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bloscpack 0.5.1

Command line interface to and serialization format for Blosc

Latest Version: 0.6.0

Description

Command line interface to and serialization format for Blosc, a high performance, multi-threaded, blocking and shuffling compressor. Uses python-blosc bindings to interface with blosc.

Dependencies

  • Python 2.6 (requires ordereddict and argparse) or Python 2.7
  • python-blosc (provides Blosc)
  • Numpy
  • The Python packages nose, nose-parameterized and cram for testing

Check the files requirements.txt and test_requirements.txt for up-to-date version numbers.

Stability of File Format

The tool is considered alpha-stage, experimental, research software. It is not unlikely that the internal storage format for the compressed files will change in future. Please do not depend critically on the files generated (unless you know what you are doing) by Bloscpack. See the warranty disclaimer in the licence at the end of this file.

Installation

The package is available on PyPi, so you may use pip to install the dependencies and bloscpack itself:

$ pip install -r requirements.txt
$ pip install bloscpack

If you want to install straight from GitHub, use pip's VCS support:

$ pip install git+https://github.com/Blosc/bloscpack

Or, of course, download the source code or clone the repository and then use the standard setup.py:

$ python setup.py install

All of the above may or may not -- depending on the incantation used -- require superuser privileges.

Alternatively, if you just need the command line interface, add the blpk file to your $PATH somehow. For example by copying using dereferencing (-L), since blpk is a sym-link to bloscpack.py:

$ cp -L blpk ~/bin

Usage

Bloscpack has a number of global options and four subcommands: [c | compress], [d | decompress], [a | append] and [i | info] most of which each have their own options.

Help for global options and subcommands:

$ ./blpk --help
[...]

Help for each one of the subcommands:

$ ./blpk compress --help
[...]
$ ./blpk decompress --help
[...]
$ ./blpk info --help
[...]
$ ./blpk append --help
[...]

Examples

Basics

Basic compression:

$ ./blpk compress data.dat

Or:

$ ./blpk c data.dat

... will compress the file data.dat to data.dat.blp

Basic decompression:

$ ./blpk decompress data.dat.blp data.dcmp

Or:

$ ./blpk d data.dat.blp data.dcmp

... will decompress the file data.dat.blp to the file data.dcmp. If you leave out the [<out_file>] argument, Bloscpack will complain that the file data.dat exists already and refuse to overwrite it:

$ ./blpk decompress data.dat.blp
blpk: error: output file 'data.dat' exists!

If you know what you are doing, you can use the global option [-f | --force] to override the overwrite checks:

$ ./blpk --force decompress data.dat.blp

Incidentally this works for compression too:

$ ./blpk compress data.dat
blpk: error: output file 'data.dat.blp' exists!
$ ./blpk --force compress data.dat

Lastly, if you want a different filename:

$ ./blpk compress data.dat custom.filename.blp

... will compress the file data.dat to custom.filename.blp

Settings

By default, the number of threads that Blosc uses during compression and decompressoion is determined by the number of cores detected on your system. You can change this using the [-n | --nthreads] option:

$ ./blpk --nthreads 1 compress data.dat

Compression with Blosc is controlled with the following options:

  • [-t | --typesize] Typesize used by Blosc (default: 8): $ ./blpk compress --typesize 8 data.dat
  • [-l | --level] Compression level (default: 7): $ ./blpk compress --level 3 data.dat
  • [-s | --no-shuffle] Deactivate shuffle: $ ./blpk compress --no-shuffle data.dat
  • [-c | --codec] Use alternative codec: $ ./blpk compress --codec lz4 data.dat

In addition, there are the following options that control the Bloscpack file:

