */
Expand Down
6 changes: 3 additions & 3 deletions src/H5Epublic.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,9 @@ typedef struct H5E_error2_t {
hid_t cls_id;
/**< Class ID */
hid_t maj_num;
/**< Major error ID */
/**< Major error ID */
hid_t min_num;
/**< Minor error number */
/**< Minor error number */
unsigned line;
/**< Line in file where error occurs */
const char *func_name;
Expand Down Expand Up @@ -308,7 +308,7 @@ H5_DLL hid_t H5Eget_current_stack(void);
* If \p close_source_stack is \c TRUE, the source error stack
* will be closed.
*
* \since 1.8.0
* \since 1.13.0
*/
H5_DLL herr_t H5Eappend_stack(hid_t dst_stack_id, hid_t src_stack_id, hbool_t close_source_stack);
/**
Expand Down
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