Guido Imperiale b074586d9e Apply filters to variable-length data (#6178) ...

Closes can_apply and set_local filter callbacks skipped for H5T_VARIABLE dtypes #5942. A more detailed explanation of the rationale for this PR is in the linked issue.

Mandatory filters can be now applied to variable-length data. This notably includes h5py object strings and NpyStrings.

Optional filters applied to variable-length data no longer skip can_apply and set_local, only to jump directly to filter. This fixes hdf5_blosc and HDF5_Blosc2, which rely on set_local. Note that all filters which have neither can_apply nor set_local have always worked fine with vlen data, as long as they were tagged as optional. Notable examples are deflate, lzf, bzip2 (from hdf5plugin), and lz4 (also from hdf5plugin).

Lossy filters, such as scale-offset, are and remain untested and most likely broken, as I expect them to treat the vlen metadata as numbers and corrupt it. The right place to ensure proper behaviour is their can_apply function, which however is broken (filters: can_apply does nothing for optional filters #6161).

2026-02-24 17:05:58 -06:00

..

API

Consistent extension for C++ (#6214)

2026-02-20 08:59:27 -06:00

testfiles

Fix bugs involving recursive link operations that could be triggered by deleting links to their parent group (#5853)

2025-09-30 12:20:49 -05:00

accum_swmr_reader.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

accum.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

app_ref.c

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2024-10-18 21:13:04 -07:00

atomic_reader.c

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2024-10-18 21:13:04 -07:00

atomic_writer.c

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2024-10-18 21:13:04 -07:00

AtomicWriterReader.txt

spelling fixes (#1561)

2022-03-31 10:42:30 -05:00

big.c

Add support for 64 bit chunks, including 64 bit chunk dimensions (#5965)

2025-11-04 11:42:24 -06:00

bittests.c

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2024-10-18 21:13:04 -07:00

btree2.c

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

cache_api.c

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

cache_common.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

cache_common.h

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

cache_image.c

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2024-10-18 21:13:04 -07:00

cache_logging.c

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2024-10-18 21:13:04 -07:00

cache_tagging.c

Change default nslots value for chunk cache to 8191 (#5956)

2025-10-31 14:48:05 -05:00

cache.c

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

chunk_info.c

Add H5Dread_chunk2() (#5506)

2025-06-17 11:11:13 -05:00

CMakeLists.txt

Enable data sieving for chunks that can't be cached (#6111)

2026-01-23 10:58:11 -06:00

CMakePassthroughVOLTests.cmake

CMake: Fix Fortran cross-compilation support

2026-02-13 14:45:02 -06:00

CMakeTests.cmake

CMake: Fix Fortran cross-compilation support

2026-02-13 14:45:02 -06:00

CMakeVFDTests.cmake

CMake: Fix Fortran cross-compilation support

2026-02-13 14:45:02 -06:00

cmpd_dset.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

cmpd_dtransform.c

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2024-10-18 21:13:04 -07:00

cork.c

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2024-10-18 21:13:04 -07:00

cross_read.c

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2024-10-18 21:13:04 -07:00

dangle.c

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2024-10-18 21:13:04 -07:00

del_many_dense_attrs.c

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2024-10-18 21:13:04 -07:00

direct_chunk.c

Add H5Dread_chunk2() (#5506)

2025-06-17 11:11:13 -05:00

dsets.c

Apply filters to variable-length data (#6178)

2026-02-24 17:05:58 -06:00

dt_arith.c

Add predefined datatypes for FP8 formats (#5882)

2025-11-03 15:10:22 -06:00

dtransform.c

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2024-10-18 21:13:04 -07:00

dtypes.c

Add predefined datatype for FP4 format (#6122)

2025-12-31 11:44:08 -06:00

earray.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

efc.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

enc_dec_plist_cross_platform.c

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2024-10-18 21:13:04 -07:00

enc_dec_plist.c

Change default page buffer size to 64MiB when using ROS3 driver (#5685)

2025-08-06 23:04:10 -05:00

enum.c

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2024-10-18 21:13:04 -07:00

err_compat.c

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2024-10-18 21:13:04 -07:00

error_test.c

Refactor warning macros (#5432)

2025-05-23 11:46:40 -05:00

event_set.c

Integrate API tests with testing framework (#5133)

