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* 1 10 Fix java data export functions (#450)Allen Byrne2021-03-101-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Byrne2021-03-053-182/+193
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Byrne2021-03-0432-368/+369
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Byrne2021-03-03134-528/+550
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Hdf5 1 10 Update license url (#403)Larry Knox2021-03-01456-458/+458
| | | | | | | | | | | | | | | | | | | | | | | * 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>
* Port PR #291 to 1.10 branch: Allow using virtual datasets in files opened ↵Neil Fortner2021-02-081-1/+29
| | | | | | | | | | 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 (#298)Allen Byrne2021-02-041-3/+5
| | | | | | | | | | | | | | | * 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 Byrne2021-01-298-35/+35
| | | | | | | | | * 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 Fortner2021-01-222-7/+31
| | | | | | | | | | | (#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.
* Add doxygen framework for CMake and autotools (#90)Allen Byrne2020-11-202-2/+46
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* Fix spelling of metadataLarry Knox2020-11-131-1/+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 Byrne2020-10-161-22/+22
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* Mostly whitespace and comment cleanup. (#39)Allen Byrne2020-10-1515-244/+238
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* Merge from develop and 1.12Allen Byrne2020-10-0825-6016/+6050
| | | | Comments and whitespace No cache, select or file-locking changes
* h5repacktest VFD fix and formatting changesAllen Byrne2020-10-051-2/+2
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* Source formattedAllen Byrne2020-10-01453-98612/+92085
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* Merge of clang-format changes from developAllen Byrne2020-09-3024-4074/+4158
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* Fixed errant commaDana Robinson2020-09-031-1/+1
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* Brings Quincey's parallel collective MD write bugfix from developDana Robinson2020-09-038-231/+25
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* Moves some H5S iterator symbols to H5Sprivate.hDana Robinson2020-08-272-29/+29
| | | | | These only need to be public in VOL branches and they show up on the binary compatibility report. It's better to hide them.
* Removes unused H5I_SPACE_SEL_ITER value from H5I_type_tDana Robinson2020-08-2711-20/+0
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* Adds helpful error messages to the HDFS VFD stubs.Dana Robinson2020-08-261-2/+14
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* Adds binary compatibility HDFS VFD stubs.Dana Robinson2020-08-262-3/+39
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* Fixes issues with HDFS VFD.Dana Robinson2020-08-242-11/+22
| | | | | | | - Warning from hdfs.h interpreted as an error under gcc - Incorrect order of headers results inn incorrect initialization - <hdfs.h> not "hdfs.h" - Other misc tidying
* Update version to 1.8.0-1 for CMake test failure.Larry Knox2020-08-241-2/+2
| | | | | | | | | | | if (H5_VERS_SUBRELEASE) set (HDF5_PACKAGE_VERSION_STRING "${HDF5_PACKAGE_VERSION}-${H5_VERS_SUBRELEASE}") else () if (${H5_VERS_SUBRELEASE} STREQUAL "") set (HDF5_PACKAGE_VERSION_STRING "${HDF5_PACKAGE_VERSION}") else () set (HDF5_PACKAGE_VERSION_STRING "${HDF5_PACKAGE_VERSION}-${H5_VERS_SUBRELEASE}") endif ()
* Brings the MPI datatype fixes from developDana Robinson2020-08-221-54/+60
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* Add missing mirror filesAllen Byrne2020-08-211-0/+3
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* Add missing '-'.Larry Knox2020-08-191-1/+1
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* Updated HDF5 1.10 support branch version number to 1.10.8-0Larry Knox2020-08-191-3/+3
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* Fixed one last trailing whitespace characterDana Robinson2020-08-181-1/+1
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* Fixed trailing whitespace from revert.Dana Robinson2020-08-183-31/+31
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* Revert "Don't track file offset position when using pread / pwrite."Dana Robinson2020-08-184-80/+32
| | | | This reverts commit 9e5a68214a5e40bb8e43c5ec2a928dc70e8a6017.
* Adds missing HDstrtoumax for S3 VFDDana Robinson2020-08-181-0/+3
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* Merge of develop PRs to 1.10Dana Robinson2020-08-185-97/+155
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* Merge pull request #2799 in HDFFV/hdf5 from ↵Larry Knox2020-08-181-0/+4
|\ | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr2020:hdf5_bmr2020_addrsani_110 to hdf5_1_10 * commit 'ede1b9b1dd53caad6dfce8ec7bc4aa7b3dbce62c': Fix HDFFV-11101
| * Fix HDFFV-11101Binh-Minh Ribler2020-08-181-0/+4
| | | | | | | | | | | | | | | | | | | | Description Added initialization to local structs in the src function H5MF_settle_raw_data_fsm() and the test function test_bt2_hdr_fd() to prevent the following error in two different occurrences: MemorySanitizer: use-of-uninitialized-value Platforms tested: Linux/64 (jelly)
* | Merge pull request #2772 in HDFFV/hdf5 from ↵Larry Knox2020-08-183-13/+92
|\ \ | |/ |/| | | | | | | | | | | ~BMRIBLER/hdf5_bmr:hdf5_bmr_HDFFV-10933_110 to hdf5_1_10 * commit '538bdb35ae932a1445f32a04e8173f8805d404f8': Updated for HDFFV-10933 Fixed HDFFV-10933
| * Fixed HDFFV-10933Binh-Minh Ribler2020-08-143-13/+92
| | | | | | | | | | | | | | | | | | | | | | Description: Fixed to allow the creation of a dataset when the combination of type, space, etc doesn't work for filter and the filter is optional. Currently, it was supposed to be skipped as indicated in the documentation, but it was not skipped and the creation failed. The function H5Z_ignore_filters was added and used in H5D__create. Platforms tested: Linux/64 (jelly)
* | Brings H5Fstart_swmr_write changes from developDana Robinson2020-08-184-7/+36
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* | Merge branch 'hdf5_1_10' into h5f_start_swmr_write_locksDana Robinson2020-08-1810-787/+2305
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| * \ Merge pull request #2789 in HDFFV/hdf5 from ↵Dana Robinson2020-08-1810-787/+2305
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:h5ac_skiplist_optimization_1_10 to hdf5_1_10 * commit '90fa429c015649fee878530817e503393e9f269c': Brings the MDC skiplist optimizations from develop
| | * | Brings the MDC skiplist optimizations from developDana Robinson2020-08-1710-787/+2305
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* | | | Merge branch 'hdf5_1_10' into h5f_start_swmr_write_locksDana Robinson2020-08-174-2425/+1310
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| * | | Brings over S3 and HDFS VFD changes from developDana Robinson2020-08-174-2425/+1310
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* | | Adds fix for H5Fstart_swmr_write lock issueDana Robinson2020-08-172-4/+16
|/ / | | | | | | Needs a final review pass.
* | Removes email and Modifications sectionsDana Robinson2020-08-1780-670/+202
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* | Minor normalizations with developDana Robinson2020-08-1666-985/+472
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* | Minor normalizations with developDana Robinson2020-08-16100-1867/+1509
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