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* Backport H5Dchunk_iter to 1.12 branch (#1970)Mark Kittisopikul2022-08-166-16/+269
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Revert "Revert H5Dchunk_iter changes in hdf5_1_12_1 (#733)" This reverts commit 10abe9a8b4985a18a0c88615686184d233d7b845. * Apply clang-format * Reincorporate spelling fix from #1166 * Incorporate H5Dchunk_iter changes from #161 * Backport to 1.12: Adds a quick for for some egregious chunk_info badness (#722) * Backport to 1.12: Converts testhdf5 macros to h5test macros in chunk_info.c (#1820) The two macro schemes were not designed to work together. Also quiets some MSVC warnings about comparing pointers and integers. * Backport to 1.12: H5Dchunk_iter now passes offsets in units of dataset elements, fix #1419 (#1969) * H5Dchunk_iter now passes chunk dimension scaled offsets, fix #1419 * Update docs for H5Dchunk_iter, H5Dget_chunk_info* Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following * offset Logical position of the chunk’s first element in units of dataset elements * filter_mask Bitmask indicating the filters used when the chunk was written * size Chunk size in bytes, 0 if the chunk does not exist * Sync H5Dchunk_iter documentation with develop * Remove H5VL_DATASET_WAIT references from 1.12 * Backport to 1.12 #161, #1474, review comments Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* [1.12 Merge] Hdf5 1 12 develop merges (#2012)jhendersonHDF2022-08-163-8/+23
| | | | | | | | | | | | | | | | | * Fix invalid comment about character encoding in H5Fint.c (#1845) * Convert assertion on (possibly corrupt) file contents to normal error check (#1861) * Convert assertion on (possibly corrupt) file contents to normal error check * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Avoid allocating chunk map for contiguous and compact dataset I/O (#1927) * Add documentation for parallel compression feature (#1981) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix Error examples (#1997)Allen Byrne2022-08-111-267/+211
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* Merge UG from 1.10 and add prelim vol section (#1980)Allen Byrne2022-08-0927-194/+14021
| | | | | | | * Merge UG from 1.10 and add prelim vol section * Spelling fixes * Merge format and autotools javadoc from 1.10
* clang 13 format #1933 (#1939)Allen Byrne2022-07-27332-3535/+3544
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* Implement support for big I/O for independent reads (#1446) (#1719)jhendersonHDF2022-05-031-16/+34
| | | | | | | | | | | | | * Implement big I/O support for independent reads. Add test for this. * Committing clang-format changes * Update big I/O code in H5FD__mpio_write() to match that in H5FD__mpio_read(). Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* [1.12 Merge]Hdf5 1 12 warnings fixes (#1715)jhendersonHDF2022-05-0339-454/+481
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Warnings fixes (#1680) * Clean stack size warnings in sio_engine (#1687) * Fixes stack size warnings in tcoords.c (#1688) * Address some warnings from casting away of const (#1684) * Fixes stack size warnings in ntypes (#1695) * Fixes stack size warnings in dtransform (#1696) * Fixes stack size warnings in set_extent test (#1698) * Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706) * Avoid a signed overflow: check the range of `entry_ptr->age` before increasing it instead of increasing it and then checking the range. This quiets a GCC warning. * Avoid the potential for signed overflow by rewriting expressions `MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`. This change quiets some GCC warnings. * Change some local variables that cannot take sensible negative values from signed to unsigned. This quiets GCC warnings about potential signed overflow. * In a handful of instances, check the range of a signed integer before increasing/decreasing it, just in case the increase/decrease overflows. This quiets a handful of GCC signed-overflow warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix object size warnings in cache.c test (#1701) * Fix some const cast and stack/static object size warnings (#1700) * Fix various warnings * Move HDfree_const to H5private.h for wider use * Print output from all ranks in parallel tests on allocation failure * Move const pointer freeing macro to h5test.h for now * Stop lying about H5S_t const-ness (#1209) Hyperslabs can be reworked inside several H5S callbacks, making H5S_t non-const in some places where it is marked const. This change switches these incorrectly const H5S_t pointer parameters and variables to non-const where appropriate. * Fix a few warnings after recent H5S const-related changes (#1225) * Adjustments for HDF5 1.12 Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 1 12 Miscellaneous warnings fixes (#1718)jhendersonHDF2022-05-039-47/+61
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixes const issues in the version 2 B-trees (#1172) The operations that were changed are fundamentally not const since the shadow operation can modify the node structure when SWMR is in use. * Quiets const warning in H5RS code (#1181) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the raw H5R_ref_t bytes to a heap buffer that's known to have the right alignment. * Committing clang-format changes * Use an automatic H5R_ref_t instead of malloc'ing one. Go ahead and initialize the H5R_ref_t to all-0s so that arbitrary stack content doesn't foul things up. Bail out with an error if `size` exceeds `sizeof(H5R_ref_t)`. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Miscellaneous warnings fixes Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix SWMR/refresh bug hidden by library free lists (#1702) (#1711)Larry Knox2022-05-021-4/+10
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* Update version to 1.12.3-1 after creating hdf5_1_12_2 releaseLarry Knox2022-04-081-3/+3
| | | | | preparation branch. Clean release note entries from RELEASE.txt.