  • [-z | --chunk-size] Desired approximate size of the chunks, where you can use human readable strings like 8M or 128K or max to use the maximum chunk size of apprx. 2GB (default: 1MB): $ ./blpk compress --chunk-size 128K data.dat or $ ./blpk c -z max data.dat
  • [-k | --checksum <checksum>] Chose which checksum to use. The following values are permissible: None, adler32, crc32, md5, sha1, sha224, sha256, sha384, sha512, (default: adler32). As described in the header format, each compressed chunk can be stored with a checksum, which aids corruption detection on decompression: $ ./blpk compress --checksum crc32 data.dat
  • [-o | --no-offsets] By default, offsets to the individual chunks are stored. These are included to allow for partial decompression in the future. This option disables that feature. Also, a certain number of offsets (default: 10 * 'nchunks') are preallocated to allow for appending data to the file: $ ./blpk compress --no-offsets data.dat

Info Subcommand

If you just need some info on how the file was compressed [i | info]:

$ ./blpk info testfile.blp
blpk: 'bloscpack_header':
blpk: {   'checksum': 'adler32',
blpk:     'chunk_size': 1048576,
blpk:     'format_version': 3,
blpk:     'last_chunk': 921600,
blpk:     'max_app_chunks': 15260,
blpk:     'metadata': False,
blpk:     'nchunks': 1526,
blpk:     'offsets': True,
blpk:     'typesize': 8}
blpk: 'offsets':
blpk: [134320,354002,552182,709597,870494,...]

Adding Metdata

Using the [-m | --metadata] option you can include JSON from a file:

$ cat meta.json
{"dtype": "float64", "shape": [200000000], "container": "numpy"}
$ ./blpk compress --metadata meta.json data.dat
$ ./blpk info data.dat.blp
blpk: 'bloscpack_header':
blpk: {   'checksum': 'adler32',
blpk:     'chunk_size': 1048576,
blpk:     'format_version': 3,
blpk:     'last_chunk': 921600,
blpk:     'max_app_chunks': 15260,
blpk:     'metadata': True,
blpk:     'nchunks': 1526,
blpk:     'offsets': True,
blpk:     'typesize': 8}
blpk: 'metadata':
blpk: {   u'container': u'numpy', u'dtype': u'float64', u'shape': [200000000]}
blpk: 'metadata_header':
blpk: {   'magic_format': 'JSON',
blpk:     'max_meta_size': 590,
blpk:     'meta_checksum': 'adler32',
blpk:     'meta_codec': 'zlib',
blpk:     'meta_comp_size': 58,
blpk:     'meta_level': 6,
blpk:     'meta_options': '00000000',
blpk:     'meta_size': 59,
blpk:     'user_codec': ''}
blpk: 'offsets':
blpk: [134946,354628,552808,710223,871120,...]

It will be printed when decompressing:

$ ./blpk d data.dat.blp
blpk: Metadata is:
blpk: '{u'dtype': u'float64', u'shape': [200000000], u'container': u'numpy'}'

Appending

You can also append data to an existing bloscpack compressed file:

$ ./blpk append data.dat.blp data.dat

However there are certain limitations on the amount of data can be appended. For example, if there is an offsets section, there must be enough room to store the offsets for the appended chunks. If no offsets exists, you may append as much data as possible given the limitations governed by the maximum number of chunks and the chunk-size. Additionally, there are limitations on the compression options. For example, one cannot change the checksum used. It is however possible to change the compression level, the typesize and the shuffle option for the appended chunks.

Also note that appending is still considered experimental as of v0.5.0.

Verbose and Debug mode

Lastly there are two mutually exclusive options to control how much output is produced.

The first causes basic info to be printed, [-v | --verbose]:

$ ./blpk --verbose compress --chunk-size 0.5G data.dat
blpk: getting ready for compression
blpk: input file is: data.dat
blpk: output file is: data.dat.blp
blpk: using 8 threads
blpk: input file size: 1.49G (1600000000B)
blpk: nchunks: 3
blpk: chunk_size: 512.0M (536870912B)
blpk: output file size: 161.9M (169759818B)
blpk: compression ratio: 0.106100
blpk: done

... and [-d | --debug] prints a detailed account of what is going on:

