v0.17.2

HDF5 v0.17.2

Diff since v0.17.1

Merged pull requests:

• mention package extension for MPI (#1122) (@ranocha)
• Update HISTORY.md (#1125) (@musm)
• Fix variable length strings as attributes (#1130) (@simonbyrne)
• Update helpers.jl with initial value for Ref{Cuint} (#1138) (@david-macmahon)
• update CompatHelper.yml and also run it for subpackages (#1139) (@antholzer)
• bump compat for filter package dependencies (#1140) (@baumgold)
• Bump codecov/codecov-action from 3 to 4 (#1141) (@dependabot[bot])
• Bump CodecZstd compat to 0.8, H5Zzstd version to 0.1.2 (#1144) (@mkitti)
• Fix H5F_LIBVER_LATEST, map lib 1.15 to H5F_LIBVER_V116 (#1145) (@mkitti)
• Add Julia 1.11 nightly to tests (#1146) (@mkitti)
• Remove unused type var in write_dataset(... (#1147) (@mkitti)

Closed issues:

• Can't get HDF5.jl work with Julia running in docker (julia:1.8-alpine3.17) - can't find libmpi.so.12 (#1123)
• Segfault when writing variable length string as attribute (#1129)
• Support szip (freely) (#1132)
• Installing HDF5.jl on ARM M1 (#1133)
• HDF5.jl triggers segfault in ccall with openmp+clang(m1) with julia 1.10 (#1134)
• h5_is_library_threadsafe() gives unreliable results due to unspecified initial value (#1137)
• The HDF Group CI (#1142)

v0.17.1

HDF5 v0.17.1

Diff since v0.17.0

Merged pull requests:

• Bump filter versions, set compat with HDF5.jl 0.17 (#1110) (@mkitti)
• Add HDF5.Filters.Registered module (#1111) (@mkitti)
• In docs, suggest passing HDF5 module to set_preferences!() instead of UUID (#1113) (@johnomotani)
• Add convenience function set_libraries! (#1115) (@JoshuaLampert)
• Update documentation about using files in memory (#1118) (@denglerchr)
• Fix h5readattr docstring (#1119) (@Sbozzolo)
• Bump version to 0.17.1 (#1120) (@mkitti)

Closed issues:

• Windows test failures for SZIP compression (#1106)
• Add to list of known preferences (#1112)
• Convenience function to use custom or system provided HDF5 binaries (#1114)

v0.17.0

HDF5 v0.17.0

HDF5 v0.17.0 includes a breaking change with regard to how system HDF5 libraries are incorporated for use with HFD5.jl as submitted in #1061 by @JoshuaLampert .

This switches to Preferences.jl for using a system-provided hdf5 library and replaces the additional build step. Please see the [note in the documentation](https://juliaio.github.io/HDF5.jl/v0.17/#Using-custom-or-system-provided-HDF5-binaries for details) on the new Preferences.jl based system and how to migrate from v0.16.x branch.

Diff since v0.16.16

Closed issues:

• Switch to Preferences for using system hdf5 (#1037)
• Juliacon 2023? (#1039)
• Test HDF5 1.14.0 from BinaryBuilder (#1053)
• compat entry for HDF5_jll (#1065)
• Copy a group of data from a file to another (#1070)
• release-0.16 branch created (#1074)
• HDF5.jl logo not optimal for dark mode (#1081)
• maxdims or max_dims in dataspace() (#1083)
• Using Type and Dataspace in create_dataset() (#1084)
• _memcpy! not defined on nightly (#1094)

Merged pull requests:

• Add initial support for H5Dchunk_iter (#1031) (@mkitti)
• Use Preferences for using custom hdf5 library (#1061) (@JoshuaLampert)
• MPI support via package extensions (weak dependency) (#1062) (@ranocha)
• Fix _typed_load fast path for Julia 1.10 (currently nightly) (#1075) (@mkitti)
• Simplify formatter check (#1078) (@simonbyrne)
• Fix #1083 maxdims -> max_dims in dataspace documentation (#1085) (@mkitti)
• Allow create_dataset to take a Type and Dataspace, Fix #1084 (#1086) (@mkitti)
• Update light and dark logos for readme (#1087) (@musm)
• Fixup readme logo links and readme style (#1088) (@musm)
• Upload logo as curves for font rendering independence (#1089) (@musm)
• Attempt to fix documentation (#1091) (@mkitti)
• doc typo: attributes(parent), not attribute(parent) (#1095) (@stevengj)
• Parse doxygen tag files (#1043) (@mkitti)
• Provide high level syntax for dealing with HDF5 files in memory (#1077) (@mkitti)
• JuliaCon 2023 Presentation (#1090) (@mkitti)
• Fix doxygen URLs from Java to C (#1099) (@mkitti)
• allow keyword args to open_group, open_dataset, open_datatype (#1100) (@simonbyrne)
• expand exported dataspace api functions (#1101) (@simonbyrne)
• Bump actions/checkout from 3 to 4 (#1103) (@dependabot[bot])
• mark SZIP tests on Windows as broken (#1107) (@simonbyrne)
• Fix datatype documentation (#1108) (@mkitti)

