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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.
* Removed mentions of Wdeclaration-after-statement now that C99 is requ… (#447)
* Removed mentions of Wdeclaration-after-statement now that C99 is required
* Remove -Werror=declaration-after-statement from error-general file.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Made private my_yyinput function static (#618)
This prevents it being exported as a public symbol.
* Adds const to a few global variables (#623)
* Committing clang-format changes
* Adds consts to a few global variables
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* (fix) Segmentation fault when using a compound type. (#143)
* (fix) Segmentation fault when using a compound type.
In the case when a compounded attribute is written to dataset
followed by writing the data with a data transform function
to the dataset will result in a segmentation fault. It turns out
the data is classified as compounded while it is not. Now, the
state is always reset first to not compounded followed by the
existing check if the variable is compounded.
* (fix) Removed undesired comment lines.
* (fix) Segmentation fault when using a compound type: added test.
* (fix) Added the missing cmpd_transform.c file to MANIFEST.
* (fix) cmpd_dtransform test: autotools and source header.
Added the cmp_dtransform test to the autotools configuration and
updated the HDF Group copyright header.
Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
* (fix) H5Z_xform_create function and scientific notation (#144)
* (fix) H5Z_xform_create function and scientific notation
Implemented a more sophisticated check to support scientific notation
in the expression of the H5Zset_data_transform function.
* (fix) H5Z_xform_create and scientific notation: Added test.
Added a test to demonstrate that the parsing of expression
which includes scientific notation works correctly. Improved
inline comment.
Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
* Committing clang-format changes
* Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)
* Cleanup tools debug build warnings (#627)
* 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
* Cleanup warnings for tools debug builds
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* h5diff subset indexing (#628)
* 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
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes gratuitous (double)x.yF casts (#632)
* Committing clang-format changes
* Removes gratuitous (double)x.yF casts
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Cleans up a const warning left over from previous constification (#633)
* Committing clang-format changes
* Adds consts to a few global variables
* Cleans up a const warning left over from previous constification
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Purges UFAIL from the library (#637)
* Committing clang-format changes
* Purges UFAIL from the library
* H5HL_insert change requested in PR
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Bmr dev hdffv 11223 (#640)
* Fixed HDFFV-11223 (CVE-2018-14460)
Description
- Added checks against buffer size to prevent segfault, in case of data
corruption, for sdim->size and sdim->max.
- Renamed data files in an existing test to shorten their length
as agreed with other developers previously.
Platforms tested:
Linux/64 (jelly)
* Committing clang-format changes
* Updated for test files
* Updated for HDFFV-11223
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)"
This reverts commit 7a682862846fa206aa3a0151c0aa08d7c759b1f7.
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>
Co-authored-by: Jan-Willem Blokland <J.W.S.Blokland@XS4All.nl>
Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.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.
* 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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* 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.
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>
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* OESS-98 fix tools test for plugins
* sync fork
* Merge of changes from dev
* Move problem option to bottom of the list until fixed
* HDFFV-11106 - fix parsing optional args
* HDFFV-11106 add note
* grammer fix
* Whitespace after clang formatting
* Undo format version 11 changes
* Update check to working version
* Merge workflow and minor changes from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge serval small changes from dev
* fix typo
* Minor non-space formatting changes
* GH #386 copyright corrections for java folder
* revert because logic requires false return
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file - files not in src or test.
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* commit '7116d82f6b685261b5b4e64fada1a0a031cd7341':
Remove mismerged code
Cherry pick of 0225e6d5969
Cleanups from PR reviews
Remove unnecessary H5CX call
Refactor H5Dvlen_get_buf_size to use optional dataset operation, with generic fallback for VOL connectors that don't implement operation
Refactor all the 'H5VL_*_optional' callbacks to move the type of operation out of the va_list, so it's at least possible for another connector to know what the operation is and decide whether to implement it or not.
Update h5debug to retrieve file pointer through VOL framework
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changes to warnhist script (and some extra improvements for condensing C++
and Java warnings), and fixed a bunch of warnings.
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from the tools code. This is all handled in H5private.h, which
should be included in all tools source files.
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Added test and new arguments to control the the input file parsing.
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Mostly replacing tabs with spaces
Removed empty mod sections
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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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Clean up warnings (from 2774 -> 1560, with my standard debug build)
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
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h5repack error handling.
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Tested on: jam (too minor for h5committest)
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gcc 4.9.2 was used to create the warning list
- implicit casts
- shadowed variables
- various enum issues
- other minor fixes (comments, unused macros, etc.)
Tested on: h5committest
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is_finalized need to be checked before making any MPI calls.
tested with h5committest.
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Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
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due to prototype" warnings by casting constants to size_t where expected by string functions.
Tested on jam, koala,ostrich and platypus with h5committest.
