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* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversi… (#2277)vchoi-hdfgroup2022-12-121-14/+11
| | | | | | | | | | | | | | | * Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion (#2153) * Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion if it is large enough, a buffer is allocated regardless so that the element in fill->buf can later be reclaimed. Valgrind is run on test/set_extent.c and there is no memory leak. * Add information of this fix to release notes. * Change macos version for CI to macos-11 until accum test failure is fixed for macos 12. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 1.12 Merge HDFGroup#2175 Implement option for using CMake GNUInstallDirs (#2221)Allen Byrne2022-11-042-6/+6
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* Merge #2198 correct CMake MPI linking (#2215)Allen Byrne2022-11-041-6/+6
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* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-11-041-0/+4
| | | | file handles (#2181) (#2207)
* Fixed an issue that could occur when combining hyperslab selections (#2122) ↵Neil Fortner2022-10-041-2/+2
| | | | (#2138)
* 1 12 doxygen merge from 1.10 (#2094)Allen Byrne2022-09-1312-17/+41
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* Address review comments from downstream merge of #2016 (#2073) (#2081)Neil Fortner2022-09-011-3/+5
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* Fix bug in attribute type conversion wiith compound types - merge to 1.12 ↵Neil Fortner2022-08-241-9/+44
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#2061) * Fix bug in attribute type conversion wiith compound types (#2016) * Fix bug in attribute type conversion where the background buffer would not be initialized with the destination contents when necessary. Other minor simplification. * Committing clang-format changes * Fix warnings. * Address review comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Add note to RELEASE.txt for GitHub #2016 (#2030) * Fix bug in attribute type conversion where the background buffer would not be initialized with the destination contents when necessary. Other minor simplification. * Committing clang-format changes * Fix warnings. * Address review comments. * Add RELEASE.txt note for PR #2016 * Add GitHub number to release note 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>
* Persist dataset access properties when using H5Fstart_swmr_write - merge to ↵Neil Fortner2022-08-224-31/+121
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1.12 branch (#2031) * Merge GitHub #1862 (HDFFV-11308) to 1.12 branch Persist dataset access properties when using H5Fstart_swmr_write (#1862) * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix bug in swmr.c introduced with recent merge (double_t) (#1913) * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes * Replace accidental use of double_t in swmr.c with double. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Add note to RELEASE.txt for HDFFV-11308 (#2029) * Add note to RELEASE.txt for HDFFV-11308 * Fix formatting error in RELEASE.txt * Committing clang-format changes * Fix inappropriate use of HGOTO_ERROR (#2055) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Spelling fixes for codespell (#2038)Dana Robinson2022-08-1842-62/+62
| | | | | | | * Spelling fixes for codespell * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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>
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