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* 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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* 1.12: Brings C++ wrappers in line with develop, minus C++11 bits (#1604)Dana Robinson2022-04-0774-1004/+670
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* Normalize Fortran code with develop (#1600)Dana Robinson2022-04-0748-189/+212
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* Normalization of Java with develop (#1607)Dana Robinson2022-04-073-13/+13
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* Normalization of HL library with develop (#1609)Dana Robinson2022-04-0720-122/+219
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* Brings skip list try_free_safe changes from develop (#1612)Dana Robinson2022-04-073-684/+206
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* Removes unused H5HP and H5MP packages (#1610)Dana Robinson2022-04-0716-3736/+4
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* Brings bin/restore.sh src/H5config.h.in cleanup from develop (#1608)Dana Robinson2022-04-071-0/+3
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* Normalized configure.ac with develop (#1599)Dana Robinson2022-04-071-49/+23
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* Normalization of 1.12 branch with develop (#1598)Dana Robinson2022-04-079-19/+24
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* Brings release timeline and github action changes from develop (#1594)Dana Robinson2022-04-064-0/+68
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* Remove c++11 keyword override. (#1587)Larry Knox2022-04-061-1/+1
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* Clang warning fixes from develop. (#1583)Larry Knox2022-04-0523-67/+77
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* Misc fixes from develop nov21 - feb22 (#1580)Larry Knox2022-04-0573-549/+594
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Add option for h5repack timing #1142 (#1575)Allen Byrne2022-04-047-51/+176
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* 1.12 New References for Dimension Scales (#1139) (#1574)Larry Knox2022-04-0218-418/+827
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* 1.12 Move error-stack text to top of usage display #1564 (#1566)Allen Byrne2022-04-0128-82/+136
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* Assume C99 fixed sized ints exist, use them (#470) (#1571)Larry Knox2022-04-0127-506/+199
| | | | | | | | | | | | | | | | * 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>
* October 2021 Pull Requests not previously merged to 1.12 (#1570)Larry Knox2022-04-014-65/+109
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* Update command format, avoid policy warning (#1551)Allen Byrne2022-04-011-3/+3
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* Remove old RELEASE.txt entries already in HISTORY-1_12.txt. (#1562)Larry Knox2022-04-011-33/+2
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* Updated RELEASE.txt (#1549)Dana Robinson2022-03-301-27/+26
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* 1.12 Merge doxygen changes from develop (#1542)Allen Byrne2022-03-3068-440/+3463
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* Brings MANIFEST removal over from develop (#1533)Dana Robinson2022-03-2911-6408/+110
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* Enable creation of RPM/DEB binaries GH#1394 #1398 (#1535)Allen Byrne2022-03-282-1/+16
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* Hdf5 1 12 parallel compression merge (#1529)jhendersonHDF2022-03-2828-3339/+9471
| | | | | | | | | | | | | | | | * 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)jhendersonHDF2022-03-2555-470/+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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