Merge issue 839 develop PRs to hdf5 1 10 - round 2 (#852)

* 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 * Squashed commit of the following: 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> * Revert references to SIZE_MAX to ((size_t)(-1)) in C header defines used by c++ code that fail on centos7 when -std=c++11 is not set. * Fix H5FD_mpio_Debug="rw" can report MPI_count instead of bytes (#699) * 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 * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes pre-C99 build and header cruft (#700) * Committing clang-format changes * Removes pre-C99 build and header cruft * Assumes ANSI C headers exist * Assumes stdbool.h, stdint.h, and inttypes.h are present * Assumes the C++ compiler can handle stdint.h * Removes all work-arounds for missing functionality, especially stdbool.h * Formats source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Clean up type size checks in configure.ac (#702) * Removes some DEC Alpha cruft from H5detect and H5private.h (#708) * Cleans up hsize_t and haddr_t size guessing (#709) * Cleans up definitions of haddr_t and hsize_t + cruft removal * Formatted source * Revert "Cleans up hsize_t and haddr_t size guessing (#709)" This reverts commit be6ad9a7a0f2d08b670fa98bbdd1ba9530c9e89a. * Updates bin/trace script to correctly wrap H5TRACE macros near clang-format column limit (#719) * Removes clang-format comments from H5O.c call * Fixes bin/trace to correctly wrap lines near the clang-format limit * Removed unused variable from bin/trace Conflicts: bin/trace src/H5O.c * 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> Conflicts: release_docs/RELEASE.txt * 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> Conflicts: release_docs/RELEASE.txt * 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> Conflicts: src/H5Gdeprec.c * Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++ (#726) * Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++ Allows C++ library to be built on older versions of gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Conflicts: src/H5public.h * Remove conflicts from RELEASE.txt * Always include inttypes.h 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> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
author: Larry Knox <lrknox@hdfgroup.org> 2021-07-26 02:20:20 (GMT)
committer: GitHub <noreply@github.com> 2021-07-26 02:20:20 (GMT)
commit: 1aa2c3421bef7ccd3610392d06c1856362c37312 (patch)
tree: bd514bb54cdbe044826a7c6f67b2b4b42f4820d6
parent: d97e989b8d1b5694ec1581d9664cb6e6e6a59880 (diff)
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27 files changed, 169 insertions, 237 deletions
diff --git a/bin/trace b/bin/trace
index 7f74e03..090b558 100755
--- a/bin/trace
+++ b/bin/trace
@@ -298,10 +298,33 @@ sub rewrite_func ($$$$$) {
     # Compose the trace macro
     $trace = "H5TRACE" . scalar(@arg_str) . "(\"$rettype\", \"";
     $trace .= join("", @arg_str) . "\"";
-    my $len = 4 + length $trace;        # Add 4, for indenting the line
-    for (@arg_name) {
-      # Wrap lines that will be longer than the limit, after ');' is added
-      if ($len + length >= ($max_trace_macro_line_len - 2)) {
+    $argtrace .= join("", @arg_str) . "\"";
+
+    # Add 4 for indenting the line
+    my $len = 4 + length($trace);
+
+    for my $i (0 .. $#arg_name) {
+      # Handle wrapping
+
+      # Be VERY careful here! clang-format and this script MUST agree
+      # on which lines get wrapped or there will be churn as each tries
+      # to undo the other's output.
+      #
+      # TWO cases must be handled:
+      # 1) The argument is that last one and ');' will be appended
+      # 2) The argument is NOT the last one and ',' will be appended
+      #
+      # NB: clang-format does NOT consider terminal newlines when
+      #     counting columns for the ColumnLimit
+      #
+      # The extra '2' added after $len includes the ', ' that would be
+      # added BEFORE the argument.
+      #
+      my $adjust = ($i + 1 == scalar(@arg_str)) ? 2 : 1;
+      my $len_if_added = $len + 2 + length($arg_name[$i]) + $adjust;
+
+      # Wrap lines that will be longer than the limit
+      if ($len_if_added > $max_trace_macro_line_len) {
         # Wrap line, with indention
         $trace .= ",\n             ";
         $len = 13;              # Set to 13, for indention
@@ -317,8 +340,11 @@ sub rewrite_func ($$$$$) {
       }
 
       # Append argument
-      $trace .= "$_";
-      $len += length;     # Add length of appended argument name
+      $trace .= "$arg_name[$i]";
+      $argtrace .= ", $arg_name[$i]";
+
+      # Add length of appended argument name
+      $len += length($arg_name[$i]);
     }
 
     # Append final ');' for macro
diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in
index 00d8097..842cfe8 100644
--- a/config/cmake/H5pubconf.h.in
+++ b/config/cmake/H5pubconf.h.in
@@ -198,15 +198,9 @@
    optimization operation */
 #cmakedefine H5_HAVE_INSTRUMENTED_LIBRARY @H5_HAVE_INSTRUMENTED_LIBRARY@
 
-/* Define to 1 if you have the <inttypes.h> header file. */
-#cmakedefine H5_HAVE_INTTYPES_H @H5_HAVE_INTTYPES_H@
-
 /* Define to 1 if you have the `ioctl' function. */
 #cmakedefine H5_HAVE_IOCTL @H5_HAVE_IOCTL@
 
-/* Define to 1 if you have the <io.h> header file. */
-#cmakedefine H5_HAVE_IO_H @H5_HAVE_IO_H@
-
 /* Define to 1 if you have the `crypto' library (-lcrypto). */
 #cmakedefine H5_HAVE_LIBCRYPTO @H5_HAVE_LIBCRYPTO@
 
