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Changelog

Observes Semantic Versioning standard and Keep a Changelog convention.

[0.3.5] - 2024-08-16

  • Fix - Improve spikeglx loader in extracting neuropixels probe type from the meta file
  • Update - Explicit call to probe.create_neuropixels_probe_types() to create entries in ProbeType

[0.3.4] - 2024-03-22

  • Add - pytest
  • Update - Ephys schema changed from ephys_acute to ephys_no_curation in tutorial.ipynb

[0.3.3] - 2024-01-24

  • Update - remove PyPi release from release.yml since it will fail after the new setup.py

[0.3.2] - 2024-01-12

  • Fix - probe_geometry bugfix for incorrect handling of probes with staggered electrode positions

[0.3.1] - 2023-11-28

  • Update - Flowchart borders for consistency with other DataJoint Elements
  • Fix - dj.config() setup moved to tutorial_pipeline.py instead of __init__.py
  • Update - Elements installed directly from GitHub instead of PyPI
  • Update - Structure of the tutorial notebook

0.3.0 - 2023-10-25

  • Add - DevContainer for codespaces
  • Add - tutorial_pipeline.py
  • Add - 60 min tutorial using Jupyter Notebooks, short demo notebook
  • Update - General improvements to increase consistency with other DataJoint Elements

0.2.11 - 2023-06-29

  • Update - Improve kilosort triggering routine - better logging, remove temporary files, robust resumable processing
  • Add - Null value for package_version to patch bug
  • Update - GitHub Actions workflows
  • Update - README instructions

0.2.10 - 2023-05-26

  • Add - Kilosort, NWB, and DANDI citations
  • Fix - CSS to improve readability of tables in dark mode
  • Update - mkdocs.yaml

0.2.9 - 2023-05-11

  • Fix - .ipynb dark mode output for all notebooks.

0.2.8 - 2023-04-28

  • Fix - .ipynb output in tutorials is not visible in dark mode.

0.2.7 - 2023-04-19

  • Bugfix - A name remapping dictionary was added to ensure consistency between the column names of the metrics.csv file and the attribute names of the QualityMetrics table

0.2.6 - 2023-04-17

  • Fix - Update Pandas DataFrame column name to insert pt_ratio in QualityMetrics.Waveform table

0.2.5 - 2023-04-12

  • Add - docstrings for quality metric tables
  • Fix - docstring errors
  • Update - concepts.md
  • Update - schema diagrams with quality metrics tables

0.2.4 - 2023-03-10

  • Update - Requirements with ipywidgets and scikit-image for plotting widget

0.2.3 - 2023-02-14

  • Add - extras_require install options for nwb and development requirement sets
  • Add - mkdocs notebook rendering
  • Add - markdown linting and spellcheck config files, with implementation edits
  • Update - license for 2023
  • Update - blackify previous updates

0.2.2 - 2022-01-11

  • Bugfix - Revert import order in __init__.py to avoid circular import error.
  • Update - .pre-commit-config.yaml to disable automatic positioning of import statement at the top.
  • Bugfix - Update docstrings to render API for documentation website.

0.2.1 - 2022-01-06

  • Add - build_electrode_layouts function in probe.py to compute the electrode layout for all types of probes.
  • Update - parameterize run_CatGT step from parameters retrieved from ClusteringParamSet table
  • Update - clustering step, update duration for "median_subtraction" step
  • Bugfix - handles single probe recording in "Neuropix-PXI" format
  • Update - safeguard in creating/inserting probe types upon probe activation
  • Add - quality control metric dashboard
  • Update & fix docstrings
  • Update - ephys_report.UnitLevelReport to add ephys.ClusterQualityLabel as a foreign key reference
  • Add - .pre-commit-config.yaml

0.2.0 - 2022-10-28

  • Add - New schema ephys_report to compute and store figures from results
  • Add - Widget to display figures
  • Add - Add ephys_no_curation and routines to trigger spike-sorting analysis using Kilosort (2.0, 2.5)
  • Add - mkdocs for Element Documentation
  • Add - New QualityMetrics table to store clusters' and waveforms' metrics after the spike sorting analysis.

0.1.4 - 2022-07-11

  • Bugfix - Handle case where spike_depths data is present.

0.1.3 - 2022-06-16

  • Update - Allow for the precluster_output_dir attribute to be nullable when no pre-clustering is performed.

0.1.2 - 2022-06-09

  • Bugfix - Handle case where pc_features.npy does not exist.

0.1.1 - 2022-06-01

  • Add - Secondary attributes to PreClusterParamSteps table

0.1.0 - 2022-05-26

  • Update - Rename module for acute probe insertions from ephys.py to ephys_acute.py.
  • Add - Module for pre-clustering steps (ephys_precluster.py), which is built off of ephys_acute.py.
  • Add - Module for chronic probe insertions (ephys_chronic.py).
  • Bugfix - Missing fileTimeSecs key in SpikeGLX meta file.
  • Update - Move common functions to element-interface package.
  • Add - NWB export function

0.1.0b4 - 2021-11-29

  • Add - Processing with Kilosort and pyKilosort for Open Ephys and SpikeGLX

0.1.0b0 - 2021-05-07

  • Update - First beta release

0.1.0a5 - 2021-05-05

  • Add - GitHub Action release process
  • Add - probe and ephys elements
  • Add - Readers for: SpikeGLX, Open Ephys, Kilosort
  • Add - Probe table supporting: Neuropixels probes 1.0 - 3A, 1.0 - 3B, 2.0 - SS, 2.0 - MS