Kilosort

This release adjusts saved template amplitudes, which fixes a template scaling issue in Phy and affects the displayed amplitude values for Phy. It also reverts a "fix" that was added to stop negative spike times from showing up for the first data batch, since that was causing a misalignment issue. Negative spike times are currently possible again, but should be rare - a message will show up after the spike detection step if any negative spike times are found, until we figure out what's causing this.

**Full Changelog**: https://github.com/MouseLand/Kilosort/compare/v4.0.6...v4.0.7

Along with miscellaneous bug fixes, this release allows some sections of the GUI to be resized. After installing, you will probably notice that the proportions have changed. You can customize this yourself by clicking and dragging on the handles shown in the image below (circled red). Any resizing will be saved and restored the next time you open the GUI.

**Full Changelog**: https://github.com/MouseLand/Kilosort/compare/v4.0.4...v4.0.6

Sorting should now work for multi-shank probes without needing to vertically stack the shanks.

This release adds distance gating for universal template positions, to match the behavior of previous versions of Kilosort. By default, templates will be excluded if they are farther than `max(dmin, dminx)` microns from the nearest active site. This can be adjusted manually by changing the new `max_channel_distance` parameter in "Extra settings." Universal template placement can be previewed in the GUI by checking "Universal Templates" under the probe plot. Note that changing any of `dmin, dminx or max_channel_distance` will change the positions of the universal templates, but this will not show on the plot until you change one of the other options or click "Preview Probe" again. The probe plot also includes axes to show scale, and a "True Aspect Ratio" checkbox to switch to a physically proportional representation.

Additionally, center points for template groupings are now determined in a way that should work well for multi-shank probes, removing the need for artificially stacking shanks on top of one another. The placement of these grouping centers can also be previewed in the GUI by checking "Grouping Centers" under the probe plot. You should see one column of centers on each shank. If this is not happening, or if you're using a 2D array, you may need to specify the new `x_centers` parameter in "Extra settings."

**Full Changelog**: https://github.com/MouseLand/Kilosort/compare/v4.0.3...v4.0.4

This release adds `pc_features.npy` and `pc_feature_ind.npy` for use with feature view in Phy. Additionally, the GUI backend was updated from PyQt5 to QtPy, which is compatible with PyQt5, PyQt6, and PySide. This should result in fewer installation issues. If you previously installed Kilosort from source, you will need to reinstall after updating the code to update your GUI dependencies.

Several bug fixes are included as well:
* `dminx` will no longer be determined automatically, the default value is 32. This removes a bug with that behavior related to checkerboard electrode layouts. You may need to update the value in the GUI under "extra settings," or click on "reset GUI," to update this.
* Setting `n_pcs` to values other than 6 will no longer cause a crash.
* Fixed bug that could cause negative spike times to be detected for first batch.
* Added informative errors related to `dminx` and electrode spacing.
* Misc fixes to GUI behavior.

**Full Changelog**: https://github.com/MouseLand/Kilosort/compare/v4.0.2...v4.0.3

Initial release of Kilosort4, linked with paper.

This release fixes both bugs for the spike holes problem (issue https://github.com/MouseLand/Kilosort/issues/594). The default value of the NT parameter has changed to 65,472 in configFile384. You need to use these defaults to fix the spike holes problem (or the rules specified in configFile384 for NT and ntbuff). Please recompile the CUDA functions with mexGPUall.

The release will be updated if further modifications are made (patch2, 3 etc).

Note: the previous release 3.0.1 had incorrect spike times and only fixed one of the two bugs.