@@ -358,18 +352,9 @@
 /* Define if `struct stat' has the `st_blocks' field */
 #cmakedefine H5_HAVE_STAT_ST_BLOCKS @H5_HAVE_STAT_ST_BLOCKS@
 
-/* Define to 1 if you have the <stdbool.h> header file. */
-#cmakedefine H5_HAVE_STDBOOL_H @H5_HAVE_STDBOOL_H@
-
 /* Define to 1 if you have the <stddef.h> header file. */
 #cmakedefine H5_HAVE_STDDEF_H @H5_HAVE_STDDEF_H@
 
-/* Define to 1 if you have the <stdint.h> header file. */
-#cmakedefine H5_HAVE_STDINT_H @H5_HAVE_STDINT_H@
-
-/* Define to 1 if you have the <stdint.h> header file for Cplusplus. */
-#cmakedefine H5_HAVE_STDINT_H_CXX @H5_HAVE_STDINT_H_CXX@
-
 /* Define to 1 if you have the <stdlib.h> header file. */
 #cmakedefine H5_HAVE_STDLIB_H @H5_HAVE_STDLIB_H@
 
@@ -713,9 +698,6 @@
 /* The size of `__int64', as computed by sizeof. */
 #define H5_SIZEOF___INT64 @H5_SIZEOF___INT64@
 
-/* Define to 1 if you have the ANSI C header files. */
-#cmakedefine H5_STDC_HEADERS @H5_STDC_HEADERS@
-
 /* Define if strict file format checks are enabled */
 #cmakedefine H5_STRICT_FORMAT_CHECKS @H5_STRICT_FORMAT_CHECKS@
 
diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake
index 004aded..d44ede7 100644
--- a/config/cmake_ext_mod/ConfigureChecks.cmake
+++ b/config/cmake_ext_mod/ConfigureChecks.cmake
@@ -120,23 +120,13 @@ CHECK_INCLUDE_FILE_CONCAT ("features.h"      ${HDF_PREFIX}_HAVE_FEATURES_H)
 CHECK_INCLUDE_FILE_CONCAT ("dirent.h"        ${HDF_PREFIX}_HAVE_DIRENT_H)
 CHECK_INCLUDE_FILE_CONCAT ("setjmp.h"        ${HDF_PREFIX}_HAVE_SETJMP_H)
 CHECK_INCLUDE_FILE_CONCAT ("stddef.h"        ${HDF_PREFIX}_HAVE_STDDEF_H)
-CHECK_INCLUDE_FILE_CONCAT ("stdint.h"        ${HDF_PREFIX}_HAVE_STDINT_H)
 CHECK_INCLUDE_FILE_CONCAT ("unistd.h"        ${HDF_PREFIX}_HAVE_UNISTD_H)
 
 # Windows
-CHECK_INCLUDE_FILE_CONCAT ("io.h"            ${HDF_PREFIX}_HAVE_IO_H)
 if (NOT CYGWIN)
   CHECK_INCLUDE_FILE_CONCAT ("winsock2.h"      ${HDF_PREFIX}_HAVE_WINSOCK2_H)
 endif ()
 
-if (CMAKE_SYSTEM_NAME MATCHES "OSF")
-  CHECK_INCLUDE_FILE_CONCAT ("sys/sysinfo.h" ${HDF_PREFIX}_HAVE_SYS_SYSINFO_H)
-  CHECK_INCLUDE_FILE_CONCAT ("sys/proc.h"    ${HDF_PREFIX}_HAVE_SYS_PROC_H)
-else ()
-  set (${HDF_PREFIX}_HAVE_SYS_SYSINFO_H "" CACHE INTERNAL "" FORCE)
-  set (${HDF_PREFIX}_HAVE_SYS_PROC_H    "" CACHE INTERNAL "" FORCE)
-endif ()
-
 CHECK_INCLUDE_FILE_CONCAT ("globus/common.h" ${HDF_PREFIX}_HAVE_GLOBUS_COMMON_H)
 CHECK_INCLUDE_FILE_CONCAT ("pdb.h"           ${HDF_PREFIX}_HAVE_PDB_H)
 CHECK_INCLUDE_FILE_CONCAT ("pthread.h"       ${HDF_PREFIX}_HAVE_PTHREAD_H)
@@ -146,12 +136,9 @@ CHECK_INCLUDE_FILE_CONCAT ("strings.h"       ${HDF_PREFIX}_HAVE_STRINGS_H)
 CHECK_INCLUDE_FILE_CONCAT ("stdlib.h"        ${HDF_PREFIX}_HAVE_STDLIB_H)
 CHECK_INCLUDE_FILE_CONCAT ("memory.h"        ${HDF_PREFIX}_HAVE_MEMORY_H)
 CHECK_INCLUDE_FILE_CONCAT ("dlfcn.h"         ${HDF_PREFIX}_HAVE_DLFCN_H)
-CHECK_INCLUDE_FILE_CONCAT ("inttypes.h"      ${HDF_PREFIX}_HAVE_INTTYPES_H)
 CHECK_INCLUDE_FILE_CONCAT ("netinet/in.h"    ${HDF_PREFIX}_HAVE_NETINET_IN_H)
 CHECK_INCLUDE_FILE_CONCAT ("netdb.h"         ${HDF_PREFIX}_HAVE_NETDB_H)
 CHECK_INCLUDE_FILE_CONCAT ("arpa/inet.h"     ${HDF_PREFIX}_HAVE_ARPA_INET_H)
-# _Bool type support
-CHECK_INCLUDE_FILE_CONCAT (stdbool.h    ${HDF_PREFIX}_HAVE_STDBOOL_H)
 
