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fix: check PSSMs #401

Merged
merged 45 commits into from May 11, 2023
Merged

fix: check PSSMs #401

merged 45 commits into from May 11, 2023

Commits on Mar 19, 2023

  1. aa profile sorted by 3-letter code

    @DaniBodor
    DaniBodor committed Mar 19, 2023
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  2. move/remove amino_acids_by_letter

    @DaniBodor
    DaniBodor committed Mar 19, 2023
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  3. delete dummy pssm file

    @DaniBodor
    DaniBodor committed Mar 19, 2023
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Commits on Mar 21, 2023

  1. Merge branch 'main' into 332_pssmformat_dbodor

    @DaniBodor
    DaniBodor committed Mar 21, 2023
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  2. allow excluding feature modules

    @DaniBodor
    DaniBodor committed Mar 21, 2023
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  3. test exception if no pssm is present

    @DaniBodor
    DaniBodor committed Mar 21, 2023
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  4. test exclude features

    @DaniBodor
    DaniBodor committed Mar 21, 2023
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  5. improve error message for no pssm file found

    @DaniBodor
    DaniBodor committed Mar 21, 2023
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  6. allow specifying chain ids in build_testgraph

    @DaniBodor
    DaniBodor committed Mar 21, 2023
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  7. fix linting

    @DaniBodor
    DaniBodor committed Mar 21, 2023
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  8. ensure that excluding works if extension is included

    @DaniBodor
    DaniBodor committed Mar 21, 2023
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  9. actually make it work with extension

    @DaniBodor
    DaniBodor committed Mar 21, 2023
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  10. allow strings for feature modules in QC

    @DaniBodor
    DaniBodor committed Mar 21, 2023
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Commits on Mar 26, 2023

  1. Merge branch 'main' into 332_pssmformat_dbodor

    @DaniBodor
    DaniBodor committed Mar 26, 2023
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  2. fix exclude with .py

    @DaniBodor
    DaniBodor committed Mar 26, 2023
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Commits on Apr 3, 2023

  1. fix bug for exclude_feature_modules = None

    @DaniBodor
    DaniBodor committed Apr 3, 2023
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  2. aa nomenclature conversion

    @DaniBodor
    DaniBodor committed Apr 3, 2023
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  3. start on sanity check

    @DaniBodor
    DaniBodor committed Apr 3, 2023
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  4. check pssm function should work

    @DaniBodor
    DaniBodor committed Apr 3, 2023
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  5. docstring and passing chain id

    @DaniBodor
    DaniBodor committed Apr 3, 2023
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  6. call pssm check

    @DaniBodor
    DaniBodor committed Apr 3, 2023
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  7. do not turn into list

    @DaniBodor
    DaniBodor committed Apr 3, 2023
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  8. better error message

    @DaniBodor
    DaniBodor committed Apr 3, 2023
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  9. remove unused import

    @DaniBodor
    DaniBodor committed Apr 3, 2023
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Commits on Apr 24, 2023

  1. test bad pssms - not working

    @DaniBodor
    DaniBodor committed Apr 24, 2023
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Commits on May 4, 2023

  1. fix test by adding build()

    @DaniBodor
    DaniBodor committed May 4, 2023
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  2. Merge branch 'main' into 332_testmerge

    @DaniBodor
    DaniBodor committed May 4, 2023
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  3. remove PATH_TEST

    @DaniBodor
    DaniBodor committed May 4, 2023
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Commits on May 11, 2023

  1. remove exclude_feature_modules parameter

    @DaniBodor
    DaniBodor committed May 11, 2023
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  2. update default feature modules

    @DaniBodor
    DaniBodor committed May 11, 2023
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  3. set defaults in single code block

    @DaniBodor
    DaniBodor committed May 11, 2023
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  4. inlcude feaure log info and improve error message

    @DaniBodor
    DaniBodor committed May 11, 2023
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  5. remove exclude option from error message

    @DaniBodor
    DaniBodor committed May 11, 2023
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  6. remove exclude_feature_modules from test

    @DaniBodor
    DaniBodor committed May 11, 2023
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  7. add _assert_correct_modules helper function

    @DaniBodor
    DaniBodor committed May 11, 2023
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  8. revamp single feature test

    @DaniBodor
    DaniBodor committed May 11, 2023
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  9. separate tests for default and all features

    @DaniBodor
    DaniBodor committed May 11, 2023
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  10. fix test integration

    @DaniBodor
    DaniBodor committed May 11, 2023
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  11. wheel does not exist for pytorch 2.0.1

    @DaniBodor
    DaniBodor committed May 11, 2023
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  12. fix typo and update readme

    @DaniBodor
    DaniBodor committed May 11, 2023
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  13. do not allow None for feature modules in query.process

    @DaniBodor
    DaniBodor committed May 11, 2023
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  14. correct versions of torchvision and torchaudio

    @DaniBodor
    DaniBodor committed May 11, 2023
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  15. fix tests

    @DaniBodor
    DaniBodor committed May 11, 2023
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  16. Merge branch 'main' into 332_pssmformat_dbodor

    @DaniBodor
    DaniBodor committed May 11, 2023
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  17. correct commands for installing pytorch 2.0.0

    @DaniBodor
    DaniBodor committed May 11, 2023
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