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Document use of mixin class for custom spyglass tables #879

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edeno opened this issue Mar 20, 2024 · 0 comments · Fixed by #903
Closed

Document use of mixin class for custom spyglass tables #879

edeno opened this issue Mar 20, 2024 · 0 comments · Fixed by #903
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@CBroz1
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documentation Improvements or additions to documentation enhancement New feature or request

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@edeno
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edeno commented Mar 20, 2024

New users may not be informed about the mixin class and its usage. We should make sure there is documentation on how to include this class for custom spyglass tables and what it does.
@edeno edeno added documentation Improvements or additions to documentation enhancement New feature or request labels Mar 20, 2024
@CBroz1 CBroz1 self-assigned this Mar 20, 2024
CBroz1 added a commit to CBroz1/spyglass that referenced this issue Mar 29, 2024
@CBroz1
LorenFrankLab#879
185e9a6
@CBroz1 CBroz1 linked a pull request Mar 29, 2024 that will close this issue
Misc Issues #903
Merged
4 tasks
@CBroz1 CBroz1 mentioned this issue Apr 2, 2024
Merged
4 tasks
edeno pushed a commit that referenced this issue Apr 19, 2024
@CBroz1
Misc Issues (#903)
995f4cd 
* #892

* #885

* #879

* Partial address of #860

* Update Changelog

* Partial solve of #886 - Ask import

* Fix failing tests

* Add note on order of inheritace

* #933

* Could not replicate fill_nan error. Reverting except clause
edeno added a commit that referenced this issue Apr 25, 2024
@CBroz1 @samuelbray32 @edeno
Part delete edits (#946)
2d9cc73 
* Add spyglass version to created analysis nwb files (#897)

* Add sg version to created analysis nwb files

* update changelog

* Change existing source script to spyglass version (#900)

* Add pynapple support (#898)

* Preliminary code

* Add retrieval of file names

* Add get_nwb_table function

* Update docstrings

* Update CHANGELOG.md

* Hot fixes for clusterless `get_ahead_behind_distance` and `get_spike_times` (#904)

* Squeeze results

* Make method and not class method

* Update CHANGELOG.md

* fix bugs in fetch_nwb (#913)

* Check for entry in merge part table prior to insert (#922)

* check for entry in merge part table prior to insert

* update changelog

* Kachery fixes (#918)

* Prioritize datajoint filepath for getting analysis file abs_path

* remove deprecated kachery tables

* update changelog

* fix lint

---------

Co-authored-by: Samuel Bray <samuelbray@som-dfvnn9m-lt.ucsf.edu>
Co-authored-by: Eric Denovellis <edeno@users.noreply.github.com>

* remove old tables from init (#925)

* Fix improper uses of strip (#929)

Strip will remove leading characters

* Update CHANGELOG.md

* Misc Issues (#903)

* #892

* #885

* #879

* Partial address of #860

* Update Changelog

* Partial solve of #886 - Ask import

* Fix failing tests

* Add note on order of inheritace

* #933

* Could not replicate fill_nan error. Reverting except clause

* Export logger (#875)

* WIP: rebase Export process

* WIP: revise doc

* ✅ : Generate working export script

* Cleanup: Expand notebook, migrate export process from graph class to export

* Revert dj_chains related edits

* Update changelog

* Revise doc

* Address review comments #875

* Remove walrus in  eval

* prevent log on preview

* Fix arg order on fetch, iterate over restr

* Add upstream analysis files during cascade. Address false positive fetch

* Avoid regen file list on revisit node

* Bump Export.Table.restr to mediumblob

* Revise Export.Table uniqueness to include export_id

* Spikesorting quality of life helpers (#910)

* add utitlity function for finding spikesorting merge ids

* add option to select v1 sorts that didn't go through artifact detection

* add option to return merge keys as dicts for future restrictions

* Add tool to get brain region and electrode info for a spikesorting merge id

* update changelog

* style cleanup

* style cleanup

* fix restriction bug for curation_id

* account for change or radiu_um argument name in spikeinterface

* only do joins with metric curastion tables if have relevant keys in the restriction

* Update tutorial to use spikesorting merge table helper functions

* fix spelling

* Add logging of AnalysisNwbfile creation time and file size (#937)

* Add logging for any func that creates AnalysisNwbfile

* Migrate create to top of respective funcs

* Use pathlib for file size. Bump creation time to top of  in spikesort

* Clear pre_create_time on create

* get/del -> pop

* Log when file accessed (#941)

* Add logging for any func that creates AnalysisNwbfile

* Fix bug on empty delete in merge table (#940)

