Deeplabcut

What's Changed
* Update beginners-guide.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2619
* Update DEEPLABCUT.yaml by EitanHemed in https://github.com/DeepLabCut/DeepLabCut/pull/2625
* Add feature to evaluate network for specfic, named snapshots. by Tetra-quark in https://github.com/DeepLabCut/DeepLabCut/pull/2508
* fixed file dialog not showing uppercase file extension video files by park-jsdev in https://github.com/DeepLabCut/DeepLabCut/pull/2645
* Swap button added to the track refinement GUI by JulianAlvarezdeGiorgi in https://github.com/DeepLabCut/DeepLabCut/pull/2680
* Fixes for testscript_3d.py by jesse-gilmer in https://github.com/DeepLabCut/DeepLabCut/pull/2443
* Allow processing of videos in MKV containers by ximion in https://github.com/DeepLabCut/DeepLabCut/pull/2701
* add in CZI EOSS badge and funding section by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2735
* Fix minimalnumberofconnections by segashin in https://github.com/DeepLabCut/DeepLabCut/pull/2718
* Benchmarking user guide by dikraMasrour in https://github.com/DeepLabCut/DeepLabCut/pull/2716
* adding docs for using data labeled elsewhere (formatting) by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2736
* Update standardDeepLabCut_UserGuide.md by bendichter in https://github.com/DeepLabCut/DeepLabCut/pull/2761
* Create citation.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2767
* Fix failing tests - `tmpdir_factory` dir creation on OSX by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2768
* Update DLC3 PyTorch docs by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2804
* Pins `numpy<2`, fix svd for `scipy>=1.11.0` by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2827
* Fix reading filtered state by maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2844
* Remove pickle5 dependency from madlc Colab by maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2846
* Fixed `dropimagesduetolackofannotation` to work with single-animal data by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2850
* Fixed conversion of dict to list for proper future indexing by m-beau in https://github.com/DeepLabCut/DeepLabCut/pull/2855
* fixes to label_frames, addition of docstring by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2858
* Pin TensorFlow according to OS; Fix DeepLabCut install in Colab to deal with new requirements. by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2862
* Remove unused GUI button in analyze videos tab by maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2875
* Fix video addition in VideoSelectionWidget by maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2878
* v2.3.11 by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2882
* improved handling of animal names when analyzing videos by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2884

New Contributors
* park-jsdev made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2645
* JulianAlvarezdeGiorgi made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2680
* jesse-gilmer made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2443
* ximion made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2701
* segashin made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2718
* dikraMasrour made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2716
* bendichter made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2761
* m-beau made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2855

maximpavliv joined the software team!

Funding includes [ChanZuckerberg Initiative's Essential Open Source Software for Science](https://chanzuckerberg.com/eoss/). Thanks!

**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.3.10...v2.3.11

What's Changed
* Doc re-arrangement in the TOC by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2523
* slight change to setup (move all TF to TF tag; pin tables, add note that python 3.9 is currently required by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2517
* Use video crop coordinates appropriately in create_video_with_all_detections by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2524
* Avoid infinite loop in `mine()` when there are no overlapping tracklets by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2525
* fix manual frame extraction with symlinks by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2527
* Update COLAB_DLC_ModelZoo.ipynb by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2533
* Adding a Quick Guide (from the wiki to the docs!) by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2532
* quick file fix by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2534
* Update installTips.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2536
* Video analysis on cropped videos: bug fixes for `extract_outlier_frames` and `create_video_with_all_detections` by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2538
* MacOS CI Fix - FFMpeg Installation by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2559
* niels/check_for_duplicate_videos by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2558
* Update setup.py by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2526
* bug fix: missing images during evaluation by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2570
* Update label and warn users of the absence of videos by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2586
* pin matplotlib version by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2583
* Correct DEEPLABCUT.yaml and DEEPLABCUT_M1.yaml reference. by midumitrescu in https://github.com/DeepLabCut/DeepLabCut/pull/2573
* minor spelling fixes by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2594
* Fix 2d line data setter by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2599
* Auto check for dlclibrary & napari-deeplabcut updates when the GUI opens by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2600
* Update README.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2601
* Release by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2602

New Contributors
* midumitrescu made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2573

**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.3.9...v2.9.10

* Add GUI help button back by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2507

What's Changed
* Pull demo data from Zenodo by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2440
* Update maDLC_UserGuide.md by Timokleia in https://github.com/DeepLabCut/DeepLabCut/pull/2446
* Fix bug dataset and metadataset fixes DeepLabCut/DeepLabCut2390 by Tetra-quark in https://github.com/DeepLabCut/DeepLabCut/pull/2405
* Bug fix: `add_new_videos(..., extract_frames=True)` by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2468
* bug fix: empty predictions during video analysis by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2467
* Update README.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2464
* Update AUTHORS by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2475
* updated macOS runner to 13 by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2484
* Update README.md by Timokleia in https://github.com/DeepLabCut/DeepLabCut/pull/2496
* Bump version of `tables` installed during CI by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2500
* updated COLAB notebooks to install a CUDA version compatible with DLC by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2506
* updated package requirements by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2513
* Test for the presence of snapshot files when using modelzoo by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2485
* Version update by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2514


**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.3.8...v2.3.9

What's Changed

* **better augmentation for maDLC:** Fix fliplr augmentation for multi animal 2 by biol-jsh in https://github.com/DeepLabCut/DeepLabCut/pull/2043
* Improved transfer learning for DLC ModelZoo by yeshaokai in https://github.com/DeepLabCut/DeepLabCut/pull/2389
* Improvements to the model zoo's GUI tab by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2431
* "deeplabcut.filterpredictions" and "deeplabcut.analyze_skeleton" return mappings by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1908
* Let user change the search window size during corner detection refinement by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2414
* Install DLC from PyPI rather than its local version in M1 Macs by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2416
* Correct link to platform specifications page by molecules in https://github.com/DeepLabCut/DeepLabCut/pull/2423
* Automatically check for napari-deeplabcut updates (in addition to DLC) by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2422
* Smartly restore pretrained model weights by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2426
* Fix video adaptation by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2436

New Contributors
* molecules made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2423

Funding includes [ChanZuckerberg Initiative's Essential Open Source Software for Science](https://chanzuckerberg.com/eoss/). Thanks!

