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* Hdf5 merge pr 509 v18 (#541)Larry Knox2021-04-052-56/+32
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. * Removes c99_(v)snprintf() calls from the standalone test code (#509) * Committing clang-format changes * Removes c99_(v)snprintf from standalone code These internal API calls were removed in a previous commit but were missed in the sio/pio_standalone code. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> 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>
* clang format push commit for 1 8 (#452)Allen Byrne2021-03-105-5/+32
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* 1 8 Merges from develop (#432)Allen Byrne2021-03-05100-1687/+1928
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Byrne2021-03-03148-541/+517
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Merge ""Fix undefined left shifting of negative numbers" (#338) to hdf5_1_ 8 ↵Larry Knox2021-02-231-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#371) * 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. 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>
* HDF5 1 8 merge of recent changes and tools (#353)Allen Byrne2021-02-22213-7878/+8753
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Knox2021-02-0912-481/+964
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* 1 8 changes for sanitize=address (#315)Allen Byrne2021-02-053-3/+3
| | | | | * Update supported platforms * Merge PR#3 changes from develop
* Update supported platforms (#302)Allen Byrne2021-02-021-6/+12
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* Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270) ↵Neil Fortner2021-01-223-7/+40
| | | | | | | | | | | (#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.
* Hdf5 1 8 (#255)Larry Knox2021-01-121-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* 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
* Stat st blocks fix 18 (#250)Larry Knox2021-01-112-7/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. * Fixes Autotools detection of the st_blocks field in stat (#246) * Fixes Autotools detection of the st_blocks field in stat The Autotools and CMake will now both correctly determine if the stat struct has the st_blocks field and set H5_HAVE_STAT_ST_BLOCKS appropriately. * Fixes a typo in configure.ac Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Remove duplicate setting (#239)Allen Byrne2021-01-051-1/+0
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* Fixed typo in an error message. (#227)bmribler2020-12-231-1/+1
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* Update pkgconfig settings with version - #218 (#223)Allen Byrne2020-12-225-10/+10
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* Update SO numbers in Hdf5 1 8 (#216)Larry Knox2020-12-217-63/+63
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Turns off autotools maintainer mode in hdf5_1_8 (#210)Dana Robinson2020-12-202-4/+16
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* Restores maintainer mode in the autotools (#200) (#204)Larry Knox2020-12-188-801/+941
| | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Brings changes to ttsafe_attr_vlen.c from develop (#202)Dana Robinson2020-12-181-20/+21
| | | | | | | * Brings changes to ttsafe_attr_vlen.c from develop Fix for exposed pthreads code that causes Windows builds to fail. * Restores license URL in ttsafe_attr_vlen.c
* close #195. (#196) (#197)Larry Knox2020-12-171-2/+2
| | | | | | | * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
* Merge branch 'hdf5_1_8' of https://github.com/HDFGroup/hdf5 into hdf5_1_8Larry Knox2020-12-170-0/+0
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| * Update version to 1.8.23-1 after creating release branch for 1.8.22. (#194)Larry Knox2020-12-179-28/+28
| | | | | | | | | | | | | | * Update version to 1.8.23-0 after creating release branch for 1.8.22. * Full version string in H5public.h was missing '-'. * Update version to 1.8.23-1.
* | Update version to 1.8.23-1.Larry Knox2020-12-177-18/+18
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* | Merge branch 'hdf5_1_8' of https://github.com/lrknox/hdf5 into hdf5_1_8Larry Knox2020-12-170-0/+0
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| * \ Merge branch 'hdf5_1_8' into hdf5_1_8Larry Knox2020-12-171-4/+6
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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 Knox2020-12-1710-28/+30
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* Partial changes to RELEASE.txt for release. (#185)Larry Knox2020-12-161-78/+95
| | | | | * Partial changes to RELEASE.txt for release. * Update supported and tested platforms.
* OESS-98 fix hdf5 link target (#191)Allen Byrne2020-12-161-2/+1
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* HDF5 1 8 fix fortran build on macs (#186)Allen Byrne2020-12-164-6/+6
| | | | | * Correct fortran and shared libs option * Fix for no shared fortran build
* 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)
* OESS-98 fix tools test for plugins (#180)Allen Byrne2020-12-152-10/+13
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* 1.8 has extra fortran CMake option (#176)Allen Byrne2020-12-155-5/+5
| | | | | * 1.8 has extra fortran CMake option * Update license URL
* OESS-98 Update plugin build option (#171)Allen Byrne2020-12-1513-174/+224
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* Update HDF5 1.8 copyright headers with updated copyright URL (#148)Larry Knox2020-12-041230-2348/+2348
| | | | | | | * 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
* hdf5 1 8 release text (#113)Allen Byrne2020-11-233-3843/+3845
| | | | | | | | | * Multiple changes to bring branch up-to-date Correct TARGET variable and CMake config file location. Add option to allow filter plugins to be built inline. Update CMake tools macros. * release text updates - mostly whitespace
* Multiple changes to bring branch up-to-date (#87)Allen Byrne2020-11-2060-1034/+1563
| | | | | Correct TARGET variable and CMake config file location. Add option to allow filter plugins to be built inline. Update CMake tools macros.
* Merge pull request #38 from byrnHDF/hdf5_1_8Larry Knox2020-11-12327-16157/+12320
|\ | | | | Reduce code differences between HDF5 1.8 and 1.10
| * Move init above executionAllen Byrne2020-10-211-4/+4
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| * Remove extra #endifAllen Byrne2020-10-201-1/+3
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| * Fix HDFS testAllen Byrne2020-10-201-146/+54
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| * Fix compile issues with vfd drivers.Allen Byrne2020-10-203-8/+8
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| * revert autoconf filesAllen Byrne2020-10-209-2267/+2104
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| * URL and options correctionsAllen Byrne2020-10-193-72/+74
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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 Byrne2020-10-1948-3972/+11300
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