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* Spelling fixes for codespell
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Make default to build high-level tools the same as default for (#1234)
high-level library.
* Updated README.txt to README.md (#1375)
* H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289
* H5Oget_info_by_name, name can be any object, not just a group
* Converted README.txt to README.md and updated files referring to README.txt to README.md.
* removed references to README.txt
* updated MANIFEST
* Snprintf2 (#1399)
* Replaced many uses of sprintf with safer snprintf
Many very straightforward, but in a few cases added a length parameter to some private functions, because buffer length was otherwise unknowable.
* Removed unnecessary use of static on small buffers
This improves thread safety.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Replaced several uses of sprintf with safer snprintf (#1383)
* Replaced several uses of sprintf with safer snprintf
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Used clang-tidy to change all floating point f suffixes to F (#1359)
* Added another missing override keyword on a dtor (#1384)
* Creating FUNDING.yml (#1427)
* Creating FUNDING.yml
Will add sponsor this project widget to the repo's page.
* Correct file name
Add sponsor widget; filename typo fixed.
* Update MANIFEST
* Fixed AbstractDs::getVarLenType documentation (#1441)
* Committing clang-format changes
* Open bsd fixes (#1195)
* Fix end of line alignment.
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: loricooperhdf <lori.cooper@hdfgroup.org>
Co-authored-by: myd7349 <myd7349@gmail.com>
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* Snapshot version 1.12 release 1-3. Update version to 1.12.1-4.
* First cut of the H5 public API documentation. (#80)
* First cut of the H5 public API documentation.
* Added H5Z "bonus track."
* Applied Quincey's patch.
* Added the missing patches from Quincey's original patch.
* H5PL (complete) and basic H5VL API documentation.
* Added H5I API docs.
* Added H5L API docs.
* First installment from Elena's H5T batch.
* Second installment of Elena's H5T batch.
* Final installment of Elena's H5T batch.
* Full set of current H5F documentation. (#105)
* First cut of the H5 public API documentation.
* Added H5Z "bonus track."
* Applied Quincey's patch.
* Added the missing patches from Quincey's original patch.
* H5PL (complete) and basic H5VL API documentation.
* Added H5I API docs.
* Added H5L API docs.
* First installment from Elena's H5T batch.
* Second installment of Elena's H5T batch.
* Final installment of Elena's H5T batch.
* Migrated documentation for SWMR functions.
* Catching up on MDC functions.
* Integrated the H5F MDC function documentation.
* Added MDC and parallel H5F functions.
* Slightly updated main page.
* Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.
* Doxygen - added (mostly) beginner functions (#112)
* Doxygen - added (mostly) beginner functions
* Removed duplicate H5Pset_szip function
* Add src/H5module.h to MANIFEST.
* close #195. (#196)
* Update HDF5PluginMacros.cmake
* Update HDF5PluginMacros.cmake
* Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206)
* Modify temporary rpath for testing in java example scripts. (#230)
* Fix undefined left shifting of negative numbers (#338)
Undefined Bahavior Sanitizer errored here about left shifting negative numbers.
* Fixes various warnings noticed on Windows (#425)
* Fixes various warnings noticed on Windows
- Adds a prototype for our implementation of vasprintf
- Return type of H5_get_utf16_str() is now non-const
- Fixes possible uninitialized return type in Wremove_utf8
- Better isolation of fork() code in accum.c:test_swmr_write_big()
- Better isolation of non-zlib code in dsets.c:test_filter_delete()
- Removed unused variable in trefer.c:test_reference_cmpnd_obj()
* Fixes clang-format issues
* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)
* Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes
Removes useless const declarations.
* Fixed most readability-non-const-parameter warnings
These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature.
* Reformat source with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Added C++11 override keyword where appropriate (#433)
Added H5_OVERRIDE macro for compatibility with both C++11 and older.
* Various clang tidy warning fixes (#448)
* Fixed clang-tidy bugprone-reserved-identifier warnings
* Fixed clang-tidy bugprone-assert-side-effect warnings
* Fixed clang-tidy bugprone-copy-constructor-init warning
* Fixed clang-tidy readability-redundant-preprocessor warning
For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block.
Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS.
