Merge PRs #498, 503, 519 to hdf5 1 10 #868
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maintain binary compatibility.
* 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>
* 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>
* 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>
* 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>
This reverts commit 426b504.
Squashed commit of the following: commit 60734e6 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 24 14:20:39 2021 -0500 Hdf5 1 10 Fix tools test (#796) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * 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 * minor whitespace * remove unneeded macro * Committing clang-format changes * 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. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem * Use only core library for testing dynamic plugins. CMake uses H5_HAVE_DIRECT instead of DIRECT_VFD Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit bfb780a Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 23 14:11:46 2021 -0500 Hdf5 1 10 Release Note (#786) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * 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 * minor whitespace * remove unneeded macro * Committing clang-format changes * 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. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners * Add known problem Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 9f50407 Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 22 07:03:26 2021 -0500 Hdf5 1 10 Update missing release note info. (#778) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * 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 * minor whitespace * remove unneeded macro * Committing clang-format changes * 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. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path * Update missing release note info. * Update code owners Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 2e80c9c Author: Dana Robinson <43805+derobins@users.noreply.github.com> Date: Fri Jun 18 06:42:23 2021 -0700 Brings hash table IDs feature from develop/1.12 (#768) * Brings updated tid test from develop * Adds empty H5Iint.c and H5Idbg.c files * H5I renaming to match 1.12/develop * Splits off H5I debug code to H5Idbg.c * Splits internal H5I.c functionality to H5Iint.c * Header cleanup * More renaming cleanup to match develop/1.12 * Adds "save last ID" optimization * Adds uthash.h * Adds hash table IDs from develop/1.12 * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 1e29bcb Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Thu Jun 17 11:21:43 2021 -0500 Hdf5 1 10 Fix cmake configure path (#762) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * 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 * minor whitespace * remove unneeded macro * Committing clang-format changes * 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. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop * Fix cmake configure path Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 475cdaf Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Wed Jun 16 15:45:58 2021 -0500 Hdf5 1 10 merge warnings changes (#756) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * 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 * minor whitespace * remove unneeded macro * Committing clang-format changes * 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. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args * Merge warnings files fixes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit e25980e Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue Jun 8 14:37:13 2021 -0500 Hdf5 1 10 merges of CMake changes (#738) * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * 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 * minor whitespace * remove unneeded macro * Committing clang-format changes * 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. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct * TRILAB-227 and tools debug merges from develop * Merge various changes from dev * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * doxygen changes merged from develop * Committing clang-format changes * Merge CMake fortran ninja changes from dev * Enable fortran to gcc yaml * Refactor Fortran CMake config tests and CMake test args Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> commit 061b23a Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jun 3 16:07:23 2021 -0500 Partial merge issue #642 develop branch PRs to Hdf5 1 10 (#718) * Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to maintain binary compatibility. * Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625) * 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> * Committing clang-format changes * Restore "error:" in line 2666. * Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)" This reverts commit 426b504. Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
commit e2578640fedf671cf11535cf22313dd477da1165
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Fri Jul 16 10:57:51 2021 -0500
Merge issue 839 changes to hdf5 1 10 (#841)
* Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to
maintain binary compatibility.
* Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)
* 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>
* Committing clang-format changes
* Restore "error:" in line 2666.
* Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)"
This reverts commit 426b50484841118cf633fd6147302a63a30fd746.
* Snapshot version 1.10 release 8-1. Update version to 1.10.8-2.
Squashed commit of the following:
commit 60734e63fe077238f10de3d6ca8f037f9a42af89
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Thu Jun 24 14:20:39 2021 -0500
Hdf5 1 10 Fix tools test (#796)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
* Merge warnings files fixes from develop
* Fix cmake configure path
* Update missing release note info.
* Update code owners
* Add known problem
* Use only core library for testing dynamic plugins.
CMake uses H5_HAVE_DIRECT instead of DIRECT_VFD
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit bfb780a4441e4ef43dd23708d415e5e3b84800f4
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Wed Jun 23 14:11:46 2021 -0500
Hdf5 1 10 Release Note (#786)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
* Merge warnings files fixes from develop
* Fix cmake configure path
* Update missing release note info.
* Update code owners
* Add known problem
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit 9f5040736868f8eec584ab5af6d2a77e4d45ae30
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Tue Jun 22 07:03:26 2021 -0500
Hdf5 1 10 Update missing release note info. (#778)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
* Merge warnings files fixes from develop
* Fix cmake configure path
* Update missing release note info.
