Merge pull request #3 from felipe-parodi/links

Correct repo links

Author: felipe-parodi

.github/CONTRIBUTING.md

@@ -5,7 +5,7 @@ Thank you for your interest in contributing to PrimateFace! We welcome contribut
 ## Ways to Contribute
 
 ### 1. Report Issues
-- Use the [GitHub Issues](https://github.com/PrimateFace/primateface_oss/issues) page
+- Use the [GitHub Issues](https://github.com/KordingLab/PrimateFace/issues) page
 - Check if the issue already exists before creating a new one
 - Provide detailed information including:
   - Your environment (OS, Python version, package versions)
@@ -17,7 +17,7 @@ Thank you for your interest in contributing to PrimateFace! We welcome contribut
 
 #### Getting Started
 1. Fork the repository
-2. Clone your fork: `git clone https://github.com/YOUR_USERNAME/primateface_oss.git`
+2. Clone your fork: `git clone https://github.com/YOUR_USERNAME/PrimateFace.git`
 3. Create a new branch: `git checkout -b feature-name`
 4. Set up your development environment:
    ```bash
@@ -88,8 +88,8 @@ Please ensure:
 ### Environment Setup
 ```bash
 # Clone the repo
-git clone https://github.com/PrimateFace/primateface_oss.git
-cd primateface_oss
+git clone https://github.com/KordingLab/PrimateFace.git
+cd PrimateFace
 
 # Create conda environment
 conda create -n primateface-dev python=3.10
@@ -130,13 +130,13 @@ pytest --cov=primateface tests/
 ## Questions?
 
 - Email: primateface@gmail.com
-- GitHub Discussions: [Link](https://github.com/PrimateFace/primateface_oss/discussions)
-- Issues: [Link](https://github.com/PrimateFace/primateface_oss/issues)
+- GitHub Discussions: [Link](https://github.com/KordingLab/PrimateFace/discussions)
+- Issues: [Link](https://github.com/KordingLab/PrimateFace/issues)
 
 ## License
 
 By contributing to PrimateFace, you agree that your contributions will be licensed under the MIT License.
 
 ## Acknowledgments
 
-Thank you to all our contributors! Your efforts help advance primate behavioral research and computer vision.
+Thank you to all our contributors! Your efforts help advance primate behavioral research and computer vision.

CHANGELOG.md

@@ -59,6 +59,6 @@ See [CONTRIBUTING.md](.github/CONTRIBUTING.md) for information on how to contrib
 ## Links
 
 - [Documentation](https://primateface.studio)
-- [Paper](https://www.biorxiv.org/content/10.1101/2025.08.12.669927v2)
+- [Paper](https://www.biorxiv.org/content/10.1101/2025.08.12.669927)
 - [Dataset](https://huggingface.co/datasets/fparodi/PrimateFace)
-- [GitHub](https://github.com/PrimateFace/primateface_oss)
+- [GitHub](https://github.com/KordingLab/PrimateFace)

README.md

@@ -3,7 +3,7 @@
 # **PrimateFace: A Machine Learning Resource for Automated Primate Face Analysis**
 
 <p align="center">
-  <a href="https://www.biorxiv.org/content/10.1101/2025.08.12.669927v2">
+  <a href="https://www.biorxiv.org/content/10.1101/2025.08.12.669927">
     <img src="https://img.shields.io/badge/Preprint-bioRxiv-orange" alt="bioRxiv">
   </a>
   &nbsp;&nbsp;
@@ -20,11 +20,11 @@
   </a>
 </p>
 
-PrimateFace contains data, models, and tutorials for analyzing facial behavior across primates ([Parodi et al., 2025](https://www.biorxiv.org/content/10.1101/2025.08.12.669927v2)). 
+PrimateFace contains data, models, and tutorials for analyzing facial behavior across primates ([Parodi et al., 2025](https://www.biorxiv.org/content/10.1101/2025.08.12.669927)). 
 
 This codebase enables you to use an off-the-shelf PrimateFace model for tracking facial movements or you can quickly fine-tune a PrimateFace model.
 
-Most of the PrimateFace modules require GPU access. If you don't have access to a GPU, you can still use PrimateFace in Google Colab (see [notebooks](https://docs.primateface.studio/notebooks/index.html)).
+Most of the PrimateFace modules require GPU access. If you don't have access to a GPU, you can still use PrimateFace in Google Colab (see [tutorials](https://docs.primateface.studio/tutorials/)).
 
 
 <p align="center">
@@ -35,7 +35,7 @@ Most of the PrimateFace modules require GPU access. If you don't have access to
 #### **Quick Start**
 1. Test the [Hugging Face demo](https://huggingface.co/datasets/fparodi/PrimateFace) to get a feel for the capabilities of PrimateFace on your own data.
 
-2. Run through the [Google Colab Notebook tutorials](https://docs.primateface.studio/notebooks/index.html) to explore several applications of PrimateFace.
