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* Update CODEOWNERS given personnel changes (#2455)Dana Robinson2023-02-111-34/+3
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* CMake: Find MPI in HDF5 CMake config (#2400) (#2411)Larry Knox2023-01-251-0/+2
| | | Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com>
* Brings mirror VFD test fixes from develop (#2392)Dana Robinson2023-01-058-1634/+1548
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* Minor change to H5private.h to bring in line with develop (#2391)Dana Robinson2023-01-051-20/+5
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* Update README.mdDana Robinson2023-01-051-1/+1
| | | Fixes incorrect version
* Brings README.md changes from develop (#2389)Dana Robinson2023-01-053-42/+43
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* 1.12: Brings the updated CI in from develop (#2311)Dana Robinson2022-12-163-385/+347
| | | | | | | | | | | | | | * Brings the updated CI in from develop Does not include the -Werror checks, changes 1.14 API to 1.12 where needed. * Fixes an API compat issue in the mirror VFD test * Committing clang-format changes * Removed pr-check.yml Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversi… (#2277)vchoi-hdfgroup2022-12-122-14/+24
| | | | | | | | | | | | | | | * 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 Byrne2022-12-127-37/+53
| | | | | | | | | * 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 Byrne2022-12-128-16/+24
| | | | | * Correct requires setting for pkgconfig files #2280 * Change macos for CI
* 1.12 Merge HDFGroup#2175 Implement option for using CMake GNUInstallDirs (#2221)Allen Byrne2022-11-0419-66/+166
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* Merge #2198 correct CMake MPI linking (#2215)Allen Byrne2022-11-048-21/+27
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* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-11-043-1/+92
| | | | file handles (#2181) (#2207)
* fixed fortran parallel testing with cmake (#2148)Scot Breitenfeld2022-10-062-1/+2
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* 1.12 Fix some Java warnings (#2146)Allen Byrne2022-10-068-183/+183
| | | | | * Fix some Java warnings * Fix accidental change
* Fixed an issue that could occur when combining hyperslab selections (#2122) ↵Neil Fortner2022-10-043-2/+61
| | | | (#2138)
* Update examples reference to single-source version 2.0.1 (#2108)Allen Byrne2022-09-246-42/+43
| | | Also fix github URL refs
* Cleanup some warnings in Java JNI code (#2034) (#2098)jhendersonHDF2022-09-134-162/+278
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* 1 12 doxygen merge from 1.10 (#2094)Allen Byrne2022-09-13109-15731/+16205
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* Address review comments from downstream merge of #2016 (#2073) (#2081)Neil Fortner2022-09-012-4/+6
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* Fix bug in attribute type conversion wiith compound types - merge to 1.12 ↵Neil Fortner2022-08-243-9/+184
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#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 Fortner2022-08-226-31/+504
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Robinson2022-08-18114-233/+223
| | | | | | | * Spelling fixes for codespell * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Correct target name for szaec lib - merge #2000 (#2001)Allen Byrne2022-08-173-10/+11
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* Backport H5Dchunk_iter to 1.12 branch (#1970)Mark Kittisopikul2022-08-168-69/+441
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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)jhendersonHDF2022-08-165-9/+346
| | | | | | | | | | | | | | | | | * 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 Byrne2022-08-09238-2206/+17695
| | | | | | | * 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 Byrne2022-07-2710-21/+78
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* clang 13 format #1933 (#1939)Allen Byrne2022-07-27658-6502/+6527
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* eliminate unnecessary errors in the error stack (#1937)Allen Byrne2022-07-262-17/+20
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* Revert "1.12 eliminate unnecessary errors in the error stack (#1880)" (#1935)Larry Knox2022-07-2638-603/+7356
| | | This reverts commit f6997681335f0b5fe2e8904f9108a71c5200fb2d.
* revert incorrect merge (#1912)Allen Byrne2022-07-191-1/+1
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* 1.12 eliminate unnecessary errors in the error stack (#1880)Allen Byrne2022-07-1839-7357/+604
| | | | | | | | | | | * 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 Byrne2022-07-184-0/+98
| | | | | | | | | | | * 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>
* Add doxygen for high level modules to hdf5 1.12 (#1901)vchoi-hdfgroup2022-07-1714-14/+4476
| | | | | | | | * Add doxygen for high level modules to hdf5 1.12 * Committing clang-format changes Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Create CODE_OF_CONDUCT.md (#1894)Dana Robinson2022-07-141-0/+128
| | | Taken directly from GitHub's suggested CoC document. We may modify this in the future.
* Cherry-pick of deprecated symbols issue (#1884) from develop (#1886)Dana Robinson2022-07-132-14/+30
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* Cherry-pick of Autotools updates from develop (#1885)Dana Robinson2022-07-132-2/+6
| | | | * Suppress Autoconf "obsolete" warnings in Java checks (#1853) * Use AC_CHECK_LIB instead of AC_HAVE_LIBRARY for Winsock (#1837)
* 1.12 HDFFV-11310 implement JNI VL support for primitive types (#1856)Allen Byrne2022-07-1219-571/+2710
| | | | | | | | | | | | | | | * 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
* revert format of parallel getenv parameter (#1808)Allen Byrne2022-06-131-1/+1
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* Hdf5 1 12 sync (#1794)Allen Byrne2022-06-1232-247/+310
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* Change TestExpress #1722 (#1776)Allen Byrne2022-05-2011-29/+79
| | | | | * Change TestExpress #1722 * Update comment
* Update VS2019 compilers (#1782)Allen Byrne2022-05-201-1/+1
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* Use windows ENV var for default install dir setting #1763 (#1767)Allen Byrne2022-05-172-2/+2
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* Replace obsolete docver arg with arg to supply branch name #1771 (#1772)Allen Byrne2022-05-151-31/+11
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* Use git command to get branch name (#1749)Allen Byrne2022-05-071-1/+1
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* Update package scripts (#1744)Allen Byrne2022-05-072-4/+5
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* Fixes a bug where t_cache fails due to a string size being too small (#1720) ↵jhendersonHDF2022-05-051-4/+6
| | | | | | | | | | | | | (#1728) * Fixes a bug where t_cache fails due to a string size being too small Recent warning reductions led to an incorrect string size being passed to h5_fileaccess, causing the test to silently fail. In addition to fixing the bug, the test will now fail noisily on setup failures. * Updates the t_cache test to fail noisily on setup errors Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* 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>
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