2024-11-26 07:34:52 -06:00

evict_on_close.c

Make test/evict_on_close.c FILENAMES static (#5989)

2025-11-07 11:51:12 -06:00

extend.c

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2024-10-18 21:13:04 -07:00

external_common.c

Fix minor Windows warnings (#5021)

2024-10-28 05:54:16 -07:00

external_common.h

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2024-10-18 21:13:04 -07:00

external_env.c

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2024-10-18 21:13:04 -07:00

external_fname.h

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2024-10-18 21:13:04 -07:00

external.c

fix for cray compiler failing test (#5347)

2025-03-03 14:11:00 -06:00

farray.c

chore: decapitalize Fixed Array (#5659)

2025-07-15 18:20:13 +02:00

fheap.c

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

file_image.c

Refactor warning macros (#5432)

2025-05-23 11:46:40 -05:00

filenotclosed.c

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2024-10-18 21:13:04 -07:00

fillval.c

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2024-10-18 21:13:04 -07:00

filter_fail.c

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2024-10-18 21:13:04 -07:00

filter_plugin1_dsets.c

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2024-10-18 21:13:04 -07:00

filter_plugin2_dsets.c

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2024-10-18 21:13:04 -07:00

filter_plugin3_dsets.c

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filter_plugin4_groups.c

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2024-10-18 21:13:04 -07:00

filter_plugin.c

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2024-10-18 21:13:04 -07:00

flush1.c

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2024-10-18 21:13:04 -07:00

flush2.c

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2024-10-18 21:13:04 -07:00

flushrefresh.c

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2024-10-18 21:13:04 -07:00

flushrefreshTest.cmake

Rework Fortran configure to allow cross compile overrides (#5720)

2025-10-12 17:30:46 -05:00

freespace.c

Fix several issues uncovered by CVE-2025-7067 (#5938)

2025-11-11 11:52:20 -06:00

gen_bad_compound.c

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2024-10-18 21:13:04 -07:00

gen_bad_offset.c

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2024-10-18 21:13:04 -07:00

gen_bad_ohdr.c

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2024-10-18 21:13:04 -07:00

gen_bogus.c

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2024-10-18 21:13:04 -07:00

gen_bounds.c

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2024-10-18 21:13:04 -07:00

gen_cross.c

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2024-10-18 21:13:04 -07:00

gen_deflate.c

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2024-10-18 21:13:04 -07:00

gen_file_image.c

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2024-10-18 21:13:04 -07:00

gen_filespace.c

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gen_filters.c

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2024-10-18 21:13:04 -07:00

gen_mergemsg.c

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2024-10-18 21:13:04 -07:00

gen_new_array.c

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gen_new_fill.c

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gen_new_group.c

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gen_new_mtime.c

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gen_new_super.c

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2024-10-18 21:13:04 -07:00

gen_noencoder.c

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2024-10-18 21:13:04 -07:00

gen_nullspace.c

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gen_old_array.c

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gen_old_group.c

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gen_old_layout.c

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2024-10-18 21:13:04 -07:00

gen_old_mtime.c

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2024-10-18 21:13:04 -07:00

gen_plist.c

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2024-10-18 21:13:04 -07:00

gen_sizes_lheap.c

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2024-10-18 21:13:04 -07:00

gen_specmetaread.c

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2024-10-18 21:13:04 -07:00

gen_udlinks.c

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2024-10-18 21:13:04 -07:00

genall5.c

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2024-10-18 21:13:04 -07:00

genall5.h

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2024-10-18 21:13:04 -07:00

getname.c

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2024-10-18 21:13:04 -07:00

gheap.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

h5test.c

Re-write ROS3 VFD S3 backend to use AWS' C S3 library (#5548)

2025-05-29 17:51:29 -05:00

h5test.h

Re-write ROS3 VFD S3 backend to use AWS' C S3 library (#5548)

2025-05-29 17:51:29 -05:00

H5srcdir_str.h.in

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2024-10-18 21:13:04 -07:00

H5srcdir.h

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2024-10-18 21:13:04 -07:00

hdfs.c

Add new multithreaded concurrency configuration (#5015)

2024-12-19 01:35:21 -08:00

hyperslab.c

Add new multithreaded concurrency configuration (#5015)

2024-12-19 01:35:21 -08:00

io_perf.c

Enable data sieving for chunks that can't be cached (#6111)

