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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.
https://tiledbsoma.readthedocs.io
MIT License
90 stars 25 forks source link

Add PointCloud class and use in Visium ingestor #2924

Closed jp-dark closed 1 month ago

jp-dark commented 1 month ago

This adds in the PointCloud class and a super class called SpatialDataFrame to the spatial prototype. A lot of the code in this PR is duplicated from the DataFrame class and will be DRY-ed up before the alpha release.

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 28.63071% with 172 lines in your changes missing coverage. Please review.

Project coverage is 82.18%. Comparing base (7ad657b) to head (d48fd3d). Report is 1 commits behind head on spatial.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## spatial #2924 +/- ## =========================================== - Coverage 84.96% 82.18% -2.78% =========================================== Files 42 44 +2 Lines 4356 4592 +236 =========================================== + Hits 3701 3774 +73 - Misses 655 818 +163 ``` | [Flag](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2924/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/2924/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `82.18% <28.63%> (-2.78%)` | :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/2924/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/2924/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `82.18% <28.63%> (-2.78%)` | :arrow_down: | | [libtiledbsoma](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2924/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `∅ <ø> (∅)` | |