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* 1.10: Add spelling check to CI and fix errors. (#2442)Allen Byrne2023-02-161-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update CI and support files to match latest from 1.14 * Correct spelling * More spelling corrections * spelling fixes in testpar * Fix spelling errors in tools * More tools spelling fixes * Spelling fixes for rest of tools and some src * Fix spelling errors in src files, pt 2 * Fix spelling in src pt3 * Fix spelling errors pt4 * Fix spelling errors pt5 * Spelling fix pt6 * fix spelling error examples * fix spelling in tests * fix spelling errors in test pt2 * Fix spelling errors in test pt3 * fix spelling in test pt4 * Fix spelling errors in hl * fix spelling errors in c++ * Spelling fixes for fortran * spelling fixes for bin and java * Add relative path * Change spelling action to use a file for list of ignore words * Fix spelling ignore list * remove unused file
* 1.10 clang 13 format #1933 (#1940)Allen Byrne2022-07-291-3/+3
| | | | | * clang 13 format #1933 * Correct workflow
* Brings random stuff over from develop (#1738)Dana Robinson2022-05-061-7/+10
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* 1.10 Fix release check version logic #1438 (#1494)Allen Byrne2022-03-121-8/+6
| | | | | * Fix release check version logic #1438 * Correct list comment
* Add cast to relnum for merge of #812 (#932)Allen Byrne2021-08-191-1/+4
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* Rework version-check for relnum in H5checkversion function (#896)Allen Byrne2021-08-121-85/+143
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* Merge issue 839 changes to hdf5 1 10 (#841)Larry Knox2021-07-161-4/+0
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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>
* Hdf5 1 10 doxygen merges (#684)Allen Byrne2021-05-261-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 merge issue 458 v110 (#465)Larry Knox2021-03-121-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update license url (#332) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories. * Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429) * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Added C++11 override keyword where appropriate (#433) Added H5_OVERRIDE macro for compatibility with both C++11 and older. * Various clang tidy warning fixes (#448) * Fixed clang-tidy bugprone-reserved-identifier warnings * Fixed clang-tidy bugprone-assert-side-effect warnings * Fixed clang-tidy bugprone-copy-constructor-init warning * Fixed clang-tidy readability-redundant-preprocessor warning For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block. Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS. * Fixed clang-tidy readability-redundant-string-init warnings * Fixed some clang-tidy performance-type-promotion-in-math-fn warnings * Fixed clang-tidy performance-unnecessary-value-param warnings * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Removed checks/workarounds for pre-C++89 compatibility (#449) After 30+ years, just assume that the following exist: - extension-less includes - namespaces - std:: - static_cast - bool * Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451) * Fixed all clang-tidy bugprone-suspicious-string-compare warnings This change was generated entirely by clang-tidy itself. * Reformat code with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Fix clang-tidy suspicious string compare in H5A.c missed in merge. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* Hdf5 merge issue 435 v110 (#462)Larry Knox2021-03-101-3/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update license url (#332) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories. * Fixed clang-tidy readability-misleading-indentation warnings (#427) * Fixed clang-tidy readability-misleading-indentation warnings * Reformatted src/H5Zscaleoffset.c with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Fixed clang-tidy readability-redundant-control-flow warnings (#428) * Fixed clang-tidy readability-redundant-control-flow warnings Just removed useless trailing return statements. * Removed blank lines from h5diffgentest.c with clang-format v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Removed bad function pointer casts (#434) * Removed bad function pointer casts In one case fixed the actual function signature to be correct. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * fix block coordinate printing example (#437) Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Mike Smith <grimbough@gmail.com>
* Hdf5 1 10 Update license url (#403)Larry Knox2021-03-011-1/+1
| | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update license url (#332) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* Source formattedAllen Byrne2020-10-011-272/+253
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* Minor normalizations with developDana Robinson2020-08-161-10/+10
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* Normalization of H5MM and H5FL with develop. Adds the newDana Robinson2020-07-081-0/+81
| | | | stats calls.