 ## Check for non-standard extenstion quadmath.h
 
@@ -238,11 +225,6 @@ macro (HDF_FUNCTION_TEST OTHER_TEST)
 endmacro ()
 
 #-----------------------------------------------------------------------------
-# Check for these functions before the time headers are checked
-#-----------------------------------------------------------------------------
-HDF_FUNCTION_TEST (STDC_HEADERS)
-
-#-----------------------------------------------------------------------------
 #  Check for large file support
 #-----------------------------------------------------------------------------
 
@@ -416,13 +398,9 @@ HDF_CHECK_TYPE_SIZE (time_t          ${HDF_PREFIX}_SIZEOF_TIME_T)
 # Extra C99 types
 #-----------------------------------------------------------------------------
 
-# _Bool type support
-if (HAVE_STDBOOL_H)
-  set (CMAKE_EXTRA_INCLUDE_FILES stdbool.h)
-  HDF_CHECK_TYPE_SIZE (bool         ${HDF_PREFIX}_SIZEOF_BOOL)
-else ()
-  HDF_CHECK_TYPE_SIZE (_Bool        ${HDF_PREFIX}_SIZEOF_BOOL)
-endif ()
+# Size of bool
+set (CMAKE_EXTRA_INCLUDE_FILES stdbool.h)
+HDF_CHECK_TYPE_SIZE (_Bool        ${HDF_PREFIX}_SIZEOF_BOOL)
 
 if (MINGW OR NOT WINDOWS)
   #-----------------------------------------------------------------------------
@@ -560,7 +538,6 @@ if (MINGW OR NOT WINDOWS)
   foreach (other_test
       HAVE_ATTRIBUTE
       HAVE_C99_FUNC
-#      STDC_HEADERS
       HAVE_FUNCTION
       HAVE_C99_DESIGNATED_INITIALIZER
       SYSTEM_SCOPE_THREADS
diff --git a/config/cmake_ext_mod/HDFTests.c b/config/cmake_ext_mod/HDFTests.c
index 2d7e1b4..0c3b7b7 100644
--- a/config/cmake_ext_mod/HDFTests.c
+++ b/config/cmake_ext_mod/HDFTests.c
@@ -88,14 +88,6 @@ int main(void)
 }
 #endif
 
-#ifdef STDC_HEADERS
-#include <stdlib.h>
-#include <stdarg.h>
-#include <string.h>
-#include <float.h>
-int main() { return 0; }
-#endif /* STDC_HEADERS */
-
 
 #ifdef HAVE_ATTRIBUTE
 
diff --git a/config/cmake_ext_mod/HDFUseCXX.cmake b/config/cmake_ext_mod/HDFUseCXX.cmake
index 580c409..423f74a 100644
--- a/config/cmake_ext_mod/HDFUseCXX.cmake
+++ b/config/cmake_ext_mod/HDFUseCXX.cmake
@@ -32,17 +32,6 @@ endif ()
 include (CheckIncludeFileCXX)
 include (TestForSTDNamespace)
 
-# IF the c compiler found stdint, check the C++ as well. On some systems this
-# file will be found by C but not C++, only do this test IF the C++ compiler
-# has been initialized (e.g. the project also includes some c++)
-if (${HDF_PREFIX}_HAVE_STDINT_H AND CMAKE_CXX_COMPILER_LOADED)
-  CHECK_INCLUDE_FILE_CXX ("stdint.h" ${HDF_PREFIX}_HAVE_STDINT_H_CXX)
-  if (NOT ${HDF_PREFIX}_HAVE_STDINT_H_CXX)
-    set (${HDF_PREFIX}_HAVE_STDINT_H "" CACHE INTERNAL "Have includes HAVE_STDINT_H")
-    set (USE_INCLUDES ${USE_INCLUDES} "stdint.h")
-  endif ()
-endif ()
-
 # For other CXX specific tests, use this MACRO.
 macro (HDF_CXX_FUNCTION_TEST OTHER_TEST)
   if (NOT DEFINED ${OTHER_TEST})
diff --git a/configure.ac b/configure.ac
index d0ce46a..d233323 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1224,8 +1224,6 @@ AC_CHECK_HEADERS([sys/resource.h sys/time.h unistd.h sys/ioctl.h sys/stat.h])
 AC_CHECK_HEADERS([sys/socket.h sys/types.h sys/file.h])
 AC_CHECK_HEADERS([stddef.h setjmp.h features.h])
 AC_CHECK_HEADERS([dirent.h])
-AC_CHECK_HEADERS([stdint.h], [C9x=yes])
-AC_CHECK_HEADERS([stdbool.h])
 AC_CHECK_HEADERS([netdb.h netinet/in.h arpa/inet.h])
 
 ## Darwin
@@ -1241,15 +1239,15 @@ esac
 ## Windows
 case "`uname`" in
   CYGWIN*)
-    AC_CHECK_HEADERS([io.h sys/timeb.h])
+    AC_CHECK_HEADERS([sys/timeb.h])
     UNAME_CYGWIN="yes"
     ;;
   MINGW*)
-    AC_CHECK_HEADERS([io.h winsock2.h sys/timeb.h])
+    AC_CHECK_HEADERS([winsock2.h sys/timeb.h])
     AC_HAVE_LIBRARY([ws2_32])
     ;;
   *)
-    AC_CHECK_HEADERS([io.h winsock2.h sys/timeb.h])
+    AC_CHECK_HEADERS([winsock2.h sys/timeb.h])
     ;;
 esac
 