* 1.12: Last round of normalizations for 1.12.2 (#1621)Dana Robinson2022-04-089-68/+105
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* Brings minor changes from headers in develop (#1618)Dana Robinson2022-04-087-38/+0
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* Merge branch 'spelling-corrections' of https://github.com/lrknox/hdf5 into ↵Larry Knox2022-04-07109-269/+271
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| * Merge branch 'hdf5_1_12' into spelling-correctionsLarry Knox2022-04-0711-2321/+204
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| * | Committing clang-format changesgithub-actions2022-04-072-3/+5
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| * | Commit codespell spelling corrections.Larry Knox2022-04-07110-273/+273
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* | | Brings free list debugging changes from develop (#1615)Dana Robinson2022-04-072-30/+72
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* | | 1.12: Brings 1.12 compiler options in line with develop (#1611)Dana Robinson2022-04-072-9/+9
| | | | | | | | | | | | | | | * Brings 1.12 compiler options in line with develop * Revert 'since' doxygen field in H5public.h
* | | Fixes H5E_ID error categores erroneously brought over from develop (#1613)Dana Robinson2022-04-073-3/+3
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* | | Fix these Doxygen warnings #1581 (#1592)Allen Byrne2022-04-073-11/+10
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* | Brings skip list try_free_safe changes from develop (#1612)Dana Robinson2022-04-072-476/+206
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* | Removes unused H5HP and H5MP packages (#1610)Dana Robinson2022-04-079-1848/+1
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* Clang warning fixes from develop. (#1583)Larry Knox2022-04-059-11/+20
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* Misc fixes from develop nov21 - feb22 (#1580)Larry Knox2022-04-0512-43/+43
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Make default to build high-level tools the same as default for (#1234) high-level library. * Updated README.txt to README.md (#1375) * H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 * H5Oget_info_by_name, name can be any object, not just a group * Converted README.txt to README.md and updated files referring to README.txt to README.md. * removed references to README.txt * updated MANIFEST * Snprintf2 (#1399) * Replaced many uses of sprintf with safer snprintf Many very straightforward, but in a few cases added a length parameter to some private functions, because buffer length was otherwise unknowable. * Removed unnecessary use of static on small buffers This improves thread safety. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Replaced several uses of sprintf with safer snprintf (#1383) * Replaced several uses of sprintf with safer snprintf * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Used clang-tidy to change all floating point f suffixes to F (#1359) * Added another missing override keyword on a dtor (#1384) * Creating FUNDING.yml (#1427) * Creating FUNDING.yml Will add sponsor this project widget to the repo's page. * Correct file name Add sponsor widget; filename typo fixed. * Update MANIFEST * Fixed AbstractDs::getVarLenType documentation (#1441) * Committing clang-format changes * Open bsd fixes (#1195) * Fix end of line alignment. Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: loricooperhdf <lori.cooper@hdfgroup.org> Co-authored-by: myd7349 <myd7349@gmail.com>
* 1.12 New References for Dimension Scales (#1139) (#1574)Larry Knox2022-04-023-25/+72
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * New references for Dimension Scale APIs (#1139) * Enable usage of new-style references with dimension scale APIs * Add API to check if an object ID represents a native connector object * Modified code to use new function H5DSwith_new_ref to determine if new references should be used with Dimension Scales. The new function return TRUE if non-native connector is used or if H5_DIMENSION_SCALES_WITH_NEW_REF varible is define at configure time (--enable-dimension-scales-with-new-ref). Tested on jelly. ToDo: generate testing file on BE system and enable the test; add flag to CMake; test netCDF-4 with the new references. * Adding new test files generated on BE system (hedgehog) created by 32 and 64-bit library. test_ds chokes on test_ds_le_new_ref.h5 on BE system; test passes for test_ds_be_new_ref-32bit.h5 for the 32-bit library and fails for the 64-bit library, and vice versa. I am checking the files for further investigation; but current implementation of the new references is not portable between LE and BE systems, and 32 and 64-bit systems. * Minor fixes for testing issues * Update test_ds.c Enabled broken test; tests pass now. * Update RELEASE.txt Documented new option to use new references with the HDF5 dimension scales APIs (H5DS*). * Update MANIFEST for new 32-bit new-style references test file for H5DS APIs * Update 'dimension scales w/ new-style refs' feature based on review Co-authored-by: Elena <epourmal@hdfgroup.org> * Fix H5DS warnings related to new H5DSwith_new_ref and H5VLobject_is_native APIs (#1184) Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Elena <epourmal@hdfgroup.org>
