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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
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[r] Implement missing `domain` argument to `DataFrame` `create` #3032

Closed johnkerl closed 2 weeks ago

johnkerl commented 3 weeks ago

Issue and/or context: As tracked on issue #2407 / [sc-51048]. Fixes #2967 / [sc-55657].

Changes:

As a legacy R/Python-parity issue, the domain argument to SOMADataFrame's create -- from the SOMA spec -- was never implemented in R. Here we remedy that.

Notes for Reviewer:

This PR is a work in progress. It is not ready for review.

Unit-test cases are not yet implemented.

johnkerl commented 3 weeks ago

~I have one more bug to fix in CI -- it's a KP~ 🙏

Update: fixed

codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 50.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 88.98%. Comparing base (2f6c442) to head (1531119). Report is 5 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #3032 +/- ## ========================================== - Coverage 89.02% 88.98% -0.04% ========================================== Files 45 45 Lines 4284 4287 +3 ========================================== + Hits 3814 3815 +1 - Misses 470 472 +2 ``` | [Flag](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3032/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/3032/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `88.98% <50.00%> (-0.04%)` | :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/3032/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/3032/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `88.98% <50.00%> (-0.04%)` | :arrow_down: | | [libtiledbsoma](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3032/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `∅ <ø> (∅)` | |
johnkerl commented 2 weeks ago

Oops, my bad @mojaveazure ! https://github.com/single-cell-data/TileDB-SOMA/pull/3032/commits/e7a2e7458aec66e724f2eb0b1be71f7f1e5eeed7