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chanzuckerberg / cellxgene-census

CZ CELLxGENE Discover Census
https://chanzuckerberg.github.io/cellxgene-census/
MIT License
72 stars 19 forks source link

[builder] cellxgene_ontology_guide integration #1094

Closed ebezzi closed 3 months ago

ebezzi commented 3 months ago

Integrate cellxgene_ontology_guide in place of the old TissueMapper.

codecov[bot] commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 91.12%. Comparing base (07d0f43) to head (cbf7187). Report is 1 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #1094 +/- ## ======================================= Coverage 91.12% 91.12% ======================================= Files 77 77 Lines 5913 5857 -56 ======================================= - Hits 5388 5337 -51 + Misses 525 520 -5 ``` | [Flag](https://app.codecov.io/gh/chanzuckerberg/cellxgene-census/pull/1094/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/1094/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=chanzuckerberg) | `91.12% <100.00%> (+<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=chanzuckerberg#carryforward-flags-in-the-pull-request-comment) to find out more.

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ebezzi commented 3 months ago

COG should also be able to replace ontology_mappy.py

Are its functionalities covered by COG? This is only used by Geneformer, which isn't part of core Census, so I wouldn't be too worried about it.

Bento007 commented 3 months ago

COG should also be able to replace ontology_mappy.py

Are its functionalities covered by COG? This is only used by Geneformer, which isn't part of core Census, so I wouldn't be too worried about it.

It's functionality is covered. I created a ticket to do this as future work.