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* Merge CMake cleanup process from develop (#2622)Allen Byrne2023-03-2385-1533/+2409
| | | | | * Merge CMake cleanup process from develop * Update test script files
* Remove getlogin work-arounds (#2620)Dana Robinson2023-03-234-22/+1
| | | Unused in the library
* Remove perf tool and standalone h5perf builds (#2619)Dana Robinson2023-03-2124-2439/+172
| | | | | | | | The small perf tool conflicts with the standard perf tool and is being removed from all HDF5 releases. Building h5perf in "standalone" mode (i.e., independently of the library) has been broken for some time, so the build code for that has also been removed.
* Add Option to not build gif tools and remove javadoc option (#2611)Allen Byrne2023-03-209-45/+58
| | | | | | | * Add Option to not build gif tools and remove javadoc option * Remove old option * Fix CMake command format
* Add missing items for hpc/scripts and release versions of extra (#2616)Allen Byrne2023-03-209-36/+67
| | | | | | | | | * Add missing items for hpc/scripts and release versions of extra * Update examples project version * Add VS2022 options to build scripts * And VS2022 added to windefs comment
* [1.10 Merge] Add Developer build mode to CMake (#2617)jhendersonHDF2023-03-2025-130/+427
| | | | | | | | | | | | | | | | | | | | | | * Add Developer build mode to CMake (#1659) * Add Developer build mode to CMake * Set a few CMake variables for Developer build modes * Refactor enabling of debug and developer-level compile definitions * Convert cache debugging macros to normal ifdef style Normal ifdef-style instead of if-style allows build system to define macros without warning about redefining macros with different values (0 vs. 1) * Add HDF5 Developer compile definitions to testing files * Temporarily disable -fanalyzer flag for GCC 12+ Developer builds * Fix Java tests for Developer build modes (#2079) * Minor adjustment of Developer build mode changes for 1.10 branch
* Normalize platform-independence code w/ develop (#2615)Dana Robinson2023-03-2019-587/+261
| | | | | | | | | | | | | | | | | | | | | | | | | | | * Normalize platform-independence code w/ develop * Use C99 types and functions in lieu of C89 work-arounds * Align key files with develop - H5public.h - H5private.h - H5system.c - H5win32defs.h * Minor fixes elsewhere to support changes in above files * Incidentally brings Fortran mod directory settings file change over This does NOT change the configure/build files. Those will still do the checks needed for the C89 work-around cruft until the perf and perform code gets cleaned up. * Add C++98 fixes * Explicitly set -std=c++98 in Autotools * Do not include cstdlib in H5public.h (requires C++11) * Remove redundant stdbool.h include * Fix alarm issues on Windows * Bring parallel alarm() changes from develop
* Gather latest CMake changes from develop (#2609)Allen Byrne2023-03-2074-223/+224
| | | | Add HDF5_SRC_INCLUDE_DIRS variable cleanup cmake comments and documentation
* Remove version specific examples from README_HPC. (#2613)Larry Knox2023-03-201-14/+10
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* Bring warning fixes from develop (#2608)Dana Robinson2023-03-2015-99/+170
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* Bring mirror VFD test improvements from develop (#2597)Dana Robinson2023-03-204-1542/+1288
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* Bring warning macro changes from develop (#2594)Dana Robinson2023-03-202-52/+100
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* Unify cmake and cmake_ext_mod like develop (#2596)Dana Robinson2023-03-2054-858/+836
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* Bring bin/ changes from develop (#2595)Dana Robinson2023-03-1916-477/+175
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* Remove bin/mkdirs and bin/newer (#2593)Dana Robinson2023-03-194-78/+11
| | | As in develop
* Move Autotools VFD list to conclude.am (#2592)Dana Robinson2023-03-195-7/+33
| | | As in develop
* Remove unused H5MP and H5HP packages (#2591)Dana Robinson2023-03-1816-3728/+4
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* Rename test scripts like develop (#2589)Dana Robinson2023-03-1816-107/+113
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* Removes dmalloc support (#2239) (#2587)Dana Robinson2023-03-187-101/+14
| | | | | | | | | | This has not been used to debug the library in a very long time. Most developers use valgrind, -fsanitize=address, or some other memory checker instead of this library. This removes: * dmalloc.h include from H5private.h * --with-dmalloc= Autotools configure option * HDF5_ENABLE_USING_DMALLOC CMake option
* Bring 'default' API value over from develop (#2588)Dana Robinson2023-03-182-3/+5
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* Align compiler flags with develop (#2586)Dana Robinson2023-03-1821-38/+157
| | | | | | Brings many compiler flag changes over from develop. Does NOT bring over -Werror changes. Also turns on Fortran silent rules, as in develop.