* Update code owners
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit 2e80c9cdec98d6cee5b4609643839a4ad2a848fb
Author: Dana Robinson <43805+derobins@users.noreply.github.com>
Date: Fri Jun 18 06:42:23 2021 -0700
Brings hash table IDs feature from develop/1.12 (#768)
* Brings updated tid test from develop
* Adds empty H5Iint.c and H5Idbg.c files
* H5I renaming to match 1.12/develop
* Splits off H5I debug code to H5Idbg.c
* Splits internal H5I.c functionality to H5Iint.c
* Header cleanup
* More renaming cleanup to match develop/1.12
* Adds "save last ID" optimization
* Adds uthash.h
* Adds hash table IDs from develop/1.12
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit 1e29bcbfe24956f0158b3363a3fbb8a42c8e7e0f
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Thu Jun 17 11:21:43 2021 -0500
Hdf5 1 10 Fix cmake configure path (#762)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
* Merge warnings files fixes from develop
* Fix cmake configure path
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit 475cdaf431c9ef5bfef6243dbc26d0005d08c49d
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Wed Jun 16 15:45:58 2021 -0500
Hdf5 1 10 merge warnings changes (#756)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
* Merge warnings files fixes from develop
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit e25980e7f35b8508db90648409ba80ee36d61c9e
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Tue Jun 8 14:37:13 2021 -0500
Hdf5 1 10 merges of CMake changes (#738)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit 061b23ac0011d3a26f660a7f4d07c40f41d63f10
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Thu Jun 3 16:07:23 2021 -0500
Partial merge issue #642 develop branch PRs to Hdf5 1 10 (#718)
* Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to
maintain binary compatibility.
* Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)
* 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>
* Committing clang-format changes
* Restore "error:" in line 2666.
* Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)"
This reverts commit 426b50484841118cf633fd6147302a63a30fd746.
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@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>
* 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>
* Made private my_yyinput function static (#618)
This prevents it being exported as a public symbol.
* Reduces overly-pedantic casting in the public headers (#644)
* Committing clang-format changes
* Fixes overly pedantic casting in public headers
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Use internal version of H5Eprint2 to avoid possible stack overflow (#661)
* Fixes for a couple of trivial warnings (#676)
* Committing clang-format changes
* Trivial warning fixes:
* Removes an unused done target in H5Tbit.c
* Add (void) to quiet "ignored return value" warnings in the generators
(which generally ignore errors)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes alternative function enter/leave macro scheme (#678)
* Committing clang-format changes
* Converted BEGIN_FUNC, etc. macros to FUNC_ENTER
* Rips out the BEGIN_FUNC, etc. macros
* Removes 'end if', etc. comments from H5HL package
* Committing clang-format changes
* Fixes an H5EA iterate issue
* Fixes an issue in the H5FA iterator code
* Further cleanup in bin/trace after macro removal
* Iterator changes in H5EA and H5FA
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Various CMake changes (#679)
* Committing clang-format changes
* Several CMake updates:
* Removes unused HDF5_ENABLE_HSIZET
* Switches TEST_SHELL_SCRIPTS to ON
* Sets SH_PROGRAM to bash instead of sh
* Set default build type back to RelWithDebInfo
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Revert "Removes alternative function enter/leave macro scheme (#678)"
This reverts commit edddb11b791adbdcaafed3ba718c95dd349a4e9a.
* err_compat test cleanup (#681)
* Committing clang-format changes
* Cleans up err_compat test and output
* Formatted source
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Sets the memory alloc sanity check option to disabled in autotools (#686)
* Revert "Sets the memory alloc sanity check option to disabled in autotools (#686)"
This reverts commit 652ffca58699388fff960c6a92c8ecfd1fc5d19b.
(Only for release branch).
* Removes alternative function enter/leave macro scheme (#678)
* Committing clang-format changes
* Converted BEGIN_FUNC, etc. macros to FUNC_ENTER
* Rips out the BEGIN_FUNC, etc. macros
* Removes 'end if', etc. comments from H5HL package
* Committing clang-format changes
* Fixes an H5EA iterate issue
* Fixes an issue in the H5FA iterator code
* Further cleanup in bin/trace after macro removal
* Iterator changes in H5EA and H5FA
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
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: Sean McBride <sean@rogue-research.com>
commit 14794490ec522fbd3ac2faa6efa0920979490fbc
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Wed Jul 14 13:50:26 2021 -0500
Update version to 1.10.8-2 after snapshot release of 1.10.8-1 (#838)
* Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to
maintain binary compatibility.
* Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)
* 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>
* Committing clang-format changes
* Restore "error:" in line 2666.
* Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)"
This reverts commit 426b50484841118cf633fd6147302a63a30fd746.
* Snapshot version 1.10 release 8-1. Update version to 1.10.8-2.
Squashed commit of the following:
commit 60734e63fe077238f10de3d6ca8f037f9a42af89
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Thu Jun 24 14:20:39 2021 -0500
Hdf5 1 10 Fix tools test (#796)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
* Merge warnings files fixes from develop
* Fix cmake configure path
* Update missing release note info.
