# Changelog

Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.

## [0.4.5] - 2025-09-17

+ Fix - Rename `env.yml` to `conda_env.yml` for consistency with other projects
+ Update - Passing tests by blackifying previous updates

## [0.4.4] - 2025-06-06

+ Update - Update params in test/tutorial
+ Fix - Moved KiloSort's template_features  to additional_files 

## [0.4.3] - 2025-06-03

+ Update - Use `Spikeinterface` official released versions (instead of install directly from source)

## [0.4.2] - 2025-03-25

+ Fix - Add key_source to `ProbeLevelReport` to filter for 'good' quality units

## [0.4.1] - 2025-02-13

+ Fix - Auto generate ProbeInsertion allows duplicate probes (e.g. probe reuse)

## [0.4.0] - 2025-01-28

+ Update - No longer support multiple variation of ephys module, keep only `ephys_no_curation` module, renamed to `ephys`
+ Update - Remove other ephys modules (e.g. `ephys_acute`, `ephys_chronic`) (moved to different branches)
+ Feat - Add support for `SpikeInterface`
+ Update - Remove support for `ecephys_spike_sorting` (moved to a different branch)
+ Update - Simplify the "activate" mechanism

## [0.3.8] - 2025-01-16

* Fix - Revert GHA Semantic Release caller and update changelog

## [0.3.7] - 2024-11-01

* Fix - robust IMAX value detection from IMEC file (metadata 3.0)

## [0.3.6] - 2024-10-01

* Fix - Minor bugfix in reading npx probe model of older versions and in reaeding probe model
* Add - New GitHub Action callers for devcontainer, mkdocs, and semantic release

## [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
* Fix - Fix regex patterns and add minimum version for scikit-image

## [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

[0.3.6]: https://github.com/datajoint/element-array-ephys/releases/tag/0.3.6
[0.3.5]: https://github.com/datajoint/element-array-ephys/releases/tag/0.3.5
[0.3.1]: https://github.com/datajoint/element-array-ephys/releases/tag/0.3.1
[0.2.11]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.11
[0.2.10]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.10
[0.2.9]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.9
[0.2.8]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.8
[0.2.7]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.7
[0.2.6]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.6
[0.2.5]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.5
[0.2.4]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.4
[0.2.3]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.3
[0.2.2]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.2
[0.2.1]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.1
[0.2.0]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.0
[0.1.4]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.4
[0.1.3]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.3
[0.1.2]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.2
[0.1.1]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.1
[0.1.0]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.0
[0.1.0b4]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.0b4
[0.1.0b0]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.0b0
[0.1.0a5]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.0a5