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Docs fixes for decoding pipeline #776
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* 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]>
Converting to draft pending merge of #772 |
* 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
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edeno
approved these changes
Jan 20, 2024
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Description
__init__
files to submodules so thatmkdocstrings
sees that is a subpackage_version
Checklist:
CITATION.cff
CHANGELOG.md