@@ -1340,16 +1338,15 @@ CFLAGS="$H5_CFLAGS $AM_CFLAGS $CFLAGS"
 ## Checkpoint the cache
 AC_CACHE_SAVE
 
-## Posix.1g types (C9x)
+## Write the confdefs.h header for checking sizes
 cat >>confdefs.h <<\EOF
-#include <sys/types.h>
-EOF
-
-if test "X$C9x" = "Xyes"; then
-  cat >>confdefs.h <<\EOF
+#include <stdbool.h>
 #include <stdint.h>
+#ifdef HAVE_UNISTD_H
+#include <sys/types.h>
+#endif
+#include <time.h>
 EOF
-fi
 
 AC_CHECK_SIZEOF(        [int8_t])
 AC_CHECK_SIZEOF(       [uint8_t])
@@ -1379,34 +1376,12 @@ AC_CHECK_SIZEOF([uint_least64_t])
 AC_CHECK_SIZEOF(  [int_fast64_t])
 AC_CHECK_SIZEOF( [uint_fast64_t])
 
+AC_CHECK_SIZEOF([bool])
+AC_CHECK_SIZEOF([off_t])
+AC_CHECK_SIZEOF([ptrdiff_t])
 AC_CHECK_SIZEOF([size_t])
 AC_CHECK_SIZEOF([ssize_t])
-AC_CHECK_SIZEOF([ptrdiff_t])
-
-cat >>confdefs.h <<\EOF
-#include <sys/types.h> /*for off_t definition*/
-EOF
-AC_CHECK_SIZEOF([off_t])
-
-if test "X$C9x" = "Xyes"; then
-  cat >>confdefs.h <<\EOF
-#ifdef HAVE_STDBOOL_H
-#include <stdbool.h> /* for bool definition */
-#else
-#define bool _Bool
-#endif
-EOF
-AC_CHECK_SIZEOF([bool])
-fi
-
-AC_CHECK_SIZEOF(time_t, [], [
-#ifdef HAVE_SYS_TYPES_H
-#include <sys/types.h>
-#endif
-#ifdef HAVE_TIME_H
-#include <time.h>
-#endif
-])
+AC_CHECK_SIZEOF([time_t])
 
 ## Checkpoint the cache
 AC_CACHE_SAVE
@@ -1911,10 +1886,8 @@ if test "X$THREADSAFE" = "Xyes"; then
     AC_CACHE_VAL([hdf5_cv_system_scope_threads],
       [AC_RUN_IFELSE(
         [AC_LANG_PROGRAM([
-            #if STDC_HEADERS
             #include <stdlib.h>
             #include <pthread.h>
-            #endif
         ],[
               pthread_attr_t attribute;
               int ret;
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 4c8fe0a..6006b1e 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -262,6 +262,49 @@ New Features
 
     Library:
     --------
+    - H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX
+
+      The size_hint value is ultimately stored in a uint32_t struct field,
+      so specifying a value larger than this on a 64-bit machine can cause
+      undefined behavior including crashing the system.
+
+      The documentation for this API call was also incorrect, stating that
+      passing a negative value would cause the library to use a default
+      value. Instead, passing a "negative" value actually passes a very large
+      value, which is probably not what the user intends and can cause
+      crashes on 64-bit systems.
+
+      The Doxygen documentation has been updated and passing values larger
+      than UINT32_MAX for size_hint will now produce a normal HDF5 error.
+      
+        (DER - 2021/04/29, HDFFV-11241)
+
+
+    - H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID
+
+      When passed an invalid fapl ID, H5Pset_fapl_log() would usually
+      segfault when attempting to free an uninitialized pointer in the error
+      handling code. This behavior is more common in release builds or
+      when the memory sanitization checks were not selected as a build
+      option.
+
+      The pointer is now correctly initialized and the API call now
+      produces a normal HDF5 error when fed an invalid fapl ID.
+
+        (DER - 2021/04/28, HDFFV-11240)
+
+    - Fixes a segfault when H5Pset_mdc_log_options() is called multiple times
+
+      The call incorrectly attempts to free an internal copy of the previous
+      log location string, which causes a segfault. This only happens
+      when the call is invoked multiple times on the same property list.
+      On the first call to a given fapl, the log location is set to NULL so
+      the segfault does not occur.
+
+      The string is now handled properly and the segfault no longer occurs.
+
+        (DER - 2021/04/27, HDFFV-11239)
+
     - HSYS_GOTO_ERROR now emits the results of GetLastError() on Windows
 
       HSYS_GOTO_ERROR is an internal macro that is used to produce error
diff --git a/src/H5FDlog.c b/src/H5FDlog.c
index aa2d6db..38ea346 100644
--- a/src/H5FDlog.c
+++ b/src/H5FDlog.c
@@ -326,12 +326,15 @@ H5Pset_fapl_log(hid_t fapl_id, const char *logfile, unsigned long long flags, si
     FUNC_ENTER_API(FAIL)
     H5TRACE4("e", "i*sULz", fapl_id, logfile, flags, buf_size);
 
+    /* Do this first, so that we don't try to free a wild pointer if
+     * H5P_object_verify() fails.
+     */
+    HDmemset(&fa, 0, sizeof(H5FD_log_fapl_t));
+
     /* Check arguments */
     if (NULL == (plist = H5P_object_verify(fapl_id, H5P_FILE_ACCESS)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file access property list")
 
-    HDmemset(&fa, 0, sizeof(H5FD_log_fapl_t));
-
     /* Duplicate the log file string
      * A little wasteful, since this string will just be copied later, but
      * passing it in as a pointer sets off a chain of impossible-to-resolve
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c
index 501ec6f..2dd7fd3 100644
--- a/src/H5FDmpio.c
+++ b/src/H5FDmpio.c
@@ -1470,6 +1470,12 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
     if (bytes_read < 0 || bytes_read > io_size)
         HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
 
