| Commit message (Collapse) | Author | Age | Files | Lines |
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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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* Revert "Revert H5Dchunk_iter changes in hdf5_1_12_1 (#733)"
This reverts commit 10abe9a8b4985a18a0c88615686184d233d7b845.
* Apply clang-format
* Reincorporate spelling fix from #1166
* Incorporate H5Dchunk_iter changes from #161
* Backport to 1.12: Adds a quick for for some egregious chunk_info badness (#722)
* Backport to 1.12: Converts testhdf5 macros to h5test macros in chunk_info.c (#1820)
The two macro schemes were not designed to work together. Also
quiets some MSVC warnings about comparing pointers and integers.
* Backport to 1.12: H5Dchunk_iter now passes offsets in units of dataset elements, fix #1419 (#1969)
* H5Dchunk_iter now passes chunk dimension scaled offsets, fix #1419
* Update docs for H5Dchunk_iter, H5Dget_chunk_info*
Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following
* offset Logical position of the chunk’s first element in units of dataset elements
* filter_mask Bitmask indicating the filters used when the chunk was written
* size Chunk size in bytes, 0 if the chunk does not exist
* Sync H5Dchunk_iter documentation with develop
* Remove H5VL_DATASET_WAIT references from 1.12
* Backport to 1.12 #161, #1474, review comments
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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* Warnings fixes (#1680)
* Clean stack size warnings in sio_engine (#1687)
* Fixes stack size warnings in tcoords.c (#1688)
* Address some warnings from casting away of const (#1684)
* Fixes stack size warnings in ntypes (#1695)
* Fixes stack size warnings in dtransform (#1696)
* Fixes stack size warnings in set_extent test (#1698)
* Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706)
* Avoid a signed overflow: check the range of `entry_ptr->age` before
increasing it instead of increasing it and then checking the range.
This quiets a GCC warning.
* Avoid the potential for signed overflow by rewriting expressions
`MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`.
This change quiets some GCC warnings.
* Change some local variables that cannot take sensible negative values
from signed to unsigned. This quiets GCC warnings about potential
signed overflow.
* In a handful of instances, check the range of a signed integer before
increasing/decreasing it, just in case the increase/decrease overflows.
This quiets a handful of GCC signed-overflow warnings.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix object size warnings in cache.c test (#1701)
* Fix some const cast and stack/static object size warnings (#1700)
* Fix various warnings
* Move HDfree_const to H5private.h for wider use
* Print output from all ranks in parallel tests on allocation failure
* Move const pointer freeing macro to h5test.h for now
* Stop lying about H5S_t const-ness (#1209)
Hyperslabs can be reworked inside several H5S callbacks, making H5S_t
non-const in some places where it is marked const. This change switches
these incorrectly const H5S_t pointer parameters and variables to
non-const where appropriate.
* Fix a few warnings after recent H5S const-related changes (#1225)
* Adjustments for HDF5 1.12
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Fixes const issues in the version 2 B-trees (#1172)
The operations that were changed are fundamentally not const since the
shadow operation can modify the node structure when SWMR is in use.
* Quiets const warning in H5RS code (#1181)
* Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171)
* Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the
raw H5R_ref_t bytes to a heap buffer that's known to have the right
alignment.
* Committing clang-format changes
* Use an automatic H5R_ref_t instead of malloc'ing one. Go ahead and
initialize the H5R_ref_t to all-0s so that arbitrary stack content
doesn't foul things up. Bail out with an error if `size` exceeds
`sizeof(H5R_ref_t)`.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Miscellaneous warnings fixes
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
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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* Fix the function cast error in H5Dchunk.c and activate (#1170)
`-Werror=cast-function-type`. Again.
* Parallel Compression improvements (#1302)
* Fix for parallel compression examples on Windows (#1459)
* Parallel compression adjustments for HDF5 1.12
* Committing clang-format changes
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@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.
* 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.
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
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Remove case statement for H5I_EVENTSET
* Correct call with versioning
* Remove tabs
* Double underscore change
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards
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file - src and test directories.
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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
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* Basic alignment with async branch - trivial changes to reduce clutter in overall diff.
* Update minor error code to reflect change within library
* Update the error output to match library
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Comments and whitespace
Skip file-locking and cache changes
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their header about this naming
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header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email
addresses from library source code (still needs cleaned from other directories).
Misc. warning, style, and whitespace cleanup.
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hdf5_1_12_small_chunk_io_opt to hdf5_1_12"
This reverts commit 331cf8c38a3ab7c8862b5645efcbe197fe3c107e, reversing
changes made to ed0985ff7fa2e64a903ea7d9c9343524d9d64ea8.
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functions. The metadata cache tagging has already been done by routines further up the call stack.
