Lightning-pose

Main contributions are functioning CI and the cropzoom pipeline (see [here](https://lightning-pose.readthedocs.io/en/latest/source/user_guide_advanced/cropzoom_pipeline.html))

What's Changed
* Minor fixes by ksikka in https://github.com/paninski-lab/lightning-pose/pull/241
* Automatically set num_workers to cpu count by ksikka in https://github.com/paninski-lab/lightning-pose/pull/243
* Add option to use steps instead of epochs by ksikka in https://github.com/paninski-lab/lightning-pose/pull/242
* add NaNPCA transform method and tests by themattinthehatt in https://github.com/paninski-lab/lightning-pose/pull/245
* Update run-tests.yml by ksikka in https://github.com/paninski-lab/lightning-pose/pull/246
* Skip failing cropzoom test for now by ksikka in https://github.com/paninski-lab/lightning-pose/pull/251
* Simplify metric code by ksikka in https://github.com/paninski-lab/lightning-pose/pull/247
* Add CI scripts and documentation by ksikka in https://github.com/paninski-lab/lightning-pose/pull/249
* CI: cancel previous build on push by ksikka in https://github.com/paninski-lab/lightning-pose/pull/252
* Add support for cropzoom pipeline by ksikka in https://github.com/paninski-lab/lightning-pose/pull/250


**Full Changelog**: https://github.com/paninski-lab/lightning-pose/compare/v1.7.0...v1.7.1

What's Changed
* make cropzoom tests compatible with python 3.8 by themattinthehatt in https://github.com/paninski-lab/lightning-pose/pull/229
* get rid of unnecessary lightning logs during inference by themattinthehatt in https://github.com/paninski-lab/lightning-pose/pull/230
* Fix issues reading labels file with empty first row by ksikka in https://github.com/paninski-lab/lightning-pose/pull/234
* Split up train, add Model class, add litpose CLI by ksikka in https://github.com/paninski-lab/lightning-pose/pull/232
* Add docs on Model, litpose by ksikka in https://github.com/paninski-lab/lightning-pose/pull/237
* Upgrade some union, list, dict annotations to 3.10 by ksikka in https://github.com/paninski-lab/lightning-pose/pull/239


**Full Changelog**: https://github.com/paninski-lab/lightning-pose/compare/v1.6.1...v1.7.0

What's Changed
* Save copy of labeled data csv to output dir by ksikka in https://github.com/paninski-lab/lightning-pose/pull/222
* Fix tests and post-training analysis behavior by ksikka in https://github.com/paninski-lab/lightning-pose/pull/221
* Save out detector artifacts on detector training by ksikka in https://github.com/paninski-lab/lightning-pose/pull/224
* fix bad import by themattinthehatt in https://github.com/paninski-lab/lightning-pose/pull/226
* add left-right flip option to augmentations by themattinthehatt in https://github.com/paninski-lab/lightning-pose/pull/227
* update version by themattinthehatt in https://github.com/paninski-lab/lightning-pose/pull/228


**Full Changelog**: https://github.com/paninski-lab/lightning-pose/compare/v1.6.0...v1.6.1

What's Changed
Major updates for this release include multi-GPU training, new imgaug transforms, and many small usability improvements
* update sleap2lp.py by themattinthehatt in https://github.com/paninski-lab/lightning-pose/pull/196
* Upgrade sphinx-rtd-theme to fix search 200 by ksikka in https://github.com/paninski-lab/lightning-pose/pull/201
* Fix search attempt 2. Fix 200 by ksikka in https://github.com/paninski-lab/lightning-pose/pull/202
* Log hydra job config to tensorboard by ksikka in https://github.com/paninski-lab/lightning-pose/pull/204
* Change backbone finetuning strategy to allow for DDP by ksikka in https://github.com/paninski-lab/lightning-pose/pull/205
* Support multi-GPU training for supervised training by ksikka in https://github.com/paninski-lab/lightning-pose/pull/206
* Multi-GPU support for unsupervised learning by ksikka in https://github.com/paninski-lab/lightning-pose/pull/207
* Continuous integration using github actions by ksikka in https://github.com/paninski-lab/lightning-pose/pull/208
* add coarse salt/pepper to imgaug transforms by themattinthehatt in https://github.com/paninski-lab/lightning-pose/pull/209
* Added option to choose colormap for labelled videos by hummuscience in https://github.com/paninski-lab/lightning-pose/pull/211
* complete config file documentation by themattinthehatt in https://github.com/paninski-lab/lightning-pose/pull/213
* Add PCA Centering method (experimental) by ksikka in https://github.com/paninski-lab/lightning-pose/pull/214
* Context frames can use any delimiter by ksikka in https://github.com/paninski-lab/lightning-pose/pull/216
* Replace relative paths with absolute paths in demo config by ksikka in https://github.com/paninski-lab/lightning-pose/pull/217
* Fix doc build failure by ksikka in https://github.com/paninski-lab/lightning-pose/pull/218
* Update README.md with downloads/week badge by ksikka in https://github.com/paninski-lab/lightning-pose/pull/219

New Contributors
* ksikka made their first contribution in https://github.com/paninski-lab/lightning-pose/pull/201

**Full Changelog**: https://github.com/paninski-lab/lightning-pose/compare/v1.5.1...v1.6.0

Several small updates, as well as reverting the default training setup to automatically save out the best model according to validation metrics, rather than the last model.

* make sure validation loader always has at least one sample
* allow for early stopping again, as well as saving out model weights every n epochs
* make training fully deterministic
* increase flexibility of LitDaliWrapper to work with custom dali video pipeline functions
* increase flexibility of keypoint correspondence array for true multiview datasets

What's Changed
* Passing vfr_check to fn.readers.video by hummuscience in https://github.com/danbider/lightning-pose/pull/179, https://github.com/danbider/lightning-pose/pull/180
* remove augmentations for val/test data by themattinthehatt in https://github.com/danbider/lightning-pose/pull/181
* implement pca object that handles NaNs by themattinthehatt in https://github.com/danbider/lightning-pose/pull/184
* support for multiple data streams by themattinthehatt farzad-ziaie Selmaan in https://github.com/danbider/lightning-pose/pull/187


**Full Changelog**: https://github.com/danbider/lightning-pose/compare/v1.4.0...v1.5.0