+#ifdef H5FDmpio_DEBUG
+    if (H5FD_mpio_debug_r_flag)
+        HDfprintf(stderr, "%s: (%d) mpi_off = %ld  bytes_read = %lld\n", FUNC, file->mpi_rank, (long)mpi_off,
+                  bytes_read);
+#endif
+
     /*
      * This gives us zeroes beyond end of physical MPI file.
      */
@@ -1659,6 +1665,12 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha
     if (bytes_written != io_size)
         HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
 
+#ifdef H5FDmpio_DEBUG
+    if (H5FD_mpio_debug_w_flag)
+        HDfprintf(stderr, "%s: (%d) mpi_off = %ld  bytes_written = %lld\n", FUNC, file->mpi_rank,
+                  (long)mpi_off, bytes_written);
+#endif
+
     /* Each process will keep track of its perceived EOF value locally, and
      * ultimately we will reduce this value to the maximum amongst all
      * processes, but until then keep the actual eof at HADDR_UNDEF just in
diff --git a/src/H5Gdeprec.c b/src/H5Gdeprec.c
index 2916198..75e47d4 100644
--- a/src/H5Gdeprec.c
+++ b/src/H5Gdeprec.c
@@ -143,10 +143,10 @@ H5G_map_obj_type(H5O_type_t obj_type)
  *		specified NAME.  The group is opened for write access
  *		and it's object ID is returned.
  *
- *		The optional SIZE_HINT specifies how much file space to
- *		reserve to store the names that will appear in this
- *		group. If a non-positive value is supplied for the SIZE_HINT
- *		then a default size is chosen.
+ *		The SIZE_HINT parameter specifies how much file space to reserve
+ *		to store the names that will appear in this group. This number
+ *		must be less than or equal to UINT32_MAX. If zero is supplied
+ *		for the SIZE_HINT then a default size is chosen.
  *
  * Note:	Deprecated in favor of H5Gcreate2
  *
@@ -177,6 +177,8 @@ H5Gcreate1(hid_t loc_id, const char *name, size_t size_hint)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location")
     if (!name || !*name)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name given")
+    if (size_hint > UINT32_MAX)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, H5I_INVALID_HID, "size_hint cannot be larger than UINT32_MAX")
 
     /* Check if we need to create a non-standard GCPL */
     if (size_hint > 0) {
diff --git a/src/H5Pfapl.c b/src/H5Pfapl.c
index fe5a81e..d7408e3 100644
--- a/src/H5Pfapl.c
+++ b/src/H5Pfapl.c
@@ -4254,7 +4254,7 @@ herr_t
 H5Pset_mdc_log_options(hid_t plist_id, hbool_t is_enabled, const char *location, hbool_t start_on_access)
 {
     H5P_genplist_t *plist;               /* Property list pointer */
-    char *          tmp_location;        /* Working location pointer */
+    char *          new_location;        /* Working location pointer */
     herr_t          ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API(FAIL)
@@ -4270,19 +4270,14 @@ H5Pset_mdc_log_options(hid_t plist_id, hbool_t is_enabled, const char *location,
     if (NULL == (plist = H5P_object_verify(plist_id, H5P_FILE_ACCESS)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "plist_id is not a file access property list")
 
-    /* Get the current location string and free it */
-    if (H5P_get(plist, H5F_ACS_MDC_LOG_LOCATION_NAME, &tmp_location) < 0)
-        HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get current log location")
-    H5MM_xfree(tmp_location);
-
     /* Make a copy of the passed-in location */
-    if (NULL == (tmp_location = H5MM_xstrdup(location)))
+    if (NULL == (new_location = H5MM_xstrdup(location)))
         HGOTO_ERROR(H5E_PLIST, H5E_CANTCOPY, FAIL, "can't copy passed-in log location")
 
     /* Set values */
     if (H5P_set(plist, H5F_ACS_USE_MDC_LOGGING_NAME, &is_enabled) < 0)
         HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set is_enabled flag")
-    if (H5P_set(plist, H5F_ACS_MDC_LOG_LOCATION_NAME, &tmp_location) < 0)
+    if (H5P_set(plist, H5F_ACS_MDC_LOG_LOCATION_NAME, &new_location) < 0)
         HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set log location")
     if (H5P_set(plist, H5F_ACS_START_MDC_LOG_ON_ACCESS_NAME, &start_on_access) < 0)
         HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set start_on_access flag")
diff --git a/src/H5detect.c b/src/H5detect.c
index 52950bb..35da85e 100644
--- a/src/H5detect.c
+++ b/src/H5detect.c
@@ -1655,21 +1655,6 @@ main(int argc, char *argv[])
     if (!rawoutstream)
         rawoutstream = stdout;
 
-#if defined(H5_HAVE_SETSYSINFO) && defined(SSI_NVPAIRS)
-#if defined(UAC_NOPRINT) && defined(UAC_SIGBUS)
-    /*
-     * Make sure unaligned access generates SIGBUS and doesn't print warning
-     * messages so that we can detect alignment constraints on the DEC Alpha.
-     */
-    int nvpairs[2];
-    nvpairs[0] = SSIN_UACPROC;
-    nvpairs[1] = UAC_NOPRINT | UAC_SIGBUS;
-    if (setsysinfo(SSI_NVPAIRS, nvpairs, 1, 0, 0) < 0) {
-        fprintf(stderr, "H5detect: unable to turn off UAC handling: %s\n", HDstrerror(errno));
-    }
-#endif
-#endif
-
 #if defined(H5SETJMP) && defined(H5_HAVE_SIGNAL)
     /* verify the SIGBUS and SIGSEGV handlers work properly */
     if (verify_signal_handlers(SIGBUS, sigbus_handler) != 0) {
diff --git a/src/H5private.h b/src/H5private.h
index 162fae4..b31ec78 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -41,10 +41,6 @@
 #endif /* H5_HAVE_WIN32_API */
 #endif /* H5_HAVE_THREADSAFE */
 
