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* Sync CMake and doxygen (#3593)Allen Byrne2023-09-261-0/+8
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* Avoid H5Ocopy in h5repack for variable-length string types (#3419) (#3469)jhendersonHDF2023-09-011-0/+4
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* Fix ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 (#3407) (#3468)jhendersonHDF2023-09-012-7/+11
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* Bring CVE fixes from develop (#3447)Dana Robinson2023-08-302-16/+2
| | | | | | | | * Bring CVE fixes from develop * Fix for CVE-2018-15671 * Fix for CVE-2016-4332 * Update the CVE matrix
* Add other types and full type to enum/str/vlen dataformat for ↵Allen Byrne2023-08-242-59/+76
| | | | structblock[begin/end] (#3358)
* Make h5dump spacing consistent when printing VLEN datatype (#3351) (#3352)jhendersonHDF2023-08-0412-26/+26
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* Set version to 1.14.3-1. (#3343)Larry Knox2023-08-031-7/+7
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* Merge Fixes the last of the -Wextra-semi-stmt warnings #3326 (#3338)Allen Byrne2023-08-033-9/+9
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* Fix h5repack for variable-length datatyped datasets (#3331) (#3333)jhendersonHDF2023-08-021-1/+12
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* Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314) (#3329)jhendersonHDF2023-08-023-30/+62
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* Sync tools with develop (#3301)Dana Robinson2023-07-2884-626/+785
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* Misc missed things from previous merges (#3295)Dana Robinson2023-07-272-2/+2
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* Remove "Programmer" lines (#3294)Dana Robinson2023-07-2746-561/+1
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* Brings over most of the HD prefix removal (#3293)Dana Robinson2023-07-2767-4427/+4413
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* Normalizes the public headers (#3292)Dana Robinson2023-07-273-35/+32
| | | * Also brings over the apostrophe fix
* Fix some warnings in developer builds (#3247) (#3291)jhendersonHDF2023-07-272-0/+5
| | | | | * Fix some warnings in developer builds * Switch approach to Winline flag
* merges from develop (#3115)Allen Byrne2023-06-131-0/+42
| | | | | | | | * Fix release action that allows files to be uploaded. * Add autotools h5copy help test. * Update cmake tools.cmake file for clang-tidy. * CMake build is missing H5FDsubfiling.h * Correct snapshot location * Add note for issue 3056
* Update version (#2971)Larry Knox2023-05-191-7/+7
| | | | | * Update version Copy RELEASE.txt from 1.14.1-2 release into HISTORY-1_14.txt Clear out RELEASE.txt
* Add h5copy help test and verify consistency (#2904)Allen Byrne2023-05-059-6/+136
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* Sync with develop (#2871)Dana Robinson2023-05-021-1/+1
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* Fix ROS3 VFD anonymous credential usage with h5dump and h5ls (#2798) (#2800)jhendersonHDF2023-04-242-4/+27
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* Merge with develop (#2790)Dana Robinson2023-04-2230-312/+30
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* Add no subsets option to h5diff like h5dump (#2759)Allen Byrne2023-04-1815-270/+196
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* Fix #2598 sanitize leak (#2675)Allen Byrne2023-04-131-4/+4
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* Minor cherry-pick merges to 1.14 (#2582)Larry Knox2023-04-043-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Enclose MESG in do...while loop (#2576) Enclose MSG macro in a do...while loop * Add a clang-format comment about permissions (#2577) * Remove an obsolete comment from the MDS test (#2578) The seed is now broadcast from rank 0, so the warning about multiple machines having different seeds is unnecessary. * Subfiling VFD - fix issues with I/O concentrator selection strategies (#2571) 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 * 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: glennsong09 <43005495+glennsong09@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Egbert Eich <eich@suse.com>
* Make sure that ONLY_SHARED_LIBS option is correctly set (#2545)Allen Byrne2023-04-0423-58/+48
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* GH issue #2538, print must have verbose on first (#2541)Allen Byrne2023-03-151-4/+6
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* Brings the following changesets over from develop: (#2328)Dana Robinson2022-12-211-2/+6
| | | | | | | | | | | | b9244a85d9f1cc5e9bbec61ca73c0cbd9c4cf249 Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074) 70cf2c390bc2eef8e57f8fa023341011e2d02d9d Removed idioms and misc. text clean-up (#2320) 8102fa8c972bdc0d8fd8f3dae604e070893150d6 Only document Fortran functions (#2319) 784061b15e176b9919c19a220ce278a9f4cddf0e moved onion VFD to FAPL group (#2321) 6b6bcdead66f0456ac0528683faac6a8e48b6565 Hdffv 11052 (#2315) 10c693a04ff0c4a5219879d7f8900157dcbece66 Update hdf5_header.html 0cb58080875070db09b5ecae92482519d58872bc Hdffv 11052 (#2303) a1c81eda203addced514ef655f7a9079f3f0bb04 added doc. warning for H5Literate_async return value (#2295) 502b32b0f22a4bcf6333c85c256db34162c2764a Updated H5ES documenation (#2293) a9036005c3916e6fda0296026323f00d043300f8 Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)
* Update versions for hdf5_1_14 develop branch after creation of (#2294)Larry Knox2022-12-131-7/+7
| | | hdf5_1-14_0 branch for 1.14.0 release.
