single-cell-data / TileDB-SOMA

Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.
https://tiledbsoma.readthedocs.io
MIT License
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[python] Move `SOMAGroup` to use C++ bindings #2675

Closed nguyenv closed 2 months ago

nguyenv commented 3 months ago

Issue and/or context:

https://github.com/single-cell-data/TileDB-SOMA/issues/2674

These changes are applied on top of https://github.com/single-cell-data/TileDB-SOMA/pull/2508

Changes:

Notes for Reviewer:

Although SOMAArray and SOMAGroup now fully use the C++ bindings, there's still areas of the code that use tiledb-py and need to be replaced in a follow up PR. For example, we use tiledb.VFS in several areas.

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 95.91837% with 4 lines in your changes missing coverage. Please review.

Project coverage is 89.89%. Comparing base (eab6557) to head (1ade53f).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #2675 +/- ## ========================================== - Coverage 89.91% 89.89% -0.03% ========================================== Files 37 37 Lines 4026 3987 -39 ========================================== - Hits 3620 3584 -36 + Misses 406 403 -3 ``` | [Flag](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2675/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | Coverage Δ | | |---|---|---| | [python](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2675/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `89.89% <95.91%> (-0.03%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data#carryforward-flags-in-the-pull-request-comment) to find out more. | [Components](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2675/components?src=pr&el=components&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | Coverage Δ | | |---|---|---| | [python_api](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2675/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `89.89% <95.91%> (-0.03%)` | :arrow_down: | | [libtiledbsoma](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2675/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `∅ <ø> (∅)` | |
nguyenv commented 2 months ago

The changes in this PR are now encompassed by: