Nwb insert config #1
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* Fix failing chains pytests * Update docstrings, changelog
* move restiction when fetch_nwb from merge table into argument * add default ripple parameters for trodes position data * update ripple detection to mediumnwb file * Add curation steps to spikesorting v0 notebook * fix spelling * change import alias --------- Co-authored-by: Eric Denovellis <[email protected]>
This is now redundant with the SpikesortingV0 tutorial
* Refine query of upstream tables on FigURL populate * Update changelog * Typo --------- Co-authored-by: Eric Denovellis <[email protected]>
* Fix dlc video and kachery cloud config * Update CHANGELOG.md --------- Co-authored-by: Chris Brozdowski <[email protected]>
* Docs updates * Exclude docs branch from gh-wf
* reduce demo data size, insert parameter sets into new database * Update spikesort v0 notebook to run on new database * Update spikesort v1 notebook * fix spelling
* update call to get_template_extremum * update changelog * make version check more robust * spelling * update location of get_template)extremum_channel_peak_shift * Remove backcompatability for spikeinterface
* Add sg version to created analysis nwb files * update changelog
* Preliminary code * Add retrieval of file names * Add get_nwb_table function * Update docstrings * Update CHANGELOG.md
…times` (LorenFrankLab#904) * Squeeze results * Make method and not class method * Update CHANGELOG.md
* check for entry in merge part table prior to insert * update changelog
* Prioritize datajoint filepath for getting analysis file abs_path * remove deprecated kachery tables * update changelog * fix lint --------- Co-authored-by: Samuel Bray <[email protected]> Co-authored-by: Eric Denovellis <[email protected]>
Strip will remove leading characters
* LorenFrankLab#892 * LorenFrankLab#885 * LorenFrankLab#879 * Partial address of LorenFrankLab#860 * Update Changelog * Partial solve of LorenFrankLab#886 - Ask import * Fix failing tests * Add note on order of inheritace * LorenFrankLab#933 * Could not replicate fill_nan error. Reverting except clause
* 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 LorenFrankLab#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
* 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
…kLab#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
* Add logging for any func that creates AnalysisNwbfile
* fix bug on empty delete in merge table * update changelog * fix spelling --------- Co-authored-by: Chris Brozdowski <[email protected]>
* Create class for group parts to help propagate deletes * spelling * update changelog * Part delete edits (LorenFrankLab#946) * Add spyglass version to created analysis nwb files (LorenFrankLab#897) * Add sg version to created analysis nwb files * update changelog * Change existing source script to spyglass version (LorenFrankLab#900) * Add pynapple support (LorenFrankLab#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` (LorenFrankLab#904) * Squeeze results * Make method and not class method * Update CHANGELOG.md * fix bugs in fetch_nwb (LorenFrankLab#913) * Check for entry in merge part table prior to insert (LorenFrankLab#922) * check for entry in merge part table prior to insert * update changelog * Kachery fixes (LorenFrankLab#918) * Prioritize datajoint filepath for getting analysis file abs_path * remove deprecated kachery tables * update changelog * fix lint --------- Co-authored-by: Samuel Bray <[email protected]> Co-authored-by: Eric Denovellis <[email protected]> * remove old tables from init (LorenFrankLab#925) * Fix improper uses of strip (LorenFrankLab#929) Strip will remove leading characters * Update CHANGELOG.md * Misc Issues (LorenFrankLab#903) * LorenFrankLab#892 * LorenFrankLab#885 * LorenFrankLab#879 * Partial address of LorenFrankLab#860 * Update Changelog * Partial solve of LorenFrankLab#886 - Ask import * Fix failing tests * Add note on order of inheritace * LorenFrankLab#933 * Could not replicate fill_nan error. Reverting except clause * Export logger (LorenFrankLab#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 LorenFrankLab#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 (LorenFrankLab#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 (LorenFrankLab#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 (LorenFrankLab#941) * Add logging for any func that creates AnalysisNwbfile * Fix bug on empty delete in merge table (LorenFrankLab#940) * fix bug on empty delete in merge table * update changelog * fix spelling --------- Co-authored-by: Chris Brozdowski <[email protected]> * Remove master restriction * Part delete takes restriction from self --------- Co-authored-by: Samuel Bray <[email protected]> Co-authored-by: Eric Denovellis <[email protected]> Co-authored-by: Samuel Bray <[email protected]> Co-authored-by: Eric Denovellis <[email protected]> * Fix linting --------- Co-authored-by: Chris Brozdowski <[email protected]> Co-authored-by: Eric Denovellis <[email protected]> Co-authored-by: Samuel Bray <[email protected]> Co-authored-by: Eric Denovellis <[email protected]>