$ ./blpk --debug compress --chunk-size 0.5G data.dat
blpk: command line argument parsing complete
blpk: command line arguments are:
blpk:   nchunks: None
blpk:   force: False
blpk:   verbose: False
blpk:   offsets: True
blpk:   checksum: adler32
blpk:   subcommand: compress
blpk:   out_file: None
blpk:   in_file: data.dat
blpk:   chunk_size: 512.0M (536870912B)
blpk:   debug: True
blpk:   shuffle: True
blpk:   typesize: 8
blpk:   clevel: 7
blpk:   nthreads: 8
blpk: getting ready for compression
blpk: blosc args are:
blpk:   typesize: 8
blpk:   shuffle: True
blpk:   clevel: 7
blpk: input file is: data.dat
blpk: output file is: data.dat.blp
blpk: using 8 threads
blpk: input file size: 1.49G (1600000000B)
blpk: 'chunk_size' proposed
blpk: nchunks: 3
blpk: chunk_size: 512.0M (536870912B)
blpk: last_chunk_size: 501.88M (526258176B)
blpk: raw_bloscpack_header: 'blpk\x02\x01\x01\x08\x00\x00\x00 \x00\x10^\x1f\x03\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
blpk: chunk '0' written, in: 512.0M (536870912B) out: 55.69M (58399001B)
blpk: checksum (adler32): '\xf7\xaa\xa3\xdf' offset: '56'
blpk: chunk '1' written, in: 512.0M (536870912B) out: 53.85M (56463343B)
blpk: checksum (adler32): '\xafo\xfe\xfd' offset: '58399061'
blpk: chunk '2' (last) written, in: 501.88M (526258176B) out: 52.35M (54897406B)
blpk: checksum (adler32): '\x91v\x07\\' offset: '114862408'
blpk: Writing '3' offsets: '[56, 58399061, 114862408]'
blpk: Raw offsets: '8\x00\x00\x00\x00\x00\x00\x00U\x19{\x03\x00\x00\x00\x00H\xa9\xd8\x06\x00\x00\x00\x00'
blpk: output file size: 161.9M (169759818B)
blpk: compression ratio: 0.106100
blpk: done

Python API

The Python API is still in flux, so this section is deliberately sparse.

Numpy

Numpy arrays can be serialized as bloscpack files, here is a very brief example:

>>> a = np.linspace(0, 1, 3e8)
>>> print a.size, a.dtype
300000000 float64
>>> bp.pack_ndarray_file(a, 'a.blp')
>>> b = bp.unpack_ndarray_file('a.blp')
>>> (a == b).all()
True

Looking at the generated file, we can see the Numpy metadata being saved:

$ lh a.blp
-rw------- 1 esc esc 266M Aug 13 23:21 a.blp
anaconda ~ esc@toolbox
$ blpk info a.blp
blpk: bloscpack header:
blpk:     format_version=3,
blpk:     offsets=True,
blpk:     metadata=True,
blpk:     checksum='adler32',
blpk:     typesize=8,
blpk:     chunk_size=1.0M (1048576B),
blpk:     last_chunk=838.0K (858112B),
blpk:     nchunks=2289,
blpk:     max_app_chunks=22890
blpk: 'metadata':
blpk: {   u'container': u'numpy',
blpk:     u'dtype': [[u'', u'<f8']],
blpk:     u'order': u'C',
blpk:     u'shape': [300000000]}
blpk: 'metadata_header':
blpk: {   'magic_format': 'JSON',
blpk:     'max_meta_size': 740,
blpk:     'meta_checksum': 'adler32',
blpk:     'meta_codec': 'zlib',
blpk:     'meta_comp_size': 68,
blpk:     'meta_level': 6,
blpk:     'meta_options': '00000000',
blpk:     'meta_size': 74,
blpk:     'user_codec': ''}
blpk: 'offsets':
blpk: [202240,408134,554982,690522,819749,...]

