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* 1.12 Merge Correct pkgconfig variables and libraries #2259 (#2478)Allen Byrne2023-02-171-0/+13
| | | | | * Merge Correct pkgconfig variables and libraries #2259 * Fix spacing
* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversi… (#2277)vchoi-hdfgroup2022-12-121-0/+13
| | | | | | | | | | | | | | | * 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 h5repack should only print if verbose (#2274)Allen Byrne2022-12-121-1/+6
| | | | | | | | | * h5repack should only print if verbose Also chage dump test to use long option * Add note * Update yaml workflows
* 1.12 Correct requires setting for pkgconfig files #2280 (#2283)Allen Byrne2022-12-121-0/+8
| | | | | * Correct requires setting for pkgconfig files #2280 * Change macos for CI
* 1.12 Merge HDFGroup#2175 Implement option for using CMake GNUInstallDirs (#2221)Allen Byrne2022-11-042-1/+28
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* Merge #2198 correct CMake MPI linking (#2215)Allen Byrne2022-11-041-1/+7
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* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-11-041-0/+10
| | | | file handles (#2181) (#2207)
* Fixed an issue that could occur when combining hyperslab selections (#2122) ↵Neil Fortner2022-10-041-0/+7
| | | | (#2138)
* Update examples reference to single-source version 2.0.1 (#2108)Allen Byrne2022-09-242-8/+8
| | | Also fix github URL refs
* Fix bug in attribute type conversion wiith compound types - merge to 1.12 ↵Neil Fortner2022-08-241-0/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#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 Fortner2022-08-221-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Robinson2022-08-184-5/+5
| | | | | | | * Spelling fixes for codespell * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* [1.12 Merge] Hdf5 1 12 develop merges (#2012)jhendersonHDF2022-08-161-1/+10
| | | | | | | | | | | | | | | | | * 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>
* Merge UG from 1.10 and add prelim vol section (#1980)Allen Byrne2022-08-091-1/+5
| | | | | | | * Merge UG from 1.10 and add prelim vol section * Spelling fixes * Merge format and autotools javadoc from 1.10
* fortran module folder from GH#1411 #1922 (#1942)Allen Byrne2022-07-272-1/+27
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* Revert "1.12 eliminate unnecessary errors in the error stack (#1880)" (#1935)Larry Knox2022-07-261-2/+45
| | | This reverts commit f6997681335f0b5fe2e8904f9108a71c5200fb2d.
* 1.12 eliminate unnecessary errors in the error stack (#1880)Allen Byrne2022-07-181-45/+2
| | | | | | | | | | | * Eliminate unnecessary error output * Fix merge typo * fix format * Fix object address to tokens * Fix conflict
* 1 12 Add utility JNI function for 1.10 style references (#1889)Allen Byrne2022-07-181-0/+7
| | | | | | | | | | | * 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>
* 1.12 HDFFV-11310 implement JNI VL support for primitive types (#1856)Allen Byrne2022-07-121-2/+38
| | | | | | | | | | | | | | | * HDFFV-11310 - implement VL read/write using List of Lists * Fix function name typo * Add JIRA issue * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Fix unreleased allocations * Fix format
* Hdf5 1 12 sync (#1794)Allen Byrne2022-06-122-19/+49
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* Change TestExpress #1722 (#1776)Allen Byrne2022-05-202-2/+2
| | | | | * Change TestExpress #1722 * Update comment
* Update VS2019 compilers (#1782)Allen Byrne2022-05-201-1/+1
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* Update version to 1.12.3-1 after creating hdf5_1_12_2 releaseLarry Knox2022-04-081-388/+10
| | | | | preparation branch. Clean release note entries from RELEASE.txt.
* Hdf5 1 12 (#1625)Larry Knox2022-04-081-223/+153
| | | * Update Platforms tested and standardize indentation in RELEASE.txt.
* Commit one more spelling correction.Larry Knox2022-04-071-1/+1
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* Commit codespell spelling corrections.Larry Knox2022-04-078-100/+100
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* Add option for h5repack timing #1142 (#1575)Allen Byrne2022-04-041-0/+8
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* 1.12 New References for Dimension Scales (#1139) (#1574)Larry Knox2022-04-021-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* October 2021 Pull Requests not previously merged to 1.12 (#1570)Larry Knox2022-04-011-58/+91
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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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* Enable creation of RPM/DEB binaries GH#1394 #1398 (#1535)Allen Byrne2022-03-281-0/+9
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* Hdf5 1 12 parallel compression merge (#1529)jhendersonHDF2022-03-281-1/+39
| | | | | | | | | | | | | | | | * 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)jhendersonHDF2022-03-251-0/+48
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Byrne2022-03-121-0/+17
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* 1 12 Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1482)Allen Byrne2022-03-111-0/+7
| | | | | | | * Merge Add -showconfig to h5cc scripts to dump libhdf5.settings file * Added note * Fix comments
* 1.12 Update HDF5_ROOT usage (#1486)Allen Byrne2022-03-112-2/+13
| | | | | * Update HDF5_ROOT usage * Fix typo
* 1 12 Merge SZ plugin changes from develop (#1455)Allen Byrne2022-02-244-22/+24
| | | | | | | * Merge SZ plugin changes from develop * Update examples version * Update examples version
* Unify handling of collective metadata reads status (#1206) (#1417)jhendersonHDF2022-02-031-0/+21
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* Re-enable collective metadata reads after disabling for chunk lookup (#1174)jhendersonHDF2021-11-121-0/+7
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* 1.12 Merge Move test utilities to utils/test folder #1109 (#1110)Allen Byrne2021-10-211-3/+11
| | | | | | | * 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 Byrne2021-10-171-1/+5
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* Fixed HDFFV-11150 (#356) (#1104)Larry Knox2021-10-151-0/+8
| | | | | | | | | | | | | | * 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 Byrne2021-10-141-0/+7
| | | | | | | (#1091) * Merge delete the noerror- variants of the compiler flags files #1033 * Remove files from MANIFEST
* Merge Corrected path searched by CMake find_package command #1041 (#1042)Allen Byrne2021-09-301-0/+17
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* Merge HDFFV-11266 - add option to build HL tools #1018 (#1020)Allen Byrne2021-09-172-0/+9
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* Fixes a bad memory read and unfreed memory in fsinfo code (#893) (#1012)Larry Knox2021-09-151-0/+16
| | | | | | | | | | | | | | | | | * 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>
* 1.12 Update examples version because of HDFFV-11269 (#999)Allen Byrne2021-09-151-1/+1
| | | | | * Update examples version because of HDFFV-11269 * Correct plugin version
* H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() … ↵Larry Knox2021-09-141-1/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#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>
* Rework of PR #826 (#972) (#978)Larry Knox2021-08-311-1/+4
| | | | | | | | * H5Fget_name_f fixed to handle correctly trailing whitespaces and newly allocated buffers. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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