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* Replaces HDgetenv with getenv (#3599)Scot Breitenfeld2023-09-2621-37/+34
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* Use HDoff_t with lseek consistently (#3600)Dana Robinson2023-09-261-1/+1
| | | | | lseek on Windows uses __int64 for both the offset and return type instead of off_t like most POSIX systems. This changes ensures we use HDoff_t (which is typdef'd correctly on Windows) w/ lseek.
* Fix docs for H5Acreate2 and H5Acreate_by_name (#3598)jhendersonHDF2023-09-262-30/+30
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* Fix typo: arange->arrange in src/H5Cmpio.c. (#3597)H. Joe Lee2023-09-261-1/+1
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* Fix docs for H5Pset_dxpl_mpio_collective_opt() (#3594)jhendersonHDF2023-09-252-15/+21
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* Fixed GH-3554 (#3584)bmribler2023-09-251-1/+1
| | | Removed the extra condition
* Correct comments about H5Z_FILTER_NONE (#3572)jhendersonHDF2023-09-222-2/+2
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* Adds link to h5fuse.sh in testpar for autotools (#3557)Scot Breitenfeld2023-09-224-1/+8
| | | | * Make the h5fuse.sh utility available to parallel subfiling tests so h5fuse testing is not skipped.
* Fix grammar (#3545)H. Joe Lee2023-09-191-1/+1
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* Strip HD prefix from string/char C API calls (#3540)Dana Robinson2023-09-15120-1036/+915
| | | | | | | | | | | | | | | | | | | | | * Strip HD prefix from string/char C API calls * HD(f)(put|get)(s|c) * HDstr* * HDv*printf * HD(s)(print|scan)f * HDperror But NOT: * HDstrcase* * HDvasprintf * HDstrtok_r * HDstrndup As those are not C99 and have portability work-around implementations. They will be handled later. * Fix th5_system.c screwup
* Remove HD prefix from math functions (#3538)Dana Robinson2023-09-1412-141/+63
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* Identify functions in a subgroup (#3530)Allen Byrne2023-09-121-21/+5
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* Add missing row for the ROS3 VFD in table #3415 (#3517)Allen Byrne2023-09-113-98/+3
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* Added new Fortran API wrappers (#3511)Scot Breitenfeld2023-09-071-2/+3
| | | | | | | | | | | | | | | | | | | * Added new wrappers for h5get_free_list_sizes_f H5Sselect_intersect_block_f H5Sselect_shape_same_f h5pget_no_selection_io_cause_f h5pget_mpio_no_collective_cause_f H5Lvisit_by_name_f H5Lvisit_f H5Fget_info_f h5dwrite_chunk_f h5dread_chunk_f * added h5pget_file_space_page_size_f, h5pset_file_space_page_size_f, h5pget_file_space_strategy_f, h5pset_file_space_strategy_f, h5info tests * added fortran tests * Update tH5F.F90
* Convert hbool_t --> bool in src (#3496)Dana Robinson2023-09-05341-7313/+7279
| | | | | | | | | | | * hbool_t --> bool in src * Does not remove TRUE/FALSE * Public header files are unchanged * Public API calls are unchanged * TRUE/FALSE --> true/false in src * Add deprecation notice for hbool_t
* Fix Subfiling VFD IOC assignment bug (#3456)jhendersonHDF2023-09-013-19/+71
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* Convert some H5MM calls to standard C equivalents (#2382)Dana Robinson2023-08-2521-172/+139
| | | | | | | | | * H5MM_calloc and malloc are now mapped to stdlib C calls * H5MM_memcpy now maps directly to memcpy in release builds * H5MM_memcpy is still implemented as a separate function that checks for buffer overlap when H5MM_DEBUG is defined (default w/ debug builds) * Switches many library memcpy calls to use H5MM_memcpy * Fixes a possible zero allocation in H5Olayout.c
* Put H5T_CONV_ab macros in do..while loops (#3432)Dana Robinson2023-08-251-521/+931
| | | | | | | | | | | Ever since a recent round of macro cleanup, bin/trace and clang-format have been bickering over what H5Tconv.c should look like and neither produces readable code. This change puts the top-level H5T_CONV_ab macros in do..while loops, adds appropriate semicolons, and adds the missing H5_CLANG_DIAG_ON|OFF and H5_GCC_CLANG_DIAG_ON|OFF macros to the list of statement macros clang-format recognizes. H5Tconv.c is now readable and both bin/trace and clang-format are happy.
* Fix for CVE-2018-15671. h5stat -S $POC will result in a crash with ↵vchoi-hdfgroup2023-08-251-15/+7
| | | | | | segmenetation fault. (#3427) It is because the object in the testfile points back to the root group. When the tool tries to traverse the object, it goes back to the root group and then back again.
* Remove intel oneapi warning (#3426)H. Joe Lee2023-08-251-1/+1
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* Revise file close assertion failure fix (#3418)jhendersonHDF2023-08-255-42/+63
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* Fix Heap-buffer-overflow WRITE in H5MM_memcpy (#3368)Alex2023-08-231-0/+3
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* Fix for CVE-2016-4332 (#3406)Dana Robinson2023-08-221-9/+7
| | | | | | | | | | | | | This CVE issue was previously listed as fixed (via HDFFV-9950) back in 2016, but with no confirmation test. Now that test files exist for the 2016 Talos CVE issues, we found that CVE-2016-4332 can raise an assert in debug builds. This fix replaces the assert with pointer checks that don't raise errors or asserts. Since the function is in cleanup code, we do our best to close and free things, even when presented with partially- initialized structs. Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo)
* Fix serial to parallel chunked dataset file space allocation bug (#3394)jhendersonHDF2023-08-221-11/+24
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* Fix valgrind warning about write of uninitialized bytes in ScaleOffset ↵jhendersonHDF2023-08-181-1/+7
| | | | filter (#3390)
* Fix valgrind warning about write of uninitialized bytes (#3389)jhendersonHDF2023-08-181-3/+14
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* Fix compile failures with H5C_DO_MEMORY_SANITY_CHECKS enabled (#3388)jhendersonHDF2023-08-182-2/+3
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* Fix assertion failure during file close on error (#3387)jhendersonHDF2023-08-181-1/+1
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* Fix possible performance regression introduced with in-place type conversion ↵Neil Fortner2023-08-151-0/+20
| | | | in 1.14.2 (#3376)
* Implementation of the mpio driver with selection I/O. (#3222)vchoi-hdfgroup2023-08-077-204/+2023
| | | | * This changes the default selection I/O to on for MPIO.