Alternatively, we can also use a string as storage:

>>> a = np.linspace(0, 1, 3e8)
>>> c = pack_ndarray_str(a)
>>> b = unpack_ndarray_str(c)
>>> (a == b).all()
True

Or use alternate compressors:

>>> blosc_args = DEFAULT_BLOSC_ARGS
>>> blosc_args['cname'] = 'lz4'
>>> a = np.linspace(0, 1, 3e8)
>>> c = pack_ndarray_str(a, blosc_args=blosc_args)
>>> b = unpack_ndarray_str(c)
>>> (a == b).all()
True

Testing

Installing Dependencies

Testing requires some additional libraries, which you can install from PyPi with:

$ pip install -r test_requirements.txt
[...]

Basic Tests

Basic tests, runs quickly:

$ nosetests test_bloscpack.py
[...]

Or, alternatively:

$ ./test_bloscpack.py
[...]

Heavier Tests

Extended tests using a larger file, may take some time, but will be nice to memory:

$ nosetests test_bloscpack.py:pack_unpack_hard
[...]

Extended tests using a huge file. This one take forever and needs loads (5G-6G) of memory and loads of disk-space (10G). Use -s to print progress:

$ nosetests -s test_bloscpack.py:pack_unpack_extreme
[...]

Note that, some compression/decompression tests create temporary files (on UNIXoid systems this is under /tmp/blpk*) which are deleted upon completion of the respective test, both successful and unsuccessful, or when the test is aborted with e.g. ctrl-c (using atexit magic).

Under rare circumstances, for example when aborting the deletion which is triggered on abort you may be left with large files polluting your temporary space. Depending on your partitioning scheme etc.. doing this repeatedly, may lead to you running out of space on the file-system.

Command Line Interface Tests

The command line interface is tested with cram:

$ ./test_bloscpack.cram
[...]

Test Runner

To run the command line interface tests and the unit tests and analyse coverage, use the convenience test runner:

$ ./test
[...]

Coverage

To determine coverage you can pool togeher the coverage from the cram tests and the unit tests:

$ COVERAGE=1 ./test_bloscpack.cram
[...]
$nosetests test_bloscpack.py --with-coverage --cover-package=bloscpack
[...]

Benchmark

Using the provided bench/blpk_vs_gzip.py script on a Intel(R) Core(TM) i7-3667U CPU @ 2.00GHz CPU with 2 cores and 4 threads (active hyperthreading), cpu frequency scaling activated but set to the performance governor (all cores scaled to 2.0 GHz), 8GB of DDR3 memory and a Luks encrypted SSD, we get:

$ PYTHONPATH=. ./bench/blpk_vs_gzip.py
create the test data..........done

Input file size: 1.49G
Will now run bloscpack...
Time: 2.06 seconds
Output file size: 198.55M
Ratio: 7.69
Will now run gzip...
Time: 134.20 seconds
Output file size: 924.05M
Ratio: 1.65

As was expected from previous benchmarks of Blosc using the python-blosc bindings, Blosc is both much faster and has a better compression ratio for this kind of structured data. One thing to note here, is that we are not dropping the system file cache after every step, so the file to read will be cached in memory. To get a more accurate picture we can use the --drop-caches switch of the benchmark which requires you however, to run the benchmark as root, since dropping the caches requires root privileges:

$ PYTHONPATH=. ./bench/blpk_vs_gzip.py --drop-caches
will drop caches
create the test data..........done

Input file size: 1.49G
Will now run bloscpack...
Time: 13.49 seconds
Output file size: 198.55M
Ratio: 7.69
Will now run gzip...
Time: 137.49 seconds
Output file size: 924.05M
Ratio: 1.65

Bloscpack Format

The input is split into chunks since a) we wish to put less stress on main memory and b) because Blosc has a buffer limit of 2GB (Version 1.0.0 and above). By default the chunk-size is a moderate 1MB which should be fine, even for less powerful machines.

