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* 1.8 Fix release check version logic #1438 (#1495)Allen Byrne2022-03-141-17/+76
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* Merge cmake custom command changes (#1362)Allen Byrne2022-01-141-32/+36
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* Fixed minor issues. (#1259)Gerd Heber2021-12-0915-27/+604
| | | | | | | | | * Fixed minor issues. * Committing clang-format changes * Fixed CMake. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add missing files for enabling doxygen and run bin/reconfigure. (#1246)Larry Knox2021-12-022-4/+51
| | | | | | * Add missing files for enabling doxygen and run bin/reconfigure. * Make default to build high-level tools the same as default for high-level library.
* TRILAB-266: Remove clang warnings. (#1202)H. Joe Lee2021-11-241-39/+45
| | | | | | | | | | | * OESS-99:Apply plugin patch from hdf5_1_10. * TRILAB-266: Remove clang warnings. * Committing clang-format changes * TRILAB-266:Restore original CMake settings. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.8 Merge cmake and flag changes from develop (#1119)Allen Byrne2021-10-221-35/+9
| | | | | | | * Merge cmake and flag changes from develop * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.8 Merge Remove clang warnings from develop (#1099)Allen Byrne2021-10-191-20/+20
| | | | | * Merge Remove clang warnings from develop * revert HD prefix
* 1.8 Merge HDFFV-11266 - add option to build HL tools #1018 (#1022)Allen Byrne2021-09-171-0/+1
| | | | | | | * Merge HDFFV-11266 - add option to build HL tools #1018 * Update configure and Makefile.ins with bin/reconfigure. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 1 8 update copyright headers (#1004)Larry Knox2021-09-167-754/+751
| | | | | | | | | | | | | | | * Update copyright headers with reproduction notice in 5 files (#993) * Update copyright headers with reproduction notice in 5 files that did not match terms in COPYING file . * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Commit changes to Makefile.ins and 4 src/H5E*.h files from running bin/reconfigure. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 1 8 doxygen merges (#683)Allen Byrne2021-05-2534-1971/+22701
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update supported platforms * Merge PR#3 changes from develop * # WARNING: head commit changed in the meantime Merge gcc 10 diagnostics option from develop Merge CMake changes from develop Merge warnings from develop Merge #318 OSX changes from develop Merge tools changes from develop Merge test macros from develop * Format updates * Fix missing semicolon and format fix * Format update * Correct actions, remove java option * Update autotools build files * Add testfiles * Fix configure issue with make flags * Init fapls to default * Update generated files and fix h5repack id closure * update format * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup whitespace cleanup tools sync * format alignment * initialize vars * revert H5private change * Merge #380 from develop * Split format source and commit changes on repo push * Change windows TS to use older VS. * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * Update unsupported types with precision * Add "option" command for clang options * CMake merges from develop h5cc scripts * Updates from develop and printf formatters * Committing clang-format changes * 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 1 8 merges from develop and format specifier updates (#670)Allen Byrne2021-05-2539-1172/+1700
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update supported platforms * Merge PR#3 changes from develop * # WARNING: head commit changed in the meantime Merge gcc 10 diagnostics option from develop Merge CMake changes from develop Merge warnings from develop Merge #318 OSX changes from develop Merge tools changes from develop Merge test macros from develop * Format updates * Fix missing semicolon and format fix * Format update * Correct actions, remove java option * Update autotools build files * Add testfiles * Fix configure issue with make flags * Init fapls to default * Update generated files and fix h5repack id closure * update format * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup whitespace cleanup tools sync * format alignment * initialize vars * revert H5private change * Merge #380 from develop * Split format source and commit changes on repo push * Change windows TS to use older VS. * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * Update unsupported types with precision * Add "option" command for clang options * CMake merges from develop h5cc scripts * Updates from develop and printf formatters * Committing clang-format changes * Issue #669 remove version from pkgcfg filename * remove version from h5cc script Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 18 copying update (#565)Larry Knox2021-04-221-13/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Restores maintainer mode in the autotools (#200) Maintainer mode should be enabled in development branches. Also adds helpful commenting. Add script bin/switch_maint_mode. Add file changes generated by bin reconfigure in src/H5Edefin.h src/H5Einit.h src/H5Epubgen.h src/H5Eterm.h * Update MANIFEST for switch_maint_mode. * Update so numbers to match 1.8.22 release. * Updated configure with reconfigure. * Updates and corrections following HDF5 1.8.22 release. * Commit Makefile.ins with so version numbers updated by bin/reconfigure. * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update top-level COPYING file and remove COPYING files from subdirectories. * Update top-level COPYING file and remove COPYING files from subdirectories (#561) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING (license) file. * Add release_docs/code-conventions.md file. * Add script to test h5py. * Fix script error. * Add file h5pytest.yml. * Test declaration of counter variables in for loops. * Committing clang-format changes * Committing clang-format changes * Added [] to line 126 of H5LTanalyze.l. Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly. * Revert "Added [] to line 126 of H5LTanalyze.l." This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266. * Revert extra commits to match canonical develop. * Update top-level COPYING file and remove COPYING files from subdirectories. * Remove subdirectory COPYING files from MANIFEST. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Remove non-existant file from MANIFEST. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 8 Merge dev changes for long double and cmake (#548)Allen Byrne2021-04-205-62/+129
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update supported platforms * Merge PR#3 changes from develop * # WARNING: head commit changed in the meantime Merge gcc 10 diagnostics option from develop Merge CMake changes from develop Merge warnings from develop Merge #318 OSX changes from develop Merge tools changes from develop Merge test macros from develop * Format updates * Fix missing semicolon and format fix * Format update * Correct actions, remove java option * Update autotools build files * Add testfiles * Fix configure issue with make flags * Init fapls to default * Update generated files and fix h5repack id closure * update format * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup whitespace cleanup tools sync * format alignment * initialize vars * revert H5private change * Merge #380 from develop * Split format source and commit changes on repo push * Change windows TS to use older VS. * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * Update unsupported types with precision Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 8 Merges from develop (#432)Allen Byrne2021-03-0535-1417/+1427
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update supported platforms * Merge PR#3 changes from develop * # WARNING: head commit changed in the meantime Merge gcc 10 diagnostics option from develop Merge CMake changes from develop Merge warnings from develop Merge #318 OSX changes from develop Merge tools changes from develop Merge test macros from develop * Format updates * Fix missing semicolon and format fix * Format update * Correct actions, remove java option * Update autotools build files * Add testfiles * Fix configure issue with make flags * Init fapls to default * Update generated files and fix h5repack id closure * update format * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup whitespace cleanup tools sync * format alignment * initialize vars * revert H5private change * Merge #380 from develop
* 1 8 Merges from develop (#418)Allen Byrne2021-03-0385-295/+282
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update supported platforms * Merge PR#3 changes from develop * # WARNING: head commit changed in the meantime Merge gcc 10 diagnostics option from develop Merge CMake changes from develop Merge warnings from develop Merge #318 OSX changes from develop Merge tools changes from develop Merge test macros from develop * Format updates * Fix missing semicolon and format fix * Format update * Correct actions, remove java option * Update autotools build files * Add testfiles * Fix configure issue with make flags * Init fapls to default * Update generated files and fix h5repack id closure * update format * Merges from develop #358 patches from vtk #361 fix header guard spelling
* HDF5 1 8 merge of recent changes and tools (#353)Allen Byrne2021-02-2212-842/+849
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update supported platforms * Merge PR#3 changes from develop * # WARNING: head commit changed in the meantime Merge gcc 10 diagnostics option from develop Merge CMake changes from develop Merge warnings from develop Merge #318 OSX changes from develop Merge tools changes from develop Merge test macros from develop * Format updates * Fix missing semicolon and format fix * Format update * Correct actions, remove java option * Update autotools build files * Add testfiles * Fix configure issue with make flags * Init fapls to default * Update generated files and fix h5repack id closure * update format
* Hdf5 1 8 (#328)Larry Knox2021-02-091-6/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Restores maintainer mode in the autotools (#200) Maintainer mode should be enabled in development branches. Also adds helpful commenting. Add script bin/switch_maint_mode. Add file changes generated by bin reconfigure in src/H5Edefin.h src/H5Einit.h src/H5Epubgen.h src/H5Eterm.h * Update MANIFEST for switch_maint_mode. * Update so numbers to match 1.8.22 release. * Updated configure with reconfigure. * Updates and corrections following HDF5 1.8.22 release. * Commit Makefile.ins with so version numbers updated by bin/reconfigure. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270) ↵Neil Fortner2021-01-222-7/+31
| | | | | | | | | | | (#277) * Cache the pointer to the next point to process after the last call to H5S__get_select_elem_pointlist. This allows the normal process of iterating over the points in batches to be much more efficient, as the library does not need to traverse the entirety of the preceding points every time the funciton is re-entered. * Update RELEASE.txt for point selection iteration performance fix.
