Add populator functions for ease of use #1279
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Copilot reviewed 16 out of 16 changed files in this pull request and generated no comments.
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src/spyglass/linearization/v1/pipeline.py:92
- Ensure that the custom method 'fetch_nwb_file_name()' returns a list of dicts containing the 'nwb_file_name' key. If the return format differs, update the subsequent code to correctly extract the NWB file name.
pos_entry = (PositionOutput & pos_key).fetch_nwb_file_name()
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Pull Request Overview
This PR introduces new high‐level populator functions to simplify the execution of multiple processing pipelines (position, DLC training/setup, MUA, linearization, decoding, and behavior) while removing some renamed or obsolete pyscripts/notebooks. The changes include updates to function signatures and docstrings for clarity, as well as the removal of unused imports and outdated scripts.
Reviewed Changes
Copilot reviewed 18 out of 18 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| src/spyglass/spikesorting/v1/recording.py | Updated the insert_selection method signature with an explicit return type and corrected a minor typo in the comments. |
| src/spyglass/spikesorting/spikesorting_merge.py | Removed an unused import. |
| src/spyglass/position/v1/pipeline_trodes.py | Added a populator function for the Trodes Position V1 pipeline. |
| src/spyglass/position/v1/pipeline_dlc_training.py | Added a new function to run DLC Model Training V1. |
| src/spyglass/position/v1/pipeline_dlc_setup.py | Introduced a new populator function for setting up DLC projects with frame extraction. |
| src/spyglass/mua/v1/pipeline.py | Added a populator function for the Multi-Unit Activity (MUA) V1 pipeline. |
| src/spyglass/linearization/v1/pipeline.py | Added a new populator function for the Position Linearization V1 pipeline. |
| src/spyglass/decoding/v1/pipeline_waveform_feature_extraction.py | Added a pipeline for Waveform Feature Extraction V1. |
| src/spyglass/decoding/v1/pipeline_sorted.py | Added a pipeline for Sorted Spikes Decoding V1. |
| src/spyglass/decoding/v1/pipeline_clusterless.py | Added a pipeline for Clusterless Decoding V1. |
| src/spyglass/behavior/v1/pipeline.py | Added a new populator function for the MoSeq Behavior V1 pipeline. |
| notebooks/py_scripts/51_MUA_Detection.py, 43_Decoding_SortedSpikes.py, 41_Extracting_Clusterless_Waveform_Features.py | Deprecated/not needed notebooks have been removed. |
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Description
Like the spikesorting.v0.spikesorting_populator, this attempts to wrap pipelines with many tables into one function for ease of use. I try to utilize any multiprocessing for parallel processing of datasets.
Also deleted some pyscripts that were renamed.
Still need to test this.
Fixes #891
Fixes #529
Checklist:
CITATION.cffaltersnippet for release notes.CHANGELOG.mdwith PR number and description.