-/*
- * Include ANSI-C header files.
- */
-#ifdef H5_STDC_HEADERS
 #include <assert.h>
 #include <ctype.h>
 #include <errno.h>
@@ -56,7 +52,6 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#endif
 
 /*
  * If _POSIX_VERSION is defined in unistd.h then this system is Posix.1
@@ -71,14 +66,7 @@
 #include <pwd.h>
 #endif
 
-/*
- * C9x integer types
- */
-#ifndef __cplusplus
-#ifdef H5_HAVE_STDINT_H
 #include <stdint.h>
-#endif
-#endif
 
 /*
  * The `struct stat' data type for stat() and fstat(). This is a Posix file
@@ -139,21 +127,6 @@
 #endif
 
 /*
- * System information. These are needed on the DEC Alpha to turn off fixing
- * of unaligned accesses by the operating system during detection of
- * alignment constraints in H5detect.c:main().
- */
-#ifdef H5_HAVE_SYS_SYSINFO_H
-#include <sys/sysinfo.h>
-#endif
-#ifdef H5_HAVE_SYS_PROC_H
-#include <sys/proc.h>
-#endif
-#ifdef H5_HAVE_IO_H
-#include <io.h>
-#endif
-
-/*
  * Dynamic library handling.  These are needed for dynamically loading I/O
  * filters and VFDs.
  */
@@ -184,6 +157,7 @@
 
 #include <windows.h>
 #include <direct.h> /* For _getcwd() */
+#include <io.h>     /* POSIX I/O */
 
 #endif /*H5_HAVE_WIN32_API*/
 
diff --git a/src/H5public.h b/src/H5public.h
index 470f8b8..8d22e9d 100644
--- a/src/H5public.h
+++ b/src/H5public.h
@@ -34,13 +34,14 @@
 #ifdef H5_HAVE_FEATURES_H
 #include <features.h> /* For setting POSIX, BSD, etc. compatibility */
 #endif
+
 #ifdef H5_HAVE_SYS_TYPES_H
 #include <sys/types.h>
 #endif
-#ifdef H5_STDC_HEADERS
+
 #include <limits.h> /* For H5T_NATIVE_CHAR defn in H5Tpublic.h  */
 #include <stdarg.h> /* For variadic functions   */
-#endif
+
 #ifndef __cplusplus
 #ifdef H5_HAVE_STDINT_H
 #include <stdint.h> /* For C9x types */
@@ -50,9 +51,13 @@
 #include <stdint.h> /* For C9x types (when included from C++) */
 #endif
 #endif
-#ifdef H5_HAVE_INTTYPES_H
-#include <inttypes.h> /* C99/POSIX.1 header for uint64_t, PRIu64 */
+
+#ifdef __cplusplus
+#define __STDC_FORMAT_MACROS
 #endif
+
+#include <inttypes.h> /* C99/POSIX.1 header for uint64_t, PRIu64 */
+
 #ifdef H5_HAVE_STDDEF_H
 #include <stddef.h>
 #endif
@@ -217,19 +222,7 @@ typedef int herr_t;
  * }
  * \endcode
  */
-#ifdef H5_HAVE_STDBOOL_H
 #include <stdbool.h>
-#else /* H5_HAVE_STDBOOL_H */
-#ifndef __cplusplus
-#if defined(H5_SIZEOF_BOOL) && (H5_SIZEOF_BOOL != 0)
-#define bool _Bool
-#else
-#define bool unsigned int
-#endif
-#define true 1
-#define false 0
-#endif /* __cplusplus */
-#endif /* H5_HAVE_STDBOOL_H */
 typedef bool hbool_t;
 typedef int  htri_t;
 
diff --git a/test/cache.c b/test/cache.c
index 85cc417..c6950ac 100644
--- a/test/cache.c
+++ b/test/cache.c
@@ -8068,19 +8068,6 @@ check_flush_cache__flush_op_test(H5F_t *file_ptr, int test_num, unsigned int flu
         if ((check[i].entry_num != i) || (check[i].entry_type < 0) ||
             (check[i].entry_type >= NUMBER_OF_ENTRY_TYPES) || (check[i].entry_index < 0) ||
             (check[i].entry_index > max_indices[check[i].entry_type]) ||
-#ifndef H5_HAVE_STDBOOL_H
-            /* Check for nonsense values if hbool_t is an integral
-             * type instead of a real Boolean.
-             */
-            ((check[i].in_cache != TRUE) && (check[i].in_cache != FALSE)) ||
-            ((check[i].at_main_addr != TRUE) && (check[i].at_main_addr != FALSE)) ||
-            ((check[i].is_dirty != TRUE) && (check[i].is_dirty != FALSE)) ||
-            ((check[i].is_protected != TRUE) && (check[i].is_protected != FALSE)) ||
-            ((check[i].is_pinned != TRUE) && (check[i].is_pinned != FALSE)) ||
-            ((check[i].expected_deserialized != TRUE) && (check[i].expected_deserialized != FALSE)) ||
-            ((check[i].expected_serialized != TRUE) && (check[i].expected_serialized != FALSE)) ||
-            ((check[i].expected_destroyed != TRUE) && (check[i].expected_destroyed != FALSE)) ||
-#endif /* H5_HAVE_STDBOOL_H */
             (check[i].expected_size <= (size_t)0)) {
 
