Update DeepLC and IM2Deep integration for their v4/v2 API rewrites#261
Merged
RalfG merged 4 commits intorelease/4.2from Apr 14, 2026
Merged
Update DeepLC and IM2Deep integration for their v4/v2 API rewrites#261RalfG merged 4 commits intorelease/4.2from
RalfG merged 4 commits intorelease/4.2from
Conversation
- Replace retention_time.py and ion_mobility.py wrapper modules with inline calls to deeplc.predict_and_calibrate() and im2deep.predict() - Both packages now take PSMList directly (no DataFrame conversion) - Lazy imports kept inside if-blocks to avoid loading PyTorch at import - Remove iRT calibration peptides (DeepLC v4 handles calibration) - Bump psm_utils requirement to >=1.5
Move DeepLC and IM2Deep calls before the batch loop so they run once on the full filtered PSMList instead of per batch. Closes #243
- Extract _add_im_rt helper for DeepLC/IM2Deep calls - Pass processes via predict_kwargs for PyTorch thread control - Use bare type: ignore for optional dep imports - Use deeplc.predict instead of predict_and_calibrate
RalfG
added
enhancement
dependencies
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Update DeepLC and IM2Deep integration for their v4/v2 API rewrites, and run RT/IM predictions once for library generation instead of per batch.
Added
rtandimoptional dependencies for DeepLC and IM2DeepChanged
deeplc.predict()functional API (replaces class-basedDeepLCwrapper)im2deep.predict()functional API (replaces legacyim2deep.im2deep.predict_ccs)predict_libraryruns RT/IM predictions once on the full filtered PSMList before batching (closes Improve runtime for predict_library by running DeepLC and IM2Deep predictions only once #243)predict_kwargsRemoved
_utils/retention_time.pyand_utils/ion_mobility.pywrapper modules (inlined in core.py)