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* 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>
* [1.12 Merge]Hdf5 1 12 warnings fixes (#1715)jhendersonHDF2022-05-0360-4691/+3686
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Warnings fixes (#1680) * Clean stack size warnings in sio_engine (#1687) * Fixes stack size warnings in tcoords.c (#1688) * Address some warnings from casting away of const (#1684) * Fixes stack size warnings in ntypes (#1695) * Fixes stack size warnings in dtransform (#1696) * Fixes stack size warnings in set_extent test (#1698) * Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706) * Avoid a signed overflow: check the range of `entry_ptr->age` before increasing it instead of increasing it and then checking the range. This quiets a GCC warning. * Avoid the potential for signed overflow by rewriting expressions `MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`. This change quiets some GCC warnings. * Change some local variables that cannot take sensible negative values from signed to unsigned. This quiets GCC warnings about potential signed overflow. * In a handful of instances, check the range of a signed integer before increasing/decreasing it, just in case the increase/decrease overflows. This quiets a handful of GCC signed-overflow warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix object size warnings in cache.c test (#1701) * Fix some const cast and stack/static object size warnings (#1700) * Fix various warnings * Move HDfree_const to H5private.h for wider use * Print output from all ranks in parallel tests on allocation failure * Move const pointer freeing macro to h5test.h for now * Stop lying about H5S_t const-ness (#1209) Hyperslabs can be reworked inside several H5S callbacks, making H5S_t non-const in some places where it is marked const. This change switches these incorrectly const H5S_t pointer parameters and variables to non-const where appropriate. * Fix a few warnings after recent H5S const-related changes (#1225) * Adjustments for HDF5 1.12 Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 1 12 Miscellaneous warnings fixes (#1718)jhendersonHDF2022-05-0315-64/+85
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixes const issues in the version 2 B-trees (#1172) The operations that were changed are fundamentally not const since the shadow operation can modify the node structure when SWMR is in use. * Quiets const warning in H5RS code (#1181) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the raw H5R_ref_t bytes to a heap buffer that's known to have the right alignment. * Committing clang-format changes * Use an automatic H5R_ref_t instead of malloc'ing one. Go ahead and initialize the H5R_ref_t to all-0s so that arbitrary stack content doesn't foul things up. Bail out with an error if `size` exceeds `sizeof(H5R_ref_t)`. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Miscellaneous warnings fixes Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix SWMR/refresh bug hidden by library free lists (#1702) (#1711)Larry Knox2022-05-021-4/+10
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* Add java clang-format (#1672)Allen Byrne2022-04-22162-10099/+13368
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* 1.12 merge: Removes HDF Group paths, adds shellcheck fixes (#1658)Dana Robinson2022-04-191-95/+41
| | | | | | For more information: https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ... https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti... https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...
* So number updates to match 1.12.2 release. (#1635)Larry Knox2022-04-151-17/+17
| | | | | | | | | * Undo increment of max_idx for addition of 1.14 verrsion from develop in make_vers. max_idx must match 1.12 version, otherwise build error results with --disable-deprecated-symbols. * Update Platforms tested and standardize indentation in RELEASE.txt. * Update so numbers to match 1.12.2 release.
* Update version to 1.12.3-1 after creating hdf5_1_12_2 releaseLarry Knox2022-04-089-407/+29
| | | | | preparation branch. Clean release note entries from RELEASE.txt.
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