+2. Run through the [Google Colab Notebook tutorials](https://docs.primateface.studio/tutorials/) to explore several applications of PrimateFace.
 
 3. Clone this repository, install the dependencies, and run through the different modules (e.g., DINOv2, image and video demos, pseudo-labeling GUI, etc.) to fully utilize PrimateFace.
 
@@ -118,18 +118,16 @@ Note: You may see a harmless `RequestsDependencyWarning` about urllib3 versions
 
 #### Links
 - [Documentation Homepage](https://docs.primateface.studio)
-- [Notebook Tutorials](https://docs.primateface.studio/notebooks/index.html)
-
-<!-- TODO: fix links for KordingLab -->
+- [Notebook Tutorials](https://docs.primateface.studio/tutorials/)
 
 | Tutorial | Open in Colab |
 |---------|----------------|
-| **1. Lemur Face Visibility Time-Stamping** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/blob/main/demos/notebooks/App1_Lemur_time_stamping.ipynb) |
-| **2. Rapid Macaque Face Recognition** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/blob/main/demos/notebooks/App2_Macaque_Face_Recognition.ipynb) |
-| **3. Howler Vocal-Motor Coupling** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/blob/main/demos/notebooks/App3_Howler_Vocal_Motor_Coupling.ipynb) |
-| **4. Human Infant Social Gaze Tracking** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/blob/main/demos/notebooks/App4_Gaze_following.ipynb) |
-| **5. Data-Driven Discovery of Facial Actions** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/blob/main/demos/notebooks/App5_Data_Driven_Discovery_of_Facial_Actions.ipynb) |
-| **6. Cross-Subject Neural Decoding of Facial Actions** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/blob/main/demos/notebooks/App6_Cross_Subject_Neural_Decoding_of_Facial_Actions.ipynb) |
+| **1. Lemur Face Visibility Time-Stamping** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/KordingLab/PrimateFace/blob/main/demos/notebooks/App1_Lemur_time_stamping.ipynb) |
+| **2. Rapid Macaque Face Recognition** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/KordingLab/PrimateFace/blob/main/demos/notebooks/App2_Macaque_Face_Recognition.ipynb) |
+| **4. Human Infant Social Gaze Tracking** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/KordingLab/PrimateFace/blob/main/demos/notebooks/App4_Gaze_following.ipynb) |
+| **3. Howler Vocal-Motor Coupling** | Coming soon |
+| **5. Data-Driven Discovery of Facial Actions** | Coming soon |
+| **6. Cross-Subject Neural Decoding of Facial Actions** | Coming soon |
 
 
 #### References

demos/notebooks/App1_Lemur_time_stamping.ipynb

@@ -23,7 +23,7 @@
         "\n",
         "| GitHub | Paper | Website |\n",
         "|---|---|---|\n",
-        "| [Code](https://github.com/KordingLab/PrimateFace) | [Preprint](https://www.biorxiv.org/content/10.1101/2025.08.12.669927v2) | [Project](https://primateface.studio/) |\n",
+        "| [Code](https://github.com/KordingLab/PrimateFace) | [Preprint](https://www.biorxiv.org/content/10.1101/2025.08.12.669927) | [Project](https://primateface.studio/) |\n",
         "\n",
         "Welcome! This tutorial notebook walks through using a **PrimateFace** detection model to automatically find and timestamp primate faces in videos, creating a 'visibility baseline' for behavioral coding.\n",
         "\n",
@@ -1568,7 +1568,7 @@
       "cell_type": "markdown",
       "source": [
         "## 9. Resources\n",
-        "1. [PrimateFace](https://github.com/PrimateFace/PrimateFace)\n",
+        "1. [PrimateFace](https://github.com/KordingLab/PrimateFace)\n",
         "2. [mmdetection](https://github.com/open-mmlab/mmdetection)\n",
         "3. [roboflow](https://roboflow.com/)"
       ],
@@ -1577,4 +1577,4 @@
       }
     }
   ]
-}
+}

demos/notebooks/App2_Macaque_Face_Recognition.ipynb

@@ -370,7 +370,7 @@
         "\n",
         "| GitHub | Paper | Website |\n",
         "|---|---|---|\n",
-        "| [Code](https://github.com/KordingLab/PrimateFace) | [Preprint](https://www.biorxiv.org/content/10.1101/2025.08.12.669927v2) | [Project](https://primateface.studio/) |\n",
+        "| [Code](https://github.com/KordingLab/PrimateFace) | [Preprint](https://www.biorxiv.org/content/10.1101/2025.08.12.669927) | [Project](https://primateface.studio/) |\n",
         "\n",