* Fixed clang-tidy readability-redundant-string-init warnings
* Fixed some clang-tidy performance-type-promotion-in-math-fn warnings
* Fixed clang-tidy performance-unnecessary-value-param warnings
* Reformat source with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Removed checks/workarounds for pre-C++89 compatibility (#449)
After 30+ years, just assume that the following exist:
- extension-less includes
- namespaces
- std::
- static_cast
- bool
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings
This change was generated entirely by clang-tidy itself.
* Reformat code with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451.
* Minor parallel improvements (#519)
* Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Clean up MPI-IO VFD tracing support (#520)
* Clean up tracing support
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Brings the native implementation of H5Fdelete() from Bitbucket (#524)
* Committing clang-format changes
* Brings the native VFD H5Fdelete() implementation from Bitbucket
Only brings the 'del' callbacks, not the 'open/close' scheme.
* Formatter changes
* Committing clang-format changes
* Fixes direct VFD callback name
* Removes UNUSED macro from family API call
* Adds barrier and rank 0 check to MPI-I/O VFD delete
* Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"
This reverts commit 909765f759d9d96e84f4b8b1cc14f7d2b3ac8143.
* Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete""
This reverts commit 9b04bef1157853fc79fcb8fcc3e8ba1371091702.
* Adds a second barrier after the delete in MPI-I/O VFD
* Only delete files in the core VFD when the backing store flag is set
* Fixes string issues in multi VFD
Also, h5test.c cleanup code now uses H5Fdelete().
* Formatted source
* Rework fapl checks for MPI-I/O VFD delete callback
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Minor warning fixes in develop (#526)
* Committing clang-format changes
* Minor warning fixes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes implementation of my_strdup() from the multi VFD (#527)
* Committing clang-format changes
* Removes my_strdup() from the multi VFD
* Use strdup directly when memory sanity checks are off
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes dead H5ST package from the library (#528)
* Committing clang-format changes
* Removes the unused H5ST package from the library
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix HDFFV-11232 (#530)
* fixed missed closing of a dataset
* fixed missed closing of a dataset
* fixed typo in error return
* Committing clang-format changes
* minor edits
* code format
* Committing clang-format changes
* code format
* minor edit
* added H5fortkit dependency for H5VLff.F90, HDFFV-11232
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes incorrect usage of H5I_BADID (#554)
* Committing clang-format changes
* Fixes incorrect use of H5I_BADID
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601)
* Committing clang-format changes
* Fixes a segfault when H5Pset_mdc_log_options() is called multiple times
An internal string is incorrectly freed when the API call is invoked
multiple times on a property list, which will usually cause a segfault
to occur. On the first call the log location is NULL so the problem
doesn't occur.
Fixes HDFFV-11239
* Fixes typos
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607)
* Committing clang-format changes
* Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid
fapl ID
This was due to a pointer-containing struct being memset after the first
internal API call. If the first call failed, the error condition would
check if the pointer was not NULL and then attempt to free it if not.
This would lead to the freeing of a wild pointer if an invalid fapl ID
were passed in.
This was fixed by reordering the memset and adding a test to ensure the
problem stays fixed.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611)
* Committing clang-format changes
* Fixes incorrect size_hint handling in H5Gcreate1
* Updates the size hint type for group creation
* Updates the RELEASE.txt note
* Revert "Updates the RELEASE.txt note"
This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff.
* Reverts previous behavior to use a uint32_t struct field
* Updates RELEASE.txt
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Revert "Brings the native implementation of H5Fdelete() from Bitbucket (#524)"
This reverts commit 38d1b121ae428138b8863c2a319518c7363c2d94.
Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Quincey Koziol <quincey@koziol.cc>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
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* Snapshot version 1.12 release 1-3. Update version to 1.12.1-4.
* First cut of the H5 public API documentation. (#80)
* First cut of the H5 public API documentation.
* Added H5Z "bonus track."
* Applied Quincey's patch.
* Added the missing patches from Quincey's original patch.
* H5PL (complete) and basic H5VL API documentation.
* Added H5I API docs.
* Added H5L API docs.
* First installment from Elena's H5T batch.
* Second installment of Elena's H5T batch.
* Final installment of Elena's H5T batch.
* Full set of current H5F documentation. (#105)
* First cut of the H5 public API documentation.
* Added H5Z "bonus track."
* Applied Quincey's patch.
* Added the missing patches from Quincey's original patch.
