DeepLabCut Files

Highlights

• New installation procedure via pyproject.toml : easier, more modern installation. Enables uv, pdm and other modern package managers use.

• Many fixes and improvements:

• PyTorch speed improvements
• CI improvements

_{Note: these changes are based on all merges since rc10}

What's Changed

• link update for COLAB_YOURDATA_SuperAnimal.ipynb by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3037
• RTMpose_x superanimal_humanbody by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3043
• skeleton fix fo RTMpose demo by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3048
• Update COLAB_HumanPose_with_RTMPose.ipynb by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/3051
• revert to working RTMPpose demo notebook by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3052
• fix for humanbody vs. others by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3050
• Save all pytorch config updates in dlc_torch.train_network() by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3062
• Save WandB run information to model folder by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3017
• Improve DLCLoader.to_coco() and add force_multi_animal argument to dlc_torch.evaluate() by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2995
• Superanimal humanbody: Use filtered detector by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3066
• ModelZoo GUI Tab fixes by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3055
• superanimal_humanbody with FilteredDetector: add video adaptation by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3086
• Expose close_figure_after_save in superanimal_analyze_images() by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3082
• Fix CTD empty conditions edge case by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3076
• Clean dlc_torch.analyze_videos() by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3079
• Fix RTMPose likelihood computation by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3078
• Fix typos in documentation and comments by @arashsm79 in https://github.com/DeepLabCut/DeepLabCut/pull/3097
• Fix snapshot index handling in PyTorch analyze_videos and extend overrides to other methods by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3092
• Updating version by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/3096
• Improve threading termination and queue handling by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3094
• Fix deeplabcut.analyze_images() with CTD model by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2990
• Log GPU memory usage by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3077
• resize the GUI by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3034
• PyTorch: Improve inference batching speed by @arashsm79 in https://github.com/DeepLabCut/DeepLabCut/pull/3099
• Hide GPU memory usage by default by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3102
• Add autocast sub-config to inference settings and disable torch.autocast by default by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3105
• Move conditions: to inference: block and document inference-related configs by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3106
• Update TensorFlow backend for Python 3.12 compatibility (Keras 2 via tf-keras) by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3087
• new version by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/3109
• Remove trailing underscore in superanimal scorer names by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3113
• update Argus documentation notes by @backyardbiomech in https://github.com/DeepLabCut/DeepLabCut/pull/3124
• Fix CI/CD failing on Mac by @arashsm79 in https://github.com/DeepLabCut/DeepLabCut/pull/3128
• PyTorch: Speed up single animal models by @arashsm79 in https://github.com/DeepLabCut/DeepLabCut/pull/3110
• PyTorch: Speed up PAF cost computation by @arashsm79 in https://github.com/DeepLabCut/DeepLabCut/pull/3117
• PyTorch: Speed up DEKR predictor by @arashsm79 in https://github.com/DeepLabCut/DeepLabCut/pull/3121
• Change bug report assignee by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3136
• docs: pin jupyter-book version by @arashsm79 in https://github.com/DeepLabCut/DeepLabCut/pull/3139
• Skip multiprocessing pytest by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3142
• Add argument max workers for multiprocessing in create_labeled_video by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3143
• Remove config editor delegate hack. by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3167
• Avoid redundant superanimal colormap calls during pytorch inference by @juan-cobos in https://github.com/DeepLabCut/DeepLabCut/pull/3159
• fix a confusing message for freeze_bn_stats by @Jiefei-Wang in https://github.com/DeepLabCut/DeepLabCut/pull/3166
• Line 355 output message updated address misleading error message for empty detections in analyze_images() function by @Ronniekev in https://github.com/DeepLabCut/DeepLabCut/pull/3157
• append, instead of rewriting, CSVLogger by @juan-cobos in https://github.com/DeepLabCut/DeepLabCut/pull/3179
• feat: Filter out low-confidence bounding box detections by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3154
• add missing init.py to pose_estimation_tensorflow/modelzoo. by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3153
• Fix GitHub Actions disk space exhaustion on Ubuntu runners by @Copilot in https://github.com/DeepLabCut/DeepLabCut/pull/3180
• Reverting PR [#3179] which breaks csv logging. by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3183
• Update napari plugin activation in launch_napari by @C-Achard in https://github.com/DeepLabCut/DeepLabCut/pull/3181
• Refactor list_videos_in_folder for clarity and correctness by @juan-cobos in https://github.com/DeepLabCut/DeepLabCut/pull/3175
• Restrict pandas dependency to version <3.0 by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3186
• hotfix extract_outlier_frames for cropped videos by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3169
• fix non-deterministic unintended failing of test_coarse_dropout by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3182
• fix ruamel.yaml dumping newline for long filenames by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3140
• fix broken links in documentation by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3145
• Close figures before plotting by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3168
• Fix huggingface_hub and filelock dependency issue by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3204
• Fix CSVLogger: read existing learning_stats.csv file when resuming previous training by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3177
• Fix hardcoded GUI icon path by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3200
• Keyword-only key argument for pd.DataFrame.to_hdf() by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3185
• Replace str, os.path with pathlib.Path by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3199
• fix rename_mapping in download_huggingface_model (change arg type str -> dict) by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3196
• improve error handling in create_training_dataset by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3146
• Update docs TOC and Sphinx excludes by @C-Achard in https://github.com/DeepLabCut/DeepLabCut/pull/3201
• Add fmpose3d functionality by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3208
• Fix: properly use unique_bodyparts and identity_scores arguments in ShelfWriter.add_prediction by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3112
• Handle tables via pip as pandas extra instead of separate conda install (and update installation instructions) by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3214
• Update conda env yaml: bump DeepLabCut and remove nb_conda by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3213
• Install through pyproject.toml (PEP 518/621) by @deruyter92 in https://github.com/DeepLabCut/DeepLabCut/pull/3184
• Fix redundant/incomplete installs in docs CI, replace with pyproject.toml optional deps by @C-Achard in https://github.com/DeepLabCut/DeepLabCut/pull/3226
• Update CircleCI for pyproject.toml-based install by @C-Achard in https://github.com/DeepLabCut/DeepLabCut/pull/3225
• DeepLabCut-live-GUI PySide6/multicamera documentation ("2.0") by @C-Achard in https://github.com/DeepLabCut/DeepLabCut/pull/3206
• rc14 release by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/3237

New Contributors

• @arashsm79 made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/3097
• @juan-cobos made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/3159
• @Jiefei-Wang made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/3166
• @Ronniekev made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/3157

Full Changelog: https://github.com/DeepLabCut/DeepLabCut/compare/v3.0.0rc10...v3.0.0rc14