chanzuckerberg / cellxgene-census

CZ CELLxGENE Discover Census
https://chanzuckerberg.github.io/cellxgene-census/
MIT License
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[python] Geneformer CLS embeddings #1225

Closed mlin closed 2 months ago

mlin commented 3 months ago

Minor updates to Geneformer scripts and WDL to use new emb_mode="cls" setting.

codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 25.00000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 91.18%. Comparing base (55d0856) to head (d58e9ed).

Files Patch % Lines
...xperimental/ml/huggingface/geneformer_tokenizer.py 25.00% 3 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #1225 +/- ## ======================================= Coverage 91.18% 91.18% ======================================= Files 80 80 Lines 6327 6327 ======================================= Hits 5769 5769 Misses 558 558 ``` | [Flag](https://app.codecov.io/gh/chanzuckerberg/cellxgene-census/pull/1225/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/1225/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=chanzuckerberg) | `91.18% <25.00%> (ø)` | | 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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