FIX noqa by using register_reader(), address many side effects #172

jalew188 · 2024-05-19T11:45:19Z

Review this PR after #171

Changes:

Remove alphabase.io.psm_reader as all functionalities are already in alphabase.psm_reader module.
register_reader() for all reader modules
register_decoy() for protein_level_decoy

review-notebook-app · 2024-05-19T11:45:24Z

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mschwoer

LGTM.. reader registration is much cleaner now

alphabase/peptide/fragment.py

alphabase/psm_reader/__init__.py

nbs_tests/psm_reader/sage_reader.ipynb

alphabase/spectral_library/base.py

alphabase/psm_reader/__init__.py

jalew188 added 3 commits May 19, 2024 12:56

FIX noqa: using register_reader() for psm_readers to avoid noqa F403

74ff17f

FIX noqa using register_decoy() for protein_level_decoy

763319a

Remove side effect when removing noqa

0d6a5e2

jalew188 added 2 commits May 19, 2024 13:51

FIX missing lxml package

8a38aa9

Merge branch 'remove_noqa' into reader_register

a6fcb55

jalew188 requested review from mschwoer and GeorgWa May 19, 2024 11:53

mschwoer changed the base branch from development to remove_noqa May 21, 2024 07:13

mschwoer approved these changes May 21, 2024

View reviewed changes

Base automatically changed from remove_noqa to development May 21, 2024 08:30

Merge branch 'remove_noqa' into reader_register

023b3d7

jalew188 mentioned this pull request May 21, 2024

Use https://charlesreid1.github.io/python-patterns-the-registry.html for registers #173

Open

jalew188 added 4 commits May 21, 2024 10:43

FIX register_sage_readers to register_sage_readers()

15a08e3

add nbmake to req

5c7e826

Add 'elution_group_idx[0] # noqa' back for TODO

29d6791

FIX pre-commit run

cd54643

jalew188 merged commit 9d8e808 into development May 21, 2024
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jalew188 deleted the reader_register branch May 21, 2024 11:16

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