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* Change compression tests reference files to use masking for compression ↵Allen Byrne2024-03-1013-40/+270
| | | | | ratios (#4083) Rework TEST_FILTER tests to handle slightly different compression ratios
* Minimize use of abort() (#4110)Dana Robinson2024-03-101-10/+11
| | | The abort() call is used at several places where it probably shouldn't.
* Refactor datatype conversion code to use pointers rather than IDs (#4104)jhendersonHDF2024-03-101-9/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | The datatype conversion code previously used IDs for the source and destination datatypes rather than pointers to the internal structures for those datatypes. This was mostly due to the need for an ID for these datatypes that can be passed to an application-registered datatype conversion function or datatype conversion exception function. However, using IDs internally caused a lot of unnecessary ID lookups and hurt performance of datatype conversions in general. This was especially problematic for compound datatype conversions, where the ID lookups were occuring on every member of every compound element of a dataset. The code has now been refactored to use pointers internally and only create IDs for datatypes when necessary. Fixed a test issue in dt_arith where a library datatype conversion function was being cast to an application conversion function. Since the two have different prototypes, this started failing after the parameters for a library conversion function changed from hid_t to H5T_t * and an extra parameter was added. This appears to have worked coincidentally in the past since the only different between a library conversion function and application conversion function was an extra DXPL parameter at the end of an application conversion function Fixed an issue where memory wasn't being freed in the h5fc_chk_idx test program. Even though the program exits quickly after allocating the memory, it still causes failures when testing with -fsanitize=address
* Clean up off_t usage (#4095)Dana Robinson2024-03-092-3/+3
| | | | * Add comments to C++ and Fortran API calls that use off_t * Remove noise casts for small integers
* Add subfiling for h5dump filedriver option help message (#3878)H. Joe Lee2024-03-088-24/+24
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* Rename incorrectly named option (#4067)Allen Byrne2024-03-0518-103/+103
| | | | | | | * Rename incorrectly named option * Restore the correct uses of USING_MEMCHECKER * Update release note
* Add options to allow tools type selection and naming (#4046)Allen Byrne2024-03-0417-161/+161
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* Grep for error messages instead of comparing files (#4024)Allen Byrne2024-02-163-19/+21
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* Issue #1824: Replaced most remaining sprintf with safer snprint (#4003)Sean McBride2024-02-131-1/+1
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* Add h5dump tests that require subfiling VFD (#3879)H. Joe Lee2024-02-018-1/+48
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* Add variable option syncing for examples (#3885)Allen Byrne2023-12-142-5/+5
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* Correct CMake command and example packaging (#3888)Allen Byrne2023-12-081-2/+2
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* Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859)Allen Byrne2023-11-2219-58/+508
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* Add extra space in comments for consistency (#3852)H. Joe Lee2023-11-141-2/+2
| | | | | * Add extra space in comments for consistency * uncomment tfloatsattrs test
* Add helpful text to h5clear (#3754)bmribler2023-10-232-4/+18
| | | | | | | Added text to the usage of h5clear to explain that this tool is not for fixing corrupted files but simply for helping in the inspection of the damage.. Fixed expected output for testing the modified usage.
* Clean up onion VFD files in tools `make clean` (#3739)Dana Robinson2023-10-212-3/+2
| | | | Cleans up h5dump and h5diff *.onion files in the Autotools when runing `make clean`.
* Test scripts now execute in-source with creation of tmp dir (#3723)Allen Byrne2023-10-2035-42/+49
| | | | | | Fixes a few issues created in #3580: * Fixes a problem where committed tools test files were deleted when cleaning after an in-source build * Fixes issues with test file paths in Autotools tools test scripts
* Sync changes that are only in 1.14 branch (#3704)jhendersonHDF2023-10-181-1/+1
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* Fix several spelling/grammar issues (#3621)jhendersonHDF2023-10-034-4/+4
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* Remove unnecessary assignment in test generator (#3603)Dana Robinson2023-09-271-1/+0
| | | | | | | Fixes what looks like a copy/paste/modify error in the format convert test file generator, where an array element is assigned one value and them immediately overwritten by another value. Fixes Coverity issue 1542285
* Develop tools move (#3580)Allen Byrne2023-09-261037-2117/+61918
| | | Reorganizes the tools files to support the VOL tests
* Replaces HDgetenv with getenv (#3599)Scot Breitenfeld2023-09-261-2/+2
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* Use HDoff_t with lseek consistently (#3600)Dana Robinson2023-09-262-5/+5
| | | | | 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.