In addition to the chunks some additional information must be added to the file for housekeeping:

header:a 32 bit header containing various pieces of information
meta:a variable length metadata section, may contain user data
offsets:a variable length section containing chunk offsets
chunk:the blosc chunk(s)
checksum:a checksum following each chunk, if desired

The layout of the file is then:

|-header-|-meta-|-offsets-|-chunk-|-checksum-|-chunk-|-checksum-|...|

Description of the header

The following 32 bit header is used for Bloscpack as of version 0.3.0. The design goals of the header format are to contain as much information as possible to achieve interesting things in the future and to be as general as possible such that the persistence layer of tools such as CArray and Blaze can be implemented without modifcation of the header format.

The following ASCII representation shows the layout of the header:

|-0-|-1-|-2-|-3-|-4-|-5-|-6-|-7-|-8-|-9-|-A-|-B-|-C-|-D-|-E-|-F-|
| b   l   p   k | ^ | ^ | ^ | ^ |   chunk-size  |  last-chunk   |
                  |   |   |   |
      version ----+   |   |   |
      options --------+   |   |
     checksum ------------+   |
     typesize ----------------+

|-0-|-1-|-2-|-3-|-4-|-5-|-6-|-7-|-8-|-9-|-A-|-B-|-C-|-D-|-E-|-F-|
|            nchunks            |        max-app-chunks         |

The first 4 bytes are the magic string blpk. Then there are 4 bytes which hold information about the activated features in this file. This is followed by 4 bytes for the chunk-size, another 4 bytes for the last-chunk-size, 8 bytes for the number of chunks, nchunks and lastly 8 bytes for the total number of chunks that can be appended to this file, max-app-chunks.

Effectively, storing the number of chunks as a signed 8 byte integer, limits the number of chunks to 2**63-1 = 9223372036854775807, but this should not be relevant in practice, since, even with the moderate default value of 1MB for chunk-size, we can still store files as large as 8ZB (!) Given that in 2012 the maximum size of a single file in the Zettabye File System (zfs) is 16EB, Bloscpack should be safe for a few more years.

Description of the header entries

All entries are little-endian.

version:

(uint8) format version of the Bloscpack header, to ensure exceptions in case of forward incompatibilities.

options:

(bitfield) A bitfield which allows for setting certain options in this file.

bit 0 (0x01):If the offsets to the chunks are present in this file.
bit 1 (0x02):If metadata is present in this file.
checksum:

(uint8) The checksum used. The following checksums, available in the python standard library should be supported. The checksum is always computed on the compressed data and placed after the chunk.

0:no checksum
1:zlib.adler32
2:zlib.crc32
3:hashlib.md5
4:hashlib.sha1
5:hashlib.sha224
6:hashlib.sha256
7:hashlib.sha384
8:hashlib.sha512
typesize:

(uint8) The typesize of the data in the chunks. Currently, assume that the typesize is uniform. The space allocated is the same as in the Blosc header.

chunk-size:

(int32) Denotes the chunk-size. Since the maximum buffer size of Blosc is 2GB having a signed 32 bit int is enough (2GB = 2**31 bytes). The special value of -1 denotes that the chunk-size is unknown or possibly non-uniform.

last-chunk:

(int32) Denotes the size of the last chunk. As with the chunk-size an int32 is enough. Again, -1 denotes that this value is unknown.

nchunks:

(int64) The total number of chunks used in the file. Given a chunk-size of one byte, the total number of chunks is 2**63. This amounts to a maximum file-size of 8EB (8EB = 2*63 bytes) which should be enough for the next couple of years. Again, -1 denotes that the number of is unknown.

max-app-chunks:

(int64) The maximum number of chunks that can be appended to this file, excluding nchunks. This is only useful if there is an offsets section and if nchunks is known (not -1), if either of these conditions do not apply this should be 0.

The overall file-size can be computed as chunk-size * (nchunks - 1) + last-chunk-size. In a streaming scenario -1 can be used as a placeholder. For example if the total number of chunks, or the size of the last chunk is not known at the time the header is created.

The following constraints exist on the header entries:

  • last-chunk must be less than or equal to chunk-size.
  • nchunks + max_app_chunks must be less than or equal to the maximum value of an int64.

