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create cg-gnn extraction script #185

Merged
merged 35 commits into from
Sep 12, 2023
Merged

create cg-gnn extraction script #185

merged 35 commits into from
Sep 12, 2023

Commits on Aug 8, 2023

  1. created cg-gnn extraction script

    @CarlinLiao
    CarlinLiao committed Aug 8, 2023
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Commits on Aug 9, 2023

  1. added a quick test for cggnn extract

    @CarlinLiao
    CarlinLiao committed Aug 9, 2023
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Commits on Aug 11, 2023

  1. hotfix importance saving

    @CarlinLiao
    CarlinLiao committed Aug 11, 2023
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Commits on Aug 15, 2023

  1. Use updated pytorch image for Python 3.11 support, cggnn extract test… 

    … passes.
    @jimmymathews
    jimmymathews committed Aug 15, 2023
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Commits on Aug 16, 2023

  1. Use python3.11 directly in test case usage of pip, now that python3.1… 

    …1 is specially installed.
    @jimmymathews
    jimmymathews committed Aug 16, 2023
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  2. Same fix applied to second test.

    @jimmymathews
    jimmymathews committed Aug 16, 2023
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  3. undo cggnn docker change

    @CarlinLiao
    CarlinLiao committed Aug 16, 2023
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  4. Merge squidpy changes into cggnn_dfs

    @CarlinLiao
    CarlinLiao committed Aug 16, 2023
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  5. Merge remote-tracking branch 'origin/main' into cggnn_dfs

    @CarlinLiao
    CarlinLiao committed Aug 16, 2023
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Commits on Aug 21, 2023

  1. added pheno, removed multistudy to FME

    @CarlinLiao
    CarlinLiao committed Aug 21, 2023
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  2. Merge branch 'main' into cggnn_dfs

    @CarlinLiao
    CarlinLiao committed Aug 21, 2023
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  3. logic hotfix

    @CarlinLiao
    CarlinLiao committed Aug 21, 2023
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  4. fix study-substudy references

    @CarlinLiao
    CarlinLiao committed Aug 21, 2023
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  5. fix test to account for phenotype columns

    @CarlinLiao
    CarlinLiao committed Aug 21, 2023
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  6. make phenotype dict key consistent

    @CarlinLiao
    CarlinLiao committed Aug 21, 2023
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Commits on Aug 22, 2023

  1. Update usage of extractor to omit study reference.

    @jimmymathews
    jimmymathews committed Aug 22, 2023
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  2. remove phenotypes from continuous dataframes

    @CarlinLiao
    CarlinLiao committed Aug 22, 2023
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Commits on Aug 24, 2023

  1. fix pheno neg expression match

    @CarlinLiao
    CarlinLiao committed Aug 24, 2023
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  2. split extract stratification, symbols in col names

    @CarlinLiao
    CarlinLiao committed Aug 24, 2023
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  3. a little formatting on FME

    @CarlinLiao
    CarlinLiao committed Aug 24, 2023
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  4. explore classes for cggnn extraction

    @CarlinLiao
    CarlinLiao committed Aug 24, 2023
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Commits on Aug 25, 2023

  1. fix FME test

    @CarlinLiao
    CarlinLiao committed Aug 25, 2023
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  2. Make test more diagnosable.

    @jimmymathews
    jimmymathews committed Aug 25, 2023
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Commits on Sep 5, 2023

  1. cggnn extract clarity refactors

    @CarlinLiao
    CarlinLiao committed Sep 5, 2023
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Commits on Sep 6, 2023

  1. update providers for new feature column names

    @CarlinLiao
    CarlinLiao committed Sep 6, 2023
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  2. add cg-gnn to toml checking

    @CarlinLiao
    CarlinLiao committed Sep 6, 2023
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Commits on Sep 7, 2023

  1. adjust squidpy clustering

    @CarlinLiao
    CarlinLiao committed Sep 7, 2023
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  2. actually handling this without a try except is better

    @CarlinLiao
    CarlinLiao committed Sep 7, 2023
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  3. any typo

    @CarlinLiao
    CarlinLiao committed Sep 7, 2023
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  4. handle malformed squidpy returns more gracefully

    @CarlinLiao
    CarlinLiao committed Sep 7, 2023
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Commits on Sep 8, 2023

  1. cggnn extract docstring

    @CarlinLiao
    CarlinLiao committed Sep 8, 2023
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  2. Merge branch 'main' into cggnn_dfs

    @CarlinLiao
    CarlinLiao committed Sep 8, 2023
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Commits on Sep 12, 2023

  1. Change dataframe to bool values to permit "all" & "all" syntax.

    @jimmymathews
    jimmymathews committed Sep 12, 2023
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  2. Fix accidentally booleanization of pixel position columns.

    @jimmymathews
    jimmymathews committed Sep 12, 2023
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  3. Make operator order precedence explicit, booleanization and negation.

    @jimmymathews
    jimmymathews committed Sep 12, 2023
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