* Reduce overhead for H5open, which is involved in the public symbols like ↵Dana Robinson2020-06-221-3/+5
| | | | H5T_NATIVE_INT, etc.
* Brought H5E package in line with develop.Dana Robinson2020-05-171-7/+9
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* OESS-29 Update HD prefix and compare against developAllen Byrne2019-08-231-10/+10
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* Replaced all MPI-1 calls with MPI-2 equivalents (from develop).Dana Robinson2018-12-311-1/+1
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* Fixed HDFFV-10404Binh-Minh Ribler2018-07-261-2/+2
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* Resolve memory leak of last API context, by freeing it in H5CX terminateQuincey Koziol2018-04-181-2/+1
| | | | routine.
* Revert "Close memory leak of last API context when shutting library down."Quincey Koziol2018-04-181-2/+2
| | | | This reverts commit 0bd3634dc5747d88582a966050896bad57acb892.
* Close memory leak of last API context when shutting library down.Quincey Koziol2018-04-171-2/+2
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-19/+17
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Normalization with VOL integration branch.Dana Robinson2017-12-051-12/+12
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* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-2/+12
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* Normalization with VOL integration branch.Dana Robinson2017-12-011-0/+1
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* Normalization with VOL integration branch.Dana Robinson2017-11-301-58/+7
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* Fix for HDFFV-10160Vailin Choi2017-06-291-0/+7
| | | | Modifications to fix the assertion/abort failure when the application does not close the file.
* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* Fixed problems that prevent bin/trace from marking up some functions.Dana Robinson2017-04-211-3/+3
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* [svn-r29350] Revert h5check_version change to check LT_VERS_XXXX numbers ↵Larry Knox2016-03-081-130/+0
| | | | | | | | | | | | | | | | | rather than HDF5 library version numbers. Svn revisions reverted: 29341, 29326 Branch features/h5check_version was created for further development. Files changed test/tcheck_version.c test/testcheck_version.sh.in src/H5public.h src/H5.c config/lt_vers.am bin/h5vers Tested with h5committest.new
* [svn-r29326] HDFFV-9536: Changed H5check_version() to use libtool shared ↵Albert Cheng2016-03-071-0/+130
| | | | | | | | | | | | | | | | | | | | | | | | library version numbers instead of the library version numbers. bin/h5vers: Changed to copy the shared lib version from lt_vers.am to H5public.h (Thanks to Larry who made the changes.) config/lt_vers.am: cosmetic change, nothing material. src/H5public.h: Changed by bin/h5vers. src/H5.c: Changed H5check_version() to use shared library version for compatibility checking. test/tcheck_version.c: test/testcheck_version.sh.in: Changed to use shared library version numbers instead of the HDF5 library version numbers for testing. Tested: tested in Jam (C only), platypus and osx1010dev (enable fortran and C++).
* [svn-r29182] Re-commit of HDFFV-8740 fix, which adds the ability to configureDana Robinson2016-02-221-1/+2
| | | | | | | | | | | | external dataset storage path behavior. This check-in fixes a bug in the original check-in where the external path stored in the file struct was not copied on reopen causing subsequent dataset operations to fail. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools serial w/ fortran and C++ autotools parallel (MPICH 3.1.4) w/ fortran
* [svn-r29084] Revert of:Dana Robinson2016-02-111-2/+1
| | | | | | | | | | | | | | | r29069 and 72 (gheap cleanup) r29041 and 43 (HDFFV-8740 external storage) These cause problems in the daily tests. They will be re-introduced when their respective problems have been addressed. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools serial (check-vfd) w/ Fortran and C++ autotools parallel w/ Fortran CMake serial
* [svn-r29041] Patch from Steffen Kiess that allows a relative path to be ↵Dana Robinson2016-02-041-1/+2
| | | | | | | | | | | specified for external dataset files set via H5Pset_external(). Resolves HDFFV-8740 Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools serial
