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* 1.12 Add fetchcontent for compression libs and fix cmake config #2487 (#2493)Allen Byrne2023-03-0122-141/+2162
| | | | | | | * Add fetchcontent for compression libs and fix cmake config #2487 * Add CI test for FetchContent * Use LINK_COMP_LIBS instead of STATIC_LIBRARY for depends
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… ↵vchoi-hdfgroup2023-02-267-26/+97
| | | | | | | | | | | | | | | | | | | | | | | | (#2291) (#2496) * Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump. When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value" all the way till the end of the routine. The user-provided corrupted file has an illegal file size causing failure when reading the image during the closing process. At the end of this routine it sets f->shared to NULL and then frees "f". This is done whether there is error or not in "ret_value". Due to the failure in reading the file earlier, the routine then returns error. The error return from H5F__dest() causes the file object "f" not being removed from the ID node table. When the library finally exits, it will try to close the file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f). Fix: a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine. b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before. c) h5debug.c main(): track error return from H5Fclose(). * 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>
* 1.12: Fix files codespell has issues with (#2489)Dana Robinson2023-02-213-44/+44
| | | | | | | * Fix files codespell has issues with * Exclude h5repack .dat test files * Fix characters in C++ HTML file * Fix header.html characters
* Remove space from toolchain name #2482 (#2484)Allen Byrne2023-02-211-0/+0
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* Merge Add build options for CMake packaging #2347 (#2465)Allen Byrne2023-02-171-24/+30
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* Merge toolchain lowercase names and updates #2426 (#2468)Allen Byrne2023-02-1710-25/+56
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* 1.12 Merge Correct pkgconfig variables and libraries #2259 (#2478)Allen Byrne2023-02-179-16/+59
| | | | | * Merge Correct pkgconfig variables and libraries #2259 * Fix spacing
* Drop non-1.12 branches in main.yml (#2447)Dana Robinson2023-02-131-1/+1
| | | | | There's no reason to list develop, etc. in the list of branches where this flavor of main.yml applies. Those branches have their own main.yml files.
* 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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