* H5PL (complete) and basic H5VL API documentation.
* Added H5I API docs.
* Added H5L API docs.
* First installment from Elena's H5T batch.
* Second installment of Elena's H5T batch.
* Final installment of Elena's H5T batch.
* Migrated documentation for SWMR functions.
* Catching up on MDC functions.
* Integrated the H5F MDC function documentation.
* Added MDC and parallel H5F functions.
* Slightly updated main page.
* Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.
* Doxygen - added (mostly) beginner functions (#112)
* Doxygen - added (mostly) beginner functions
* Removed duplicate H5Pset_szip function
* Add src/H5module.h to MANIFEST.
* close #195. (#196)
* Update HDF5PluginMacros.cmake
* Update HDF5PluginMacros.cmake
* Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206)
* Modify temporary rpath for testing in java example scripts. (#230)
* Fix undefined left shifting of negative numbers (#338)
Undefined Bahavior Sanitizer errored here about left shifting negative numbers.
* Fixes various warnings noticed on Windows (#425)
* Fixes various warnings noticed on Windows
- Adds a prototype for our implementation of vasprintf
- Return type of H5_get_utf16_str() is now non-const
- Fixes possible uninitialized return type in Wremove_utf8
- Better isolation of fork() code in accum.c:test_swmr_write_big()
- Better isolation of non-zlib code in dsets.c:test_filter_delete()
- Removed unused variable in trefer.c:test_reference_cmpnd_obj()
* Fixes clang-format issues
* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)
* Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes
Removes useless const declarations.
* Fixed most readability-non-const-parameter warnings
These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature.
* Reformat source with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Added C++11 override keyword where appropriate (#433)
Added H5_OVERRIDE macro for compatibility with both C++11 and older.
* Various clang tidy warning fixes (#448)
* Fixed clang-tidy bugprone-reserved-identifier warnings
* Fixed clang-tidy bugprone-assert-side-effect warnings
* Fixed clang-tidy bugprone-copy-constructor-init warning
* Fixed clang-tidy readability-redundant-preprocessor warning
For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block.
Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS.
* Fixed clang-tidy readability-redundant-string-init warnings
* Fixed some clang-tidy performance-type-promotion-in-math-fn warnings
* Fixed clang-tidy performance-unnecessary-value-param warnings
* Reformat source with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Removed checks/workarounds for pre-C++89 compatibility (#449)
After 30+ years, just assume that the following exist:
- extension-less includes
- namespaces
- std::
- static_cast
- bool
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings
This change was generated entirely by clang-tidy itself.
* Reformat code with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451.
* Simplified hl parsing (#399)
* Stop using global variables to share parse context with the lexer.
The lexer uses an unconventional strategy for parsing lexical categories
NUMBER (decimal numbers) and STRING (double-quoted strings) that involves
sharing the parse context with the lexer using global variables. There
are a couple of problems with that. First, the lexer is too complicated
for the simple tokenization it performs—it's hard to tell if it is
correct. Second, as @seanm points out, the shared global variables
spill into the namespace shared by other libraries and application
programs—e.g., VTK.
* Regenerate source files from *.[yl].
* Replace strndup, which isn't available on Windows, with a custom
routine, `trim_quotes`, that produces a copy of its `const char *`
argument with leading and trailing double quotes ('"') removed.
While I am here, remove the unnecessary statement `BEGIN INITIAL;`,
which I should have deleted in a previous commit.
* Regenerate .c from .l.
* You haven't programmed in C until you have programmed in High-Definition
(HD) C.
* \#include "H5private.h" for HD* definitions.
* Regenerate *.[ch] from *.[yl].
* Removed workarounds for pre-standard inline keyword (#423)
Fixes -Wreserved-identifier warnings due to multiple underscores in H5_HAVE___INLINE.
* Replaces checks for fork, etc. with checks for unistd.h (#457)
* Replaces checks for fork, etc. with H5_HAVE_UNISTD_H
Code previously checked for individual POSIX API calls using
H5_HAVE_FORK, etc. The calls we use have been standardized for
decades and available via unistd.h.
Some test messages that were missing when tests are skipped
due to a lack of unistd.h were also added.
The configure checks for individual POSIX API calls will be
removed in a later commit.
