Pretrained SuperAnimal Models Support, Multi-Animal support, DLC 3.x Compatibility, and Docker Testing

.dockerignore

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+# Docker ignore file
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Virtual environments
+venv/
+env/
+ENV/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+
+# Documentation
+docs/_build/
+
+# Git
+.git/
+.gitignore
+
+# Docker
+Dockerfile
+docker-compose*.yaml
+.dockerignore
+
+# Test data (will be mounted as volume)
+test_videos/
+
+# Local config (will be mounted as volume)
+dj_local_conf.json
+
+# OS
+.DS_Store
+Thumbs.db
+
+

CONDA_ENV_SETUP.md

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+# Conda Environment Setup Guide
+
+## Quick Start
+
+```bash
+# Create environment (Python 3.10+ required for DeepLabCut 3.x)
+conda create -n element-deeplabcut python=3.10
+conda activate element-deeplabcut
+
+# Install system dependencies
+conda install -c conda-forge graphviz
+
+# Install package
+pip install -e ".[elements,tests]"
+```
+
+## With DeepLabCut
+
+```bash
+# Full setup with DeepLabCut
+pip install -e ".[elements,dlc_default,tests]"
+```
+
+## Verify Installation
+
+```bash
+python -c "import element_deeplabcut; print('✅ Package installed')"
+python -c "import datajoint as dj; print('✅ DataJoint available')"
+```
+
+## Troubleshooting
+
+| Issue | Solution |
+|-------|----------|
+| Package conflicts | `conda env remove -n element-deeplabcut` and recreate |
+| Graphviz not found | `conda install -c conda-forge graphviz` |
+
+## Next Steps
+
+1. Configure database: See `tests/ENVIRONMENT_SETUP.md`
+2. Run tests: `pytest tests/ -v`

DOCKER_TEST_README.md

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+# Docker Testing
+
+## Quick Start
+
+```bash
+# Start database and container
+docker compose up -d
+
+# Run tests
+docker compose run --rm client python test_trained_inference.py
+docker compose run --rm client python test_video_inference.py superanimal_quadruped
+
+# Or use Makefile
+make test-trained
+make test-pretrained
+```
+
+## Configuration
+
+Create `.env` file (optional):
+
+```env
+DJ_PASS=simple
+DB_PORT=3306
+DATABASE_PREFIX=test_
+```
+
+## Volumes
+
+| Mount | Container Path | Description |
+|-------|----------------|-------------|
+| `./test_videos` | `/app/data` | Test videos |
+| `.` | `/app` | Project directory |
+| `./dj_local_conf.json` | `/app/dj_local_conf.json` | Database config |
+
+## Troubleshooting
+
+| Issue | Solution |
+|-------|----------|
+| Database connection | `docker compose ps` to check health |
+| Permission issues | `sudo chown -R $USER:$USER test_videos/` |
+| Code changes | `docker compose build` |
+| Clean up | `docker compose down -v` |
+
+## Development
+
+```bash
+make shell  # Interactive shell
+```

Dockerfile

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+# Dockerfile for element-deeplabcut client environment
+# Uses DeepLabCut's official Docker image as base
+# Pinned to specific version for reproducibility
+FROM deeplabcut/deeplabcut:3.0.0rc13-jupyter
+
+# Set working directory
+WORKDIR /app
+
+# Install additional system dependencies if needed
+RUN apt-get update && apt-get install -y \
+    git \
+    graphviz \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy the entire project
+COPY . .
+
+# Install element-deeplabcut and its dependencies
+# The DLC image already has DeepLabCut installed, so we just need element-deeplabcut
+# Note: We explicitly constrain dlclibrary version to avoid ModelZoo download bug
+# (rename_mapping being a string instead of dict - fixed with runtime monkey patch)
+RUN pip install -e .[dlc_default,elements,tests] && \
+    pip install "dlclibrary>=0.1.0,<0.2.0" || true
+
+# Set environment variables
+ENV PYTHONUNBUFFERED=1
+
+# Set entrypoint to bash
+ENTRYPOINT ["/bin/bash"]
+
+# Default command - interactive bash shell
+# Users can override with: docker compose run client -c "python your_script.py"
+CMD ["-i"]
+