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Clean up warnings, enable new compiler warning flag(s) and bring back
changes from Coverity branch:
r20813:
Remove the dead code as listed for coverity bug #1722. h5committested.
r20814:
Issue 69: Check return value and throw error if negative return. Also free datatype id on error
r20815:
Use HDstrncpy. --gh
r20816:
Replaced one last HDstrcat call with HDstrncat to resolve coverity issue 832.
r20817:
Use HDstrncpy and HDstrncat. --gh
r20818:
Purpose: Fix valgrind issues with h5jam
Description:
Modified h5jam to free strings strdup'd in parse_command_line before exit. Note
that they may still not be freed in case of error, due to the widespread use of
exit().
r20819:
Issue 80: change loop to use int as loop index.
r20820:
Maintenance: Fixed the bug found by coverity CID 788
There were two problems with this function:
1) it tried to unnecessary free NULL pointer
2) it tried to allocate c_name buffer that is done by H5Pget_class_name
Tested on:
Mac OSX 10.8.4 (amazon) w/gcc 4.8.1, C++ & FORTRAN
(too minor to require h5committest)
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Clean up a few warnings
Tested on:
Mac OSX 10.8.4 (amazon) w/C++ & FORTRAN
(too minor to require h5committest)
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Tested: local linux
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Tested: local linux
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Clean up warnings in H5Tconv.c (down to _only_ 9000 lines of output now!)
Merge changes from Coverity branch back to trunk:
r20684:
Fix for coverity bug #1721 which was due to the fix for coverity bug #943.
r20685:
Use HDstrncpy. --gh
r20761:
Purpose: Fix valgrind issues
Description:
Free image_data and data as appropriate in test_image.
r20762:
Purpose: Fix coverity issue 600
Description:
Add check for return value of H5O_close in H5Ocopy. Also cleaned up various
warnings.
r20763:
Purpose: Fix valgrind issues with h5stat
Description:
Modified h5stat to free "iter" before exit, and free "hand" before exit if
parse_command_line exits directly.
r20764:
fixed coverity issues:
69, 327, 614, 684, 685, 696, 697, 1681, 967, 826, 660, 80
r20765:
Fixed coverity bug 668
Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning.
No actual integer overflow tests are performed since it's just a test program but I did add a check that n_elements is >= 1.
I also changed an error condition from doing its own close and returning -1 to "goto out;" like the rest of the program.
r20766:
Fixed coverity bug 667
Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning.
No actual integer overflow tests are performed since it's just a test program.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
(h5committest upcoming)
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for filename F to be optional.
Tested: local linux
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Bring reviewed changes from Coverity branch back to trunk (QK & JK):
r20457:
Coverity issue 691: return of H5duo could be negative. Fixed by using
STDOUT_FILENO and redesign parse_command_line and main to cleanup file
allocations. The output_file var is null when using stdout. In cleanup do not
close output_file if NULL.
r20510:
Initialize ufid = -1 and predicate HDclose call on ufid != -1
r20511:
Purpose: Fix coverity issue 1715
Description: Free "file" and nested data on failure in H5FD_core_open.
r20512:
Initialize ifid = -1 and predicate HDclose call on ifid != -1
r20514:
Initialize h5fid = -1 and predicate HDclose call on h5fid != -1
r20516:
Added else branch to the if (ret_value < 0) check.
r20522:
Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor
potential buffer overwrite bugs, or coverity errors. Fixed by replacing
strcpy and sprintf with strncpy and snprintf.
r20523:
fixed coverity issues 68, 1120, 1116i
r20524:
Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence.
r20601:
Purpose: Fix coverity issues 1703-1705
Description: Modified the cleanup code in test_free in accum.c to reset
allocated buffers to NULL after they are freed, and modified the error cleanup
code to check if these buffers are NULL before freeing them. Also fixed some
unrelated warnings in accum.c.
r20602:
Use HDsnprintf and HDstrncat
r20603:
Purpose: Fix coverity issues 808-809
Description: Modified test_core in vfd.c to check the returns from malloc, and
keep track of whether points and check are allocated by setting them to NULL
when they are not. Added code to free points and check on error if they are
not NULL. Also fixed unrelated warnings in vfd.c.
r20604:
Use HDstrncpy.
r20605:
Use HDstrncpy and HDstrncat.
r20606:
Purpose: Fix coverity issue 807
Description: Modified long_compact in stab.c to keep track of whether objname is
allocated by setting it to NULL when it is not. Added code to free objname on
error if it is not NULL.
r20607:
Changed string function calls to use versions that specify the string length
to fix coverity issues 832 and 839.
Tested on:
Mac OSX/64 10.8.2 (amazon)
(Too minor to require h5committest)
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Tested: local linux
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Tested: local linux
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Issue on windows
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