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* Update corrected so numbers including java. (#2652)Larry Knox2023-03-302-16/+16
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* Update hdf5 1 10 10 (#2647)Larry Knox2023-03-289-0/+9
| | | | | | | | | | * Update with autogen.sh using autoconf 2.71, automake 1.16.2 and libtool 2.4.6. Update RELEASE.txt with NVIDIA 22.5 instead of PGI 19.4. --------- Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update hdf5 1 10 10 (#2642)Larry Knox2023-03-281-0/+1
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* Update hdf5 1 10 10 (#2640)Larry Knox2023-03-284-0/+195
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* Update version to HDF5 1.10.10-3 for initial release branch version. (#2634)Larry Knox2023-03-279-0/+13261
| | | | | | | | | | | * Update version to HDF5 1.10.10-3 for initial release branch version. Update RELEASE.txt Update configure.ac for release: switch to production mode, disable maintainer mode Set HDF5_GENERATE_HEADERS to OFF in src/CMakeLists.txt Add files generated by autogen.sh for release. * Fix codespell issues for autotools files generated by autogen.sh. Remove generated autom4te.cache files.
* Merge CMake cleanup process from develop (#2622)Allen Byrne2023-03-235-13/+86
| | | | | * Merge CMake cleanup process from develop * Update test script files
* Add Option to not build gif tools and remove javadoc option (#2611)Allen Byrne2023-03-201-12/+0
| | | | | | | * Add Option to not build gif tools and remove javadoc option * Remove old option * Fix CMake command format
* [1.10 Merge] Add Developer build mode to CMake (#2617)jhendersonHDF2023-03-205-5/+5
| | | | | | | | | | | | | | | | | | | | | | * Add Developer build mode to CMake (#1659) * Add Developer build mode to CMake * Set a few CMake variables for Developer build modes * Refactor enabling of debug and developer-level compile definitions * Convert cache debugging macros to normal ifdef style Normal ifdef-style instead of if-style allows build system to define macros without warning about redefining macros with different values (0 vs. 1) * Add HDF5 Developer compile definitions to testing files * Temporarily disable -fanalyzer flag for GCC 12+ Developer builds * Fix Java tests for Developer build modes (#2079) * Minor adjustment of Developer build mode changes for 1.10 branch
* Gather latest CMake changes from develop (#2609)Allen Byrne2023-03-208-8/+10
| | | | Add HDF5_SRC_INCLUDE_DIRS variable cleanup cmake comments and documentation
* Unify cmake and cmake_ext_mod like develop (#2596)Dana Robinson2023-03-201-1/+1
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* Update copyright headers. (#2527)Larry Knox2023-03-1044-44/+0
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* 1.10: Add spelling check to CI and fix errors. (#2442)Allen Byrne2023-02-166-7/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update CI and support files to match latest from 1.14 * Correct spelling * More spelling corrections * spelling fixes in testpar * Fix spelling errors in tools * More tools spelling fixes * Spelling fixes for rest of tools and some src * Fix spelling errors in src files, pt 2 * Fix spelling in src pt3 * Fix spelling errors pt4 * Fix spelling errors pt5 * Spelling fix pt6 * fix spelling error examples * fix spelling in tests * fix spelling errors in test pt2 * Fix spelling errors in test pt3 * fix spelling in test pt4 * Fix spelling errors in hl * fix spelling errors in c++ * Spelling fixes for fortran * spelling fixes for bin and java * Add relative path * Change spelling action to use a file for list of ignore words * Fix spelling ignore list * remove unused file
* 1.10 Merge HDFGroup#2175 Implement option for using CMake GNUInstallDirs (#2222)Allen Byrne2022-11-051-1/+1
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* 1.10 Fix some Java warnings (#2147)Allen Byrne2022-10-066-184/+187
| | | | | * Fix some Java warnings * fix formatting
* Cleanup some warnings in Java JNI code (#2034) (#2099)jhendersonHDF2022-09-164-108/+146
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* Main Getting Started page and the three HDF Resources have pages. (#2092)Allen Byrne2022-09-092-4/+61
| | | | | | | | HDFView is still under construction, but mostly there. Merge the Fortran doxygen changes from develop PR, updated RM index. Adjusted references to UG and created some TODOs for missing UG modules Some may just need a reference back to a section of the user guide. Made some Fortran doxygen changes for overall consistency.
* Update java code with doxygen tags, add menu files. (#1972)Allen Byrne2022-08-0955-979/+2198
| | | | | | | | | | | | | | | | | * Update java code with doxygen tags, add menu files. * Add -Xdoclint:none to autotools javadoc command * Committing clang-format changes * Add fortran RM list descriptions * delete empty file * doc tag location changes * Spelling corrections Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.10 clang 13 format #1933 (#1940)Allen Byrne2022-07-2937-375/+376
| | | | | * clang 13 format #1933 * Correct workflow
* 1 10 Add utility JNI function for 1.10 style references (#1890)Allen Byrne2022-07-183-0/+91
| | | | | | | | | | | * Add utility JNI function for 1.10 style references * Clarify text * Correct signature * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 10 HDFFV-11310 implement JNI VL support for primitive types (#1858)Allen Byrne2022-07-1214-501/+2383
| | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-11310 - implement vlen read/write for atomic types. * HDFFV-11310 - VL read/write function for primitive types * Add read/write VL option * fix function name typo * remove debugging prints * Remove more debugging code * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Fix unreleased allocations, fix debug * Fix format * Fix formatting * Correct typo
* Add datasets UG chapter, plus fix doxygen refs (#1841)Allen Byrne2022-07-052-23/+45
| | | | | * Add datasets UG chapter, plus fix doxygen refs * Remove duplicates
* Hdf5 1 10 sync (#1795)Allen Byrne2022-06-096-39/+56
| | | | | * Branch sync updates and spelling * Revert format of getenv
* Update version to 1.10.10-1 (#1783)Larry Knox2022-05-192-2/+2
| | | | Update so numbers to match 1.10.9 release. Clear 1.10.9 entries from RELEASE.txt.