Description of the metadata section

This section goes after the header. It consists of a metadata-section header followed by a serialized and potentially compressed data section, followed by preallocated space to resize the data section, possibly followed by a checksum.

The layout of the section is thus:

|-metadata-header-|-data-|-prealloc-|-checksum-|

The header has the following layout:

|-0-|-1-|-2-|-3-|-4-|-5-|-6-|-7-|-8-|-9-|-A-|-B-|-C-|-D-|-E-|-F-|
|         magic-format          | ^ | ^ | ^ | ^ |   meta-size   |
                                  |   |   |   |
              meta-options -------+   |   |   |
              meta-checksum ----------+   |   |
              meta-codec -----------------+   |
              meta-level ---------------------+

|-0-|-1-|-2-|-3-|-4-|-5-|-6-|-7-|-8-|-9-|-A-|-B-|-C-|-D-|-E-|-F-|
| max-meta-size |meta-comp-size |            user-codec         |
magic-format:

(8 byte ASCII string) The data will usually be some kind of binary serialized string data, for example JSON, BSON, YAML or Protocol-Buffers. The format identifier is to be placed in this field.

meta-options:

(bitfield) A bitfield which allows for setting certain options in this metadata section. Currently unused

meta-checksum:

The checksum used for the metadata. The same checksums as for the data are available.

meta-codec:

(unit8) The codec used for compressing the metadata. As of Bloscpack version 0.3.0 the following codecs are supported.

0:no codec
1:zlib (DEFLATE)
meta-level:

(unit8) The compression level used for the codec. If codec is 0 i.e. the metadata is not compressed, this must be 0 too.

meta-size:

(uint32) The size of the uncompressed metadata.

max-meta-size:

(uint32) The total allocated space for the data section.

meta-comp-size:

(uint32) If the metadata is compressed, this gives the total space the metadata occupies. If the data is not compressed this is the same as meta-size. In a sense this is the true amount of space in the metadata section that is used.

user-codec:

Space reserved for usage of additional codecs. E.g. 4 byte magic string for codec identification and 4 bytes for encoding of codec parameters.

The total space left for enlarging the metadata section is simply: max-meta-size - meta-comp-size.

JSON Example of serialized metadata:

'{"dtype": "float64", "shape": [1024], "others": []}'

If compression is requested, but not beneficial, because the compressed size would be larger than the uncompressed size, compression of the metadata is automatically deactivated.

As of Bloscpack version 0.3.0 only the JSON serializer is supported and used the string JSON followed by four whitespace bytes as identifier. Since JSON and any other of the suggested serializers has limitations, only a subset of Python structures can be stored, so probably some additional object handling must be done prior to serialize certain kinds of metadata.

Description of the offsets entries

Following the metadata section, comes a variable length section of chunk offsets. Offsets of the chunks into the file are to be used for accelerated seeking. The offsets (if activated) follow the header. Each offset is a 64 bit signed little-endian integer (int64). A value of -1 denotes an unknown offset. Initially, all offsets should be initialized to -1 and filled in after writing all chunks. Thus, If the compression of the file fails prematurely or is aborted, all offsets should have the value -1. Also, any unused offset entries preallocated to allow the file to grow should be set to -1. Each offset denotes the exact position of the chunk in the file such that seeking to the offset, will position the file pointer such that, reading the next 16 bytes gives the Blosc header, which is at the start of the desired chunk.

