Python-Blosc2#

A Python wrapper for the extremely fast Blosc2 compression library#

Author:

The Blosc development team

Contact:

blosc@blosc.org

Github:

Blosc/python-blosc2

Actions:

actions

PyPi:

version

NumFOCUS:

numfocus

Code of Conduct:

Contributor Covenant

What it is#

C-Blosc2 is the new major version of C-Blosc, and is backward compatible with both the C-Blosc1 API and its in-memory format. Python-Blosc2 is a Python package that wraps C-Blosc2, the newest version of the Blosc compressor.

Currently Python-Blosc2 already reproduces the API of Python-Blosc, so it can be used as a drop-in replacement. However, there are a few exceptions for a full compatibility.

In addition, Python-Blosc2 aims to leverage the new C-Blosc2 API so as to support super-chunks, multi-dimensional arrays (NDArray), serialization and other bells and whistles introduced in C-Blosc2. Although this is always and endless process, we have already catch up with most of the C-Blosc2 API capabilities.

Note: Python-Blosc2 is meant to be backward compatible with Python-Blosc data. That means that it can read data generated with Python-Blosc, but the opposite is not true (i.e. there is no forward compatibility).

SChunk: a 64-bit compressed store#

SChunk is the simple data container that handles setting, expanding and getting data and metadata. Contrarily to chunks, a super-chunk can update and resize the data that it contains, supports user metadata, and it does not have the 2 GB storage limitation.

Additionally, you can convert a SChunk into a contiguous, serialized buffer (aka cframe) and vice-versa; as a bonus, the serialization/deserialization process also works with NumPy arrays and PyTorch/TensorFlow tensors at a blazing speed:

Compression speed for different codecs

Decompression speed for different codecs

while reaching excellent compression ratios:

Compression ratio for different codecs

Also, if you are a Mac M1/M2 owner, make you a favor and use its native arm64 arch (yes, we are distributing Mac arm64 wheels too; you are welcome ;-):

Compression speed for different codecs on Apple M1

Decompression speed for different codecs on Apple M1

Read more about SChunk features in our blog entry at: https://www.blosc.org/posts/python-blosc2-improvements

NDArray: an N-Dimensional store#

One of the latest and more exciting additions in Python-Blosc2 is the NDArray object. It can write and read n-dimensional datasets in an extremely efficient way thanks to a n-dim 2-level partitioning, allowing to slice and dice arbitrary large and compressed data in a more fine-grained way:

https://github.com/Blosc/python-blosc2/blob/main/images/b2nd-2level-parts.png?raw=true

To wet you appetite, here it is how the NDArray object performs on getting slices orthogonal to the different axis of a 4-dim dataset:

https://github.com/Blosc/python-blosc2/blob/main/images/Read-Partial-Slices-B2ND.png?raw=true

We have blogged about this: https://www.blosc.org/posts/blosc2-ndim-intro

We also have a ~2 min explanatory video on why slicing in a pineapple-style (aka double partition) is useful:

Slicing a dataset in pineapple-style

Installing#

Blosc is now offering Python wheels for the main OS (Win, Mac and Linux) and platforms. You can install binary packages from PyPi using pip:

pip install blosc2

Documentation#

The documentation is here:

https://blosc.org/python-blosc2/python-blosc2.html

Also, some examples are available on:

Blosc/python-blosc2

Building from sources#

python-blosc2 comes with the C-Blosc2 sources with it and can be built in-place:

git clone https://github.com/Blosc/python-blosc2/
cd python-blosc2
git submodule update --init --recursive
python -m pip install -r requirements-build.txt
python setup.py build_ext --inplace

That’s all. You can proceed with testing section now.

Testing#

After compiling, you can quickly check that the package is sane by running the tests:

python -m pip install -r requirements-tests.txt
python -m pytest  (add -v for verbose mode)

Benchmarking#

If curious, you may want to run a small benchmark that compares a plain NumPy array copy against compression through different compressors in your Blosc build:

PYTHONPATH=. python bench/pack_compress.py

License#

The software is licenses under a 3-Clause BSD license. A copy of the python-blosc2 license can be found in LICENSE.txt.

Mailing list#

Discussion about this module is welcome in the Blosc list:

blosc@googlegroups.com

https://groups.google.es/group/blosc

Twitter#

Please follow @Blosc2 to get informed about the latest developments.

Enjoy data!

Contents#