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Proof of concept for depending on external blosc python package #571

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dstansby
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@dstansby dstansby commented Aug 31, 2024

This is a proof of concept for depending on the blosc Python package for blosc compression, instead of using the sources we build ourselves. The goal here is to proove it's possible in as few as lines as possible.

If we go ahead with this we would need to first deprecate the following functions in numcodecs.blosc before the replacement could be done:

[
'destroy',
'init',
'compname_to_compcode',
'cbuffer_sizes',
'cbuffer_metainfo',
'err_bad_cname',
'decompress_partial'
]

TODO:

  • Unit tests and/or doctests in docstrings
  • Tests pass locally
  • Docstrings and API docs for any new/modified user-facing classes and functions
  • Changes documented in docs/release.rst
  • Docs build locally
  • GitHub Actions CI passes
  • Test coverage to 100% (Codecov passes)

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codecov bot commented Aug 31, 2024

Codecov Report

Attention: Patch coverage is 91.02564% with 7 lines in your changes missing coverage. Please review.

Project coverage is 98.17%. Comparing base (2a7bf9c) to head (44f1c36).
Report is 3 commits behind head on main.

Files with missing lines Patch % Lines
numcodecs/blosc.py 90.14% 7 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #571      +/-   ##
==========================================
- Coverage   99.91%   98.17%   -1.75%     
==========================================
  Files          59       60       +1     
  Lines        2334     2353      +19     
==========================================
- Hits         2332     2310      -22     
- Misses          2       43      +41     
Files with missing lines Coverage Δ
numcodecs/__init__.py 100.00% <ø> (ø)
numcodecs/tests/test_blosc.py 100.00% <100.00%> (ø)
numcodecs/blosc.py 90.14% <90.14%> (ø)

... and 1 file with indirect coverage changes

@d-v-b
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d-v-b commented Sep 1, 2024

looking back at the commit history, it seems like blosc has been vendored in this repo for a very long time. @alimanfoo and / or @jakirkham what do you think about this PR?

@normanrz
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normanrz commented Nov 9, 2024

Since we are using the zstd and lz4 code from within the c-blosc repo, how would we deliver those codecs when using the blosc wheels?

@alimanfoo
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Hi @dstansby, this was a while ago now but IIRC part of the original motivation for vendoring was to be able to minimise memory copies. So maybe worth a check on whether using the Python blosc package would introduce any extra memory copies.

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4 participants