* Add H5P doxygen chapter (#1762)Allen Byrne2022-05-142-2/+2
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* Reinstate java API removed in 1.10.8 (#1697)Allen Byrne2022-04-293-5/+108
| | | | | | | * Revert java API removal with JNI private function * Fix name typo * Correct format
* Add java to format source (#1690)Allen Byrne2022-04-26152-9186/+12098
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* Hdf5 1 10 merges (#1633)jhendersonHDF2022-04-141-16/+3
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* Merge various cleanup java test, test files, comments (#1364)Allen Byrne2022-01-1911-38/+43
| | | Plus some spelling corrections
* Merge Update the java slf4j logging jars to latest 1.7.33 (#1371)Allen Byrne2022-01-1417-21/+21
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* 1.10 Merge Add javadoc to packages - HDFFV-11285 (#1199)Allen Byrne2021-11-206-9/+278
| | | | | * Merge Add javadoc to packages - HDFFV-11285 * Correct list
* Merge Correct java exception declarations #1121 (#1123)Allen Byrne2021-10-251-6/+9
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* 1.10 Merge Add missing dataset reference text #1081 (#1083)Allen Byrne2021-10-092-13/+46
| | | | | * Merge Add missing dataset reference text #1081 * Only print name if not printing data
* Update version to 1.10.9-1. (#1069)Larry Knox2021-10-032-4/+4
| | | Clear 1.10.8 entries out of RELEASE.txt.
* Fix javadoc and java warnings (#1011)Allen Byrne2021-09-164-47/+462
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* Update copyright headers with reproduction notice in 5 files (#993) (#1002)Larry Knox2021-09-092-16/+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>
* 1.10 merge clang tidy of examples and hl (#966)Allen Byrne2021-08-251-2/+1
| | | | | | | * Merge of clang tidy of examples and hl from 1.12 * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Correct dataset close in java test #919 (#921)Allen Byrne2021-08-191-1/+1
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* Hdf5 1 10 merge of printf specifiers and VS2015 min changes (#612)Allen Byrne2021-04-301-1/+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 * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 110 copying update (#564)Larry Knox2021-04-261-13/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. * Cleans up a couple of MSVC warnings in testhdf5 (#475) * Fixes a few testhdf5 warnings raised in Visual Studio Visual Studio is grumpier about treating pointers like integers than gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix typos and grammar errors. (#476) * Suppresses the tcheck_version test's abort dialog on Windows (#477) * Suppresses the tcheck_version test's abort dialog on Windows Windows raises a modal abort/retry/ignore dialog box when CRT calls abort(). This change installs a report hook that suppresses the dialog so that the CMake tests don't time out waiting for a nonexistent user to click a dialog box. * Committing clang-format changes * Removes __cdecl from callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Update top-level COPYING file and remove COPYING files from subdirectories. * Update top-level COPYING file and remove COPYING files from subdirectories (#561) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING (license) file. * Add release_docs/code-conventions.md file. * Add script to test h5py. * Fix script error. * Add file h5pytest.yml. * Test declaration of counter variables in for loops. * Committing clang-format changes * Committing clang-format changes * Added [] to line 126 of H5LTanalyze.l. Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly. * Revert "Added [] to line 126 of H5LTanalyze.l." This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266. * Revert extra commits to match canonical develop. * Update top-level COPYING file and remove COPYING files from subdirectories. * Remove subdirectory COPYING files from MANIFEST. 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: Sean McBride <sean@rogue-research.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>
* 1 10 Merge of long double fix and compiler flags (#531)Allen Byrne2021-04-198-2/+907
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 merge issue 487 v110 (#533)Larry Knox2021-04-011-2/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Cleans up a couple of MSVC warnings in testhdf5 (#475) * Fixes a few testhdf5 warnings raised in Visual Studio Visual Studio is grumpier about treating pointers like integers than gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix typos and grammar errors. (#476) * Suppresses the tcheck_version test's abort dialog on Windows (#477) * Suppresses the tcheck_version test's abort dialog on Windows Windows raises a modal abort/retry/ignore dialog box when CRT calls abort(). This change installs a report hook that suppresses the dialog so that the CMake tests don't time out waiting for a nonexistent user to click a dialog box. * Committing clang-format changes * Removes __cdecl from callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
* 1 10 - Mostly all javadoc warning fixes (#508)Allen Byrne2021-03-2514-57/+388
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 10 Fix java data export functions (#450)Allen Byrne2021-03-1093-1038/+1309
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Merges from develop (#424)Allen Byrne2021-03-0436-413/+321
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* 1 10 merge java copyright header changes (#392)Allen Byrne2021-03-01190-190/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Knox2021-03-01235-235/+235
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* 1 10 merges from develop (#298)Allen Byrne2021-02-041-3/+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
* 1 10 Whitespace changes after clang-format run (#287)Allen Byrne2021-01-291-2/+2
| | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes
* 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>
* HDFFV-10865 - merge from dev, HDFArray perf fix. (#234)Allen Byrne2020-12-291-184/+120
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