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* Comment cleanup (#2689)Quincey Koziol2023-04-11126-2959/+154
| | | * Clean up content and redundant logging in comments.
* Remove dead code hidden behind #ifdef LATER (#2686)Dana Robinson2023-04-1012-300/+4
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* Fix #2598 sanitize leak (#2660)Allen Byrne2023-04-072-5/+10
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* Minor fixes for CMake code and install docs (#2623)Allen Byrne2023-04-0313-73/+90
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* Update java logger version (#2643)Allen Byrne2023-04-0321-30/+33
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* Minor fixes for Subfiling VFD tests (#2633)jhendersonHDF2023-04-032-26/+109
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* Synchronize HDF5 tests with VOL tests (#2628)jhendersonHDF2023-04-0318-236/+799
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* Fix memory leaks and aborts in H5O EFL decode (#2656)Dana Robinson2023-04-031-48/+61
| | | | | | | | | | | | | | | | | | | | | * Convert asserts to error handling in efl decode 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
* CMake - Match Autotools behavior for library instrumentation (#2648)jhendersonHDF2023-04-012-1/+17
| | | Enable library instrumentation by default for parallel debug builds
* chore: make comment consistent (#2654)H. Joe Lee2023-04-011-1/+1
| | | Use a 3rd person verb to match "Does not" in the next sentence.
* Avoid suppressing error output for non-tentative file opens (#2632)jhendersonHDF2023-04-011-11/+41
| | | | | * Avoid suppressing error output for non-tentative file opens * Update comment about tentative file opens
* Fix a memory corruption issue in H5S__point_project_simple (#2626)jhendersonHDF2023-03-242-1/+15
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* Fix minor things noted when doing 1.10 merges (#2610)Dana Robinson2023-03-245-6/+6
| | | | * Duplicated HDF_RESOURCES_DIR from cmake_ext_mod merge * Typos in comments
* Bring new release_docs scheme from 1.14 (#2614)Dana Robinson2023-03-238-21897/+884
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* Fix test script names in cleanup code (#2590)Dana Robinson2023-03-201-6/+9
| | | | When the test scripts were renamed, DISTCLEANFILES in Makefile.am was not updated.
* Subfiling VFD - fix issues with I/O concentrator selection strategies (#2571)jhendersonHDF2023-03-173-39/+286
| | | | | Fix multiple bugs with the SELECT_IOC_EVERY_NTH_RANK and SELECT_IOC_TOTAL I/O concentrator selection strategies and add a regression test for them
* Add a clang-format comment about permissions (#2577)Dana Robinson2023-03-171-0/+9
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* Remove an obsolete comment from the MDS test (#2578)Dana Robinson2023-03-171-4/+0
| | | | The seed is now broadcast from rank 0, so the warning about multiple machines having different seeds is unnecessary.
* Fix 2nd argument of Java H5Fis_accessible (#2535)Mark Kittisopikul2023-03-172-5/+5
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* Enclose MESG in do...while loop (#2576)glennsong092023-03-171-2/+5
| | | Enclose MSG macro in a do...while loop
* Change libaec URL to actively maintained repo GH#2552 (#2559)Allen Byrne2023-03-153-6/+6
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* Rename clang-format fix action (#2550)Dana Robinson2023-03-142-4/+4
| | | | The clang-format fix and check actions have the same name. This also makes some small changes to the action's text fields.
* Add Glenn Song to the CODEOWNERS file (#2551)Dana Robinson2023-03-141-1/+1
| | | Also removes Ray Lu
* Make sure that ONLY_SHARED_LIBS option is correctly set (#2544)Allen Byrne2023-03-1337-125/+117
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* Add concurrency option to cancel in-progress jobs (#2539)Scot Breitenfeld2023-03-131-1/+6
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* GH issue #1142, print must have verbose on first (#2540)Allen Byrne2023-03-131-4/+6
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* Addressed various Doxygen grammar issues. (#2524)Scot Breitenfeld2023-03-1343-210/+210
| | | | | | | | | | * reviewed H5A * Addressed various grammar issues. * remove double words, spelling fixes * replace the use of rawdata with raw data
* Elaborate how cd_values get stored (#2522)Mark (he/his) C. Miller2023-03-081-4/+7
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* docs: in -> out (#2514) (#2516)H. Joe Lee2023-03-081-1/+1
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* Update ReferenceManual.dox (#2517)mattjala2023-03-081-1/+1
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* Fix H5Dchunk_iter doxygen example, cherry-pick of ef3bed6 (#2519)Mark Kittisopikul2023-03-081-3/+3
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* Remove redundant and flawed documentation of H5D_chunk_iter_op_t from H5D.c ↵Mark Kittisopikul2023-03-081-26/+0
| | | | | (#2512) Forward port of 9f252f1 from #2329
* Fix new codespell issues (#2521)Mark Kittisopikul2023-03-0812-12/+12
| | | | | * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake
* Update cross compile checks and files (#2497)Allen Byrne2023-03-023-54/+138
