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chanzuckerberg / cellxgene-census

CZ CELLxGENE Discover Census
https://chanzuckerberg.github.io/cellxgene-census/
MIT License
78 stars 20 forks source link

[python] New embeddings API #1023

Closed ebezzi closed 5 months ago

ebezzi commented 6 months ago

New embeddings API. Provides a unified access pattern to embeddings (regardless of whether they're collaboration or hosted) through get_anndata.

metakuni commented 6 months ago

Sorry, my clumsy fingers clicked the wrong button!

codecov[bot] commented 5 months ago

Codecov Report

Attention: Patch coverage is 93.26425% with 13 lines in your changes are missing coverage. Please review.

Project coverage is 82.32%. Comparing base (a5dbdef) to head (520941e). Report is 2 commits behind head on main.

Files Patch % Lines
...us/src/cellxgene_census/experimental/_embedding.py 87.09% 8 Missing :warning:
...hon/cellxgene_census/src/cellxgene_census/_util.py 71.42% 2 Missing :warning:
...xgene_census/tests/experimental/test_embeddings.py 95.23% 2 Missing :warning:
...lxgene_census/src/cellxgene_census/_get_anndata.py 96.55% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #1023 +/- ## ========================================== + Coverage 81.33% 82.32% +0.99% ========================================== Files 73 74 +1 Lines 5566 5714 +148 ========================================== + Hits 4527 4704 +177 + Misses 1039 1010 -29 ``` | [Flag](https://app.codecov.io/gh/chanzuckerberg/cellxgene-census/pull/1023/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=chanzuckerberg) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/chanzuckerberg/cellxgene-census/pull/1023/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=chanzuckerberg) | `82.32% <93.26%> (+0.99%)` | :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=chanzuckerberg#carryforward-flags-in-the-pull-request-comment) to find out more.

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ebezzi commented 5 months ago

@ebezzi have you considered the convenience API to get all available Census version for a given embedding name?

@pablo-gar get_all_census_versions_with_embedding that would be the function.