v1.1.0

What's Changed

• 295 readme for using ephys data module by @abuzarmahmood in #296
• Add force statements to and and other checks to pipeline shell scripts by @abuzarmahmood in #298
• 303 similarity matrix plot for units similarity by @abuzarmahmood in #304
• update docstrings by @abuzarmahmood in #311
• Add pre-commit config file by @abuzarmahmood in #306
• 302 drift detection using spike counts by @abuzarmahmood in #315
• 317 allow fitting rnn to each region separately can use flag as argument for separate regions vs all together by @abuzarmahmood in #319
• 320 add infer rnn ratespy to prefect pipeline for testing by @abuzarmahmood in #321
• refactor(infer-rnn-rates): simplify argument handling and config loading by @abuzarmahmood in #323
• added line in blech_exp_info.py that will turn bad_dig_ins into strings by @emmalala123 in #337
• fix(logging): properly close 'tee' in pipeline_graph_check by @abuzarmahmood in #345
• 341 allow option to either separately train on different tastes or train on all tastes together for infer rnn rates by @abuzarmahmood in #343
• 349 plot all channels as part of qa output by @abuzarmahmood in #351
• Fix elbo_drift.py warnings by @Mraymon5 in #362
• ci: Add workflow_dispatch trigger to enable manual workflow runs by @abuzarmahmood in #364
• ci: Update GitHub workflow to run Prefect pipeline in blech_clust conda environment by @abuzarmahmood in #368
• ci: Standardize concurrency group names across workflow jobs by @abuzarmahmood in #357
• docs: Add blog section to README with link to project blog page by @abuzarmahmood in #371
• ci: Update job dependencies to enforce Spike → EMG → Spike-EMG workflow order by @abuzarmahmood in #373
• feat: Add conditional GitHub Action for installation on 'install' tag push by @abuzarmahmood in #350
• feat: Add error handling for QA tests and update dependency graph by @abuzarmahmood in #392
• feat: Add method to load drift check results and mark unit stability by @abuzarmahmood in #393
• feat: Implement Bayesian Gaussian Mixture clustering for CAR groups by @abuzarmahmood in #401
• Patch re-running post-process by @Mraymon5 in #408
• feat: Update blech_exp_info.py to support multiple opto conditions and laser parameters by @abuzarmahmood in #400
• update make_arrays for multi-opto by @abuzarmahmood in #415
• update units characteristics plotting by @abuzarmahmood in #416
• refactor: Remove redundant spike-only test from Prefect pipeline by @abuzarmahmood in #420
• feat: Enhance blech_exp_info.py with caching and default value support by @abuzarmahmood in #419
• 307 allow over riding default classifier threshold by @abuzarmahmood in #426
• feat: Add S3 upload functionality for pipeline test outputs by @abuzarmahmood in #358
• refactor: Replace BGM with K-Means clustering using BIC for electrode selection by @abuzarmahmood in #425
• refactor: Improve modularity and reduce class interdependencies in spike processing pipeline by @abuzarmahmood in #435

New Contributors

• @emmalala123 made their first contribution in #337

Full Changelog: 1.0.0...1.1.0

1.0.0

• Improved handling of digital input names and indices
• Remove redundancy in reading digital inputs between blech_exp_info and downstream processing
• Support (and testing) for processing Intan traditional file format

Note

• Since dig-ins are now read using the dig_in_frame.csv during downstream processing, this version is not backwards compatible with earlier versions

0.0.1

Updates over OG blech_clust:

• Metadata handling
• Functionality for auto-sorting
• Ability to handle uneven trials in EMG
• Pipeline testing
• Improved plotting
• Streamlined setup and dependency management (including merging EMG environment into main blech_clust environment)
• Interface with BlechRNN to infer firing rates using population-based RNN