* Reverts lock/unlock callback signature to 1.8.21 version (#254)Dana Robinson2021-01-123-120/+6
| | | | | | | | | | * Reverts lock/unlock callback signature to 1.8.21 version This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs that have the lock callback implemented and that is just as no-op stubs. These stubs were removed so the callbacks are now NULL pointers, like the other VFDs in 1.8. * Trivial whitespace fix
* Fixed typo in an error message. (#227)bmribler2020-12-231-1/+1
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* Update SO numbers in Hdf5 1 8 (#216)Larry Knox2020-12-211-9/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Restores maintainer mode in the autotools (#200) Maintainer mode should be enabled in development branches. Also adds helpful commenting. Add script bin/switch_maint_mode. Add file changes generated by bin reconfigure in src/H5Edefin.h src/H5Einit.h src/H5Epubgen.h src/H5Eterm.h * Update MANIFEST for switch_maint_mode. * Update so numbers to match 1.8.22 release. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Restores maintainer mode in the autotools (#200) (#204)Larry Knox2020-12-184-777/+777
| | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Restores maintainer mode in the autotools (#200) Maintainer mode should be enabled in development branches. Also adds helpful commenting. Add script bin/switch_maint_mode. Add file changes generated by bin reconfigure in src/H5Edefin.h src/H5Einit.h src/H5Epubgen.h src/H5Eterm.h * Update MANIFEST for switch_maint_mode. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Update version to 1.8.23-1.Larry Knox2020-12-171-2/+2
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* Merge branch 'hdf5_1_8' of https://github.com/HDFGroup/hdf5 into hdf5_1_8Larry Knox2020-12-171-4/+4
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| * Correct func enter/leave macros in hdfs VFD (#192)Dana Robinson2020-12-161-4/+6
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* | Full version string in H5public.h was missing '-'.Larry Knox2020-12-171-1/+1
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* | Update version to 1.8.23-0 after creating release branch for 1.8.22.Larry Knox2020-12-172-3/+5
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* Hdf5 1 8 (#169)bmribler2020-12-162-2/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed HDFFV-10480 and HDFFV-11159 Description Checked against buffer size to prevent segfault, in case of data corruption. + HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode + HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode and A user's patch was applied to this previously, but it is redone for a more correct fix, that is the check now accounted for the previous advance of the buffer pointer. Platforms tested: Linux/64 (jelly) * Fixed typo * Fixed HDFFV-11150 Description Replaced an HDassert with a check for null pointer in H5O_dec_rc() to catch null pointer in corrupted data situation. Reversed the fix in svn-r24463 in which a check for null pointer prior to calling H5O_dec_rc() Platforms tested: Linux/64 (jelly)
* Update HDF5 1.8 copyright headers with updated copyright URL (#148)Larry Knox2020-12-04362-364/+364
| | | | | | | * Update URL for COPYING file in copyright headers. * Make fortran copyright headers uniformly spaced. * Update url for Copyright file in c++/src/footer.html.
* Fixed HDFFV-10480 and HDFFV-11159 (#145)bmribler2020-12-032-3/+23
| | | | | | | | | | | | | | | | | * Fixed HDFFV-10480 and HDFFV-11159 Description Checked against buffer size to prevent segfault, in case of data corruption. + HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode + HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode and A user's patch was applied to this previously, but it is redone for a more correct fix, that is the check now accounted for the previous advance of the buffer pointer. Platforms tested: Linux/64 (jelly) * Fixed typo
* Multiple changes to bring branch up-to-date (#87)Allen Byrne2020-11-205-799/+799
| | | | | Correct TARGET variable and CMake config file location. Add option to allow filter plugins to be built inline. Update CMake tools macros.
* Fix compile issues with vfd drivers.Allen Byrne2020-10-202-2/+4
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* Correct boolean value and missing defineAllen Byrne2020-10-192-24/+23
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* Revert autotools files to previous versionAllen Byrne2020-10-195-1689/+1067
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* Fix macro argumentAllen Byrne2020-10-191-4/+4
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* Comment fixesAllen Byrne2020-10-192-10/+10
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* More merges from 1.10 comments and initsAllen Byrne2020-10-1597-3406/+2882
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* Update FD sourceAllen Byrne2020-10-158-34/+8
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* Update autotools filesAllen Byrne2020-10-1529-3396/+3736
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* Merge from 1.10Allen Byrne2020-10-15272-9512/+6591
| | | | | Comments, whitespace Simple init and if block brackets. Minimal code changes limited to return value and spelling
* Snapshot 1.8.22-snap11. Update version to 1.8.22-snap12.Larry Knox2020-10-141-2/+2
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* Fix comment whitespaceAllen Byrne2020-10-051-258/+241
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* Update formatingAllen Byrne2020-10-053-4/+4
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* Source formattedAllen Byrne2020-10-01355-79280/+73657
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* Merge clang-format changes from developAllen Byrne2020-10-0123-6470/+6532
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* Snapshot 1.8.22-snap10. Update version to 1.8.22-snap11.hdftest2020-08-311-2/+2
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* Remove extra parensAllen Byrne2020-08-131-1/+1
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* HDFFV-11127 - force RTLD_LOCAL in dlopenAllen Byrne2020-08-121-11/+11
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* Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)Binh-Minh Ribler2020-08-021-1/+18
| | | | | | | | | | | Description: When a buffer overflow occurred because a name length was corrupted and became very large, h5dump produced a segfault on one file and a memcpy parameter overlap on another file. This commit added checks that detect a read pass the end of the buffer to prevent these error conditions. Platforms tested: Linux/64 (jelly)
* Merge pull request #2708 in HDFFV/hdf5 from ↵Vailin Choi2020-07-231-0/+4
|\ | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/18_HDFFV-11080-heap-use-after-free-by-the-call to hdf5_1_8 * commit '2d7a23887a6c5121b4dac858a50792a18087c5bf': Incorporate pull request #2693 from develop for the fix to HDFFV-11080: (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads (3) Update MANIFEST (4) Add new test to Cmake
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