* Strip HD prefix from string/char C API calls (#3540)Dana Robinson2023-09-1519-183/+183
| | | | | | | | | | | | | | | | | | | | | * 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 Robinson2023-09-141-18/+18
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* hbool_t/TRUE/FALSE --> bool/true/false in tools (#3491)Dana Robinson2023-09-0512-159/+155
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* Fix ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 (#3407)jhendersonHDF2023-08-221-3/+5
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* Another round of fixing -Wextra-semi-stmt warnings (#3264)Sean McBride2023-07-241-2/+2
| | | Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* removed the use of encoded single apostrophe (#3261)Scot Breitenfeld2023-07-202-2/+2
| | | | | | * removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read * updated sanitizer paragraph * fixed brief description for H5Fget_info
* Remove HD from HDmem* calls (#3211)Dana Robinson2023-06-297-28/+28
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* Remove programmer/date from comments (#3210)Dana Robinson2023-06-2920-227/+1
| | | | * Removes Programmer: and Date: fields * Fixes a few Modifications: fields leftover from previous work
* Remove HD from C std lib file ops (#3206)Dana Robinson2023-06-297-53/+53
| | | | | | | | | * HDfclose * HDferror * HDfeof * HDfflush * HDfopen * HDfread * HDfwrite
* Remove HD from strto* calls (#3204)Dana Robinson2023-06-291-2/+2
| | | | | | | | * HDstrtod * HDstrtol * HDstrtoll * HDstrtoul * HDstrtoull * HDstrtoumax
* Rename HDexit() and related to exit(), etc. (#3202)Dana Robinson2023-06-298-32/+32
| | | | | * HDatexit * HDexit * HD_exit
* Remove HD from protected POSIX calls (#3203)Dana Robinson2023-06-291-14/+14
| | | | | | | | | | | These calls are non-C99 but protected by ifdefs and have no Windows equivalents: * HDalarm * HDasprintf * HDclock_gettime * HDfcntl * HDgethostname * HDgetrusage * HDsymlink
* Remove HD from memory allocate/free calls (#3195)Dana Robinson2023-06-2814-293/+293
| | | | | | * HDcalloc * HDfree * HDmalloc * HDrealloc
* Rename HDsystem() to system() (#3197)Dana Robinson2023-06-281-2/+2
| | | | system() is only used in the iopipe test and the things it calls (which are POSIX-y) are protected by an ifdef.
* Add note about HDF5_VOL_CONNECTOR to tools usage (#3159)mattjala2023-06-2811-0/+33
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* Rename HD(f)printf() to (f)printf() (#3194)Dana Robinson2023-06-2822-587/+584
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* Rename HDassert() to assert() (#3191)Dana Robinson2023-06-284-516/+516
| | | | | * Change HDassert to assert * Fix bin/make_err
* Many fixes to various compiler warnings (#3124)Sean McBride2023-06-1911-47/+59
| | | | | | | | | | | * Fixed various -Wmissing-variable-declarations by adding static keyword * In a few cases, renamed the variable suffix from _g to _s. * Fixed some -Wmissing-variable-declarations by using different declaration macros * Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero * Fixed various -Wcomma warnings * Fixed clang -Wstrict-prototypes warnings * Fixed various -Wunused-variable warnings * Updated some casts to fix the only 3 -Wcast-qual warnings * Fixed the only -Wsometimes-uninitialized warning
* Many clang -Wextra-semi-stmt fixes (#2537)Sean McBride2023-06-1611-63/+63
| | | | | * Adds semicolons to function-like macros * Adds a do..while(0) loop to some macros * Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END
* Add h5copy help test and verify consistency (#2902)Allen Byrne2023-05-177-3/+175
| | | * Add autotools test for help
* Add no subsets option to h5diff like h5dump #2688 (#2756)Allen Byrne2023-04-1810-0/+20
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* Comment cleanup (#2689)Quincey Koziol2023-04-118-66/+2
| | | * Clean up content and redundant logging in comments.
* Remove dead code hidden behind #ifdef LATER (#2686)Dana Robinson2023-04-101-20/+0
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* Make sure that ONLY_SHARED_LIBS option is correctly set (#2544)Allen Byrne2023-03-1310-31/+21
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* Check for overflow when calculating on-disk attribute data size (#2459)Egbert Eich2023-03-022-0/+10
| | | | | | | | | | | | | | | | | * 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
* Play nice with existing plugin paths (#2394)Quincey Koziol2023-01-064-4/+4
| | | | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. * Play nice with existing plugin paths Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* H5F_LIBVER_LATEST changes for move to 1.15 (#2288)Allen Byrne2022-12-212-8/+9
| | | | | | | | | | | | | | | * H5F_LIBVER_LATEST changes for move to 1.15 * Add new default api check * Format fixes * Fix default configure * fix lib version tests * Fix another version variable * Add 1.14 doc link
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