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Decoding pipeline edits for imported data #782

Merged
merged 197 commits into from
Jan 25, 2024
Merged

Decoding pipeline edits for imported data #782

merged 197 commits into from
Jan 25, 2024

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edeno
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@edeno edeno commented Jan 21, 2024

Description

This is a series of fixes to get external data to work with our pipelines.

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

edeno and others added 30 commits October 19, 2023 08:05
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edeno commented Jan 23, 2024

Note: There are a lot of functions that could be refactored into a single place that would work on both clusterless and sorted spikes, but due to time constraints, I am not worrying about that right now.

@edeno edeno requested a review from CBroz1 January 23, 2024 17:43
khl02007 and others added 2 commits January 23, 2024 11:59
@edeno edeno changed the title [WIP] Decoding pipeline edits for imported data Decoding pipeline edits for imported data Jan 24, 2024
@edeno edeno marked this pull request as ready for review January 24, 2024 17:03
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edeno commented Jan 24, 2024

Still would like to add the ability to filter units. Will see if there is time for that.

* Addressing #789. See details.

- Edit settings.py to permit fail to load config on startup
- Simplify instructions to use func to generate config, negating need
  for config.py script
- Edit notebook 00 and installation doc to point to save-config func
- Expand example config to demonstrate all possible values
- Lint dj_merge_table.py to remove unused import and `var is True`

* #794

* Fix failing tests

* Update Changelog

* Typo: chared -> shared
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src/spyglass/common/common_position.py Outdated Show resolved Hide resolved
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src/spyglass/common/common_position.py Outdated Show resolved Hide resolved
src/spyglass/common/common_behav.py Outdated Show resolved Hide resolved
src/spyglass/decoding/decoding_merge.py Show resolved Hide resolved
src/spyglass/decoding/v1/sorted_spikes.py Show resolved Hide resolved
src/spyglass/decoding/v1/sorted_spikes.py Show resolved Hide resolved
src/spyglass/decoding/v1/sorted_spikes.py Show resolved Hide resolved
src/spyglass/settings.py Outdated Show resolved Hide resolved
src/spyglass/spikesorting/merge.py Outdated Show resolved Hide resolved
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edeno commented Jan 25, 2024

To Do:

  • Implement filtering of units
  • Rename load_ functions to fetch for consistency
  • Clean up redundancy in table methods
  • Refactor methods to use merge table methods
  • Rename SortedSpikesGroup.SortGroup to Units? Sorting?

@CBroz1 CBroz1 merged commit c5bf75b into master Jan 25, 2024
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