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* Remove 1.12 release schedule (#2744)Dana Robinson2023-04-143-64/+0
| | | | | | There is no need to maintain the release schedule in each branch, so it's being removed from all branches aside from develop. Also removes the badges that don't pertain to 1.12
* Fix for github issue #2599: (#2665) (#2735)vchoi-hdfgroup2023-04-142-1/+20
| | | | | | | | | | | | As indicated in the description, memory leak is detected when running "./h5dump pov". The problem is: when calling H5O__add_cont_msg() from H5O__chunk_deserialize(), memory is allocated for cont_msg_info->msgs. Eventually, when the library tries to load the continuation message via H5AC_protect() in H5O_protect(), error is encountered due to illegal info in the continuation message. Due to the error, H5O_protect() exits but the memory allocated for cont_msg_info->msgs is not freed. When we figure out how to handle fuzzed files that we didn't generate, a test needs to be added to run h5dump with the provided "pov" file.
* Add Elena to CODEOWNERS for FortranDana Robinson2023-04-141-1/+1
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* CMake - Match Autotools behavior for library instrumentation (#2648) (#2673)jhendersonHDF2023-04-132-1/+17
| | | Enable library instrumentation by default for parallel debug builds
* Avoid suppressing error output for non-tentative file opens (#2632) (#2669)jhendersonHDF2023-04-131-7/+43
| | | | | * Avoid suppressing error output for non-tentative file opens * Update comment about tentative file opens
* Fix #2598 sanitize leak (#2676)Allen Byrne2023-04-132-4/+11
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* Change name of test file to avoid conflict (#2705)Allen Byrne2023-04-131-2/+2
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* * Convert asserts to error handling in efl decode (#2709)Dana Robinson2023-04-131-48/+61
| | | | | | | | | | | | | | | | | | | The function that decodes external data files object header messages would call assert() when parsing malformed files, causing applications to crash when linked against the debug library. This change converts these assert() calls to HDF5 error checks, so the messages are sanity checked in both release and debug mode and debug mode no longer crashes applications. Also cleaned up some error handling usage and debug checks. * Free memory on H5O efl decode errors * Add buffer size checks to efl msg decode * Add parentheses to math expressions Fixes GitHub #2605
* Fix CMake for version less then 3.18 (#2651)Allen Byrne2023-03-3018-62/+112
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* Port h5dchunk_iter_hsizet_size #2074 to hdf5_1_12 branch (#2329)Mark Kittisopikul2023-03-294-38/+12
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* Minor cherry-pick merges to 1.12 (#2581)Larry Knox2023-03-2911-20/+53
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* Update cross compile checks and files #2497 (#2565)Allen Byrne2023-03-293-87/+174
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* Revert the removal of HDF5GroupInfo class and deprecate. (#2637)Allen Byrne2023-03-294-0/+198
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* Fix a memory corruption issue in H5S__point_project_simple (#2626) (#2630)jhendersonHDF2023-03-292-1/+15
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* Bring release_docs scheme from develop (#2612)Dana Robinson2023-03-205-21001/+127
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* Change libaec URL to actively maintained repo GH#2552 (#2561)Allen Byrne2023-03-183-6/+6
| | | | | * Change libaec URL to actively maintained repo GH#2552 * Remove duplicated https
* Fix H5Dchunk_iter doxygen example, cherry-pick of ef3bed6 (#2519) (#2549)Larry Knox2023-03-141-3/+3
| | | Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* Make sure that ONLY_SHARED_LIBS option is correctly set (#2546)Allen Byrne2023-03-1436-124/+116
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* GH issue #2538, print must have verbose on first (#2542)Allen Byrne2023-03-141-4/+6
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* Fix up the H5Pencode2 test for virtual layout. (#2325) (#2356)vchoi-hdfgroup2023-03-141-115/+111
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* Update Copyright headers. (#2534)Larry Knox2023-03-131203-1303/+58
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* Fix new codespell issues (#2521) (#2530)Larry Knox2023-03-1013-14/+14
| | | | | | | | | | | | | * Fix new codespell issues (#2521) * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake * Fix typo in genparser. --------- Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* 1.12 Merge doxygen plist tables changes #2470 from develop (#2505)Allen Byrne2023-03-0147-13543/+15939
| | | | | | | | | * Merge doxygen plist tables changes #2470 from develop * Add new/moved files * More add new/moved files * Doxy corrections
* 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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