             pass = FALSE;
diff --git a/test/cache_common.c b/test/cache_common.c
index 3762196..089f9a0 100644
--- a/test/cache_common.c
+++ b/test/cache_common.c
@@ -1508,12 +1508,6 @@ add_flush_op(int target_type, int target_idx, int op_code, int type, int idx, hb
     HDassert((0 <= type) && (type < NUMBER_OF_ENTRY_TYPES));
     HDassert((0 <= idx) && (idx <= max_indices[type]));
     HDassert(new_size <= VARIABLE_ENTRY_SIZE);
-#ifndef H5_HAVE_STDBOOL_H
-    /* Check for TRUE or FALSE if we're using an integer type instead
-     * of a real Boolean type.
-     */
-    HDassert((flag == TRUE) || (flag == FALSE));
-#endif /* H5_HAVE_STDBOOL_H */
 
     if (pass) {
 
@@ -1713,12 +1707,6 @@ execute_flush_op(H5F_t *file_ptr, struct test_entry_t *entry_ptr, struct flush_o
     HDassert((0 <= op_ptr->type) && (op_ptr->type < NUMBER_OF_ENTRY_TYPES));
     HDassert((0 <= op_ptr->idx) && (op_ptr->idx <= max_indices[op_ptr->type]));
     HDassert(flags_ptr != NULL);
-#ifndef H5_HAVE_STDBOOL_H
-    /* Check for TRUE or FALSE if we're using an integer type instead
-     * of a real Boolean type.
-     */
-    HDassert((op_ptr->flag == FALSE) || (op_ptr->flag == TRUE));
-#endif /* H5_HAVE_STDBOOL_H */
 
     if (pass) {
 
diff --git a/test/cache_logging.c b/test/cache_logging.c
index 448e12b..af43845 100644
--- a/test/cache_logging.c
+++ b/test/cache_logging.c
@@ -58,6 +58,12 @@ test_logging_api(void)
     if (H5Pset_mdc_log_options(fapl, is_enabled, LOG_LOCATION, start_on_access) < 0)
         TEST_ERROR;
 
+    /* Ensure that setting the property twice doesn't cause problems
+     * (addresses a previous bug).
+     */
+    if (H5Pset_mdc_log_options(fapl, is_enabled, LOG_LOCATION, start_on_access) < 0)
+        TEST_ERROR;
+
     /* Check to make sure that the property list getter returns the correct
      * location string buffer size;
      */
diff --git a/test/tmisc.c b/test/tmisc.c
index a559191..fbb3ca8 100644
--- a/test/tmisc.c
+++ b/test/tmisc.c
@@ -3998,9 +3998,31 @@ test_misc23(void)
     H5E_END_TRY;
     VERIFY(tmp_id, FAIL, "H5Gcreate1");
 
-    tmp_id = H5Gcreate1(file_id, "/A/grp", (size_t)0);
+    /* Make sure that size_hint values that can't fit into a 32-bit
+     * unsigned integer are rejected. Only necessary on systems where
+     * size_t is a 64-bit type.
+     */
+    if (SIZE_MAX > UINT32_MAX) {
+        H5E_BEGIN_TRY
+        {
+            tmp_id = H5Gcreate1(file_id, "/size_hint_too_large", SIZE_MAX);
+        }
+        H5E_END_TRY;
+        VERIFY(tmp_id, FAIL, "H5Gcreate1");
+    }
+
+    /* Make sure the largest size_hint value works */
+    H5E_BEGIN_TRY
+    {
+        tmp_id = H5Gcreate1(file_id, "/largest_size_hint", UINT32_MAX);
+    }
+    H5E_END_TRY;
     CHECK(tmp_id, FAIL, "H5Gcreate1");
+    status = H5Gclose(tmp_id);
+    CHECK(status, FAIL, "H5Gclose");
 
+    tmp_id = H5Gcreate1(file_id, "/A/grp", (size_t)0);
+    CHECK(tmp_id, FAIL, "H5Gcreate1");
     status = H5Gclose(tmp_id);
     CHECK(status, FAIL, "H5Gclose");
 
@@ -4013,7 +4035,6 @@ test_misc23(void)
 
     tmp_id = H5Dcreate1(file_id, "/A/dset", type_id, space_id, create_id);
     CHECK(tmp_id, FAIL, "H5Dcreate1");
-
     status = H5Dclose(tmp_id);
     CHECK(status, FAIL, "H5Dclose");
 #endif /* H5_NO_DEPRECATED_SYMBOLS */
diff --git a/test/vfd.c b/test/vfd.c
index 843c772..af734d8 100644
--- a/test/vfd.c
+++ b/test/vfd.c
@@ -1835,12 +1835,23 @@ test_log(void)
     hsize_t       file_size = 0;
     unsigned int  flags     = H5FD_LOG_ALL;
     size_t        buf_size  = 4 * KB;
+    herr_t        ret       = SUCCEED;
 
     TESTING("LOG file driver");
 
