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Installation

Prerequisites

  • Python 3.8 or higher
  • pip package manager
  • Git (for development installation)

Installation Methods

For development or the latest features:

# Clone the repository
git clone <repository-url>
cd ethopy_analysis

# Create virtual environment
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

# Install in development mode
pip install -e .

Package Installation

pip install ethopy-analysis

Optional Dependencies

Documentation Tools

pip install -e ".[docs]"

Includes: - mkdocs - mkdocs-material - mkdocstrings

Development Tools

pip install -e ".[dev]"

Includes: - pytest (testing) - black (code formatting) - isort (import sorting) - flake8 (linting) - mypy (type checking) - jupyter (notebooks)

Verify Installation

Test that the package is installed correctly:

# Test CLI
ethopy-analysis --help

# Test Python import
python -c "import ethopy_analysis; print('Installation successful')"

Dependencies

Core Dependencies

  • datajoint (≥0.13.0) - Database connectivity
  • matplotlib (≥3.5.0) - Plotting
  • pandas (≥1.3.0) - Data manipulation
  • numpy (≥1.20.0) - Numerical computing
  • seaborn (≥0.11.0) - Statistical visualization
  • plotly (≥5.0.0) - Interactive plots
  • opencv-python (≥4.5.0) - Video analysis
  • click (≥8.0.0) - Command-line interface
  • tqdm (≥4.60.0) - Progress bars
  • ipykernel (≥6.0.0) - Jupyter support

Database Setup

The package works without database configuration, but for full functionality:

  1. Configure database connection (see Configuration Guide)
  2. Test connection: 
    ethopy-analysis test-db-connection

Troubleshooting

Common Issues

Import errors: 

# Reinstall with all dependencies
pip install -e ".[dev,docs]"

Permission errors: 

# Use user installation
pip install --user -e .

Database connection issues: - Check network connectivity - Verify database credentials - See Configuration Guide

Getting Help

If you encounter issues: 1. Check the Troubleshooting Guide 2. Search existing GitHub issues 3. Create a new issue with error details