* Update code owners
* Add known problem
* Use only core library for testing dynamic plugins.
CMake uses H5_HAVE_DIRECT instead of DIRECT_VFD
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit bfb780a4441e4ef43dd23708d415e5e3b84800f4
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Wed Jun 23 14:11:46 2021 -0500
Hdf5 1 10 Release Note (#786)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
* Merge warnings files fixes from develop
* Fix cmake configure path
* Update missing release note info.
* Update code owners
* Add known problem
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit 9f5040736868f8eec584ab5af6d2a77e4d45ae30
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Tue Jun 22 07:03:26 2021 -0500
Hdf5 1 10 Update missing release note info. (#778)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
* Merge warnings files fixes from develop
* Fix cmake configure path
* Update missing release note info.
* Update code owners
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit 2e80c9cdec98d6cee5b4609643839a4ad2a848fb
Author: Dana Robinson <43805+derobins@users.noreply.github.com>
Date: Fri Jun 18 06:42:23 2021 -0700
Brings hash table IDs feature from develop/1.12 (#768)
* Brings updated tid test from develop
* Adds empty H5Iint.c and H5Idbg.c files
* H5I renaming to match 1.12/develop
* Splits off H5I debug code to H5Idbg.c
* Splits internal H5I.c functionality to H5Iint.c
* Header cleanup
* More renaming cleanup to match develop/1.12
* Adds "save last ID" optimization
* Adds uthash.h
* Adds hash table IDs from develop/1.12
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit 1e29bcbfe24956f0158b3363a3fbb8a42c8e7e0f
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Thu Jun 17 11:21:43 2021 -0500
Hdf5 1 10 Fix cmake configure path (#762)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
* Merge warnings files fixes from develop
* Fix cmake configure path
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit 475cdaf431c9ef5bfef6243dbc26d0005d08c49d
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Wed Jun 16 15:45:58 2021 -0500
Hdf5 1 10 merge warnings changes (#756)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
* Merge warnings files fixes from develop
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit e25980e7f35b8508db90648409ba80ee36d61c9e
Author: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Tue Jun 8 14:37:13 2021 -0500
Hdf5 1 10 merges of CMake changes (#738)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
* Change windows TS to use older VS.
* Mostly all javadoc fixes, one argument rename.
* synch file
* Merge of long double fix and compiler flags
* HDFFV-11229 merge changes from develop
* HDFFV-11229 correct test script
* 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
* minor whitespace
* remove unneeded macro
* Committing clang-format changes
* 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.
* Fortran target depends
* Remove incorrect source attribute
* Revert define removal
* printf specifiers and VS2015 min changes
* Committing clang-format changes
* Add time struct
* TRILAB-227 and tools debug merges from develop
* Merge various changes from dev
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* doxygen changes merged from develop
* Committing clang-format changes
* Merge CMake fortran ninja changes from dev
* Enable fortran to gcc yaml
* Refactor Fortran CMake config tests and CMake test args
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
commit 061b23ac0011d3a26f660a7f4d07c40f41d63f10
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Thu Jun 3 16:07:23 2021 -0500
Partial merge issue #642 develop branch PRs to Hdf5 1 10 (#718)
* Revert addition of & to 2 parameters in DSetCreatPropList::setVirtual to
maintain binary compatibility.
* Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)
* 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>
* Committing clang-format changes
* Restore "error:" in line 2666.
* Revert "Fix H5Eget_auto2/H5Eauto_is_v2 to not clear error stack (#625)"
This reverts commit 426b50484841118cf633fd6147302a63a30fd746.
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
…sed by c++ code that fail on centos7 when -std=c++11 is not set.
* Fixed use of null pointer identified by UBSan UBSan warned: runtime error: member access within null pointer of type 'named_dt_t' (aka 'struct named_dt_t') with these two tests: H5REPACK-committed_dt_DFF H5REPACK-committed_dt Reformulated per @gnuoyd suggestion. * Fixed undefined float -> unsigned char conversion in HL_test_image * Removed dead skip_overflow_tests_g global The global `skip_overflow_tests_g` was being set but never read. * Don't treat 2d array as 1d array, fixing UBSan complaint in `CPP_testhdf5` * Committing clang-format changes * Remove extra ']' in line 730. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 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 <bmribler@hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 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>
hdf5_1_10. H5O_info2_t isn't available in HDF5 1.10.
lrknox
requested review from
bmribler,
fortnern,
jhendersonHDF,
jrmainzer,
rawarren and
soumagne
as code owners
derobins
approved these changes
Jul 29, 2021
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498 Ubsan fixes 3899e09 Note: 3 files merged, changes to the 4th file, h5repack.c were not merged because the change used H5)_info2_t which was introduced in 1.12.
503 BUG: DataSet assignment operator is missing d179f9d
519 Minor parallel improvements cb0a883