2026-01-23 10:58:11 -06:00

istore.c

build(haiku): make chunk_dims static in test/istore.c (#6049)

2025-12-01 13:16:51 -06:00

lheap.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

links_env.c

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2024-10-18 21:13:04 -07:00

links.c

Fixes buffer underflow (#6143)

2026-01-26 18:07:23 -06:00

mdset.c

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2024-10-18 21:13:04 -07:00

mf.c

Fix several issues uncovered by CVE-2025-7067 (#5938)

2025-11-11 11:52:20 -06:00

mirror_vfd.c

Fix codespell issues (#5256)

2025-01-21 17:36:27 -06:00

mount.c

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2024-10-18 21:13:04 -07:00

mtime.c

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2024-10-18 21:13:04 -07:00

ntypes.c

Add predefined datatype for FP4 format (#6122)

2025-12-31 11:44:08 -06:00

null_vfd_plugin.c

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2024-10-18 21:13:04 -07:00

null_vfd_plugin.h

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2024-10-18 21:13:04 -07:00

null_vol_connector.c

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2024-10-18 21:13:04 -07:00

null_vol_connector.h

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2024-10-18 21:13:04 -07:00

objcopy_ref.c

Refactor warning macros (#5432)

2025-05-23 11:46:40 -05:00

objcopy.c

Refactor warning macros (#5432)

2025-05-23 11:46:40 -05:00

ohdr.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

onion.c

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2024-10-18 21:13:04 -07:00

page_buffer.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

POSIX_Order_Write_Test_Report.docx

Moved remaining SWMR-related test files to develop.

2017-01-26 14:34:12 -05:00

POSIX_Order_Write_Test_Report.pdf

Moved remaining SWMR-related test files to develop.

2017-01-26 14:34:12 -05:00

reserved.c

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2024-10-18 21:13:04 -07:00

ros3.c

Add documentation and s3proxy testing for ROS3 VFD (#5560)

2025-06-19 16:22:49 -05:00

rtree.c

Fix zero-element reads on virtual dsets with r-trees (#6083)

2025-12-12 09:24:09 -06:00

s3comms.c

Add documentation and s3proxy testing for ROS3 VFD (#5560)

2025-06-19 16:22:49 -05:00

select_io_dset.c

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2024-10-18 21:13:04 -07:00

set_extent.c

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2024-10-18 21:13:04 -07:00

ShellTests.cmake

Add check for PERL_FOUND around actual test (#5130)

2024-11-19 16:18:17 -06:00

space_overflow.c

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2024-10-18 21:13:04 -07:00

stab.c

Change default file format to 1.8 (#5949)

2025-10-30 15:26:12 -05:00

swmr_addrem_writer.c

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2024-10-18 21:13:04 -07:00

swmr_common.c

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2024-10-18 21:13:04 -07:00

swmr_common.h

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2024-10-18 21:13:04 -07:00

swmr_generator.c

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2024-10-18 21:13:04 -07:00

SWMR_POSIX_Order_UG.txt

Fixed Spelling Errors (#1166)

2021-12-07 08:27:29 -06:00

swmr_reader.c

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2024-10-18 21:13:04 -07:00

swmr_remove_reader.c

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2024-10-18 21:13:04 -07:00

swmr_remove_writer.c

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2024-10-18 21:13:04 -07:00

swmr_sparse_reader.c

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2024-10-18 21:13:04 -07:00

swmr_sparse_writer.c

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2024-10-18 21:13:04 -07:00

swmr_start_write.c

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2024-10-18 21:13:04 -07:00

SWMR_UseCase_UG.txt

Fixed Spelling Errors (#1166)

2021-12-07 08:27:29 -06:00

swmr_writer.c

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2024-10-18 21:13:04 -07:00

swmr.c

Change default file format to 1.8 (#5949)

2025-10-30 15:26:12 -05:00

tarray.c

Remove const from testing parameters in testframe framework (#5214)

2025-01-08 13:33:00 -06:00

tattr.c

Fixes buffer underflow (#6143)

2026-01-26 18:07:23 -06:00

tcheck_version.c

Semantic versioning update (#5944)

