v2.3.10

What's Changed

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

New Contributors

• @midumitrescu made their first contribution in #2573

Full Changelog: v2.3.9...v2.9.10

Updates and bug fixes

• Add GUI help button back by @jeylau in #2507

What's Changed

• Pull demo data from Zenodo by @jeylau in #2440
• Update maDLC_UserGuide.md by @Timokleia in #2446
• Fix bug dataset and metadataset fixes #2390 by @Tetra-quark in #2405
• Bug fix: add_new_videos(..., extract_frames=True) by @n-poulsen in #2468
• bug fix: empty predictions during video analysis by @n-poulsen in #2467
• Update README.md by @MMathisLab in #2464
• Update AUTHORS by @MMathisLab in #2475
• updated macOS runner to 13 by @n-poulsen in #2484
• Update README.md by @Timokleia in #2496
• Bump version of tables installed during CI by @jeylau in #2500
• updated COLAB notebooks to install a CUDA version compatible with DLC by @n-poulsen in #2506
• updated package requirements by @n-poulsen in #2513
• Test for the presence of snapshot files when using modelzoo by @jeylau in #2485
• Version update by @AlexEMG in #2514

Full Changelog: v2.3.8...v2.3.9

Expanded GUI features for the DLC ModelZoo

What's Changed

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

New Contributors

• @molecules made their first contribution in #2423

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!

Full Changelog: v2.3.7...v2.3.8

Minor fixes

What's Changed

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

Full Changelog: v2.3.6...v2.3.7

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!

Bug fixes and minor updates

What's Changed

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

New Contributors

• @rizarae-p made their first contribution in #2271
• @yowayb made their first contribution in #2368
• @Tetra-quark made their first contribution in #2360

Full Changelog: v2.3.5...v2.3.6

v2.3.5

What's Changed

• Fetch mice demo data from Zenodo by @jeylau in #2223
• Changing except Error type to match no files found by @nattse in #2226
• Fix randomly failing multi-animal test script by @jeylau in #2233
• Fix rectangle selector by @n-poulsen in #2227
• Moved sections from H3 to H2 by @aoot in #2231
• removed deprecated install tips for mac m1/m2 by @n-poulsen in #2234
• Fix docstring in video_inference_superanimal by @stes in #2236
• 4 additional unit-tests by @AlexEMG in #2239
• Update URL for deeplabcut-docker by @stes in #2249
• Update bug_report.yml by @MMathisLab in #2250
• Allow frame extraction on a video subset in GUI by @jeylau in #2238
• Basicformatting by @AlexEMG in #2241
• Explicitely use QRegularExpression instead of implicit string conversion by @hmaarrfk in #2244
• Use QFrame.Shape.StyledPanel instead of QFrame.StyledPanel by @hmaarrfk in #2243
• Update use of .Directory for PySide6.5.0 by @hmaarrfk in #2247
• Additions to modelzoo APIs by @yeshaokai in #2198
• Update setup.py, docs by @MMathisLab in #2255
• version update by @AlexEMG in #2257

New Contributors

• @nattse made their first contribution in #2226
• @n-poulsen made their first contribution in #2227
• @aoot made their first contribution in #2231

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!

Full Changelog: v2.3.4...v2.3.5

Minor updates and bug fixes

What's Changed

• Fix model zoo video adaptation by @jeylau in #2181
• GUI fixes by @KonradDanielewski in #2126
• Guarantee tracks are sorted by predicted identity by @jeylau in #2194
• Improved thread-safety of tracklet refinement GUI by @jeylau in #2191
• Catch ValueError when tracklet dict is empty by @jeylau in #2189
• Copy rather than move video files when symlink creation fails by @jeylau in #2187
• Auto default to ellipse in create_labeled_video for multi-animal projects by @jeylau in #2188
• Fix deprecated features in pandas 2.0 by @jeylau in #2160
• Update installation.md by @MMathisLab in #2214
• Fix AttributeError in Analyze Video tab with single animal projects by @jeylau in #2210
• Fix ArtistList's AttributeError by @jeylau in #2216
• Update multiple_individuals_trainingsetmanipulation.py by @MMathisLab in #2219
• codespell: config, action and a few typos fixed by @yarikoptic in #2217
• Fix typo in refine_tracklets.py by @xun468 in #2221
• v2.3.4 -- Update version for release by @AlexEMG in #2222

New Contributors

• @yarikoptic made their first contribution in #2217
• @xun468 made their first contribution in #2221

Full Changelog: v2.3.2...v2.3.4

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!

Minor updates and bug fixes

This release note summarizes changes in v2.3.1 and 2.3.2 jointly.

