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* Hdf5 1 12 merges (#1528)jhendersonHDF2022-03-2555-470/+855
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Windows and *nix use different forms for warnings #1515 (#1524)Allen Byrne2022-03-254-5/+7
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* Change ENV to CMake var #1520 (#1521)Allen Byrne2022-03-251-2/+1
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* Merge free an MPI communicator #1503 (#1511)Allen Byrne2022-03-211-7/+8
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* Fix java test name conflict #1467 (#1496)Allen Byrne2022-03-121-2/+1
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* 1.12 Fix release check version logic #1438 (#1493)Allen Byrne2022-03-124-10/+25
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* Implemented suggestion in #1381 for dtransform test (#1490)Allen Byrne2022-03-112-18/+22
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* 1 12 Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1482)Allen Byrne2022-03-112-1/+29
| | | | | | | * Merge Add -showconfig to h5cc scripts to dump libhdf5.settings file * Added note * Fix comments
* 1.12 Update HDF5_ROOT usage (#1486)Allen Byrne2022-03-113-3/+14
| | | | | * Update HDF5_ROOT usage * Fix typo
* Merge Mingw fixes from develop (#1477)Baljak2022-03-106-35/+34
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* 1 12 Merge SZ plugin changes from develop (#1455)Allen Byrne2022-02-2441-115/+119
| | | | | | | * Merge SZ plugin changes from develop * Update examples version * Update examples version
* 1.12 Fix tools incompatibility (#1448)Allen Byrne2022-02-2122-531/+751
| | | | | | | | | * fix tools incompatibility with get_option #1443 * Fix get_option function * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Unify handling of collective metadata reads status (#1206) (#1417)jhendersonHDF2022-02-0311-137/+366
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* 1 12 Remove const from the argv tools/tests main sig. #1390 (#1404)Allen Byrne2022-01-2941-107/+111
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* Merge Update code owners file with more names #1386 (#1407)Allen Byrne2022-01-291-15/+15
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* Merge various cleanup java test, test files, comments (#1365)Allen Byrne2022-01-245-14/+19
| | | Plus some spelling corrections
* Merge Update the java slf4j logging jars to latest 1.7.33 (#1370)Allen Byrne2022-01-2421-32/+32
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* Fix cmake dynamic analysis on windows (#1374)Allen Byrne2022-01-242-5/+21
| | | | Fix sanitizer flag form on windows Add search paths to windows code-coverage
* Merge cmake custom command changes (#1360)Allen Byrne2022-01-141-32/+36
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* 1.12 Merge Add tests for H5Ocopy of new object refs (#1339)Allen Byrne2022-01-1420-503/+910
| | | | | | | | | | | | | * Add tests for H5Ocopy of new object refs * Correct class name * Skip test because of issue with debug assertions * Update reference file * Fix object examples for new refs and spelling fixs * Fix ref try-catch blocks
* 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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* Merge Fix directory variable in shell scripts #1273 (#1278)Allen Byrne2021-12-119-113/+40
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* Make default to build high-level tools the same as default for (#1258)Larry Knox2021-12-071-0/+2
| | | | | | * Make default to build high-level tools the same as default for high-level library. * Correct default HDF5_HL_TOOLS
* change windows os from 2016 to latest (#1242)Allen Byrne2021-12-022-8/+8
| | | | | | | * change windows os from 2016 to latest * Upgrade the VS version used. * specify windows VS version
* Merge #1237 Add check for SDK version on windows (#1238)Allen Byrne2021-12-021-1/+1
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* Merge Fix Fortran REGEX and newlines #1226 (#1228)Allen Byrne2021-12-023-9/+9
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* Merge Github #969 Use stdout instead of file for configure check #1089 (#1204)Allen Byrne2021-11-194-158/+93
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* 1.12 Merge Add javadoc to packages - HDFFV-11285 (#1198)Allen Byrne2021-11-197-9/+282
| | | | | * Merge Add javadoc to packages - HDFFV-11285 * Correct list
* 1.12 TRILAB-266: Remove clang warnings. (#1193)H. Joe Lee2021-11-138-108/+119
| | | | | | | | | | | | | | | | | | | | | | | * 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)jhendersonHDF2021-11-122-7/+28
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* Update CODEOWNERS (#1161)Allen Byrne2021-11-031-5/+5
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* Merge Fix Java VOL tests #1158 (#1160)Allen Byrne2021-11-035-317/+16
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* Merge Github #1019 - add Fortran developer flags #1090 (#1147)Allen Byrne2021-10-315-10/+11
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* 1.12 Merge Consolidate VFD create list macro #1132 (#1133)Allen Byrne2021-10-319-31/+36
| | | | | | | * Merge Consolidate VFD create list macro #1132 * Split dir create into separate macro * fix VFD settings
* Merge Set the plugin path to the library default #1144 (#1150)Allen Byrne2021-10-311-0/+2
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* Merge Correct java exception declarations #1121 (#1122)Allen Byrne2021-10-211-16/+19
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* 1.12 Merge Move test utilities to utils/test folder #1109 (#1110)Allen Byrne2021-10-2132-256/+342
| | | | | | | * Merge Move test utilities to utils/test folder #1109 * Merge Correct shell tests and c++ flag warning * Fix typo
* Merge Fixed HL_test_packet, incorrect length assignment (#1101)Allen Byrne2021-10-172-3/+7
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* 1 12 Merge Remove clang warnings from develop (#1097)Allen Byrne2021-10-1714-695/+695
| | | | | * Merge Remove clang warnings from develop * Correct test data typo
* Fixed HDFFV-11150 (#356) (#1104)Larry Knox2021-10-153-3/+12
| | | | | | | | | | | | | | * 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>
* 1.12 Merge delete the noerror- variants of the compiler flags files #1033 ↵Allen Byrne2021-10-1416-356/+75
| | | | | | | (#1091) * Merge delete the noerror- variants of the compiler flags files #1033 * Remove files from MANIFEST
* 1.12 Merge Add missing dataset reference text #1081 (#1082)Allen Byrne2021-10-081-4/+4
| | | | | * Merge Add missing dataset reference text #1081 * Only print name if not printing data
* 1.12 Merge ASAN fixes (#1059)Allen Byrne2021-10-063-37/+37
| | | | | | | | * Merge ASAN fixes Fix ASAN issue in h5dump error path #1051 ASAN fix for test_ld - free sub-allocation of fields #1052 * Merge Rework error allocation free.
* Merge Upgrade libaec to 1.0.6 #1037 (#1038)Allen Byrne2021-09-301-1/+7
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* Merge Corrected path searched by CMake find_package command #1041 (#1042)Allen Byrne2021-09-304-9/+26
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* 1.12 Merge Need to match clang and versions not just "Clang" #1029 (#1030)Allen Byrne2021-09-244-22/+14
| | | | | * Merge Need to match clang and versions not just "Clang" * Merge MS clang needs EHsc flag #1035
* Merge Correction of pkg-config compile script #974 (#1025)Allen Byrne2021-09-181-1/+1
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* Merge HDFFV-11266 - add option to build HL tools #1018 (#1020)Allen Byrne2021-09-177-2/+45
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* Merge Disable fortran warning #1014 (#1015)Allen Byrne2021-09-172-7/+8
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