Merge pull request #284 from KumarLabJax/task/add-jabs-vision-package

Task/add jabs vision package

Author: bergsalex

packages/jabs-vision/README.md

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+# JABS Vision (`jabs-vision`)
+
+This package handles raw video processing and deep learning training and inference.
+
+## Overview
+
+`jabs-vision` is responsible for converting raw video frames into pose estimation data.
+It houses the heavy machine learning frameworks and GPU-accelerated code.
+
+## Responsibilities
+
+- **Pose Estimation Inference**: Running deep learning models (PyTorch) on video frames
+  to detect keypoints.
+- **Static Object Detection**
+- **Segmentation Masking**
+- **Identity Matching**: Tracking individual animals across frames using vectorized
+  features.
+- **Video Processing**: Handling frame extraction and normalization for input to vision
+  models.
+
+## Key Components
+
+- `jabs.vision.inference`: Wrappers for pose estimation model execution.
+- `jabs.vision.tracking`: Identity matching and re-identification logic.
+
+## Dependencies
+
+- `torch` / `torchvision`
+- `opencv-python-headless`
+- `jabs-io`, `jabs-core`

packages/jabs-vision/pyproject.toml

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+[project]
+name = "jabs-vision"
+version = "0.1.0"
+description = ""
+readme = "README.md"
+requires-python = ">=3.10,<3.15"
+license = { text = "Proprietary" }
+
+authors = [
+  { name = "Glen Beane" },
+  { name = "Alexander Berger-Liedtka" },
+  { name = "Keith Sheppard" },
+]
+
+dependencies = [
+    "jabs-io",
+    "jabs-core",
+    "hydra-core>=1.3.2",
+    "torch>=2.9.1",
+    "torchvision>=0.24.1",
+]
+
+[tool.uv.sources]
+jabs-io = { workspace = true }
+jabs-core = { workspace = true }
+
+[project.optional-dependencies]
+plot = [
+    "matplotlib>=3.10.8",
+]
+mlflow = [
+    "mlflow>=3.8.1",
+]
+wandb = [
+    "wandb>=0.24.0",
+]
+submitit = [
+    "submitit>=1.5.4",
+]
+timm = [
+    "timm>=1.0.0",
+]
+
+[dependency-groups]
+dev = [
+  {include-group = "lint"},
+  {include-group = "test"},
+  "pre-commit>=4.2.0,<5.0.0",
+  "matplotlib>=3.9.3,<4.0.0",
+]
+test = [
+  "pytest>=8.3.4,<9.0.0",
+  "pytest-cov>=7.0.0",
+]
+lint = [
+  "ruff>=0.11.5,<0.12.0",
+]
+
+[project.urls]
+Repository = "https://github.com/KumarLabJax/JABS-behavior-classifier"
+Issues = "https://github.com/KumarLabJax/JABS-behavior-classifier/issues"
+
+[build-system]
+requires = ["uv_build>=0.9.26,<0.10.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-name = "jabs.vision"

packages/jabs-vision/src/jabs/vision/__init__.py

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+"""The jabs.vision package."""

packages/jabs-vision/tests/__init__.py

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+"""Tests for the jabs.vision package."""

zensical.toml

@@ -1,17 +1,17 @@
 [project]
 site_name = "JABS Documentation"
 site_description = "End-user and developer documentation for JABS (Jax Animal Behavior System)."
-site_author = "Alexander Berger-Liedtka, Glen Beane, Keith Sheppard"
+site_author = "Glen Beane, Alexander Berger-Liedtka, Keith Sheppard"
 repo_name = "JABS-behavior-classifier"
 repo_url = "https://github.com/KumarLabJax/JABS-behavior-classifier"
 copyright = """
-Copyright © 2026 The Jackson Laboratory
+Copyright © 2026 The Kumar Lab & The Jackson Laboratory
 """
 
 # The site_url is the canonical URL for your site. When building online
 # documentation you should set this.
 # Read more: https://zensical.org/docs/setup/basics/#site_url
-#site_url = "https://www.example.com/"
+site_url = "https://kumarlabjax.github.io/JABS-behavior-classifier/"
 
 # Read more: https://zensical.org/docs/setup/navigation/
  nav = [