Quickfix for fetch_nwb #913
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
CBroz1
approved these changes
Apr 3, 2024
CBroz1
approved these changes
Apr 3, 2024
edeno
added a commit
that referenced
this pull request
Apr 25, 2024
* 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 pull request
May 6, 2024
* 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>
This pull request was closed.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
fixes #912
fetch_nwb