* Use new scheme in release_docs (#2585)Dana Robinson2023-03-184-14439/+127
| | | | | * Add README.md and NEWSLETTER.txt files * Remove HISTORY-1_8.txt * Rename HISTORY-1_0-1_8_0_rc3.txt to HISTORY-1_0-1_8_0.txt
* Allow parallel thread-safe builds (#2584)Dana Robinson2023-03-183-17/+9
| | | | | | | | * Allow parallel + thread-safe builds No longer require the "enable unsupported" option to build this configuration in CMake and the Autotools. * Add a release note for parallel thread-safety
* Minor merges to 1.10 (#2579)Larry Knox2023-03-188-10/+46
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Elaborate how cd_values get stored (#2522) * Enclose MESG in do...while loop (#2576) Enclose MSG macro in a do...while loop * Add a clang-format comment about permissions (#2577) * Check for overflow when calculating on-disk attribute data size (#2459) * 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 --------- Co-authored-by: Mark (he/his) C. Miller <miller86@llnl.gov> Co-authored-by: glennsong09 <43005495+glennsong09@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Egbert Eich <eich@suse.com>
* Merge minor configure.ac changes from develop (#2583)Dana Robinson2023-03-181-11/+8
| | | | | | * Comment & whitespace differences * Minor tweak to the "find szip" code * Yank a STDC_HEADERS block * Remove ST from the list of debug packages
* Merge MD cache tag slist --> hash table change (#2580)Dana Robinson2023-03-174-129/+89
| | | PR #1925 from develop
* Update cross compile checks and files #2497 (#2567)Allen Byrne2023-03-173-87/+174
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* Change libaec URL to actively maintained repo GH#2552 (#2562)Allen Byrne2023-03-173-6/+6
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* Add Glenn Song to the CODEOWNERS file (#2551) (#2557)Larry Knox2023-03-153-5/+5
| | | | | | | | | | | | | | * Add Glenn Song to the CODEOWNERS file (#2551) Also removes Ray Lu * Rename clang-format fix action (#2550) The clang-format fix and check actions have the same name. This also makes some small changes to the action's text fields. --------- Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Add concurrency option to cancel in-progress jobs (#2539) (#2556)Larry Knox2023-03-141-1/+6
| | | Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* GH issue #2538, print must have verbose on first (#2543)Allen Byrne2023-03-141-4/+6
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* Make sure that ONLY_SHARED_LIBS option is correctly set (#2547)Allen Byrne2023-03-1436-124/+116
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* docs: in->out (#2514) (#2532)H. Joe Lee2023-03-121-1/+1
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* Update copyright headers. (#2527)Larry Knox2023-03-101197-1335/+35
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* Fix H5Dchunk_iter doxygen example (#2520)Mark Kittisopikul2023-03-101-3/+3
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* Fix 1.10 new codespell issues (#2521) (#2525)Larry Knox2023-03-0913-14/+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>
* Remove redundant and flawed documentation of H5D_chunk_iter_op_t from H5D.c ↵Mark Kittisopikul2023-03-081-26/+0
| | | | (#2513)
* Fix an errant bracket that confused formatter (#2511)Dana Robinson2023-03-061-4525/+4539
| | | An extra { in an ifdef'd-out block caused bad indentation in H5C.c
* 1.10 Merge doxygen plist tables changes #2470 from develop (#2506)Allen Byrne2023-03-0136-13503/+15015
| | | | | | | | | * Add new/moved files * Doxy corrections * Aother Doxy correction * Remove type not in 1.10
* Merge uthash version update from develop (#2502)Dana Robinson2023-02-263-68/+47
| | | * Merege uthash version update from develop
* Use LINK_COMP_LIBS instead of STATIC_LIBRARY for depends (#2500)Allen Byrne2023-02-243-29/+28
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* 1.10 Add fetchcontent for compression libs and fix cmake config #2487 (#2494)Allen Byrne2023-02-2221-119/+2136
| | | | | * Add fetchcontent for compression libs and fix cmake config #2487 * Add CI test for FetchContent
* 1.10: Fix weird characters in C2Cppfunction_map.htm (#2490)Dana Robinson2023-02-212-43/+43
| | | | | * Fix weird characters in C2Cppfunction_map.htm * Fix header.html
* Backport H5Dchunk_iter to 1.10 branch (#1968)Mark Kittisopikul2023-02-216-1/+659
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Backport H5Dchunk_iter to 1.10 branch * Add some accessory files, test still needs work * Apply proper formatting, and fix compile errors * Remove const from H5D__chunk_iter as per #1700 * Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074) * Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info * Modify chunk_info test to for unsigned / hsize_t types * Fix types in test * Add test_basic_query, helper functions to test/chunk_info.c 1_10 * 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 * Fix regression of #1419 * Add a note about return fail in 1.12 and older for invalid chunk index * Committing clang-format changes * Run clang-format on test/chunk_info.c --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove space from toolchain name #2482 (#2485)Allen Byrne2023-02-211-0/+0
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* 1.10 Merge Merge CMake generated pkg-config file is incorrect #2259 (#2479)Allen Byrne2023-02-179-16/+59
| | | | | * Merge Merge CMake generated pkg-config file is incorrect #2259 * Fix spacing
* Merge toolchain lowercase names and updates #2426 (#2469)Allen Byrne2023-02-165-14/+24
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* Merge Add build options for CMake packaging #2347 (#2466)Allen Byrne2023-02-161-24/+30
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* 1.10: Add spelling check to CI and fix errors. (#2442)Allen Byrne2023-02-16367-1305/+1345
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Update CI and support files to match latest from 1.14 * Correct spelling * More spelling corrections * spelling fixes in testpar * Fix spelling errors in tools * More tools spelling fixes * Spelling fixes for rest of tools and some src * Fix spelling errors in src files, pt 2 * Fix spelling in src pt3 * Fix spelling errors pt4 * Fix spelling errors pt5 * Spelling fix pt6 * fix spelling error examples * fix spelling in tests * fix spelling errors in test pt2 * Fix spelling errors in test pt3 * fix spelling in test pt4 * Fix spelling errors in hl * fix spelling errors in c++ * Spelling fixes for fortran * spelling fixes for bin and java * Add relative path * Change spelling action to use a file for list of ignore words * Fix spelling ignore list * remove unused file
* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion ↵vchoi-hdfgroup2023-02-132-14/+24
| | | | | | | | | | (#2153) (#2278) * 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.
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