Description of the chunk format

As mentioned previously, each chunk is just a Blosc compressed string including header. The Blosc header (as of v1.0.0) is 16 bytes as follows:

|-0-|-1-|-2-|-3-|-4-|-5-|-6-|-7-|-8-|-9-|-A-|-B-|-C-|-D-|-E-|-F-|
  ^   ^   ^   ^ |     nbytes    |   blocksize   |    ctbytes    |
  |   |   |   |
  |   |   |   +--typesize
  |   |   +------flags
  |   +----------versionlz
  +--------------version

The first four are simply bytes, the last three are are each unsigned ints (uint32) each occupying 4 bytes. The header is always little-endian. ctbytes is the length of the buffer including header and nbytes is the length of the data when uncompressed. A more detailed description of the Blosc header can be found in the README_HEADER.rst of the Blosc repository

Overhead

Depending on which configuration for the file is used a constant, or linear overhead may be added to the file. The Bloscpack header adds 32 bytes in any case. If the data is non-compressible, Blosc will add 16 bytes of header to each chunk. The metadata section obviously adds a constant overhead, and if used, both the checksum and the offsets will add overhead to the file. The offsets add 8 bytes per chunk and the checksum adds a fixed constant value which depends on the checksum to each chunk. For example, 32 bytes for the adler32 checksum.

Coding Conventions

  • Numpy rst style docstrings
  • README cli examples should use long options
  • testing: expected before received nt.assert_equal(expected, received)
  • Debug messages: as close to where the data was generated
  • Single quotes around ambiguities in messages overwriting existing file: 'testfile'
  • Exceptions instead of exit
  • nose-parametrized for parameterized tests

Maintainers Notes on Cutting a Release

  1. Update the changelog
  2. Set the version number in bloscpack.py
  3. Commit with git commit -m "$VERSION"
  4. Make the tag using git tag -s -m "Bloscpack $VERSION" $VERSION
  5. Push the tag to Blosc github git push blosc $VERSION
  6. Push the tag to own github git push esc $VERSION
  7. Upload tp PyPi using python setup.py sdist upload
  8. Bump version number to next dev version
  9. Announce release on the Blosc list
  10. Announce release via Twitter

TODO

  • list prior art
  • quiet verbosity level
  • possibly provide a BloscPackFile abstraction, like GzipFile
  • document library usage
  • Expose the ability to set 'max_app_chunks' from the command line
  • Allow to save metadata to a file during decompression
  • Allow to not-prealloc additional space for metadata
  • Refactor certain collections of functions that operate on data into objects
    • BloscHeader
    • MetadataHeader
    • Offsets (maybe)
  • subcommand e or estimate to estimate the size of the uncompressed data.
  • subcommand v or verify to verify the integrity of the data
  • partial decompression?
  • add --raw-input and --raw-output switches to allow stuff like: cat file | blpk --raw-input --raw-output compress > file.blp
  • since we now have potentially small chunks, the progressbar becomes relevant again
  • configuration file to store commonly used options on a given machine
  • check Python 3.x compatibility
  • make a note in the README that the chunk-size benchmark can be used to tune
  • print the compression time, either as verbose or debug
  • Announcement RST
  • Announce on scipy/numpy lists, comp.compression, freshmeat, ohloh ...
  • Debian packages (for python-blosc and bloscpack)
  • Establish and document proper exit codes
  • Use tox for testing multiple python versions
  • Investigate if we can use a StringIO object that returns memoryviews on read.
  • Implement a memoryview Compressed/PlainSource
  • Use a bytearray to read chunks from a file. Then re-use that bytearray during every read to avoid allocating deallocating strings the whole time.
  • Document the metadata saved during Numpy serialization
  • The keyword arguments to many functions are global dicts, this is a bad idea, Make the immutable with a forzendict.
  • Check that source and sink are of the correct type
  • Use more of nose-parametrized
  • Use the faster version of struct where you have a single string
  • Memory profiler, might be able to reduce memory used by reusing the buffer during compression and decompression
  • Benchmark different codecs