**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.3.7...v2.3.8

What's Changed

* update the lr when switching to adam optimizer by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2393
* Update maDLC_UserGuide.md by Timokleia in https://github.com/DeepLabCut/DeepLabCut/pull/2394
* Fix `testscript.py` execution: set `max_iters` when training network by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2395
* Update python-package.yml by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2401
* Bump python to 3.9 in DEEPLABCUT.yaml environment file by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2402
* Address underlying compatibility issue with scipy 1.11.0 by hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/2396
* Update standardDeepLabCut_UserGuide.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2403
* Unifying docs on Napari DeepLabCut by Timokleia in https://github.com/DeepLabCut/DeepLabCut/pull/2399
* Update publish-book.yml by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2404
* Napari Flowchart by Timokleia in https://github.com/DeepLabCut/DeepLabCut/pull/2406
* Minor modifications to deploy_book github action by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2407
* Update URL of napari shortcuts SVG by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2408
* update notebooks and COLAB by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2411
* GUI - Fix config YAML edition (start list indexing at 0) by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2412
* Fix link typos and conversion by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2409
* Update version by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2413


**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.3.6...v2.3.7

Funding includes [ChanZuckerberg Initiative's Essential Open Source Software for Science](https://chanzuckerberg.com/eoss/). Thanks!

What's Changed

* Fix deprecated numpy builtin type by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2270
* Fix display bodyparts by KonradDanielewski in https://github.com/DeepLabCut/DeepLabCut/pull/2264
* fix drawing of skeleton when displayedbodyparts != all by KonradDanielewski in https://github.com/DeepLabCut/DeepLabCut/pull/2274
* stitch_tracklets crashes when not enough tracks are found by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2273
* Pass train/test indices to create_multianimaltraining_dataset by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2272
* renamed attempttomakefolder to attempt_to_make_folder by rizarae-p in https://github.com/DeepLabCut/DeepLabCut/pull/2271
* pin scipy to less than 1.11.0 by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2290
* Fixed draw_bbox when pyplot is in non-interactive mode by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2288
* Bug fix spatiotemporal adaptation kwargs by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2291
* Update README.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2294
* Avoid creating training dataset with multiple scorers by KonradDanielewski in https://github.com/DeepLabCut/DeepLabCut/pull/2287
* handles empty frame in video adaptation by yeshaokai in https://github.com/DeepLabCut/DeepLabCut/pull/2258
* Update DEEPLABCUT.yaml by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2299
* pinned tensorflow to <2.13.0 by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2308
* Manual outlier_frame_extraction bugfix by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2307
* Fix windows video selection for extraction in the GUI by KonradDanielewski in https://github.com/DeepLabCut/DeepLabCut/pull/2286
* Add function to get per-bodypart RMSE by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2315
* Plot keypoint confidence as alpha value by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2319
* Some usability improvements to the main GUI by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2275
* fix broken gputouse by ludovicbellier in https://github.com/DeepLabCut/DeepLabCut/pull/2320
* Avoid assembling if already done and overwrite == False by KonradDanielewski in https://github.com/DeepLabCut/DeepLabCut/pull/2317
* Pose_cfg.yaml recipe by KonradDanielewski in https://github.com/DeepLabCut/DeepLabCut/pull/2331
* Add link to hyperparams/augmentation guide by KonradDanielewski in https://github.com/DeepLabCut/DeepLabCut/pull/2333
* Update DEEPLABCUT.yaml by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2325
* bug fix: assemblies filename print by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2346
* Fixed `analyze_videos` docstring by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2354
* ortholonal -> orthogonal by yowayb in https://github.com/DeepLabCut/DeepLabCut/pull/2368
* Do not unpickle unit test data with pandas by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2373
* Updated deeplabcut installation in colab notebooks by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2376
* Added a new recipe on how to publish new recipes by rizarae-p in https://github.com/DeepLabCut/DeepLabCut/pull/2334
* Remove unused parameter `num_shuffles` from `check_for_weights` function. by Tetra-quark in https://github.com/DeepLabCut/DeepLabCut/pull/2360
* Update installation.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2378
* Update installation.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2379
* updated Model Zoo Colab notebook by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2381
* Doc clean up by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2380
* Clean up Model Zoo superanimal notebook by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2382
* Fix `interp` kwarg in `imresize` function. by Tetra-quark in https://github.com/DeepLabCut/DeepLabCut/pull/2374
* Add build matrix for docker images, update images by stes in https://github.com/DeepLabCut/DeepLabCut/pull/1936
* Update UseOverviewGuide and docker guide by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2384
* Update README.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2385
* Bug fixes VideoWriter: video names with spaces by n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2388
* Branch for new version by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2392

New Contributors
* rizarae-p made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2271
* yowayb made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2368
* Tetra-quark made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2360

**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.3.5...v2.3.6