         "Welcome! This tutorial notebook demonstrates a complete, closed-set face recognition pipeline. That is, given a set of images with corresponding primate IDs, we will chain together PrimateFace models with off-the-shelf face recognition models to achieve rapid identity recognition.\n",
         "\n",
@@ -2668,7 +2668,7 @@
       "cell_type": "markdown",
       "source": [
         "## 7. Resources\n",
-        "1. [PrimateFace](https://github.com/PrimateFace/PrimateFace)\n",
+        "1. [PrimateFace](https://github.com/KordingLab/PrimateFace)\n",
         "2. [mmdetection](https://github.com/open-mmlab/mmdetection)\n",
         "3. [mmpose](https://github.com/open-mmlab/mmpose)\n",
         "4. [InsightFace](https://github.com/deepinsight/insightface)"
@@ -2678,4 +2678,4 @@
       }
     }
   ]
-}
+}

demos/notebooks/App4_Gaze_following.ipynb

@@ -24,7 +24,7 @@
         "\n",
         "| GitHub Repo | Paper | Project Page |\n",
         "|---|---|---|\n",
-        "| [PrimateFace](https://github.com/PrimateFace/PrimateFace) | [PrimateFace](https://arxiv.org/abs/10000) | [PrimateFace](https://primateface.github.io/) |\n",
+        "| [PrimateFace](https://github.com/KordingLab/PrimateFace) | [PrimateFace](https://www.biorxiv.org/content/10.1101/2025.08.12.669927) | [PrimateFace](https://docs.primateface.studio/) |\n",
         "\n",
         "Welcome! This tutorial notebook demonstrates a gaze-following heuristic for videos containing two primates. It uses models from the **PrimateFace** and **Gazelle** projects to analyze social attention dynamics.\n",
         "\n",
@@ -496,7 +496,7 @@
       "source": [
         "\n",
         "## 8. Resources\n",
-        "1. [PrimateFace](https://github.com/PrimateFace/PrimateFace)\n",
+        "1. [PrimateFace](https://github.com/KordingLab/PrimateFace)\n",
         "2. [Gazelle](https://gazelle-gaze.github.io/)\n",
         "3. [mmdetection](https://github.com/open-mmlab/mmdetection)"
       ],
@@ -505,4 +505,4 @@
       }
     }
   ]
-}
+}

demos/notebooks/README.md

@@ -2,13 +2,13 @@
 
 These notebooks are designed to help you get started with PrimateFace.
 
-These correspond to the scientific applications outlined in the PrimateFace [paper](https://www.biorxiv.org/content/10.1101/2025.08.12.669927v2).
+These correspond to the scientific applications outlined in the PrimateFace [paper](https://www.biorxiv.org/content/10.1101/2025.08.12.669927).
 
 | Tutorial | Open in Colab |
 |---------|----------------|
-| **1. Lemur Face Visibility Time-Stamping** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/demos/notebooks/App1_Lemur_time_stamping.ipynb) |
-| **2. Rapid Macaque Face Recognition** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/demos/notebooks/App2_Macaque_Face_Recognition.ipynb) |
-| **3. Howler Vocal-Motor Coupling** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/demos/notebooks/App3_Howler_Vocal_Motor_Coupling.ipynb) |
-| **4. Human Infant Social Gaze Tracking** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/demos/notebooks/App4_Gaze_following.ipynb) |
-| **5. Data-Driven Discovery of Facial Actions** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/demos/notebooks/App5_Data_Driven_Discovery_of_Facial_Actions.ipynb) |
-| **6. Cross-Subject Neural Decoding of Facial Actions** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PrimateFace/primateface_oss/demos/notebooks/App6_Cross_Subject_Neural_Decoding_of_Facial_Actions.ipynb) |
+| **1. Lemur Face Visibility Time-Stamping** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/KordingLab/PrimateFace/blob/main/demos/notebooks/App1_Lemur_time_stamping.ipynb) |
+| **2. Rapid Macaque Face Recognition** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/KordingLab/PrimateFace/blob/main/demos/notebooks/App2_Macaque_Face_Recognition.ipynb) |
+| **4. Human Infant Social Gaze Tracking** | [![Open](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/KordingLab/PrimateFace/blob/main/demos/notebooks/App4_Gaze_following.ipynb) |
+| **3. Howler Vocal-Motor Coupling** | Coming soon |
+| **5. Data-Driven Discovery of Facial Actions** | Coming soon |
+| **6. Cross-Subject Neural Decoding of Facial Actions** | Coming soon |

docs/index.md

@@ -132,7 +132,7 @@ For pressing questions or collaborations, reach out via:
 
 If you use PrimateFace in your research, please cite:
 
-[Parodi et al., 2025](https://www.biorxiv.org/content/10.1101/2025.08.12.669927v2)
+[Parodi et al., 2025](https://www.biorxiv.org/content/10.1101/2025.08.12.669927)
 