What's Changed

• improve model zoo install and docs by @MMathisLab in #2105
• depreciated modelzoo urls by @MMathisLab in #2113
• Auto-load video and data when manually extracting outliers by @jeylau in #2114
• Fix typo by @jeylau in #2119
• Better handling failures in video creating GUI by @kngwyu in #2075
• Fix typo in add_new_videos function documentation. by @rojasgabriel in #2129
• Fix typo by @jeylau in #2135
• Add warning message during calibration when no complete poses are found by @jeylau in #2131
• extracted defs from main functions by @xarisot in #2122
• Label video when num_outputs > 1 (and overwriting flag) by @ludovicbellier in #2096
• Fix keypoint location in create_labeled_video after cropped analysis by @jeylau in #2147
• Fix typo in argument given to GUI's deeplabcut.filterpredictions by @jeylau in #2148
• Refine manual frames by @jonahpearl in #2045
• pin torch to less than 1.12 by @MMathisLab in #2156
• Model Zoo new API by @MMathisLab in #2109
• V2.3.1 by @AlexEMG in #2168
• Add missing data file in setup.py by @jeylau in #2170
• Update README.md by @MMathisLab in #2175
• v232 by @AlexEMG in #2176

New Contributors

• @rojasgabriel made their first contribution in #2129
• @xarisot made their first contribution in #2122
• @jonahpearl made their first contribution in #2045

Full Changelog: v2.3...v2.3.2

Major release with new GUI and paving the way for the Model Zoo!

This is a major release for DeepLabCut v2.3. We switch from a wxPython based GUI to a Pyside2 based GUI with napari support!

Try it out with:

pip install 'deeplabcut[tf,gui]'==2.3

Happy Holidays!!

-->> Check out the end of the year blog!
https://deeplabcut.medium.com/2022-year-in-review-4f6546d84710

What's Changed

• Transition from wxpython to PySide2 project management GUI by @jeylau in #1984
• Fix failing tests by @jeylau in #2007
• Mwm/docs fix by @MMathisLab in #2005
• Add style.qss to data_files in setup.py by @jeylau in #2015
• Fix failing tests by @jeylau in #2021
• Update installation.md by @MMathisLab in #2020
• Add benchmark API by @stes in #1777
• Update installation.md by @alesantuz in #2029
• Straightforward, functional installation on Apple Silicon // moving to PySide6 // rc2 by @jeylau in #2022
• Fix corrupted video analysis by @jeylau in #2025
• Avoid sampling of NaN center location by @jeylau in #2037
• Update docs by @MMathisLab in #2038
• Code for automatically updating license headers by @stes in #2028
• Fix project folder property in GUI by @jeylau in #2039
• Use video-specific crop params in extract_outlier_frames by @jeylau in #2040
• Fix broken API docs by @jeylau in #2049
• Get an empty list if "recent_files" is None by @jeylau in #2051
• Clarification on installation on M1/2 Mac by @KonradDanielewski in #2055
• Loading model zoo weights from hugging face. by @AlexEMG in #2059
• V2.3rc3 by @AlexEMG in #2060
• Fix video with all detections checkbox by @jeylau in #2054
• Adding dogs and cats back to model zoo (from Hugging Face). by @AlexEMG in #2064
• minor change to colab notebook by @MMathisLab in #2066
• Fix circular imports on python3.7 by @jeylau in #2069
• do not write when frame is None by @jh85 in #2065
• Test DLC on Ubuntu & python 3.7 by @jeylau in #2070
• Fix an outdated relative import and a missing member by @kngwyu in #2074
• Move Hugging Face's pre-trained weights to the right target directory by @jeylau in #2076
• Fix matched frame extraction for 3d projects by @jeylau in #2077
• Cap TF version to 2.10 by @jeylau in #2087
• Update branch name to "main" in GitHub's CI workflow by @jeylau in #2089
• Fix "merge datasets" button action by @jeylau in #2085
• Do not add a new video if it already exists by @jeylau in #2063
• prevents replotting of existing plots during model evaluation by @ludovicbellier in #2091
• Add dlclibrary for model download from zoo by @jeylau in #2088
• Pin napari-deeplabcut to >=0.0.9 by @jeylau in #2101
• Backwardscompatpath by @AlexEMG in #2099
• Model Zoo Docs by @MMathisLab in #2100
• Minor COLAB modelzoo improvements by @jeylau in #2103

New Contributors

• @jh85 made their first contribution in #2065
• @kngwyu made their first contribution in #2074
• @ludovicbellier made their first contribution in #2091

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!

Full Changelog: v2.2.3...v2.3

Updated Release candidate for new GUI.

What's Changed

• Fix failing tests by @jeylau in #2007
• Mwm/docs fix by @MMathisLab in #2005
• Add style.qss to data_files in setup.py by @jeylau in #2015
• Fix failing tests by @jeylau in #2021
• Update installation.md by @MMathisLab in #2020
• Add benchmark API by @stes in #1777
• Update installation.md by @alesantuz in #2029
• Straightforward, functional installation on Apple Silicon // moving to PySide6 // rc2 by @jeylau in #2022
• Fix corrupted video analysis by @jeylau in #2025
• Avoid sampling of NaN center location by @jeylau in #2037
• Update docs by @MMathisLab in #2038
• Code for automatically updating license headers by @stes in #2028
• Fix project folder property in GUI by @jeylau in #2039
• Use video-specific crop params in extract_outlier_frames by @jeylau in #2040
• Fix broken API docs by @jeylau in #2049
• Get an empty list if "recent_files" is None by @jeylau in #2051
• Clarification on installation on M1/2 Mac by @KonradDanielewski in #2055
• Loading model zoo weights from hugging face. by @AlexEMG in #2059

Full Changelog: v2.3rc1...v2.3rc3

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!