Changelog

  • v0.5.1 - Sat Feb 22 2014
    • Documentation fixes and improvements
  • v0.5.0 - Sun Feb 02 2014
  • v0.5.0-rc1 - Thu Jan 30 2014
    • Support for Blosc 1.3.x (alternative codecs)
  • v0.4.1 - Fri Sep 27 2013
    • Fixed the pack_unpack_hard test suite
    • Fixed handling Numpy record and nested record arrays
  • v0.4.0 - Sun Sep 15 2013
    • Fix a bug when serializing numpy arrays to strings
  • v0.4.0-rc2 - Tue Sep 03 2013
    • Package available via PyPi (since 0.4.0-rc1)
    • Support for packing/unpacking numpy arrays to/from string
    • Check that string and record arrays work
    • Fix installation problems with PyPi package (Thanks to Olivier Grisel)
  • v0.4.0-rc1 - Sun Aug 18 2013
    • BloscpackHeader class introduced
    • The info subcommand shows human readable sizes when printing the header
    • Now using Travis-CI for testing and Coveralls for coverage
    • Further work on the Plain/Compressed-Source/Sink abstractions
    • Start using memoryview in places
    • Learned to serialize Numpy arrays
  • v0.3.0 - Sun Aug 04 2013
    • Minor readme fixes
    • Increase number of cram tests
  • v0.3.0-rc1 - Thu Aug 01 2013
    • Bloscpack format changes (format version 3)
      • Variable length metadata section with it's own header
      • Ability to preallocate offsets for appending data (max_app_chunks)
    • Refactor compression and decompression to use file pointers instead of file name strings, allows using StringIO/cStringIO.
    • Sanitize calculation of nchunks and chunk-size
    • Special keyword max for use with chunk-size in the CLI
    • Support appending to a file and append subcommand (including the ability to preallocate offsets)
    • Support rudimentary info subcommand
    • Add tests of the command line interface using cram
    • Minor bugfixes and corrections as usual
  • v0.2.1 - Mon Nov 26 2012
    • Backport to Python 2.6
    • Typo fixes in documentation
  • v0.2.0 - Fri Sep 21 2012
    • Use atexit magic to remove test data on abort
    • Change prefix of temp directory to /tmp/blpk*
    • Merge header RFC into monolithic readme
  • v0.2.0-rc2 - Tue Sep 18 2012
    • Don't bail out if the file is smaller than default chunk
    • Set the default typesize to 8 bytes
    • Upgrade dependencies to python-blosc v1.0.5 and fix tests
    • Make extreme test less resource intensive
    • Minor bugfixes and corrections
  • v0.2.0-rc1 - Thu Sep 13 2012
    • Implement new header format as described in RFC
    • Implement checksumming compressed chunks with various checksums
    • Implement offsets of the chunks into the file
    • Efforts to make the library re-entrant, better control of side-effects
    • README is now rst not md (flirting with sphinx)
    • Tons of trivial fixes, typos, wording, refactoring, renaming, pep8 etc..
  • v0.1.1 - Sun Jul 15 2012
    • Fix the memory issue with the tests
    • Two new suites: hard and extreme
    • Minor typo fixes and corrections
  • v0.1.0 - Thu Jun 14 2012
    • Freeze the first 8 bytes of the header (hopefully for ever)
    • Fail to decompress on non-matching format version
    • Minor typo fixes and corrections
  • v0.1.0-rc3 - Tue Jun 12 2012
    • Limit the chunk-size benchmark to a narrower range
    • After more careful experiments, a default chunk-size of 1MB was deemed most appropriate
    • Fixed a terrible bug, where during testing and benchmarking, temporary files were not removed, oups...
    • Adapted the header to have space for more chunks, include special marker for unknown chunk number (-1) and format version of the compressed file
    • Added a note in the README about instability of the file format
    • Various minor fixes and enhancements
  • v0.1.0-rc2 - Sat Jun 09 2012
    • Default chunk-size now 4MB
    • Human readable chunk-size argument
    • Last chunk now contains remainder
    • Pure python benchmark to compare against gzip
    • Benchmark to measure the effect of chunk-size
    • Various minor fixes and enhancements
  • v0.1.0-rc1 - Sun May 27 2012
    • Initial version
    • Compression/decompression
    • Command line argument parser
    • README, setup.py, tests and benchmark

Thanks

  • Fracesc Alted for writing Blosc in the first place, for providing continual code-review and feedback on Bloscpack and for co-authoring the Bloscpack file-format specification.
 
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