-    /* Set property list and file name for log driver. */
     if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
         TEST_ERROR;
+
+    /* Make sure calling with an invalid fapl doesn't crash */
+    H5E_BEGIN_TRY
+    {
+        ret = H5Pset_fapl_log(H5I_INVALID_HID, LOG_FILENAME, 0, 0);
+    }
+    H5E_END_TRY;
+    if (SUCCEED == ret)
+        TEST_ERROR;
+
+    /* Set property list and file name for log driver. */
     if (H5Pset_fapl_log(fapl, LOG_FILENAME, flags, buf_size) < 0)
         TEST_ERROR;
     h5_fixname(FILENAME[6], fapl, filename, sizeof filename);
diff --git a/tools/test/perform/chunk.c b/tools/test/perform/chunk.c
index 1b6793a..1b08e95 100644
--- a/tools/test/perform/chunk.c
+++ b/tools/test/perform/chunk.c
@@ -24,12 +24,10 @@
 #undef NDEBUG
 #include "hdf5.h"
 
-#ifdef H5_STDC_HEADERS
 #include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#endif
 
 /* Solaris Studio defines attribute, but for the attributes we need */
 #if !defined(H5_HAVE_ATTRIBUTE) || defined __cplusplus || defined(__SUNPRO_C)
diff --git a/tools/test/perform/direct_write_perf.c b/tools/test/perform/direct_write_perf.c
index b3ae54d..6537215 100644
--- a/tools/test/perform/direct_write_perf.c
+++ b/tools/test/perform/direct_write_perf.c
@@ -23,14 +23,11 @@
 
 #if !defined(WIN32) && !defined(__MINGW32__)
 
-#include <math.h>
-
-#ifdef H5_STDC_HEADERS
 #include <errno.h>
 #include <fcntl.h>
+#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
-#endif
 
 #ifdef H5_HAVE_UNISTD_H
 #include <sys/types.h>
diff --git a/tools/test/perform/overhead.c b/tools/test/perform/overhead.c
index dba8220..60ec8d8 100644
--- a/tools/test/perform/overhead.c
+++ b/tools/test/perform/overhead.c
@@ -23,17 +23,11 @@
 #include "hdf5.h"
 #include "H5private.h"
 
-#ifdef H5_STDC_HEADERS
 #include <ctype.h>
 #include <fcntl.h>
 #include <stdlib.h>
 #include <sys/stat.h>
 #include <string.h>
-#endif
-
-#ifdef H5_HAVE_IO_H
-#include <io.h>
-#endif
 
 #ifdef H5_HAVE_UNISTD_H
 #include <sys/types.h>
diff --git a/tools/test/perform/perf.c b/tools/test/perform/perf.c
index bf4b2a9..a06fb77 100644
--- a/tools/test/perform/perf.c
+++ b/tools/test/perform/perf.c
@@ -26,13 +26,11 @@
 
 #ifdef H5_HAVE_PARALLEL
 
-#ifdef H5_STDC_HEADERS
 #include <errno.h>
 #include <fcntl.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#endif
 
 #ifdef H5_HAVE_UNISTD_H
 #include <sys/types.h>
diff --git a/tools/test/perform/pio_engine.c b/tools/test/perform/pio_engine.c
index 65194b0..cac36d7 100644
--- a/tools/test/perform/pio_engine.c
+++ b/tools/test/perform/pio_engine.c
@@ -16,12 +16,10 @@
 
 #include "hdf5.h"
 
-#ifdef H5_STDC_HEADERS
 #include <errno.h>
 #include <fcntl.h>
 #include <stdio.h>
 #include <stdlib.h>
-#endif
 
 #ifdef H5_HAVE_UNISTD_H
 #include <sys/types.h>
diff --git a/tools/test/perform/pio_standalone.h b/tools/test/perform/pio_standalone.h
index 35a5217..82fabdc 100644
--- a/tools/test/perform/pio_standalone.h
+++ b/tools/test/perform/pio_standalone.h
@@ -21,10 +21,6 @@
 
 #include "H5public.h" /* Include Public Definitions    */
 
-/*
- * Include ANSI-C header files.
- */
-#ifdef H5_STDC_HEADERS
 #include <assert.h>
 #include <ctype.h>
 #include <errno.h>
@@ -37,7 +33,6 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#endif
 
 /*
  * Redefine all the POSIX functions.  We should never see a POSIX
diff --git a/tools/test/perform/sio_engine.c b/tools/test/perform/sio_engine.c
index e5a0ec8..f67a7a6 100644
--- a/tools/test/perform/sio_engine.c
+++ b/tools/test/perform/sio_engine.c
@@ -16,12 +16,10 @@
 
 #include "hdf5.h"
 
-#ifdef H5_STDC_HEADERS
 #include <errno.h>
 #include <fcntl.h>
 #include <stdio.h>
 #include <stdlib.h>
-#endif
 
 #ifdef H5_HAVE_UNISTD_H
 #include <sys/types.h>
diff --git a/tools/test/perform/sio_standalone.h b/tools/test/perform/sio_standalone.h
index d8b6412..54e82fa 100644
--- a/tools/test/perform/sio_standalone.h
+++ b/tools/test/perform/sio_standalone.h
@@ -21,10 +21,6 @@
 
 #include "H5public.h" /* Include Public Definitions    */
 
-/*
- * Include ANSI-C header files.
- */
-#ifdef H5_STDC_HEADERS
 #include <assert.h>
 #include <ctype.h>
 #include <errno.h>
@@ -37,7 +33,6 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#endif
 
 /* maximum of two, three, or four values */
 #undef MAX
author	Larry Knox <lrknox@hdfgroup.org>	2021-07-26 02:20:20 (GMT)
committer	GitHub <noreply@github.com>	2021-07-26 02:20:20 (GMT)
commit	1aa2c3421bef7ccd3610392d06c1856362c37312 (patch)
tree	bd514bb54cdbe044826a7c6f67b2b4b42f4820d6
parent	d97e989b8d1b5694ec1581d9664cb6e6e6a59880 (diff)
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