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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 Robinson2024-03-093-5/+4
| | | | * 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 Lee2024-03-089-28/+32
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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
* Improve error messages when tools attempt to use non-enabled S3 and HDFS ↵Larry Knox2024-03-044-7/+12
| | | | VFDs. (#4047)
* Add options to allow tools type selection and naming (#4046)Allen Byrne2024-03-0428-543/+364
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* Grep for error messages instead of comparing files (#4024)Allen Byrne2024-02-163-19/+21
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* Fix some output issues with ph5diff (#4008)jhendersonHDF2024-02-132-6/+8
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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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* Remove check for MPI initialization in tools library when using parallel VFDsH. Joe Lee2024-01-091-13/+16
| | | The tools library no longer checks for whether MPI is initialized when attempting to use a parallel VFD, such as the MPI I/O VFD or Subfiling VFD. This requires that parallel VFDs check for this situation and initialize MPI on their own if need be, but also allows parallel VFDs to be used with non-parallel HDF5 tools, such as h5dump.
* Add 'warning density' computation to the warnhist script (#3910)Quincey Koziol2023-12-291-42/+42
| | | | | | | | | * Add 'warning density' computation to the warnhist script, along with several cleanups to it. Add "--enable-show-all-warnings" configure (and CMake) option to disable compiler diagnostic suppression (and therefore show all the otherwise suppressed compiler diagnostics), disabled by default. Clean up a buncn of misc. warnings. Signed-off-by: Quincey Koziol <qkoziol@amazon.com>
* Add variable option syncing for examples (#3885)Allen Byrne2023-12-1413-38/+38
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* Correct CMake command and example packaging (#3888)Allen Byrne2023-12-081-2/+2
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* Fix h5dump segmentation fault when --vfd-value option is used (#3873)H. Joe Lee2023-11-281-1/+1
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* Complete the `if command line option` sentence. (#3868)H. Joe Lee2023-11-241-1/+1
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* Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859)Allen Byrne2023-11-2220-58/+511
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* Fix typo: look -> loop (#3866)H. Joe Lee2023-11-211-1/+1
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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
* Fix misc. warnings from GCC when compiling with -fsanitize=undefined (#3787)jhendersonHDF2023-11-011-0/+8
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* Don't build util tests when HDF5_EXTERNALLY_CONFIGURED=ON (#3781)Robert Adam2023-10-301-1/+1
| | | | Fixes #3780
* Don't install h5tools_test_utils test program on system (#3793)jhendersonHDF2023-10-301-1/+1
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* Add helpful text to h5clear (#3754)bmribler2023-10-233-6/+27
| | | | | | | 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`.
* Add tools/libtest to Autotools builds (#3735)Dana Robinson2023-10-202-5/+5
| | | | | This was only added to CMake many years ago and tests the tools library.
* 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
* Fix issue with unmatched messages in ph5diff (#3719)jhendersonHDF2023-10-192-7/+4
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* 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)jhendersonHDF2023-10-035-5/+5
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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
* Fix potential uninitialized variable (#3602)Dana Robinson2023-09-271-3/+4
| | | | | | | | | | Moves a union initialization up a bit so it's performed before code that can jump to the cleanup target, where file descriptors could be checked without being initialized. This could only happen in test code and only in an out-of-memory situation. Fixes Coverity 1542254
* Develop tools move (#3580)Allen Byrne2023-09-261037-2117/+2184
| | | Reorganizes the tools files to support the VOL tests
* Replaces HDgetenv with getenv (#3599)Scot Breitenfeld2023-09-267-14/+14
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* Use HDoff_t with lseek consistently (#3600)Dana Robinson2023-09-263-8/+8
| | | | | 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 Robinson2023-09-1560-1078/+1078
| | | | | | | | | | | | | | | | | | | | | * 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 Robinson2023-09-142-42/+42
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* hbool_t/TRUE/FALSE --> bool/true/false in tools (#3491)Dana Robinson2023-09-0557-1409/+1405
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* Fix for CVE-2018-15671. h5stat -S $POC will result in a crash with ↵vchoi-hdfgroup2023-08-252-16/+2
| | | | | | 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.
* Avoid H5Ocopy in h5repack for variable-length string types (#3419)jhendersonHDF2023-08-241-0/+4
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* Add other types and full type to enum/str/vlen dataformat for ↵Allen Byrne2023-08-242-59/+76
| | | | structblock[begin/end] (#3353)
* Fix ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 (#3407)jhendersonHDF2023-08-222-7/+11
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* Make h5dump spacing consistent when printing VLEN datatype (#3351)jhendersonHDF2023-08-0412-26/+26
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* Fixes the last of the -Wextra-semi-stmt warnings (#3326)Sean McBride2023-08-023-9/+9
| | | | | | | | | | | | | | | | | | | | | | | * 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 h5repack for variable-length datatyped datasets (#3331)jhendersonHDF2023-08-021-1/+12
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* Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314)jhendersonHDF2023-08-023-30/+62
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* Another round of fixing -Wextra-semi-stmt warnings (#3264)Sean McBride2023-07-247-16/+16
| | | Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* removed the use of encoded single apostrophe (#3261)Scot Breitenfeld2023-07-203-3/+3
| | | | | | * 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 some warnings in developer builds (#3247)jhendersonHDF2023-07-182-0/+5
| | | | | * Fix some warnings in developer builds * Switch approach to Winline flag
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