* Fix bug report template html * Update changelog
* Fix errored test teardown * Docs build pin, docstring fixes * Update overview page * Update changelog * Fix 0.X -> 1.X, remove sponsor-only option
* initial commit for restrict_from_upstream * Add tests for RestrGraph * WIP: ABC for RestrGraph * WIP: ABC for RestrGraph 2 * WIP: ABC for RestrGraph 3 * WIP: Operator for 'find upstream key' * WIP: Handle all alias cases in _bridge_restr * WIP: Add tests * WIP: Cascade through merge tables * WIP: add docs * WIP: Revise tests * WIP: Add way to ban item from search * Revert pytest options * Fix failing tests * Bail on cascade if restr empty * Update src/spyglass/utils/dj_mixin.py Co-authored-by: Samuel Bray <[email protected]> * Permit dict/list-of-dict restr on long-distance restrict --------- Co-authored-by: Sam Bray <[email protected]> Co-authored-by: Eric Denovellis <[email protected]>
* WIP: transaction on populate_all_common * ✅ : Seperate rollback and raise err options
* Permit multiple restrict_by * Update Changelog * Fix typo
…Lab#970) * fix dlc pose estimation populate if no raw position data * allow dlc pipeline to run without raw spatial data * update changelog * string formatting * fix analysis nwb create time
…renFrankLab#970)" (LorenFrankLab#972) This reverts commit 113ce9a. Co-authored-by: Chris Brozdowski <[email protected]>
* Address failing tests * Revert to bare make for no transaction * Update changelog
…Lab#973) * fix dlc pose estimation populate if no raw position data * allow dlc pipeline to run without raw spatial data * update changelog * string formatting * fix analysis nwb create time * review changes * allow empty returns from convert_epoch_interval_name_ without error * switch to getattr --------- Co-authored-by: Sam Bray <[email protected]> Co-authored-by: Chris Brozdowski <[email protected]>
* wrong function call * get epoch directly from table key * default to opencv for speed * update changelog
* LorenFrankLab#981: -> * Update changelog
LorenFrankLab#985) * Separate optional fields * Provide default for filtering * Black * Use get
* WIP: Add vid downloader, start position pytests * WIP: Full coverage on common_position.py * WIP: Start add tests for DLC * WIP: pytests for position 2 * WIP: Align yml files * WIP: Add DLC Centroid tests * WIP: tests for centoid, model, orietation * WIP: Subpackage coverage 72% * WIP: Run tests on main * WIP: Add prints to debug data download * WIP: remove redundant slash * WIP: download full directory * WIP: let pytests down dlc items * WIP: gh-action managed container * WIP: use mysql as service * WIP: fix container ID * WIP: revise no-docker arg name * WIP: Box vars available to test step * WIP: Only first test * WIP: remove duplicate installs from conda deps -> pyproject * WIP: Add cuda driver * WIP: Cuda method selective * WIP: unpin DLC * WIP: parameterize skipping dlc tests * WIP: Add back Checkout * WIP: All download in action * WIP: custom wget func * WIP: revise data downloader * WIP: Run all * WIP: no docker container id in test database_settings * WIP: revise utils tests for --no-docker * WIP: add password to DatabaseSettings no-docker run * WIP: Spellcheck * WIP: debug mysql add role command * WIP: fix typo * 🎉 : Update changelog * Edit PR template to remind of local tests * Revert conda-installed dependencies * Return mountainsort to conda pip list * Upgrade action versions per node.js 16 deprecation
* Save LFP as pynwb.ecephys.LFP * Fix formatting * Fix formatting * Don't reinsert name * Recompose name * Fix second referece to * Update CHANGELOG.md --------- Co-authored-by: Eric Denovellis <[email protected]> Co-authored-by: CBroz1 <[email protected]> Co-authored-by: Eric Denovellis <[email protected]>
…ab#996) * Add docstrings * update changelog * fix spelling --------- Co-authored-by: Samuel Bray <[email protected]>
* Add Common Errors * Update changelog
* documented some of mua notebook * mua notebook documented * documented some of mua notebook * synced py script
* compile exported files, download dandiset, and organize * add function to translate files into dandi-compatible names * add table to store dandi name translation and steps to populate * add dandiset validation * add function to fetch nwb from dandi * add function to change obj_id of nwb_file * add dandi upload call and fix circular import * debug dandi file streaming * fix circular import * resolve dandi-streamed files with fetch_nwb * implement review comments * add admin tools to fix common dandi discrepencies * implement tool to cleanup common dandi errors * add dandi export to tutorial * fix linting * update changelog * fix spelling * style changes from review * reorganize function locations * fix circular import * make dandi dependency optional in imports * store dandi instance of data in DandiPath * resolve case of pre-existing dandi entries for export * cleanup bugs from refactor * update notebook * Apply suggestions from code review Co-authored-by: Chris Broz <[email protected]> * add requested changes from review * make method check_admin_privilege in LabMember --------- Co-authored-by: Chris Broz <[email protected]>
