Merge branch 'main' into latest

Author: xiu-cs

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -25,7 +25,7 @@ body:
     attributes:
       label: DeepLabCut version
       description: What version of DLC are you using? Please check with `import deeplabcut`, `deeplabcut.__version__`
-      placeholder: 3.0.0rc8
+      placeholder: 3.0.0rc9
     validations:
       required: true
   - type: dropdown

README.md

@@ -10,12 +10,14 @@ parts:
   - file: docs/installation
   - file: docs/recipes/installTips
   - file: docs/docker
+
 - caption: Main User Guides
   chapters:
   - file: docs/standardDeepLabCut_UserGuide
   - file: docs/maDLC_UserGuide
   - file: docs/Overviewof3D
   - file: docs/HelperFunctions
+  
 - caption: Graphical User Interfaces (GUIs)
   chapters:
   - file: docs/gui/PROJECT_GUI
@@ -36,16 +38,28 @@ parts:
   - file: docs/beginner-guides/labeling
   - file: docs/beginner-guides/Training-Evaluation
   - file: docs/beginner-guides/video-analysis
-- caption: Hardware Tips
+- caption: 🚀 Main Demo Notebooks
   chapters:
-  - file: docs/recipes/TechHardware
-- caption: DeepLabCut-Live!
+  - file: examples/COLAB/COLAB_DEMO_SuperAnimal
+  - file: examples/COLAB/COLAB_DEMO_mouse_openfield
+  - file: examples/COLAB/COLAB_3miceDemo
+  - file: examples/COLAB/COLAB_HumanPose_with_RTMPose
+
+
+  
+- caption: 🚀 Notebooks For Your Data
   chapters:
-  - file: docs/deeplabcutlive
-- caption: 🦄 DeepLabCut Model Zoo
+  - file: examples/COLAB/COLAB_YOURDATA_SuperAnimal
+  - file: examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis
+  - file: examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis
+
+- caption: 🚀 Special Feature Demos
   chapters:
-  - file: docs/ModelZoo
-  - file: docs/recipes/UsingModelZooPupil
+  - file: examples/COLAB/COLAB_transformer_reID
+  - file: examples/COLAB/COLAB_BUCTD_and_CTD_tracking
+  - file: examples/JUPYTER/Demo_3D_DeepLabCut
+  - file: examples/COLAB/COLAB_DLC_ModelZoo
+
 - caption: 🧑‍🍳 Cookbook (detailed helper guides)
   chapters:
   - file: docs/convert_maDLC
@@ -60,15 +74,30 @@ parts:
   - file: docs/recipes/flip_and_rotate
   - file: docs/recipes/pose_cfg_file_breakdown
   - file: docs/recipes/publishing_notebooks_into_the_DLC_main_cookbook
+
+- caption: Hardware Tips
+  chapters:
+  - file: docs/recipes/TechHardware
+- caption: DeepLabCut-Live!
+  chapters:
+  - file: docs/deeplabcutlive
+- caption: 🦄 DeepLabCut Model Zoo
+  chapters:
+  - file: docs/ModelZoo
+  - file: docs/recipes/UsingModelZooPupil
+
 - caption: DeepLabCut Benchmarking
   chapters:
   - file: docs/benchmark
   - file: docs/pytorch/Benchmarking_shuffle_guide
+
 - caption: Mission & Contribute
   chapters:
   - file: docs/MISSION_AND_VALUES
   - file: docs/roadmap
   - file: docs/Governance
+  - file: CONTRIBUTING
+
 - caption: Citations for DeepLabCut
   chapters:
   - file: docs/citation

_toc.yml

@@ -35,4 +35,4 @@ dependencies:
   - pip:
     - torch
     - torchvision
-    - deeplabcut[gui,modelzoo,wandb]==3.0.0rc8
+    - deeplabcut[gui,modelzoo,wandb]==3.0.0rc9

conda-environments/DEEPLABCUT.yaml

@@ -1 +1 @@
-### Please head over to [Installation](/docs/installation.md) to see how to utilize our supplied conda envs!
+# Please head over to [Installation](/docs/installation.md) to see how to utilize our supplied conda envs!

conda-environments/README.md

@@ -60,6 +60,7 @@
 )
 
 from deeplabcut.modelzoo.video_inference import video_inference_superanimal
+from deeplabcut.pose_estimation_pytorch.modelzoo.superanimal_humanbody_video_inference import analyze_videos_superanimal_humanbody
 
 from deeplabcut.utils import (
     create_labeled_video,

deeplabcut/__init__.py

@@ -741,7 +741,6 @@ def analyze_videos(
         Change batch size for inference; if given overwrites value in ``pose_cfg.yaml``.
 
     cropping: list or None, optional, default=None
-        Currently not supported by the PyTorch engine.
         List of cropping coordinates as [x1, x2, y1, y2].
         Note that the same cropping parameters will then be used for all videos.
         If different video crops are desired, run ``analyze_videos`` on individual

deeplabcut/compat.py

@@ -17,6 +17,8 @@
 
 from unittest.mock import Mock, patch
 
+from datetime import datetime
+
 import numpy as np
 
 try:
@@ -66,6 +68,7 @@ def compute_bbox_metrics(
     coco.dataset["annotations"] = []
     coco.dataset["categories"] = [{"id": 1, "name": "animals", "supercategory": "obj"}]
     coco.dataset["images"] = []
+    coco.dataset['info'] = {"description": "Generated by DeepLabCut","year": datetime.now().year,"date_created": datetime.now().strftime("%Y-%m-%d")}
     predictions = []
     for idx, (img, gt) in enumerate(ground_truth.items()):
         img_id = idx + 1

deeplabcut/core/metrics/bbox.py

@@ -133,7 +133,7 @@ def create_pretrained_project(
     net_name: str | None = None,
     detector_name: str | None = None,
 ):
-    """
+    r"""
     Creates a new project directory, sub-directories and a basic configuration file.
     Change its parameters to your projects need.
 
@@ -265,7 +265,7 @@ def create_pretrained_project_pytorch(
     net_name: str | None = None,
     detector_name: str | None = None,
 ):
-    """
+    r"""
     Method used specifically for Pytorch-based ModelZoo models.
 
     Creates a new project directory, sub-directories and a basic configuration file.
@@ -488,7 +488,7 @@ def create_pretrained_project_tensorflow(
     createlabeledvideo: bool = True,
     trainFraction: float | None = None,
 ):
-    """
+    r"""
     Method used specifically for Tensorflow-based ModelZoo models.
 
     Creates a new project directory, sub-directories and a basic configuration file.

deeplabcut/create_project/modelzoo.py

@@ -17,7 +17,7 @@
 
 
 def create_new_project_3d(project, experimenter, num_cameras=2, working_directory=None):
-    """Creates a new project directory, sub-directories and a basic configuration file for 3d project.
+    r"""Creates a new project directory, sub-directories and a basic configuration file for 3d project.
     The configuration file is loaded with the default values. Adjust the parameters to your project's needs.
 
     Parameters
@@ -42,7 +42,7 @@ def create_new_project_3d(project, experimenter, num_cameras=2, working_director
 
     Windows:
     >>> deeplabcut.create_new_project('reaching-task','Bill',2)
-    Users must format paths with either:  r'C:\ OR 'C:\\ <- i.e. a double backslash \ \ )
+    Users must format paths with either:  r'C:\ OR 'C:\\ <- i.e. a double backslash \\ )
 
     """
     from datetime import datetime as dt