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commit ff7a9a34de2fcd78f5d32a1532f3d0e224b20d94
Author: Kimmy Mu <kmu@hdfgroup.org>
Date: Wed Jan 29 14:12:18 2020 -0600
Merge pull request #2324 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12
* commit '781fa57f6ee816e037dd12fff02d37ff7ec9c2b1':
pick up missing piece from merge
Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop
remove redundent definition
Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop
Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop
Merge pull request #2315 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop
missing prototype warning
prototype issue
Merge pull request #2306 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop
Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to develop
Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized to develop
Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop
Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop
Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to develop
commit 9f3d808c05d2a3b308f32c958c6671fcac0a432c
Author: David Young <dyoung@hdfgroup.org>
Date: Wed Jan 29 11:43:55 2020 -0600
testpar/t_2Gio.c: Fix a typo that I think was introduced by a
previous warnings PR. An array element was assigned to
itself---shape[2]Â =Â shape[2];---instead of being assigned to
chunk[2].
fortran/src/H5Pf.c: move conditional compilation controlled by
H5_NO_DEPRECATED_SYMBOLS outside of a function for readability.
fortran/src/H5match_types.c: put a variable's declaration under the same
conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its
use.
For now, skip compilation of some unused debug dump routines in the JNI.
While I'm in the JNI, delete a set-but-unused variable.
src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS
so that it's not declared but unused or vice versa.
test/cache_common.h: add an #include in to get some symbols we need to
avoid implicit declaration warnings.
test/dsets.c: use a more conventional conditional-compilation syntax.
test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized
variables before use.
test/vfd.c: pass the expected type of `void **` to posix_memalign(3)
instead of `int **`.
testpar/t_bigio.c: explicitly compare with 0 instead of using ! when
"equal to 0?" is the question not "is false?" Repair some
indentation while I'm here.
testpar/testpar.h: repair misaligned line-continuation backslashes in a
macro that probably should be a function so that we don't have
to fiddle with the line continuation to begin with.
tools/src/h5repack/h5repack_main.c: fix some compiler fussing about
enums.
tools/test/perform/pio_engine.c: the compiler fusses if you cast a
function call returning double directly to off_t. It's ok if
you cast a variable that's a double to off_t, however. Write
and use a new function, sqrto(), to avoid the cast warnings.
commit 43a4b80b21c0329fbc1f9a0e2854795189f0bb50
Author: David Young <dyoung@hdfgroup.org>
Date: Wed Jan 29 10:47:30 2020 -0600
Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required.
Reduce gratuitous casts---e.g., (size_t)1.
Use the right format string for a pointer.
In the H5C sanity checks, change a "size increase" variable from ssize_t
(too narrow) to int64_t (wide enough).
Parenthesize every appearance of `storage` in the macro
`H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an
expression like &sc and it works properly.
Disallow re-assignment of the `dset` parameter to H5D__chunk_init()
because it helped assure me that it's safe to replace the repeating
expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout.
Replace lengthy expressions such as
`&dset->shared->layout.storage.u.chunk` with `sc` throughout several
functions in H5Dchunk.c ISTR that the compiler warned that `sc` was
declared but unused in a couple of functions, and then I found that `sc`
could be used in many places. Maybe the disused `sc` appeared because a
bunch of code was copied and pasted, I don't know. Anyway, it's a lot
tighter code now that I use `sc`.
In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete()
I actually expand `sc` and another temporary variable, `pline`,
because they're used only in !defined(NDEBUG) code. This squashes
unused-variable warnings in the defined(NDEBUG) configuration.
Don't drop the `volatile` qualification with a cast in
tools/src/h5import/h5import.c.
commit 035bfa0769a4012881fc659b673bacf44d146537
Author: David Young <dyoung@hdfgroup.org>
Date: Tue Jan 28 20:35:28 2020 -0600
Reduce differences between my -Werror branch and `develop`:
Rename index -> idx, fileno -> fnumber, fileno -> fno to avoid GCC
shadowed declaration warnings about index(3).
Convert #pragma GCC diagnostic push/pop/ignored to the HDF5 library's
H5_GCC_DIAG_OFF()/H5_GCC_DIAG_ON() macros.
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* commit 'af5c33afabdae2e39bb45eb1b3e9c8366da01145':
remove unnecessary stuff
squash cast warning fix
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* commit '145ef3ceee20c28a443bd11507c58858bea3f889':
more cleanup
change it back
pick up missing piece
fix unused related warnings
removed unused parameter
more fix and address comments
remove unsed var,function,macro, etc
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to develop
* commit '0a2bb11b248df6841daabca3970df5d8504adfc7':
address problems from comments
fix and address comments
change according to previous comments
add missing piece
remove unnecessary check macro
fix intel compile warnings
Revert "fix warnings from Intel compiler"
Revert "fix warnings and some text alignment"
Revert "let hdf5 pick up the right compiler in Intel environment"
Revert "fix issues from previous PR comments"
Revert "using a different MACRO"
using a different MACRO
fix issues from previous PR comments
let hdf5 pick up the right compiler in Intel environment
fix warnings and some text alignment
fix warnings from Intel compiler
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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.