 ```bibtex
 @article{parodi2025primateface,

gui/pseudolabel.py

@@ -492,7 +492,7 @@ def cmd_refine(args: argparse.Namespace) -> None:
     print("  2. Edit COCO JSON files directly")
     print("  3. Use annotation tools like CVAT, Label Studio, or VGG VIA")
     print("     that support COCO format import/export")
-    print("\nFor updates, check: https://github.com/PrimateFace/primateface_oss")
+    print("\nFor updates, check: https://github.com/KordingLab/PrimateFace")
     sys.exit(0)
 
 
@@ -624,4 +624,4 @@ def main() -> None:
 
 
 if __name__ == "__main__":
-    main()
+    main()

pyproject.toml

@@ -123,10 +123,10 @@ all = [
 
 [project.urls]
 Homepage = "https://primateface.studio"
-Documentation = "https://primateface.studio/docs"
-Repository = "https://github.com/PrimateFace/primateface_oss"
-"Bug Reports" = "https://github.com/PrimateFace/primateface_oss/issues"
-Paper = "https://www.biorxiv.org/content/10.1101/2025.08.12.669927v1"
+Documentation = "https://docs.primateface.studio"
+Repository = "https://github.com/KordingLab/PrimateFace"
+"Bug Reports" = "https://github.com/KordingLab/PrimateFace/issues"
+Paper = "https://www.biorxiv.org/content/10.1101/2025.08.12.669927"
 "Hugging Face" = "https://huggingface.co/datasets/fparodi/PrimateFace"
 
 [tool.setuptools.packages.find]
@@ -135,4 +135,4 @@ include = ["primateface*", "dataset*", "demos*", "dinov2*", "evals*", "gui*", "l
 exclude = ["tests*", "docs*", "notebooks*"]
 
 [tool.setuptools.package-data]
-"*" = ["*.json", "*.yaml", "*.yml", "*.txt", "*.md"]
+"*" = ["*.json", "*.yaml", "*.yml", "*.txt", "*.md"]