* Fix for the bug exposed from running test/set_extent.c when selection… (#3319)vchoi-hdfgroup2023-08-045-74/+161
| | | | | * Fix for the bug exposed from running test/set_extent.c when selection I/O is enabled. This is a fix from Neil. The test/set_extent.c is modified to test for selection I/O enabled.
* Fix assertion failure in H5D__mpio_collective_filtered_vec_io (#3340)jhendersonHDF2023-08-031-3/+3
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* Fixes the last of the -Wextra-semi-stmt warnings (#3326)Sean McBride2023-08-024-29/+29
| | | | | | | | | | | | | | | | | | | | | | | * Fixed extra semi warning by adjusting alternative macro definitions * Find-replace H5E_END_TRY; -> H5E_END_TRY * Made H5Epush_goto a do-while loop, fixed indentation * Made GOTOERROR and ERRMSG do-while loops * Made Hgoto_error and Hgoto_done do-while loops * Made vrfy_cint_type and vrfy_ctype do-while loops * Made TEST_TYPE_CONTIG and others do-while loops * Removed extraneous semi-colons * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix CVE-2018-13867 (#3336)Dana Robinson2023-08-021-0/+6
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* Fix CVE-2018-11202 (#3330)Dana Robinson2023-08-021-0/+9
| | | | | | | | | | | | | A malformed file could result in chunk index memory leaks. Under most conditions (i.e., when the --enable-using-memchecker option is NOT used), this would result in a small memory leak and and infinite loop and abort when shutting down the library. The infinite loop would be due to the "free list" package not being able to clear its resources so the library couldn't shut down. When the "using a memory checker" option is used, the free lists are disabled so there is just a memory leak with no abort on library shutdown. The chunk index resources are now correctly cleaned up when reading misparsed files and valgrind confirms no memory leaks.
* Made HGOTO_ERROR a do-while loop (#3308)Sean McBride2023-08-02319-13942/+14080
| | | | | * Made HGOTO_ERROR a do-while loop
* Fix loading plugin fails with missing directory GH issue #3248 (#3315)Allen Byrne2023-08-021-2/+1
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* Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314)jhendersonHDF2023-08-021-6/+10
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* Fix incorrect error check in H5Ofill.c for undefined fill values (#3312)jhendersonHDF2023-08-021-1/+1
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* Switch parallel compression to use vector I/O (#3245)jhendersonHDF2023-08-022-816/+544
| | | | | Updates parallel compression feature to use vector I/O instead of creating and passing down MPI derived types to VFD
* Another round of fixing -Wextra-semi-stmt warnings (#3264)Sean McBride2023-07-24176-1178/+1190
| | | Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* ROS3: (fix) Replaced HDfprintf (#3266)Jan-Willem Blokland2023-07-241-3/+3
| | | | - Replaced the HDfprintf() functions by fprintf() to be consistent with other parts of the library.
* removed the use of encoded single apostrophe (#3261)Scot Breitenfeld2023-07-2033-294/+294
| | | | | | * removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read * updated sanitizer paragraph * fixed brief description for H5Fget_info
* Fix warning in H5C__UPDATE_STATS_FOR_DIRTY_PIN macro (#3259)jhendersonHDF2023-07-181-1/+1
| | | | Add braces to H5C__UPDATE_STATS_FOR_DIRTY_PIN macro to fix warning causing Werror Release builds to fail
* Fixed more warnings about extra semicolons (#3249)Sean McBride2023-07-1896-1671/+1299
| | | | | | | * Require semi-colon after H5_CHECK_OVERFLOW calls Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix some warnings in developer builds (#3247)jhendersonHDF2023-07-188-196/+185
| | | | | * Fix some warnings in developer builds * Switch approach to Winline flag
* Fix CMake builds when Subfiling VFD isn't enabled (#3250)jhendersonHDF2023-07-172-33/+40
| | | | | * Fix CMake builds when Subfiling VFD isn't enabled * Add Subfiling VFD entry to hdf5-config.cmake.in
* ROS3: (feature) Temporary security credentials (#3030)Jan-Willem Blokland2023-07-144-36/+468
| | | | | | | | | | - Implemented support for AWS temporary security credentials. For this kind of credentials also a session/security token should be included in the request by adding the x-amz-security-token header. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Subfiling VFD source cleanup (#3241)jhendersonHDF2023-07-1331-3287/+105
| | | | | | | | | | | | | | | | * Subfiling VFD source cleanup Modularize Subfiling CMake code into separate CMakeLists.txt file Update Mercury util code to latest version and update Copyright Generate mercury_util_config.h header file instead of using pre-generated file Remove unnecessary Mercury functionality Fix minor warning in Subfiling VFD code * Remove Mercury headers from Autotools publicly-distributed header list
* Fix doc for H5allocate_memory (#3240)Nicolas Cornu2023-07-121-1/+1
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