* [svn-r28996] Autotools configure updates to allow separation of build type, ↵Dana Robinson2016-01-271-64/+69
| | | | | | | | | | | | | | debug symbols, asserts, profiling, and optimization. Also much refactoring, improved help, and --enable-<foo> options will now emit errors on nonsense (e.g.: --enable-foo="asdfasdf"). The libhdf5.settings.in file was also reformatted. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial and parallel autotools w/ various options
* [svn-r28777] Description:Quincey Koziol2016-01-031-0/+5
| | | | | | | | | | Add --enable-memory-alloc-sanity-check option to configure, to track and sanity check memory allocations within the library. This is orthogonal to the --enable-using-memchecker option and can be used with/without it. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28761] Description:Quincey Koziol2016-01-011-4/+1
| | | | | | | | | | | | Clean up many mismatches between malloc/free and H5MM_malloc/H5MM_xfree in the library and tests (and use of H5free_memory and H5Dvlen_reclaim). Also make H5Ocopy use a private version of H5Lexists, which doesn't internally throw (and suppress) errors when an object (or the path to it) isn't found in the destination. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r27879] Move property list shutdown earlier in H5_term_library, since ↵Neil Fortner2015-09-251-4/+8
| | | | | | | | with VDS layout it needs to call into the H5D package. Tested: ummon
* [svn-r27834] Description:Quincey Koziol2015-09-211-1/+1
| | | | | | | | Close FAPL for external link test, to fix infinite loop closing the library. Tested on: MacOSX/64 10.10.5 (amazon) w/serial (too minor to require h5committest)
* [svn-r27768] Description:Quincey Koziol2015-09-141-8/+43
| | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* [svn-r27601] Removed the H5TSprivate.h include from H5.c. It's not needed ↵Dana Robinson2015-08-271-1/+0
| | | | | | | | and causes problems on Windows. Tested on: jam, with and without --enable-threadsafe
* [svn-r27587] Added a new API call (H5is_library_threadsafe) to the library. ↵Dana Robinson2015-08-261-9/+39
| | | | | | | | | | This call can be used to determine at runtime if the library was built with thread-safety. Fixes HDFFV-9496 Tested on: h5committest
* [svn-r27427] - free comm keyval after setting atribute on comm_selfMohamad Chaarawi2015-07-231-0/+3
| | | | | | - free allocated buffer in t_file_image test tested on jam with parallel.
* [svn-r27162] fix for HDFFV-9412:Mohamad Chaarawi2015-06-081-11/+15
| | | | | | | - Check for mpi is_initialized and is_finalized before making MPI calls in init/terminate of HDF5. - Add a test to make sure we can make serial HDF5 calls from rank 0 after MPI_Finalize is called. tested with h5committest
* [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-1/+1
| | | | | | | | * H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z))) - Rename UNUSED attribute characterstic to H5_ATTR_UNUSED. - Rename NORETURN attribute characterstic to H5_ATTR_NORETURN tested with h5committest.
* [svn-r26392] Reinstates r26327-8, which had been reverted due to failures onDana Robinson2015-03-091-3/+86
| | | | | | | | | | | | | | Solaris and OS X. Added public API functions that expose the C library's memory allocator for use in filter functions that need to allocate or resize buffers. Intended for use with filter plugins, particularly on Windows, where C runtime (CRT) issues can cause problems. Fixes: HDFFV-9100 Tested on: h5committest + OS X (quail) + Solaris (emu)
* [svn-r26331] Revert checking r 26327&8, which added new code and test that ↵Larry Knox2015-02-281-86/+3
| | | | | | fails on solaris and macs. Tested h5committest + emu and quail.
* [svn-r26327] Added public API functions that expose the C library's memory ↵Dana Robinson2015-02-271-3/+86
| | | | | | | | | | | | allocator for use in filter functions that need to allocate or resize buffers. Intended for use with filter plugins, particularly on Windows, where C runtime (CRT) issues can cause problems. Fixes: HDFFV-9100 tested on: jam (minor, localized change)
* [svn-r26279] re-commit 26260 that Dana moved out fixing the versioning of ↵Mohamad Chaarawi2015-02-231-19/+61
| | | | functions to work with v16 default API.
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