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[python] Use bindings for SparseNDArray readpath#2133

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nguyenv merged 4 commits intomainfrom
viviannguyen/use-bindings-for-sparse-ndarray
Feb 27, 2024
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[python] Use bindings for SparseNDArray readpath#2133
nguyenv merged 4 commits intomainfrom
viviannguyen/use-bindings-for-sparse-ndarray

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@nguyenv
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@nguyenv nguyenv commented Feb 13, 2024

Issue and/or context:

#2077

Changes:

Use clib.SparseNDArray for read path, replacing usage of tiledb.Array.

These changes were picked out of #1817.

Notes for Reviewer:

These changes are on top of #2132.

@nguyenv nguyenv linked an issue Feb 13, 2024 that may be closed by this pull request
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codecov Bot commented Feb 13, 2024

Codecov Report

Merging #2133 (85f188e) into main (e74810a) will decrease coverage by 6.60%.
The diff coverage is 0.00%.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #2133      +/-   ##
==========================================
- Coverage   78.65%   72.05%   -6.60%     
==========================================
  Files         136      102      -34     
  Lines       10666     6881    -3785     
  Branches      215      215              
==========================================
- Hits         8389     4958    -3431     
+ Misses       2178     1824     -354     
  Partials       99       99              
Flag Coverage Δ
libtiledbsoma 67.54% <0.00%> (-0.03%) ⬇️
python ?
r 74.68% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Components Coverage Δ
python_api ∅ <ø> (∅)
libtiledbsoma 48.75% <0.00%> (-0.04%) ⬇️

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nguyenv commented Feb 21, 2024

Needs to be updated to use SOMAContext once #2158 is merged.

@nguyenv nguyenv force-pushed the viviannguyen/use-bindings-for-dense-ndarray branch from 229e297 to a185f8a Compare February 23, 2024 17:33
@nguyenv nguyenv force-pushed the viviannguyen/use-bindings-for-sparse-ndarray branch 2 times, most recently from 06bcbe9 to e60bb37 Compare February 23, 2024 20:07
@nguyenv nguyenv force-pushed the viviannguyen/use-bindings-for-dense-ndarray branch from d0a2f6c to 7185a5e Compare February 23, 2024 21:56
@nguyenv nguyenv force-pushed the viviannguyen/use-bindings-for-sparse-ndarray branch 3 times, most recently from c1a78b0 to 7a0c6b2 Compare February 24, 2024 00:41
Base automatically changed from viviannguyen/use-bindings-for-dense-ndarray to main February 24, 2024 12:57
@nguyenv nguyenv force-pushed the viviannguyen/use-bindings-for-sparse-ndarray branch from 7a0c6b2 to 41efdf7 Compare February 24, 2024 15:14
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nguyenv commented Feb 26, 2024

This is ready for review.

Comment thread apis/python/src/tiledbsoma/_sparse_nd_array.py Outdated
Comment thread apis/python/src/tiledbsoma/soma_object.cc Outdated
@nguyenv nguyenv merged commit 2310054 into main Feb 27, 2024
@nguyenv nguyenv deleted the viviannguyen/use-bindings-for-sparse-ndarray branch February 27, 2024 00:36
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[sc-40220]

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[python] Use SOMASparseNDArray bindings in class SparseNDArray

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