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Docs fixes for decoding pipeline #776

Merged
merged 10 commits into from
Jan 20, 2024
Merged

Docs fixes for decoding pipeline #776

merged 10 commits into from
Jan 20, 2024

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CBroz1
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@CBroz1 CBroz1 commented Jan 18, 2024

Description

  • Decoding pipeline fixes: tidy docstrings for auto-rendering.
  • Add __init__ files to submodules so that mkdocstrings sees that is a subpackage
  • hatch cli no longer prints version to stdout, so using grep to fetch from _version

Checklist:

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

@CBroz1 CBroz1 linked an issue Jan 19, 2024 that may be closed by this pull request
CBroz1 and others added 2 commits January 19, 2024 11:15
* WIP: Pull from old stash, resolve conflicts

* Pytest WIP. Position centriod fix. Centralize device prompt logic

* Add tests for all tables in

* WIP: Improve coverage behav, dio

* WIP: Add coverage, see details:

- Add `return_fig` param to plotting helper functions to permit tests
  - `common_filter`
  - `common_interval`
- Add coverage for ~1/2 of `common`
  - `common_behav`
  - `common_device`
  - `common_ephys`
  - `common_filter`
  - `common_interval` - with helper funcs tested seperately
  - `common_lab`
  - `common_nwbfile` - partial

* WIP pytest common 2nd half, start lfp

* WIP lfp tests, ahead of fetch upstream

* Add lfp pipeline tests

* Run pre-commit checks

* Fix bug

* Unpin position_tools for CI

* Change download data dir

* Change download data dir 2

* Fix teardown. Coverage 67%

* Update changelog

* logger.warn -> logger.warning
* Add non-local detector and remove replay_trajectory_classification

* Reorganize

* Fix formatting and imports

* Update .gitignore

* Remove because of circular import

* Fix name of parameter

* Handle case where ther is only one interval

* Fix settings

* Handle single interval

* from_unit_dict does not exist in 0.98.2 of spike interface

* Simplify call

* Update for SpikeSorting merge table and add spyglass mixin

* Fix dependencies

* Fix merge conflict

* Update src/spyglass/decoding/v1/clusterless.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/decoding/v1/clusterless.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/decoding/v1/clusterless.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/decoding/v1/clusterless.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Apply suggestions from code review

Co-authored-by: Chris Brozdowski <[email protected]>

* Remove unused imports and format

* Add saving of waveform features

* Don't store electrodes, full waveforms, waveform mean

* Fix spike times and add convenience method

* Add spike location and some formatting

* Remove circular import

* Fix dict expansion

* Initial working clusterless pipeline

* Add position group

* Rename classifier to decoding

* Handle encoding and decoding intervals

* Put old files under v0, try/except for old decoding package

* Rename visualization and remove from v0

v0 visualization is redundant with visualization

* Place parameters and position group in core.py

* Add sorted spikes decoding

* Add objects to init for convenience

* Remove unused imports

* Fix fetching of spike times

* Insert into merge table

* Update CHANGELOG.md

* Function for removing decoding outputs not in DecodingOutput

* Fix name

* Add draft of tutorials and rearrange notebooks

* Fix config loading

* Add 1D decoding and some notes on estimate_parameters kwarg

* Update 43_Decoding_SortedSpikes.ipynb

* Remove old decoding notebook

* Save initial conditions and discrete transitions

* Apply suggestions from code review

Co-authored-by: Chris Brozdowski <[email protected]>

* Be more specific with import error

* Remove unneeded comments

* Remove incorrect dimension name

* Project merge_id from SpikeSortingOutput for clarity

* Update src/spyglass/decoding/v0/clusterless.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/decoding/v0/clusterless.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/decoding/v0/clusterless.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Fix linting

* Update notebooks

* Ignore .pem

* Add session as a primary key for Groups

* Add some helper methods

* Update notebooks

* Update README.md

* Update pyscripts

* Update 42_Decoding_Clusterless.ipynb

* Update CHANGELOG.md

* Add fetch and insert

* Simplify class conversion

* Do the dictionary conversion of class for the user

* Update CHANGELOG.md

* Update .gitignore

* Use methods in populate

* Avoid fetching interval range if not needed

* Generalize finding class from modules

* Use args/kwargs

* Simplify tuple unpacking

* Make decoding kwargs nullable

* Add function for get_recording and get_sorting to the spikesorting merge table

* make decoding waveform features agnostic to spikesorting source

* Fix spelling

* Use fetch1_dataframe for position

* Use self instead of class

* Update src/spyglass/decoding/v1/sorted_spikes.py

Co-authored-by: Samuel Bray <[email protected]>

* Be more careful about populating select keys

* Make more readable/remove unused imports

* Save classifier

* Clean up saved model paths

* add function load_linear_position_info

* Update src/spyglass/decoding/v1/sorted_spikes.py

Co-authored-by: Samuel Bray <[email protected]>

* Update 41_Extracting_Clusterless_Waveform_Features.py

* Update docstring

* Apply suggestions from code review

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/decoding/v1/clusterless.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/decoding/v1/clusterless.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Fix linting

* Fix syntax

* Rename variable to avoid confusion

* Restrict UnitWaveformFeaturesGroup and SortedSpikesGroup

* Concatenate linear position and position dataframes

* Static methods don't require instantiating class

* Avoid merge restrict

* Add version to defaults

* Remove unused import

* Fix classifier path

* Add dry run

* Remove non-default

* Handle permissions and file not found

* Keep position info within encoding/decoding interval

* Add methods to get the spike_times, spike_indicators, firing rate

* Fix docstring to match default

* Implement function rather than import

* Remove unused broken imports

* Add decoding cleanup

* Fix import

* Put old vis code back

* Fix import

* Add draft helper functions

* Limit options on input

* Fix logic

* Fix where the key is passed

* Update notebooks

* Host main visualizations in non_local_detector repo

* Update notebooks/py_scripts/41_Extracting_Clusterless_Waveform_Features.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/spikesorting/merge.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Update src/spyglass/decoding/decoding_merge.py

Co-authored-by: Chris Brozdowski <[email protected]>

* Revert "Limit options on input"

This reverts commit 386714c.

* Use f-string for version

* Add useful imports to the top level

This would have to change a bit if there were multiple versions of the pipeline.

* Make source class a hidden attribute

* Update CHANGELOG.md

---------

Co-authored-by: Chris Brozdowski <[email protected]>
Co-authored-by: Sam Bray <[email protected]>
@CBroz1 CBroz1 marked this pull request as draft January 19, 2024 22:38
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CBroz1 commented Jan 19, 2024

Converting to draft pending merge of #772

emreybroyles and others added 5 commits January 19, 2024 16:49
* add envs to bashrc; multi cam addition

* 12/11/23 using TackEpoch to define interval_names

* 12/11/23 remove comment

* del smooth duration

* jan 10 again

* DLC noteboks 5 and 6

* 5 and 6

* fix ignore and 21

* Removed submodule

* removed .gitignore

* DLC notebooks
@CBroz1 CBroz1 marked this pull request as ready for review January 19, 2024 23:31
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@edeno edeno merged commit e504c74 into LorenFrankLab:master Jan 20, 2024
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Update docs to reflect new notebook structure
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