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4 release notes for HDF5 1.12.1 from RELEASE.txt for HDF5 1.10.7 (#780)
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* Hdf5 1 12 doxygen version correction (#658)

* 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

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

* TRILAB-227 and tools debug merge from develop

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES in compiler id compare, merge from dev

* Revert test enable

* Add file to list

* doxygen version errors

* if blocks needed for build modes

* Update list of test platforms

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Attempt format uniformity in RELEASE.txt.

* BUG: DataSet assignment operator is missing (#503)

* BUG: DataSet assignment operator is missing

* Some compilers complain if the copy constructor is given explicitly
  but the assignment operator is implicitly set to default.

* Explicitly defining the assignment operator allows us to properly
  handle reference counters for shared resources.

* BUG: DataSet assignment operator is missing.

* Mimicking code of H5DataType::operator() as suggested by @bmribler.

* Added test

Description:
    Added test for DataSet::operator= that Leengit added
Platform tested:
    Linux/64 (jelly)

* Removed Author field.

* Commit clang format changes.

* Entry for Leengit's github PR #503

* Removed lines left by mistake

Co-authored-by: Binh-Minh Ribler <[email protected]>
Co-authored-by: Larry Knox <[email protected]>

* Add H5Dchunk_iter method for iterating over chunks (#6)

* Add H5Dchunk_iter method for iterating over chunks

This method iterates over all chunks in dataset, calling a user-supplied
callback with the chunk information and optional user supplied data.

The iterator is stopped when ITER_STOP is returned by the user-supplied
callback or the iterator is exhausted.

Existing methods to get chunk_info performs an iteration each time, so
to get many or all chunks causes SUM(i) for i = 0 -> N operations for N
chunks, as opposed to N operations when using this iterator for this use case.

* H5Dchunk_iter: test iterating all chunks, some chunks and failing iteration.

* H5D: move H5Dchunk_iter private methods to specific

* trace: add H5D_chunk_iter_op_t and trace H5D.c

* chunks-iter: document chunk_iter

* chunk-iter: chunk add FUNC_ENTER/FUNC_LEAVE macros

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Set initial doxygen version for H5Dchunk_iter().

* Revert "Set initial doxygen version for H5Dchunk_iter()."

This reverts commit d739e46.

* Revert "Add H5Dchunk_iter method for iterating over chunks (#6)"

This reverts commit 53e1139.

* Add flushrefresh errors with check-passthrough-vol to known problems in
RELEASE.txt.

* Minor RELEASE.txt updates.

* Hdf5 1 12 Remove version from pkgcfg file names (#672)

* 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

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

* TRILAB-227 and tools debug merge from develop

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES in compiler id compare, merge from dev

* Revert test enable

* Add file to list

* doxygen version errors

* if blocks needed for build modes

* Update list of test platforms

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* More minor updates.

* Update configure disablhing memory alloc sanity check for release.
Last 50 lines of
/mnt/scr1/SnapTest/snapshots-hdf5-branchtest4/log/moohan_0525Tue_1021
Last 50 lines of
/mnt/scr1/SnapTest/snapshots-hdf5-branchtest4/log/moohan_0525Tue

* Set version to 1.12.1.

* Hdf5 1 12 fix warnings files (#755)

* 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

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

* TRILAB-227 and tools debug merge from develop

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES in compiler id compare, merge from dev

* Revert test enable

* Add file to list

* doxygen version errors

* if blocks needed for build modes

* Update list of test platforms

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

* Merge CMake and java refs from dev

* Reworked CMake Fortran configure macros to allow multiple runs.

* Fix CMake issue with tests not comparing test argument properly.

* MAX_PRECISION defines must be defined with a value

* Fix warnings files and -std

* remove std for c++11

* Replace file

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes an array issue flagged by PGI in a C++ test (#763)

* Hdf5 1 12 Fix cmake configure path (#761)

* 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

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

* TRILAB-227 and tools debug merge from develop

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES in compiler id compare, merge from dev

* Revert test enable

* Add file to list

* doxygen version errors

* if blocks needed for build modes

* Update list of test platforms

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

* Merge CMake and java refs from dev

* Reworked CMake Fortran configure macros to allow multiple runs.

* Fix CMake issue with tests not comparing test argument properly.

* MAX_PRECISION defines must be defined with a value

* Fix warnings files and -std

* remove std for c++11

* Replace file

* Fix cmake configure path

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Restore initials to release notes.

* Copy release notes from 1.10.7 RELEASE.txt ffor fixes also in 1.12.1.

* emove 2 entries added in PR #777.

Co-authored-by: Allen Byrne <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Lee Newberg <[email protected]>
Co-authored-by: Binh-Minh Ribler <[email protected]>
Co-authored-by: Gaute Hope <[email protected]>
Co-authored-by: Dana Robinson <[email protected]>
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Original file line number Diff line number Diff line change
Expand Up @@ -680,6 +680,24 @@ Bug Fixes since HDF5-1.12.0 release

(QAK - 2020/08/21)

- Fixed use-of-uninitialized-value error

Appropriate initialization of local structs was added to remove the
use-of-uninitialized-value errors reported by MemorySanitizer.

(BMR - 2020/8/13, HDFFV-11101)

- Creation of dataset with optional filter

When the combination of type, space, etc doesn't work for filter
and the filter is optional, it was supposed to be skipped but it was
not skipped and the creation failed.

A fix is applied to allow the creation of a dataset in such
situation, as specified in the user documentation.

(BMR - 2020/8/13, HDFFV-10933)

- Explicitly declared dlopen to use RTLD_LOCAL

dlopen documentation states that if neither RTLD_GLOBAL nor
Expand All @@ -689,6 +707,17 @@ Bug Fixes since HDF5-1.12.0 release

(ADB - 2020/08/12, HDFFV-11127)

- Fixed issues CVE-2018-13870 and CVE-2018-13869

When a buffer overflow occurred because a name length was corrupted
and became very large, h5dump crashed on memory access violation.

A check for reading past the end of the buffer was added to multiple
locations to prevent the crashes and h5dump now simply fails with an
error message when this error condition occurs.

(BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121)

- H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which
causes asserts/errors when passed to other dataspace API calls.

Expand Down Expand Up @@ -718,6 +747,17 @@ Bug Fixes since HDF5-1.12.0 release

(VC - 2020/07/13, HDFFV-11080)

- Fixed CVE-2018-17435

The tool h52gif produced a segfault when the size of an attribute message
was corrupted and caused a buffer overflow.

The problem was fixed by verifying the attribute message's size against the
buffer size before accessing the buffer. h52gif was also fixed to display
the failure instead of silently exiting after the segfault was eliminated.

(BMR - 2020/6/19, HDFFV-10591)

- Reduce overhead for H5open(), which is involved in public symbols like
H5T_NATIVE_INT, etc.

Expand Down Expand Up @@ -826,6 +866,16 @@ Bug Fixes since HDF5-1.12.0 release

(DER - 2021/01/07, HDFFV-11201)

- Stopped addition of szip header and include directory path for
incompatible libsz

szlib.h is the same for both 32-bit and 64-bit szip, and the header file
and its path were added to the HDF5 binary even though the configure
check of a function in libsz later failed and szip compression was not
enabled. The header file and include path are now added only when the
libsz function passes the configure check.

(LRK - 2020/08/17, HDFFV-10830)

Tools
-----
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