* fix bug on empty delete in merge table

* update changelog

* fix spelling

---------

Co-authored-by: Chris Brozdowski <Chris.Broz@ucsf.edu>

* Remove master restriction

* Part delete takes restriction from self

---------

Co-authored-by: Samuel Bray <sam.bray@ucsf.edu>
Co-authored-by: Eric Denovellis <edeno@users.noreply.github.com>
Co-authored-by: Samuel Bray <samuelbray@som-dfvnn9m-lt.ucsf.edu>
Co-authored-by: Eric Denovellis <edeno@bu.edu>
edeno added a commit that referenced this issue May 6, 2024
@samuelbray32 @CBroz1 @edeno
Group part delete propagation (#899)
435b0f3 
* Create class for group parts to help propagate deletes

* spelling

* update changelog

* Part delete edits (#946)

* Add spyglass version to created analysis nwb files (#897)

* Add sg version to created analysis nwb files

* update changelog

* Change existing source script to spyglass version (#900)

* Add pynapple support (#898)

* Preliminary code

* Add retrieval of file names

* Add get_nwb_table function

* Update docstrings

* Update CHANGELOG.md

* Hot fixes for clusterless `get_ahead_behind_distance` and `get_spike_times` (#904)

* Squeeze results

* Make method and not class method

* Update CHANGELOG.md

* fix bugs in fetch_nwb (#913)

* Check for entry in merge part table prior to insert (#922)

* check for entry in merge part table prior to insert

* update changelog

* Kachery fixes (#918)

* Prioritize datajoint filepath for getting analysis file abs_path

* remove deprecated kachery tables

* update changelog

* fix lint

---------

Co-authored-by: Samuel Bray <samuelbray@som-dfvnn9m-lt.ucsf.edu>
Co-authored-by: Eric Denovellis <edeno@users.noreply.github.com>

* remove old tables from init (#925)

* Fix improper uses of strip (#929)

Strip will remove leading characters

* Update CHANGELOG.md

* Misc Issues (#903)

* #892

* #885

* #879

* Partial address of #860

* Update Changelog

* Partial solve of #886 - Ask import

* Fix failing tests

* Add note on order of inheritace

* #933

* Could not replicate fill_nan error. Reverting except clause

* Export logger (#875)

* WIP: rebase Export process

* WIP: revise doc

* ✅ : Generate working export script

* Cleanup: Expand notebook, migrate export process from graph class to export

* Revert dj_chains related edits

* Update changelog

* Revise doc

* Address review comments #875

* Remove walrus in  eval

* prevent log on preview

* Fix arg order on fetch, iterate over restr

* Add upstream analysis files during cascade. Address false positive fetch

* Avoid regen file list on revisit node

* Bump Export.Table.restr to mediumblob

* Revise Export.Table uniqueness to include export_id

* Spikesorting quality of life helpers (#910)

* add utitlity function for finding spikesorting merge ids

* add option to select v1 sorts that didn't go through artifact detection

* add option to return merge keys as dicts for future restrictions

* Add tool to get brain region and electrode info for a spikesorting merge id

* update changelog

* style cleanup

* style cleanup

* fix restriction bug for curation_id

* account for change or radiu_um argument name in spikeinterface

* only do joins with metric curastion tables if have relevant keys in the restriction

* Update tutorial to use spikesorting merge table helper functions

* fix spelling

* Add logging of AnalysisNwbfile creation time and file size (#937)

* Add logging for any func that creates AnalysisNwbfile

* Migrate create to top of respective funcs

* Use pathlib for file size. Bump creation time to top of  in spikesort

* Clear pre_create_time on create

* get/del -> pop

* Log when file accessed (#941)

* Add logging for any func that creates AnalysisNwbfile

* Fix bug on empty delete in merge table (#940)

* fix bug on empty delete in merge table

* update changelog

* fix spelling

---------

Co-authored-by: Chris Brozdowski <Chris.Broz@ucsf.edu>

* Remove master restriction

* Part delete takes restriction from self

---------

Co-authored-by: Samuel Bray <sam.bray@ucsf.edu>
Co-authored-by: Eric Denovellis <edeno@users.noreply.github.com>
Co-authored-by: Samuel Bray <samuelbray@som-dfvnn9m-lt.ucsf.edu>
Co-authored-by: Eric Denovellis <edeno@bu.edu>

* Fix linting

---------

Co-authored-by: Chris Brozdowski <Chris.Broz@ucsf.edu>
Co-authored-by: Eric Denovellis <edeno@users.noreply.github.com>
Co-authored-by: Samuel Bray <samuelbray@som-dfvnn9m-lt.ucsf.edu>
Co-authored-by: Eric Denovellis <edeno@bu.edu>
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