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* Check for overflow when calculating on-disk attribute data size (#2459)Egbert Eich2023-03-025-4/+26
| | | | | | | | | | | | | | | | | * Remove duplicate code Signed-off-by: Egbert Eich <eich@suse.com> * Add test case for CVE-2021-37501 Bogus sizes in this test case causes the on-disk data size calculation in H5O__attr_decode() to overflow so that the calculated size becomes 0. This causes the read to overflow and h5dump to segfault. This test case was crafted, the test file was not directly generated by HDF5. Test case from: https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.md
* Missing or misplaced entries in API reference tables #2470 (#2472)Allen Byrne2023-03-013-65/+208
| | | | | * Missing or misplaced entries in API reference tables #2470 * Doxy corrections
* Add fetchcontent for compression libs and fix cmake config (#2487)Allen Byrne2023-02-2620-141/+2150
| | | | | | | | | | | | | * Add fetchcontent for compression libs and fix cmake config * MSDOS is a reserved define name * Add release note and update install doc for FetchContent * Add CI test for FetchContent * Use LINK_COMP_LIBS instead of STATIC_LIBRARY for depends * Use general link
* Subfiling VFD - add option to specify config file prefix (#2495)jhendersonHDF2023-02-267-24/+273
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* HDFFV-10368 (OESS-319): Making two useful macros (H5L_EXT_FLAGS_ALL and ↵raylu-hdf2023-02-214-8/+119
| | | | | | | | | | | | | | | | | | | | | H5L_EXT_VERSION) public (#2386) * HDFFV-10368 (OESS-319): Move two useful macros (H5L_EXT_FLAGS_ALL and H5L_EXT_VERSION) from H5Lpkg.h to H5Lpublic.h for public usage. The test in vol.c only envokes H5Lcreate_external using the passthru VOL. To test if the macros are public, one can use them in the link creation of the passthru VOL, such as printing out their values. * Committing clang-format changes * Moved the test for the external link public macros (H5L_EXT_FLAGS_ALL and H5L_EXT_VERSION) from vol.c to links.c. * Committing clang-format changes * Minor change: changed a pointer variable to an integer. * Committing clang-format changes * Moved two macros (H5L_EXT_VERSION and H5L_EXT_FLAGS_ALL) to H5Ldevelop.h for only developers to use. --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove space from toolchain name (#2482)Allen Byrne2023-02-211-0/+0
| | | | | * Remove space from toolchain name * Another space removed
* OESS-330/HDFFV-11282: Improve failure message when a VOL connector can't be ↵raylu-hdf2023-02-202-3/+8
| | | | | | | | | | | loaded (#2481) * OESS-330/HDFFV-11282: Improve failure message when a VOL connector can't be loaded. Made the error message clearer when the library can't find a plugin in the path table that contains the paths set by HDF5_PLUGIN_PATH and the default location and maybe set by H5PLxxx functions. * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix issue with collective metadata writes of global heap data (#2480)jhendersonHDF2023-02-207-4/+105
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* Develop toolchain lowercase names and updates (#2426)Allen Byrne2023-02-179-24/+28
| | | | | | | | | | | | | * lowercase the toolchain filenames * Change name of option define * Update CI with changed toolchain name * Correct Intel compiler names * Account for Intels name for compiler based on clang * Make icx default and rename classic to icc
* CMake generated pkg-config file is incorrect #2259 (#2476)Allen Byrne2023-02-179-16/+59
| | | | | | | | | | | | | * CMake generated pkg-config file is incorrect #2259 * Fix fortran pc template * hdf5.pc is incorrect for debug builds #1546 * Correct pkg name and lib name * Fix typo * Fix missing space
* GitHub #2417: to avoid the pass-through VOL failing in unexpected places, ↵raylu-hdf2023-02-171-0/+31
| | | | | | | | | | | make sure the underneath VOL ID is specified. (#2475) * GitHub #2417: to avoid the pass-through VOL failing in unexpected places, make sure the underneath VOL ID is specified. * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add build options for CMake packaging #2347 (#2462)Allen Byrne2023-02-151-24/+30
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* Add parallel Autotools -Werror checks (#2384)Dana Robinson2023-02-131-0/+46
| | | New actions added to GitHub CI to build parallel HDF5 w/ CFLAGS=-Werror. Since the GitHub runners are so underpowered, we just configure, build, and install but do not run tests. This covers Autotools only, both debug and release.
* Fix uninitialized variable in pio_engine.c (#2463)Dana Robinson2023-02-131-11/+11
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* Fix a possible uninitialized variable in pio_perf (#2461)Dana Robinson2023-02-131-1/+1
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* Fix parallel warnings in H5Dmpio.c (#2457)Dana Robinson2023-02-131-2/+8
| | | | | | | * Mark a parameter as unused when not using a special debug define * Check for a chunk_entry NULL pointer after using HASH_FIND These should be the last parallel warnings so we can start building parallel with -Werror.
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