h5_threads() sets how many threads h5lite uses for parallel work, currently the Blosc and Blosc2 codecs. The H5LITE_NTHREADS environment variable sets the default. Threads need hdf5lib 2.2.0.1 or later.start). start and count must now be whole numbers."bytes" encoding are now rejected before writing starts.h5_move() no longer deletes a group moved into itself (e.g. "g" to "g/sub"); this is now an error.names, dimnames, and row.names) are now kept consistent: h5_move() moves a dataset's scales with it, h5_delete() and overwriting delete them with it (scales not named after the dataset, such as netCDF coordinate variables, are detached but kept), deleting a scale detaches it, and writing a scale never overwrites an unrelated object (previously, writing x replaced anything named x_names, and could rewrite the names of a moved dataset).h5_write(list, file, name, attr = ...) no longer replaces the dataset name with a group; lists can't be written as attributes.list(a = 1, 2), deleting the group).POSIXct times are now stored in UTC (previously local times were labelled Z), with fractional seconds. POSIXlt is now written like POSIXct instead of as an empty group.utf8[n] and fixed-length strings are no longer truncated in the middle of a multibyte character, and their width is measured in UTF-8 bytes.as = "ascii" now transliterates every string, not just the first.70000 as float16, 2^63 as int64) are now an error instead of becoming Inf or wrapping around.blosc2_truncate no longer corrupts 32- and 64-bit integers, including those in data frames (it zeroed their low bits: with blosc2_truncate = 10, every int32 below 8192 read back as 0), or turns NA into NaN or Inf. It now applies only to float32 and float64 data without NA or NaN.int64 NA values now read back as NA instead of -9.22e18, and uint64 values above the int64 range read with as = "bit64" become NA (with a warning) instead of being clamped.dim, class, ...), no longer produce malformed or reshaped results. Factors with empty-string levels can no longer be written.h5_write(list, file, "/"), h5$write(list)).h5_create_file() and h5_open() now work on read-only files.as fixes: an unnamed as (or non-@ key) no longer applies to attributes when writing; as is now honored for factors (which can be stored as strings, e.g. as = c(grade = "ascii[1]")), raw, complex, integer64, NULL, and nested lists; "skip" and "null" must be spelled out rather than abbreviated; type-class keys like .int only match numeric data when reading; "auto" keeps the automatic type; attributes read or written directly accept plain or @ keys; and "null" drops data frame columns when reading.start on a data frame is now an error, and start/count on a group apply to each of its datasets.h5_length() returns 0 for NULL datasets and attributes.h5_ls() and h5_names() (for groups) now return names in the order sort() puts them, instead of an arbitrary order, and full.names = TRUE returns absolute paths. h5_read() on a group and h5_str() now follow the order objects were created (in files written by this version; name order otherwise), so lists read back in the order they were written.h5_str() shows names longer than 255 bytes, and h5_str() and h5_attr_names() no longer show HDF5's DIMENSION_LIST/REFERENCE_LIST attributes.h5_write() and h5_read() fail on Windows with older versions of R (such as R 4.2), and as keys now match an object named ~. Both came from R's basename(), which is meant for file paths.h5_open() handle methods now accept the same arguments as the corresponding functions (e.g. h5$read(name, start, count)), ".." works in absolute paths, and a relative file path keeps working after setwd().I() around a length-one POSIXct now writes a scalar, and its warning for longer objects appears once.h5_inspect() reports filter parameters as non-negative numbers."blosc1", "blosc2", "blosc2-ndlz", "blosc1-snappy", standard "blosc*-lz4") and "blosc2-zfp-acc-*" storing data uncompressed."blosc1-gzip" and "blosc2-gzip" now use Blosc instead of plain gzip.float_rounding no longer corrupt NA, NaN, or Inf: ZFP falls back to gzip and float_rounding is skipped for data containing them.print(h5_inspect()) reads Blosc2's settings in the new layout as well as those written by earlier versions (including the blosc2_truncate bits of 1-D datasets and of negative settings) and by other software, lists the pre-filters in the order they run (truncation, delta, shuffle), and shows when Blosc2's ZFP codecs declined a dataset.blosc2_delta and blosc2_truncate are no longer passed to "blosc2-ndlz" and "blosc2-zfp-...", which never ran them. print(h5_inspect()) listed them anyway, and blosc2_truncate = 8 made NDLZ use 8x8 cells. print(h5_compression("blosc2-ndlz")) no longer claims a bitshuffle.blosc2_truncate must be between -51 and 52, and not 0. A setting that keeps no bits or drops a whole mantissa used to leave the data uncompressed. For float32 data, settings that would drop 23 bits or more are skipped."lz4-[level]" now passes the requested LZ4-HC level instead of always using level 9."blosc2-zfp-acc-0", which silently used a tolerance of 1) is now an error.float_rounding on float16 or bfloat16 data no longer makes the write fail; HDF5's Scale-Offset filter can't handle them, so it is skipped.compress = "none" no longer chunks or shuffles the data, and compress = TRUE now selects gzip instead of no compression."blosc2-zfp-*" now falls back to the default shuffle + gzip pipeline."zfp-...") now falls back to the default shuffle + gzip pipeline for data whose chunks have no dimension longer than one (e.g. a single value) or more than four, which ZFP can't compress. The write used to fail.h5_inspect() no longer prints large chunk dimensions in scientific notation.vignette('compression') now covers every bundled codec, lossy compression, sharing files with other software, and chunk tuning.These take effect when h5lite is built with hdf5lib 2.2.0.1 or later.
h5_threads().blosc2_truncate bits into the first. So hdf5plugin describes them by their last pre-filter, h5py can append to them, and h5py can read 1-D Blosc2 datasets. hdf5plugin used to read the pre-filter bitmask h5lite recorded as a single filter code, which isn't a valid one with blosc2_delta or blosc2_truncate. 1-D Blosc2 datasets written earlier can't be read by h5py until they are rewritten."blosc2-zfp-..." now compresses arrays of more than four dimensions, and chunks with a dimension shorter than 4, which it used to store uncompressed. Data of fewer than four values is stored uncompressed, and print(h5_inspect()) shows e.g. blosc2 [zfp-acc] (declined: stored uncompressed).int_packing or float_rounding. It used to refuse every chunk with two or more dimensions after Scale-Offset, leaving them packed but otherwise uncompressed."snappy" datasets are written in the block layout of snappy-cuda, the filter registered for Snappy's HDF5 filter ID. h5lite built with hdf5lib 2.2.0.0 or earlier can't read them; older ones can still be read.HDF5_PLUGIN_PATH. hdf5lib's read-only BitRound shim claimed SZ3's ID, which made them unreadable; it now uses BitRound's own, 32032, which h5_inspect() names bitround.‘%d’ directive output may be truncated in utils.c.h5_compression() and h5_inspect().vignette('compression').vignette('partial-reading').h5_length() and h5_dim() now return numeric values instead of integer to support very large datasets.