* Stupid formatter
* develop JNI export references and java updates (#467)
* 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
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix display of long double in tools (#469)
* 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
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update clang config (#473)
* Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Correct syntax error. (#474)
a Fortran compile -> a Fortran compiler
* Cleans up a couple of MSVC warnings in testhdf5 (#475)
* Fixes a few testhdf5 warnings raised in Visual Studio
Visual Studio is grumpier about treating pointers like integers than
gcc.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix typos and grammar errors. (#476)
* Suppresses the tcheck_version test's abort dialog on Windows (#477)
* Suppresses the tcheck_version test's abort dialog on Windows
Windows raises a modal abort/retry/ignore dialog box when CRT
calls abort(). This change installs a report hook that suppresses
the dialog so that the CMake tests don't time out waiting for a
nonexistent user to click a dialog box.
* Committing clang-format changes
* Removes __cdecl from callback
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Rerun genparser.
* Fix merge issues and rerun genparser.
Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Quincey Koziol <quincey@koziol.cc>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
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file - src and test directories.
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hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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Correct a minor error in file free space allocation which was affecting
the 'multi' VFD and preventing some tests from fully working with it.
Wholesale revisitation of all the places where tests were disabled
with various VFDs and remove or correct all these so that _only_ the tests
which _really_ can't work with particular VFDs are skipped during a
'make check-vfd' test.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
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Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Tested on:
Mac OS X/32 10.5.5 (amazon)
No need for h5committest, just whitespace changes...
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Changed H5Acreate2 -> H5Acreate_by_name, to be more consistent with
other new API routines.
Re-added simpler form of H5Acreate2, which creates attributes directly
on an object.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Add H5Dcreate to API versioned routines, replacing internal usage with
H5Dcreate2
Fix thread-safe error stack initialization for API versioned error
stack printing routines.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Make H5Dopen versioned and change all internal usage to use H5Dopen2
Add simple regression test for H5Dopen1
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Put H5Acreate() under API versioning, with all internal usage shifted
to H5Acreate2().
Add regression tests for H5Acreate1().
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Fix problems with 'check-vfd' target, that were [mostly] introduced with
the recent "unique, but sharable" ISOHM optimization.
The problems were mostly with using the 'core' VFD, so the
H5Pset_fapl_core() API call was changed to re-open existing files (therefore
operating more list the sec2, stdio, etc. VFDs). This allows many more of
the tests to run using the 'core' VFD, so those were enabled also.
Tested on:
Linux/64 2.6 (chicago2) w/check-vfd
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copyright notice.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
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Altix (cobalt). There's a configure
option --enable-direct-vfd/--disable-direct-vfd to enable/disable Direct I/O support. The default
is enabled. There's a small test in test/vfd.c. Another way to test it is to set environment
variable HDF5_DRIVER to "direct" and run "make check" in the test/ directory. There'll be some
further improvement in the following checkin including allowing user to provide memory boundary
value, file block size, and copying buffer size.
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Add "use the latest format" support for dataspace object header encode/
decode routines and clean up format a bit for the latest format (new to 1.8.x
releases)
Remove storing 'perm' parameter for array datatypes in memory and the file,
and add test to make certain that if any user applications are attempting to
store them, we get some reports back. (Should be unlikely, since the RefMan
says that the parameter is not implemented and is unsupported).
Carry those changes into the tests, etc.
Clean up a bunch more compiler warnings.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-1.6-compat
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Tested on heping.
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"make check-vfd" will now run all tests in the test directory with different
file drivers (at least, all of those tests that use the testing framework's
FAPL). Tests that fail will be skipped.
This is not a perfect fix, but is better than nothing.
Along with this change, check-vfd should be added to the Daily Tests.
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Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
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Code cleanup
Description:
Fixed reserved.c test to use h5_fileaccess/h5_fixname/h5_cleanup.
Updated RELEASE.txt for previous bug fix
Platforms tested:
sleipnir, verbena
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Code cleanup
Description:
Clean up a bunch of warnings and bring new code better inline with current
library coding practice.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Misc. update:
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Purpose:
Bug fix
Description:
Replaced "unsigned long long" with hsize_t in H5MF
Added "return 0" at end of reserved.c test
Platforms tested:
arabica, sleipnir
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Purpose:
Description:
Missed adding a test file in previous commit.
Solution:
Platforms tested:
Misc. update:
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