v0.16.16

HDF5 v0.16.16

Diff since v0.16.15

This the last significant change in the v0.16.x minor version branch of HDF5.jl.

** Merged pull requests **

• Port non-breaking changes for 0.16.16 (#1098) (@mkitti)

v0.16.15

What's Changed

• Update docs on system-provided MPI by @JoshuaLampert in #1059
• enable dependabot for GitHub actions by @ranocha in #1058
• Update HDF5_jll compat to 1.14, bump version number by @mkitti in #1054
• Update Project.toml to 0.16.15 by @mkitti in #1063
• Fixes create_dataset for compound types by @tamasgal in #1069
• Functional API with Strings / variable-size strings by @mkitti in #1067
• Tuple support by @lxvm in #1060
• Handle partial chunks by @0 in #1072
• [CI] Extend integration timeout to 30 min by @mkitti in #1073
• Docstrings for the function copy_object by @linwaytin in #1071

New Contributors

• @JoshuaLampert made their first contribution in #1059
• @lxvm made their first contribution in #1060
• @0 made their first contribution in #1072
• @linwaytin made their first contribution in #1071

Full Changelog: v0.16.14...v0.16.15

v0.16.14

HDF5 v0.16.14

Diff since v0.16.13

Closed issues:

• Windows mmap test failures (#89)
• threadsafe? (#139)
• thread safety? (#259)
• FYI: HDF5 query language [needs support?] (#322)
• Cannot create mmap file on windows (#357)
• Create our own binary artifacts (#569)
• Base.show method for Properties (#763)
• v0.16 tracker and discussion (#802)
• It seems h5info is not implemented: is there an alternative? (#815)
• Crash when using from multiple threads (#835)
• Finalizing correctly when using MPI (#852)
• safe multi-threaded writing (#853)
• Read all attributes into a dictionary (or structure) (#857)
• Empty (extensible) dataset cannot be read back (#859)
• create_dset triggers race condition (#862)
• Finalizers cause exception_access_violation while using HDF5 from a thread. (#990)
• add branch protection to master (#1036)
• OrderedCollections, an implicit dependency (#1046)
• Finalizer error when rapidly writing to HDF5 (#1048)
• Not compatible with TerminalMenus in the stdlib (#1050)
• Unexpected create_group key from readdlm string data (#1055)

Merged pull requests:

• Make begin as the first index of a Dataset work (#1027) (@machakann)
• correct docs on JULIA_HDF5_PATH search path (#1032) (@stevengj)
• add missing docstring for Group (#1034) (@simonbyrne)
• close property lists, simplify mpio test (#1035) (@simonbyrne)
• Clean up MPI (#1038) (@simonbyrne)
• Bump H5Zblosc version to 0.1.1 (#1040) (@mkitti)
• Update docs/Manifest.toml for H5Zblosc v0.1.1 (#1041) (@mkitti)
• some fixes for docs (#1042) (@simonbyrne)
• fix implicit OrderedCollections dependency on FileIO (#1047) (@simonbyrne)
• Implement try_close_finalizer, fix #1048 (#1049) (@mkitti)
• Always load even if deps aren't satisfied (#1051) (@jpsamaroo)
• docs: mention that low-level functions are in API submodule (#1052) (@jwahlstrand)
• use Cstring in ccall (#1056) (@simonbyrne)

v0.16.13

HDF5 v0.16.13

Diff since v0.16.12

Merged pull requests:

• add support for read-only s3 virtual driver (#1010) (@gszep)
• Add built-in support to write compound data types (#1013) (@tamasgal)
• Update HISTORY.md (#1017) (@musm)
• Fix virtual dataset tests (#1019) (@mkitti)
• Add JuliaFormatterTool and format.jl script (#1020) (@mkitti)
• add lock around all API calls (#1021) (@simonbyrne)
• Fix virtual dataset tests, from mkitti/api_lock_preferences (#1023) (@mkitti)
• Remove use of tempname() from setindex! of an AttributeDict (#1026) (@nhz2)
• fix invalidations from loading LoopVectorization.jl (#1028) (@ranocha)

v0.16.12

HDF5 v0.16.12

Diff since v0.16.11

Closed issues:

• Release 6.11 (#1005)

Merged pull requests:

• Add Invalidations.yml [ci skip] [skip tests] (#1009) (@ranocha)
• add BlockRange object to represent a dimension of a hyperslab (#1011) (@simonbyrne)
• Add virtual dataset support (#1012) (@simonbyrne)
• More informative errors when missing a filter (#1014) (@nhz2)
• Correct readme link for build instructions (#1016) (@musm)

v0.16.11

HDF5 v0.16.11

Diff since v0.16.10

Closed issues:

• create_group probably should throw a custom exception (#829)
• track_order only used with FileIO & OrderedDict (#939)
• Split up and rearrange files (#945)
• write on attribute doesn't check bounds (#954)
• Use of H5P_SET_FILE_LOCKING env var is unreliable (#959)
• StackOverflowError during initialization of module Drivers (#960)
• macOS x86_64 Julia nightly CI fails (#964)
• H5O_info[1]_t type definition is incorrect (#980)
• BITSHUFFLE filter not supported out of the box for HDF5 reading (#981)
• Use task_local_storage as a context instead of global state. (#985)
• Summer maintainership? (#991)
• Failed to precompile HDF5 on macOS (#997)

Merged pull requests:

• Move code into datasets.jl, readwrite.jl, and types.jl (#955) (@mkitti)
• move dataspace-related functions to new file (#961) (@simonbyrne)
• Add Core driver to docs (#965) (@mkitti)
• move type-unwrapping to unsafe_convert (#966) (@simonbyrne)
• Avoid calling non-public h5fd_xxx_init() functions (#967) (@david-macmahon)
• move Reference pieces to new file (#968) (@simonbyrne)
• move file-related functions to new file (#970) (@simonbyrne)
• move group and link functions to new file (#971) (@simonbyrne)
• Make Core init lazy, revise FileAccessProperty interface, fix file locking (#972) (@mkitti)
• Remove confusing example of create_dataset (#974) (@nhz2)
• move datatype functions to new file (#975) (@simonbyrne)
• move object-related functions to new file (#976) (@simonbyrne)
• h5o_get_info update to h5o_get_info3, deprecate object_info (#979) (@mkitti)
• Fix track_order usage in do block (#982) (@t-bltg)
• Check buf size on attr or dset write (#983) (@t-bltg)
• Add formatting check action and apply an initial format (#984) (@t-bltg)
• Add bitshuffle (#986) (@jamesrhester)
• Fix typo in H5Zbitshuffle, add API to H5Z_FLAG_REVERSE (#987) (@mkitti)
• Focus testing on H5Zbitshuffle (#988) (@mkitti)
• Add missing H5P functions (#989) (@mkitti)
• Ignore src/api/functions.jl for code coverage (#992) (@mkitti)
• Initialize properties on get. (#993) (@mkitti)
• Change set_track_order to set_track_order!, spelling and whitespace (#994) (@mkitti)
• Implement Base.copy(::Properties) (#995) (@mkitti)
• Debug 32-bit windows (#998) (@mkitti)
• Remove extraneous debug statement (#999) (@musm)
• Fix failing tests by revising H5O_get_info* API on library version (#1000) (@mkitti)
• Move code to highlevel.jl (#1002) (@mkitti)
• move MPI docs to their own page (#1004) (@simonbyrne)
• Cleanup group code (#1006) (@simonbyrne)
• fix fileno type (#1007) (@simonbyrne)

v0.16.10

HDF5 v0.16.10

Diff since v0.16.9

Closed issues:

• Permit reading values into a preexisting array buffer (#580)
• how to copy the file structure of a hdf5 file (#941)
• StackOverflowError during initialization of module Drivers (#960)

Merged pull requests:

• Add copyto! and similar for Datasets (#937) (@mkitti)
• CompatHelper: bump compat for Compat to 4, (keep existing compat) (#942) (@github-actions[bot])
• move attributes to new file, add docs (#943) (@simonbyrne)
• Add dset_no_attrs_hint support, h5f coverage up to v1.12 (#944) (@mkitti)
• Define AttributeDict (#948) (@simonbyrne)
• Expand DatasetAccessProperties coverage, add helpers (#949) (@mkitti)
• make iterators safe for error handling (#950) (@simonbyrne)
• fix error message on write_attribute (#951) (@simonbyrne)
• Refer to HDF5.API.H5Error rather than HDF5.H5Error (#956) (@mkitti)
• Fix attribute docs for attrs and rename_attribute, export it. (#958) (@mkitti)