* Assume C99 fixed sized ints exist, use them (#470) (#1571)Larry Knox2022-04-0112-245/+126
| | | | | | | | | | | | | | | | * Committing clang-format changes * Assume C99 fixed sized ints exist, use them * Assume H5_SIZEOF_LONG_DOUBLE != 0, `long double` has existed since C89 Note, this is only assuming that `long double` exists, no assumptions about its size have been touched. Didn't remove any code that does things like test if `long double` and `double` have different sizes. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@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>
* 1.12 Merge doxygen changes from develop (#1542)Allen Byrne2022-03-3035-355/+376
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* Hdf5 1 12 parallel compression merge (#1529)jhendersonHDF2022-03-2812-1581/+4813
| | | | | | | | | | | | | | | | * Fix the function cast error in H5Dchunk.c and activate (#1170) `-Werror=cast-function-type`. Again. * Parallel Compression improvements (#1302) * Fix for parallel compression examples on Windows (#1459) * Parallel compression adjustments for HDF5 1.12 * Committing clang-format changes Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 1 12 merges (#1528)jhendersonHDF2022-03-2538-407/+724
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Use internal version of H5Eprint2 to avoid possible stack overflow (#661) * Add support for parallel filters to h5repack (#832) * Allow parallel filters feature for comm size of 1 (#840) * Avoid popping API context when one wasn't pushed (#848) * Fix several warnings (#720) * Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201) * Fix free list tracking and cleanup cast alignment warnings (#1288) * Fix free list tracking and cleanup cast alignment warnings * Add free list tracking code to H5FL 'arr' routines * Fix usage of several HDfprintf format specifiers after HDfprintf removal (#1324) * Use appropriate printf format specifiers for haddr_t and hsize_t types directly (#1340) * Fix H5ACmpio dirty bytes creation debugging (#1357) * Fix documentation for H5D_space_status_t enum values (#1372) * Parallel rank0 deadlock fixes (#1183) * Fix several places where rank 0 can skip past collective MPI operations on failure * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix a few issues noted by LGTM (#1421) * Fix cache sanity checking code by moving functions to wider scope (#1435) * Fix metadata cache bug when resizing a pinned/protected entry (v2) (#1463) * Disable memory alloc sanity checks by default for Autotools debug builds (#1468) * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.12 Fix release check version logic #1438 (#1493)Allen Byrne2022-03-121-7/+5
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* Merge Mingw fixes from develop (#1477)Baljak2022-03-101-5/+4
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* Unify handling of collective metadata reads status (#1206) (#1417)jhendersonHDF2022-02-038-81/+268
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* 1 12 Remove const from the argv tools/tests main sig. #1390 (#1404)Allen Byrne2022-01-292-3/+4
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* Merge cmake custom command changes (#1360)Allen Byrne2022-01-141-32/+36
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* Remove duplicate memcpy in chunk_file_cb (#1286)jhendersonHDF2021-12-131-1/+0
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* Initialize filter mask and chunk nbytes for 'Single' chunk index (#1261) (#1276)jhendersonHDF2021-12-111-1/+7
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* 1.12 TRILAB-266: Remove clang warnings. (#1193)H. Joe Lee2021-11-134-48/+58
| | | | | | | | | | | | | | | | | | | | | | | * TRILAB-266: Remove clang warnings in src/H5Zscaleoffset.c. (PR #1105) * Committing clang-format changes * TRILAB-266: Remove clang warnings in H5private.h and uthash.h. (PR #1124) * TRILAB-266: Remove clang warnings in H5FDcore.c. (PR #1127) * Committing clang-format changes * TRILAB-266: Remove clang warnings in test/testmeta.c. (PR #1135) * TRILAB-266: Remove clang warnings in test/swmr.c. (PR #1136) * TRILAB-266: Remove clang warnings in test/cork.c. (PR #1137) * Committing clang-format changes * TRILAB-266: Remove clang warnings in test/cork.c. (PR #1146) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Re-enable collective metadata reads after disabling for chunk lookup (#1174)jhendersonHDF2021-11-121-7/+21