* give analysis nwb new uuid when created * fix function argument * update changelog
* fix bug in change in analysis_file_object_id * update changelog
* LorenFrankLab#976 * Remove notebook reference
* initial non daemon parallel commit * resolve namespace and pickling errors * fix linting * update changelog * implement review comments * add parallel_make flag to spikesorting recording tables * fix multiprocessing spawn error on mac * move propert --------- Co-authored-by: Samuel Bray <[email protected]>
* Give UUID to artifact interval * Add ability to set smoothing sigma in get_firing_rate (LorenFrankLab#994) * add option to set spike smoothing sigma * update changelog * Add docstrings to SortedSpikesGroup and Decoding methods (LorenFrankLab#996) * Add docstrings * update changelog * fix spelling --------- Co-authored-by: Samuel Bray <[email protected]> * Add Common Errors doc (LorenFrankLab#997) * Add Common Errors * Update changelog * Mua notebook (LorenFrankLab#998) * documented some of mua notebook * mua notebook documented * documented some of mua notebook * synced py script * Dandi export and read (LorenFrankLab#956) * compile exported files, download dandiset, and organize * add function to translate files into dandi-compatible names * add table to store dandi name translation and steps to populate * add dandiset validation * add function to fetch nwb from dandi * add function to change obj_id of nwb_file * add dandi upload call and fix circular import * debug dandi file streaming * fix circular import * resolve dandi-streamed files with fetch_nwb * implement review comments * add admin tools to fix common dandi discrepencies * implement tool to cleanup common dandi errors * add dandi export to tutorial * fix linting * update changelog * fix spelling * style changes from review * reorganize function locations * fix circular import * make dandi dependency optional in imports * store dandi instance of data in DandiPath * resolve case of pre-existing dandi entries for export * cleanup bugs from refactor * update notebook * Apply suggestions from code review Co-authored-by: Chris Broz <[email protected]> * add requested changes from review * make method check_admin_privilege in LabMember --------- Co-authored-by: Chris Broz <[email protected]> * Minor fixes (LorenFrankLab#999) * give analysis nwb new uuid when created * fix function argument * update changelog * Fix bug in change in analysis_file object_id (LorenFrankLab#1004) * fix bug in change in analysis_file_object_id * update changelog * Remove classes for usused tables (LorenFrankLab#1003) * LorenFrankLab#976 * Remove notebook reference * Non-daemon parallel populate (LorenFrankLab#1001) * initial non daemon parallel commit * resolve namespace and pickling errors * fix linting * update changelog * implement review comments * add parallel_make flag to spikesorting recording tables * fix multiprocessing spawn error on mac * move propert --------- Co-authored-by: Samuel Bray <[email protected]> * Update pipeline column for IntervalList --------- Co-authored-by: Samuel Bray <[email protected]> Co-authored-by: Samuel Bray <[email protected]> Co-authored-by: Chris Broz <[email protected]> Co-authored-by: Denisse Morales-Rodriguez <[email protected]> Co-authored-by: Samuel Bray <[email protected]>
* Fix artifact list_triggers * Black * Update changelog
* remove problem key in DLCPosV1 fetch_nwb attrs * update changelog
* WIP: pytests for common & lfp * WIP: pytests for utils 1 * ✅ : pytests for utils, position, linearization * Remove unnecessary lfp_band checks. Add deprecation warn on permission set * WIP: Tidy position 1 * WIP: Tidy position 2 * Spellcheck tests * Reduce pop_all_common redundancy * PosIntervalMap LorenFrankLab#849 * Logger decorator, unify make_video logic * Update changelog/requirements * Misc edits * Change deprecation warning * Video func name specificity * Revise centroid calc * Fix errors * Vectorize orient calc. Remove multitable stack warn * Revert blit
* WIP: No Orphans downstream * WIP: Bidirectional RestrGraph, remove TableChains * WIP: bridge up to interval list * Add tests for new delete * Update changelog * Fix typo * WIP: topological sort of deletes * ✅ : Topological sort * Revise downloads * Update src/spyglass/utils/dj_helper_fn.py Co-authored-by: Samuel Bray <[email protected]> * Ignore unimported non-spyglass in cascade * Load part-master cache before graph * Add more automatic imports * Pin twine req for build --------- Co-authored-by: Samuel Bray <[email protected]>
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Description
Merges master branch and implements default arguments requested in PR