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* 1 10 Fix java data export functions (#450)Allen Byrne2021-03-1098-1041/+1339
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* 1 10 Merge #380 from develop (#439)Allen Byrne2021-03-054-182/+203
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* 1 10 Merges from develop (#424)Allen Byrne2021-03-04133-956/+1132
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) (#417)bmribler2021-03-042-15/+31
| | | | | | | | | | | | | | | * Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) 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 format issues with clang formatter.
* 1 10 merges from develop (#419)Allen Byrne2021-03-03207-737/+753
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* 1 10 merge java copyright header changes (#392)Allen Byrne2021-03-01192-196/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Hdf5 1 10 update license url part2 (#404)Larry Knox2021-03-01982-991/+991
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. * Update license url part2 (#333) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - files not in src or test. * Update URL in source file Copyright headers for web. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* Hdf5 1 10 Update license url (#403)Larry Knox2021-03-01651-653/+653
| | | | | | | | | | | | | | | | | | | | | | | * 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>
* Merge "Fix undefined left shifting of negative numbers" (#338) to hdf5_1_10 ↵Larry Knox2021-02-231-2/+2
| | | | | | | | | | | | | | | | | | (#370) * 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. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* 1 10 Minor non-space formatting changes (#355)Allen Byrne2021-02-191-14/+15
| | | | | | | | | | | | | | | | | | | | | | | | | * 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
* 1 10 merge recent changes from develop (#345)Allen Byrne2021-02-178-11/+38
| | | | | | | | | | | | | | | | | | | | | | | * 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
* 1 10 Merge #318 OSX changes from develop (#327)Allen Byrne2021-02-093-18/+7
| | | | | | | | | | | | | | | | | | | | | * 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
* Port PR #291 to 1.10 branch: Allow using virtual datasets in files opened ↵Neil Fortner2021-02-082-2419/+2544
| | | | | | | | | | with H5F_CLOSE_SEMI and H5F_CLOSE_STRONG (#323) * Modify VDS code to always open source files with H5F_CLOSE_WEAK close (#291) degree. Add test cases to VDS test for this, and reduce the amount of output from that test. * Run formatter on H5Dvirtual.c and test/vds.c
* 1 10 merges from develop (#320)Allen Byrne2021-02-088-0/+121
| | | | | | | | | | | | | | | | | | | * 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
* 1 10 changes for sanitize=address (#313)Allen Byrne2021-02-055-12/+14
| | | | | | | | | | | | | | | | | * 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
* Warnings merge 110 (#300)Allen Byrne2021-02-0424-85/+572
| | | | | | | | | | | | | * 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 * Merge dev warnings refactor from develop
* 1 10 merges from develop (#298)Allen Byrne2021-02-0439-264/+465
| | | | | | | | | | | | | | | * 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
* 1 10 Whitespace changes after clang-format run (#287)Allen Byrne2021-01-2919-75/+264
| | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes
* Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270) ↵Neil Fortner2021-01-223-8/+39
| | | | | | | | | | | (#276) * 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.
* Stat st blocks fix 110 (#249)Larry Knox2021-01-112-3/+12
| | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * 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>
* Hdf5 1 10 - Modify temporary rpath for testing in java example scripts (#243)Larry Knox2021-01-064-5/+37
| | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
* 1 10 Remove duplicate setting (#238)Allen Byrne2021-01-051-1/+0
| | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting
* HDFFV-10865 - merge from dev, HDFArray perf fix. (#234)Allen Byrne2020-12-292-185/+130
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* Update pkgconfig settings with version - #218 (#222)Allen Byrne2020-12-225-10/+10
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* close #195. (#196) (#198)Larry Knox2020-12-171-2/+2
| | | | | | | * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
* OESS-98 fix hdf5 link target (#190)Allen Byrne2020-12-161-2/+1
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* OESS-98 fix tools test for plugins (#179)Allen Byrne2020-12-152-15/+18
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* OESS-98 Update plugin build option (#172)Allen Byrne2020-12-1511-172/+222
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* Add Makefile.ins in utils directory to MANIFEST. (#156)Larry Knox2020-12-111-0/+2
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* hdf5 1 10 release text (#111)Allen Byrne2020-11-235-1192/+4166
| | | | | | | * Merge changes from 1.12/dev * Add chkmanifest * Update release text files, mostly whitespace
* hdf5 1 10 merge changes from dev (#107)Allen Byrne2020-11-205-4/+4
| | | | | * Merge changes from 1.12/dev * Add chkmanifest
* Add doxygen framework for CMake and autotools (#90)Allen Byrne2020-11-2020-9/+4525
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* Merge pull request #94 from lrknox/hdf5_1_10Larry Knox2020-11-131-1/+1
|\ | | | | Fix spelling of metadata
| * Fix spelling of metadataLarry Knox2020-11-131-1/+1
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* Merge pull request #86 from byrnHDF/hdf5_1_10Larry Knox2020-11-1222-91/+64
|\ | | | | Correct TARGET variable and CMake config file location
| * Correct TARGET variable and CMake config file locationAllen Byrne2020-11-1222-91/+64
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* Merge pull request #74 from byrnHDF/hdf5_1_10Larry Knox2020-11-0548-330/+4691
|\ | | | | HDFFV-10868 1 10 java merge from develop
| * HDFFV-10868 add release noteAllen Byrne2020-11-051-1/+8
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| * HDFFV-10868 merge java changes from developAllen Byrne2020-11-0347-329/+4683
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* Merge pull request #58 from byrnHDF/hdf5_1_10Larry Knox2020-10-247-14/+14
|\ | | | | OESS-98 - add option to build plugin library with hdf5
| * OESS-98 - add option to build plugin library with hdf5Allen Byrne2020-10-237-14/+14
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* Merge pull request #54 from byrnHDF/hdf5_1_10Larry Knox2020-10-221-0/+14
|\ | | | | 1.10 Close test allocations
| * Close test allocationsAllen Byrne2020-10-211-0/+14
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* | Merge pull request #51 from byrnHDF/hdf5_1_10Larry Knox2020-10-203-3/+5
|\ \ | |/ | | URL and options corrections
| * URL and options correctionsAllen Byrne2020-10-193-3/+5
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* | Merge pull request #44 from byrnHDF/hdf5_1_10Larry Knox2020-10-1966-196/+705
|\ \ | |/ | | OESS-98 add CMake option to build plugins project within hdf5
| * Add missing file referenceAllen Byrne2020-10-191-0/+1
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| * Whitespace changesAllen Byrne2020-10-194-23/+23
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| * OESS-98 add CMake option to build plugins project within hdf5Allen Byrne2020-10-1661-173/+681
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* Mostly whitespace and comment cleanup. (#39)Allen Byrne2020-10-1516-249/+243
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