What's Changed

• Abu collab by @abuzarmahmood in #1
• Cluster approx by @abuzarmahmood in #14
• Abu master by @abuzarmahmood in #15
• Emg updates by @abuzarmahmood in #35
• Updates to support one file per signal type by @hfgem in #38
• Blech process refactor by @abuzarmahmood in #60
• Blech process refactor by @abuzarmahmood in #61
• Add faster algorithm for calculating collisions by @abuzarmahmood in #64
• Include all-trial plot with envelope and detected gapes by @abuzarmahmood in #66
• Workflow by @abuzarmahmood in #69
• using relative path from script to find blech_clust path by @abuzarmahmood in #71
• Extract waveforms hannah by @abuzarmahmood in #73
• Allow session to not contain any taste info by @abuzarmahmood in #77
• bug fixes for waveform_classifier "throw_out_noise" setting by @abuzarmahmood in #78
• Emg updates by @abuzarmahmood in #83
• Restructure car by @abuzarmahmood in #84
• 80 test for bridges channels by @abuzarmahmood in #86
• Allow handling uneven trials... by @abuzarmahmood in #98
• 88 bash parallel step should take directory as input by @abuzarmahmood in #91
• Add subplots for ISI dist and spike-counts over time by @abuzarmahmood in #99
• Plot datashader waveforms, avg waveform, ISI dist, and spike raster, … by @abuzarmahmood in #102
• 103 hierarchical plot for classified positive neurons by @abuzarmahmood in #104
• Fix digin numbering by @abuzarmahmood in #105
• Fix digin numbering by @abuzarmahmood in #106
• Add blech_run_process.sh file + fix classifier plot issues. by @abuzarmahmood in #109
• 108 making changes to params folders prevents future git pulls by @abuzarmahmood in #114
• Add OMP_NUM_THREADS limit to blech_process_single, and remove generat… by @abuzarmahmood in #115
• 110 update readme to align with latest code by @abuzarmahmood in #112
• [HOTFIX] Fix big with exporting OMP_NUM_THREADS...not needed as blech… by @abuzarmahmood in #117
• [HOTFIX] rename variable to correct name by @abuzarmahmood in #118
• Refactor blech_post_process for fixing bugs and improving readability by @abuzarmahmood in #123
• Generate 2 plots for every merge: 1) color each cluster, 2) show all … by @abuzarmahmood in #124
• Create a directory for quality control scripts by @abuzarmahmood in #125
• [FIX] Fix issues with HDF5 handling during post-process by @abuzarmahmood in #126
• Add file to run QA steps by @abuzarmahmood in #128
• Provide STFT as an alternative option for BSA in EMG processing by @abuzarmahmood in #130
• 26 auto clustering by @abuzarmahmood in #127
• Hierarchical clustering plot to better assess cluster stability by @abuzarmahmood in #138
• 119 overlay psth add heatmaps by @abuzarmahmood in #139
• Add plot with dig-in order to QA_output dir by @abuzarmahmood in #140
• Functionality to automatically post-process if clustering was also automatic by @abuzarmahmood in #142
• 148 separate emg outputs in hdf5 by dig in by @abuzarmahmood in #153
• Adding my changes to a test branch by @Mraymon5 in #177
• Bat safer edits by @Mraymon5 in #178
• Update conda_requirements_base.sh by @Mraymon5 in #187
• Update blech_process.py by @Mraymon5 in #185
• Update cluster_stability.py by @Mraymon5 in #184
• Remove agg backend from blech_process_utils by @abuzarmahmood in #194
• Make primary positional argument to blech_post_process.py by @abuzarmahmood in #195
• Set seed for all mixture models to ensure repeatibility of clustering by @abuzarmahmood in #196
• 155 change npint to int by @Mraymon5 in #192
• Add progress bar / report while removing raw recordings by @abuzarmahmood in #198
• Update blech_process_utils.py by @Mraymon5 in #200
• 176 blech run qa error by @abuzarmahmood in #202
• 171 make faq with deleting resultslog for blech run processpy by @Mraymon5 in #190
• 45 workflow management -- only run next step if dependencies have been fulfilled by @abuzarmahmood in #204
• 208 python only setup for emg by @abuzarmahmood in #211
• 209 no emg dataset for testing can simply be done by using a different exp info file by @abuzarmahmood in #212
• Add ephys_data as a utility by @abuzarmahmood in #215
• Do not coerce digin names to int by @Mraymon5 in #220
• 176 blech run qa error, part 2: spike train plotting by @Mraymon5 in #207
• 225 Add code to infer firing rates using BlechRNN by @abuzarmahmood in #226
• Update blech_process_utils.py by @Mraymon5 in #181
• 206 issues with emg data or lack thereof in blech make arrayspy by @Mraymon5 in #219
• Add missing sampling_rate argument by @Mraymon5 in #222
• 8 add testing and cicd for repo by @abuzarmahmood in #224
• Palatability calc by @abuzarmahmood in #230
• 228 add opto + emg regions to info files by @abuzarmahmood in #231
• Refactor palatability identity setup and plot by @abuzarmahmood in #234

New Contributors

• @abuzarmahmood made their first contribution in #1
• @hfgem made their first contribution in #38
• @Mraymon5 made their first contribution in #177

Full Changelog: https://github.com/katzlabbrandeis/blech_clust/commits/0.0.1