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feat: add cli annotation subcommand #2539

Merged
merged 63 commits into from
Jul 29, 2022

Commits on May 12, 2022

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  2. format: fmt, lint

    atolopko-czi committed May 12, 2022
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Commits on May 18, 2022

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Commits on May 19, 2022

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  2. add cli annotate tests

    atolopko-czi committed May 19, 2022
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Commits on May 20, 2022

  1. more cli annotate tests

    atolopko-czi committed May 20, 2022
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Commits on May 24, 2022

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  2. rm todo

    no longer a req
    atolopko-czi committed May 24, 2022
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Commits on May 25, 2022

  1. cli tweaks, test fix

    atolopko-czi committed May 25, 2022
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  4. todo

    atolopko-czi committed May 25, 2022
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Commits on Jun 1, 2022

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  2. add test

    atolopko-czi committed Jun 1, 2022
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Commits on Jun 8, 2022

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Commits on Jun 9, 2022

  1. overhaul for use with new trained models

    - "model" is actually two models now, one for ref mapping (scvi pytorch) and
    one for classifier (XGBoost)
    - remove all gene column congruency logic, as that is handled by scvi
    - tests currently broken
    atolopko-czi committed Jun 9, 2022
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  2. refactoring

    atolopko-czi committed Jun 9, 2022
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  4. grammar

    atolopko-czi committed Jun 9, 2022
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  5. cleanup

    atolopko-czi committed Jun 9, 2022
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Commits on Jun 14, 2022

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  2. pkg fixes

    atolopko-czi committed Jun 14, 2022
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Commits on Jun 15, 2022

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Commits on Jun 24, 2022

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Commits on Jun 28, 2022

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Commits on Jul 20, 2022

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Commits on Jul 21, 2022

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Commits on Jul 22, 2022

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Commits on Jul 25, 2022

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  2. rename

    atolopko-czi committed Jul 25, 2022
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  3. fmt, lint

    atolopko-czi committed Jul 25, 2022
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  7. Merge branch 'atolopko/2518-cell-type-prediction-cli-cmd' of github.c…

    …om:chanzuckerberg/cellxgene into atolopko/2518-cell-type-prediction-cli-cmd
    atolopko-czi committed Jul 25, 2022
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  12. reinstate gha jobs

    atolopko-czi committed Jul 25, 2022
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Commits on Jul 26, 2022

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  2. fix embedding selection

    reverted code to previous implementation that was presumably changed due to
    destructuring assignment lint error; explicitly ignoring error
    atolopko-czi committed Jul 26, 2022
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Commits on Jul 27, 2022

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  3. add annotate cli tests

    atolopko-czi committed Jul 27, 2022
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Commits on Jul 28, 2022

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  2. test fix

    atolopko-czi committed Jul 28, 2022
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  4. cli fixes

    atolopko-czi committed Jul 28, 2022
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  6. Merge branch 'atolopko/2535-fix-embedding-selection' into atolopko/25…

    …18-cell-type-prediction-cli-cmd
    atolopko-czi committed Jul 28, 2022
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  8. fmt

    atolopko-czi committed Jul 28, 2022
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Commits on Jul 29, 2022

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  2. lint

    atolopko-czi committed Jul 29, 2022
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