* Output should only be printed if verbose. (#2273)Allen Byrne2022-12-021-26/+36
| | | | | * Output should only be printed if verbose. * Add note
* Add aarch64 toolchain and change dump test to long opt (#2271)Allen Byrne2022-12-011-1/+1
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* Correct the CMake link for MPI (#2198)Allen Byrne2022-11-013-6/+6
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* Update copyright headers (#2184)Larry Knox2022-11-01149-150/+12
| | | | | * Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
* Update develop branch version to 1.13.4-1 (#2189)Larry Knox2022-10-261-7/+7
| | | | | | * Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3 release. Added new version to exceptions in lines 74-5 of src/H5.c
* Update CMake code to 3.18 minimum version (#2080)Allen Byrne2022-09-0330-37/+32
| | | | | * Update CMake code to 3.18 minimum version * Updated release note
* Removes cmake_ext_mod (files moved to cmake) (#2041)Dana Robinson2022-08-1916-89/+89
| | | | At one time this content was a git submodule shared between several projects but that time has long passed.
* Fixes codespell issues (#2032)Dana Robinson2022-08-171-1/+1
| | | | | * Fixes codespell issues * Fixed another typo
* Update version to 1.13.3-1 after creating hdf5_1_13_2 branch for 1.13.2 (#2004)Larry Knox2022-08-121-7/+7
| | | | release. Added new version to exceptions in line 75 of src/H5.c.
* Revert "Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for ↵Larry Knox2022-08-121-7/+7
| | | | | | | | release" This reverts commit c58558e872d529da6eda327183ca2d14cfa91b95. H5TEST-tcheck_version-release failed.
* Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for releaseLarry Knox2022-08-121-7/+7
| | | | of HDF5 1.13.2.
* Only use Subfiling VFD in tools if MPI was initialized previously (#1998)jhendersonHDF2022-08-111-3/+11
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* Fix typos found in the rest of the hdf5 code-base (#1985)luzpaz2022-08-109-11/+11
| | | | | | | | | | | * Fix typos found in the rest of the hdf5 code-base * Typo in tool.cmake * Revert "Typo in tool.cmake" This reverts commit 06b8403d99757c7d20f1eed530cf317c3d84de4b. * Fix clang-format styling
* Fix CMake macro code commands (#1989)Allen Byrne2022-08-101-3/+0
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* Revert for older cmake versions (#1974)Allen Byrne2022-08-086-157/+0
| | | | | * Revert for older cmake versions * Remove unneeded clear/clean tests because of changes to test macro
* Develop cmake clean (#1971)Allen Byrne2022-08-0742-1080/+1058
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* Fix issues in tools code after Subfiling VFD updates (#1973)jhendersonHDF2022-08-061-2/+13
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* Subfiling updates for release (#1963)jhendersonHDF2022-08-042-9/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Remove generated file h5fuse.sh * Link pthreads library when Subfiling VFD is built * Switch to MPI I/O driver for Subfiling HDF5 stub file * Rough first implementation for Subfiling file deletion * Subfiling VFD - get file dirname for file deletion * Subfiling VFD - set lock callback to NULL for now to avoid performance issues * Committing clang-format changes * Minor tidying up of Subfiling testing * Fixups for Subfiling VFD support in tools * Tidy up Subfiling public interface and add Doxygen * Respect Subfiling configuration settings from application * Add release note for Subfiling VFD * Committing clang-format changes * Committing clang-format changes * Shorten some Subfiling environment variable names Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Corrects some bad format strings in the tools (#1964)Dana Robinson2022-08-032-8/+11
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* Onion VFD (#1953)Dana Robinson2022-08-0236-33/+1908
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Onion VFD feature * Fixes onion VFD errors with non-sec2 backing store VFDs * Disables the onion VFD tests w/ ph5diff * Disables non-sec2 VFDs as onion VFD backing stores * Committing clang-format changes * Formatted source * Typo * Adds onion VFD tools tests to CMake * Fixes for v16 API compatibility * Memset structs to avoid bad frees on errors * H5Dwrite() calls now use H5T_NATIVE_INT as the memory type vs LE * Properly decodes checksums on BE machines * Be more careful about uint64_t to haddr_t/hsize_t conversions * Another fix for BE data comparison * Removed double underscores from onion constants * Replace hard-coded onion header string w/ constant * Fixes cleanup paths in H5FD__onion_ingest_history() * Fixed use of size_t revision numbers * Fix h5dump revision count format string Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop clang 13 format (#1933)Allen Byrne2022-07-2669-504/+502
| | | | | * Update format source to clang 13 * More format changes
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