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Savitha/scdl geneformer integration #363

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Savitha/scdl geneformer integration #363

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Commits on Oct 22, 2024

  1. Bug fix for row index creation in concat function when collating mult… 

    …iple datasets; added unit test that checks for regression
    Savitha Srinivasan committed Oct 22, 2024
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  2. Merge branch 'main' into savitha/scdl-concat-fix

    @savitha-eng
    savitha-eng authored Oct 22, 2024
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  3. Installed precommit and ran on files to fix formatting issues

    Savitha Srinivasan committed Oct 22, 2024
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  4. Merge branch 'savitha/scdl-concat-fix' of github.com:NVIDIA/bionemo-f… 

    …w-ea into savitha/scdl-concat-fix
    Savitha Srinivasan committed Oct 22, 2024
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Commits on Oct 23, 2024

  1. Changes for testing geneformer integration with scdl

    Savitha Srinivasan committed Oct 23, 2024
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Commits on Oct 24, 2024

  1. changes to debug

    Savitha Srinivasan committed Oct 24, 2024
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Commits on Oct 25, 2024

  1. unit tests for dataset changes

    Savitha Srinivasan committed Oct 25, 2024
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  2. Adding unit tests

    Savitha Srinivasan committed Oct 25, 2024
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  3. Add tests for genes not in tokenizer covab and for assertions on the … 

    …cellx dataset
    Savitha Srinivasan committed Oct 25, 2024
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  4. Modified comments and documentation

    Savitha Srinivasan committed Oct 25, 2024
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  5. changes for bypassing tokenizer vocab

    Savitha Srinivasan committed Oct 25, 2024
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  6. Added conftest with pytest fixtures for unitt ests

    Savitha Srinivasan committed Oct 25, 2024
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  7. Remove debugging changes

    Savitha Srinivasan committed Oct 25, 2024
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  8. Remove unneeded prints

    Savitha Srinivasan committed Oct 25, 2024
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  9. Add logic to bypass checking for gene name in vocab to train script a… 

    …nd corresponding pytest
    Savitha Srinivasan committed Oct 25, 2024
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  10. Add SCDl as a dependency for geneformer

    Savitha Srinivasan committed Oct 25, 2024
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  11. remove randomization from test case to prevent random failure

    Savitha Srinivasan committed Oct 25, 2024
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