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* 1 12 Merge Remove clang warnings from develop (#1097)Allen Byrne2021-10-171-17/+17
| | | | | * Merge Remove clang warnings from develop * Correct test data typo
* Fixed HDFFV-11150 (#356) (#1104)Larry Knox2021-10-152-3/+4
| | | | | | | | | | | | | | * Fixed HDFFV-11150 (#356) Description Replaced an HDassert with a check for null pointer in H5O_dec_rc() to catch null pointer in corrupted data situation. As a result, removed the null check prior to H5O_dec_rc() calls. Platforms tested: Linux/64 (jelly) * Add release note for HDFFV-11150 fix. Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Fixes a bad memory read and unfreed memory in fsinfo code (#893) (#1012)Larry Knox2021-09-152-14/+22
| | | | | | | | | | | | | | | | | * Fixes a bad memory read and unfreed memory in fsinfo code The segfaul from CVE-2020-10810 was fixed some time ago, but the illegal memory read and unfreed memory were not. This fix tracks some buffer sizes and errors out gracefully on errors, ensuring buffers are cleaned up and avoiding the H5FL infinite loop + abort on library close. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() … ↵Larry Knox2021-09-141-5/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#933) (#1008) * H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() function - Made a small improvement for H5Z_xform_noop() function. Now, the function will also return TRUE if the data transform function expression = "x". For this case, the HDF5 library behaves in a similar fashion as the case when no data transform function has been specified. - Improved the inline documentation of the function H5Z_xform_create() such it is more inline with the rest of the code. * Committing clang-format changes * H5Ztrans: (feature) Added 3 tests for improved H5Z_xform_noop() function - Added serial test with data transform expression = "x" to verify the improved H5Z_xform_noop() function behaves as expected. - Added 2 parallel tests with data transform expression = "x" in combination with a filter. Before, these tests will fail but with the improved H5Z_xform_noop() function they work and result in the expected behavior. - Small bug fix for one of parallel filter tests. * Committing clang-format changes * H5Ztrans: (feature) Added release note about detection of the simple data transform function "x". - Added a brief explanation about the implemented improvement of the detection of the simple data transform function "x" to the RELEASE.txt file. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Merge Fix various warnings and issues in doxygen doc generation #994 (#996)Allen Byrne2021-09-103-42/+10
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* Update copyright headers with reproduction notice in 5 files (#993) (#1003)Larry Knox2021-09-092-17/+14
| | | | | | | | | | | * 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> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.12 Merge A batch of life-cycle examples for different modules #654 (#987)Allen Byrne2021-09-0729-1362/+1151
| | | | | | | * Merge A batch of life-cycle examples for different modules #654 * Remove generated file * Change doxygen generated file location
* Merge clang-tidy changes to public headers (#962)Allen Byrne2021-08-2510-39/+57
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* 1.12 Tools merges from develop (#949)Allen Byrne2021-08-233-460/+711
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Tools merges from develop Brings the tools getopt(3) replacement into the main library (#803) Perform option arg variables (#834) Removes unused commented-out code from h5jamgentest.c (#851) Reorg tools perform to provide h5perf for installation (#884) * Fix missing files * Remove empty files * Remove empty file * Resync defines * Fix endif typo * Add Makfile to list * Fix typo * Remove H5_GCC_DIAG_ON line to match removal of H5_GCC_DIAG_OFF line in sio_engine.c/ Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Merge windows compiler fixes #912 (#948)Allen Byrne2021-08-211-0/+3
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* 1.12 Rework version-check for relnum in H5check. Merge of #812 (#931)Allen Byrne2021-08-191-84/+145
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* Reverts PR 906 and 907 due to binary compatibility issues (#918)Dana Robinson2021-08-1720-495/+237
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