Added a new VOL sub-class called "introspect" where callbacks that report
information about the connector or container can be placed. Added an
'opt_query' callback to this sub-class, for a connector to report back
to the library whether a particular optional callback operation is supported.
Also added a 'get_conn_cls' introspection callback, to retrieve the H5VL_class_t
of a connector (either the "current" connector, H5VL_GET_CONN_LVL_CURR, or
the terminal connector, H5VL_GET_CONN_LVL_TERM).
Moved the "post open" operation from a file 'specific' operation to a file
'optional' operation, now that it's possible to detect (with the 'opt_query'
introspection callback) whether a VOL connector implements an optional
operation, without just returning an error.
Added new internal VOL helper routines: H5VL_object_is_native, to determine
if an object is in (or is a) native file, and H5VL_file_is_same, to determine
if two objects are in (or are) the same terminal VOL connector's container.
(And moved the special handling for FILE_IS_EQUAL operation out of internal VOL
callback routine into H5VL_file_is_same)
Made new dataset 'get' operation for H5Dvlen_get_buf_size, aligning it better
with other 'get' operations in API.
Fixed several issues with pass-through connectors, which are now passing the
'make check-passthrough-vol' tests again.
A bunch of warning and style cleanups as well.
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https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12"
This reverts commit 9f9336a5bd541752f472bab4c93da8de89f862cd, reversing
changes made to 437a1919e7ba60fe75a33a466d264183a0255319.
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H5Sselect_adjust. Implement "adjust_s" callback for all selection
types. Add range checking to H5Sselect_adjust().
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to hdf5_1_12
* commit '5d2545ee26d4b7013ed363545705f16a67087549':
Fix func enter macro in H5T_ref_reclaim()
Update RELEASE.txt for reference changes
Fix reference type comparison in h5dump
Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()
Add new H5R API that abstracts object, region and attribute reference types
Remove ability to loc by ref from H5VL layer
Add support for retrieving object name by token
Add H5VL_OBJECT_GET_TYPE to get object type
Add H5VL_MAX_TOKEN_SIZE and H5VL_token_t
Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info.
Fix H5VL_blob_get to return size of blob
Add 'blob' callbacks to VOL, along with a native implementation to store them in the global heap, and changed the VL datatype conversion code to use blobs.
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Also support references to external files
Add new H5T_REF type and type conversion routines
Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF
Add H5Treclaim() API to reclaim memory of vlen/reference types
Deprecate H5Dvlen_reclaim()
Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback
Add H5T_ref_reclaim()
Move previous H5R APIs to H5Rdeprec.c
Clean up H5Ocopy
Separate H5O_copy_expand_ref() to H5Ocopy_ref()
Add support for copying new reference types
Clean up deprecated routines to go through VOL and same code path
Fix return codes in existing trefer.c test
Rename trefer.c to trefer_deprec.c
trefer.c is for new references
Add performance test for trefer
Add additional obj_copy_ref test
Make use of tokens and blobs to store references
Skip blob encoding for object references
Start adding new reference examples
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~VCHOI/my_third_fork:bugfix/HDFFV-10585-investigate-slowness-of-regular to develop
* commit '7924eee0e5ee0745b784c635042b8633886fb799':
(1) Address the feedback from the PR review (2) Add release notes
Fix for HDFFV-10585 investigate hyperslab slowness: 1) Improve hyperslab performance when doing I/O from 1-d disjoint file dataspace to 1-d contiguous memory dataspace. 2) Move coding in H5D__chunk_io_init() that is constructing the chunk mappings to a separate routine.
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Description:
- Added functions to query chunk information:
H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
Gets the number of written chunks that intersect with the given
dataspace. However, in this version, the intersection is not
yet completed. Thus, the number of all written chunks will be
returned.
H5Dget_chunk_info_by_coord(dset_id, *offset, *filter_mask, *addr, *size)
Given a chunk's logical coordinates, returns the chunk's filter,
address, and size.
H5Dget_chunk_info(dset_id, fspace_id, index, *offset, *filter_mask, *addr, *size)
Given a chunk's index, returns the chunk's logical coordinates, filter,
address, and size. The chunk belongs to a set of chunks that have
nonempty intersection with the specified dataspace. However, in
this version, the intersection is not yet completed, and the index
is of all the written chunks.
These functions comply with VOL.
- Fixed some oversights found in the library for the tests in chunk_info.c
to work correctly. The returned value from a callback function was not
checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate().
This oversight caused a callback function to continue iterating even though
it's supposed to stop.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
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