2025-11-04 05:11:46 -06:00

tchecksum.c

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2025-01-08 13:33:00 -06:00

tconfig.c

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2025-01-08 13:33:00 -06:00

tcoords.c

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2025-01-08 13:33:00 -06:00

test_flush_refresh.sh.in

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2024-10-18 21:13:04 -07:00

test_swmr.pwsh.in

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test_swmr.sh.in

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test_use_cases.sh.in

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2024-10-18 21:13:04 -07:00

test_vds_swmr.pwsh.in

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2024-10-18 21:13:04 -07:00

test_vds_swmr.sh.in

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2024-10-18 21:13:04 -07:00

testframe.c

Move TestAlarmOn()/TestAlarmOff() back into PerformTests() (#5307)

2025-02-10 15:23:54 -06:00

testframe.h

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

testhdf5.c

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2024-10-18 21:13:04 -07:00

testhdf5.h

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2025-01-08 13:33:00 -06:00

testmeta.c

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2024-10-18 21:13:04 -07:00

tfile.c

Fixes buffer underflow (#6143)

2026-01-26 18:07:23 -06:00

tgenprop.c

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2025-01-08 13:33:00 -06:00

th5_system.c

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2025-01-08 13:33:00 -06:00

th5o.c

Remove const from testing parameters in testframe framework (#5214)

2025-01-08 13:33:00 -06:00

th5s.c

Fix segfault in H5S__get_select_hyper_blocklist() (#5353)

2025-03-18 11:06:36 -05:00

tid.c

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2025-01-08 13:33:00 -06:00

timer.c

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2024-10-18 21:13:04 -07:00

titerate.c

Fixes buffer underflow (#6143)

2026-01-26 18:07:23 -06:00

tmeta.c

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2025-01-08 13:33:00 -06:00

tmisc.c

Add support for 64 bit chunks, including 64 bit chunk dimensions (#5965)

2025-11-04 11:42:24 -06:00

trefer_deprec.c

Remove const from testing parameters in testframe framework (#5214)

2025-01-08 13:33:00 -06:00

trefer_shutdown.c

Rename HD(f)printf() to (f)printf() (#3194)

2023-06-28 08:31:32 -07:00

trefer.c

Fixes buffer underflow (#6143)

2026-01-26 18:07:23 -06:00

trefstr.c

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2025-01-08 13:33:00 -06:00

tselect.c

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2025-01-08 13:33:00 -06:00

tskiplist.c

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2025-01-08 13:33:00 -06:00

tsohm.c

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

ttime.c

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2025-01-08 13:33:00 -06:00

ttsafe_acreate.c

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ttsafe_atomic.c

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ttsafe_attr_vlen.c

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ttsafe_cancel.c

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ttsafe_dcreate.c

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ttsafe_develop.c

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ttsafe_error_stacks.c

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ttsafe_error.c

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2025-01-08 13:33:00 -06:00

ttsafe_rec_rwlock.c

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ttsafe_rwlock.c

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2025-01-08 13:33:00 -06:00

ttsafe_semaphore.c

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2025-01-08 13:33:00 -06:00

ttsafe_thread_id.c

Fix codespell issues (#5256)

2025-01-21 17:36:27 -06:00

ttsafe_thread_pool.c

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2025-01-08 13:33:00 -06:00

ttsafe.c

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2025-01-08 13:33:00 -06:00

ttsafe.h

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2025-01-08 13:33:00 -06:00

tunicode.c

Skip unicode tests for specific VFDs (#5823)

2025-09-15 11:42:54 -05:00

tvlstr.c

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2025-01-08 13:33:00 -06:00

tvltypes.c

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2025-01-08 13:33:00 -06:00

twriteorder.c

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unlink.c

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2024-10-18 21:13:04 -07:00

unregister.c

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2024-10-24 10:09:22 -07:00

use_append_chunk_mirror.c

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use_append_chunk.c

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use_append_mchunks.c

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2024-10-18 21:13:04 -07:00

use_common.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

use_disable_mdc_flushes.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

use.h

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds_env.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds_swmr_gen.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds_swmr_reader.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds_swmr_writer.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds_swmr.h

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vfd_plugin.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vfd.c

Change default file format to 1.8 (#5949)

2025-10-30 15:26:12 -05:00

vol_plugin.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vol.c

Fix checking of HDF5_VOL_CONNECTOR env. var. in some tests (#6073)

2025-12-01 11:21:19 -06:00