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[python] Use bindings for DenseNDArray readpath#2132

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nguyenv merged 9 commits intomainfrom
viviannguyen/use-bindings-for-dense-ndarray
Feb 24, 2024
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[python] Use bindings for DenseNDArray readpath#2132
nguyenv merged 9 commits intomainfrom
viviannguyen/use-bindings-for-dense-ndarray

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@nguyenv nguyenv commented Feb 13, 2024

Issue and/or context:

#2078

Changes:

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

These changes were picked out of #1817.

Notes for Reviewer:

These changes are on top of #2129.

@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 #2132 (a8c3836) into main (05e9592) will decrease coverage by 6.65%.
The diff coverage is 100.00%.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #2132      +/-   ##
==========================================
- Coverage   78.63%   71.99%   -6.65%     
==========================================
  Files         136      102      -34     
  Lines       10653     6880    -3773     
  Branches      215      215              
==========================================
- Hits         8377     4953    -3424     
+ Misses       2177     1827     -350     
- Partials       99      100       +1     
Flag Coverage Δ
libtiledbsoma 67.37% <100.00%> (-0.27%) ⬇️
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 48.79% <100.00%> (+0.04%) ⬆️

Base automatically changed from viviannguyen/add-pybind11-ndarray-bindings to main February 15, 2024 19:15
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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
Comment thread apis/python/src/tiledbsoma/_tdb_handles.py Outdated
Comment thread apis/python/src/tiledbsoma/_tdb_handles.py Outdated
Comment thread apis/python/src/tiledbsoma/_tdb_handles.py Outdated
@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-dense-ndarray branch from ca77ace to 614d886 Compare February 23, 2024 22:15
Comment thread apis/python/src/tiledbsoma/_dense_nd_array.py Outdated
Comment thread apis/python/src/tiledbsoma/_dense_nd_array.py Outdated
Comment thread apis/python/src/tiledbsoma/_tdb_handles.py Outdated
Comment thread apis/python/src/tiledbsoma/_tiledb_object.py Outdated
@nguyenv nguyenv merged commit e74810a into main Feb 24, 2024
@nguyenv nguyenv deleted the viviannguyen/use-bindings-for-dense-ndarray branch February 24, 2024 12:57
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[python] Use SOMADenseNDArray bindings in class DenseNDArray

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