Feature: DLomix integration #250
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Refactor the methods in oktoberfest::predict to use a predictor class abstracted from Koina. Add a new oktoberfest::predict::dlomix module with a bare-bones interface for using DLomix models for local prediction of intensity.
- manually merge changes to predict functions from divergent development branch - rename predict::predict.py to predict::alignment.py to better reflect the static methods left in it - get rid of unnecessary imports - consistently use generic type annotations from typing instead of built-in ones
picciama
requested changes
Jul 27, 2024
pyupgrade will otherwise reformat GenericType[] from typing to 3.10+ genericType[] if `from __future__ import annotations` is present
new spectrum_fundamentals & spectrum_io releases, new dlomix release in development, updated dependencies
Refactor for legibility, actually use frag_dict, enable keeping additional columns, remove decoys from data, add stub for filtering by Andromeda score
Add sections where necessary, expand & split up some existing paragraphs Add some cross-references
added koinapy and extend superclass
…erface implementation to satisfy mypy
picciama
force-pushed
the
feature/dlomix-integration
branch
2 times, most recently
from
cf76872 to
395373f
Compare
picciama
force-pushed
the
feature/dlomix-integration
branch
from
395373f to
3490afa
Compare
picciama
approved these changes
Sep 13, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
PR Checklist
docsis updatedDescription of changes
Enable off-line prediction of intensity using DLomix.
Technical details
Caveats