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single-cell-data / TileDB-SOMA

Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.
MIT License
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[python] Deprecate `tiledb_ctx` usage in `TileDBSOMAContext` #2693

Closed nguyenv closed 1 month ago

nguyenv commented 1 month ago

Issue and/or context:

[sc-49124]

Deprecating usage of tiledb.Ctx for users is necessary for the complete removal of tiledb-py. Internally, the codebase now passes around a TileDBSOMAContext.native_context which is a C++ SOMAContext binding. We no longer use tiledb.Ctx anywhere.

Changes:

Notes for Reviewer:

I have set the deprecation for 1.14.

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 86.36364% with 3 lines in your changes missing coverage. Please review.

Project coverage is 90.17%. Comparing base (54e3b8c) to head (8d59689).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #2693 +/- ## ========================================== + Coverage 90.16% 90.17% +0.01% ========================================== Files 37 37 Lines 4005 4022 +17 ========================================== + Hits 3611 3627 +16 - Misses 394 395 +1 ``` | [Flag](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2693/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/2693/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `90.17% <86.36%> (+0.01%)` | :arrow_up: | 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/2693/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/2693/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `90.17% <86.36%> (+0.01%)` | :arrow_up: | | [libtiledbsoma](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2693/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `∅ <ø> (∅)` | |