Decoding pipeline

[edeno]

Description

This PR will:

• update the existing pipeline to use merge tables
• have a table to store the decoding results
• use the new non_local_detector package for decoding

• Fixes Add clusterless / clustered decoding parameter schema and decoded data schema #14

Checklist:

• This PR should be accompanied by a release: (yes/no/unsure)
• (If release) I have updated the CITATION.cff
• I have updated the CHANGELOG.md
• I have added/edited docs/notebooks to reflect the changes

To-do:

• Position Group for multiple position entries
• Waveform Group for grouping clusterless marks
• Sorted Spikes Group for grouping sorted units
• Convert model classes into dictionaries and back again
• Write file cleanup for .nc files
• Write notebooks for each step of the pipeline
• Document 1D decoding requires setting track_graph, track_order, track_spacing in environment variable
• Document the difference between estimate parameters and not estimate parameters
• Save initial conditions and discrete transition matrix (possibly just in the xarray)
• Update notebook on using GPUs with decoding
• Load spatial environments easily
• Add section on decoding visualization with figurl in notebook
• Decoding parameters override insert
• Test adding track_graph to Environment and storing in decoding table
• Test on production data to make sure there is a reasonable decode

[edeno]

@CBroz1 would you mind taking a look at src/spyglass/decoding/v1/waveform_features.py? The saving of the waveform features is still not working but the rest should be good to review.

[samuelbray32]

• Added functions to the SpikesortingOutput table to make it easier to fetch information from upstream tables.
• Used these and other changes to allow UnitWaveformFeatures to accept from the spikesorting v0 pipeline

[edeno]

@samuelbray32 was able to get existing data through to decoding.
Clusterless:

Sorted Spikes:

[CBroz1]

Looks good. I think the last step is to make a decision about #749 - to add, add/tweak and place elsewhere, or to close

[edeno]

Looks good. I think the last step is to make a decision about #749 - to add, add/tweak and place elsewhere, or to close

I would like to merge this in master as is and then in a separate PR think about how to add that since I haven't tested it out.