Environment Setup Guide

This guide explains how to set up the development environment for the Neurological LRD Analysis project.

Quick Setup

Run the automated setup script:

bash scripts/setup_venv.sh

This script will:

Check for Python 3.11+ compatibility
Create a virtual environment named neurological_env
Install all required dependencies
Install development and optional dependencies

Manual Setup

If you prefer to set up the environment manually:

1. Create Virtual Environment

python3 -m venv neurological_env

2. Activate Virtual Environment

Linux/macOS:

source neurological_env/bin/activate

Windows:

neurological_env\Scripts\activate

3. Install Dependencies

# Upgrade pip
pip install --upgrade pip

# Install project in development mode
pip install -e .

# Install development dependencies
pip install pytest pytest-cov pytest-html pytest-json-report pytest-timeout black isort flake8 mypy

# Install optional dependencies for enhanced functionality
pip install jax jaxlib numba scikit-learn matplotlib seaborn pywavelets

Environment Management

Activating the Environment

Before working on the project, always activate the virtual environment:

source neurological_env/bin/activate  # Linux/macOS
# or
neurological_env\Scripts\activate     # Windows

You should see (neurological_env) at the beginning of your command prompt when the environment is active.

Deactivating the Environment

To deactivate the virtual environment:

deactivate

Checking Environment Status

To verify the environment is working correctly:

# Check Python version (should be 3.11+)
python --version

# Check installed packages
pip list

# Run tests to verify installation
python -m pytest tests/ -v

Project Structure

The virtual environment (neurological_env/) should be created in the project root directory:

neurological_lrd_analysis/
├── neurological_env/          # Virtual environment (created by setup)
├── neurological_lrd_analysis/ # Main package directory
├── docs/                      # Documentation
├── scripts/                   # Setup and demo scripts
├── tests/                     # Test suite
├── pyproject.toml             # Project configuration
└── README.md                  # Project overview

Troubleshooting

Python Version Issues

If you encounter Python version issues:

Check your Python version: python3 --version
Ensure you have Python 3.11 or later installed
If using a different Python version, specify it explicitly:
```
python3.11 -m venv neurological_env
```

Permission Issues

If you encounter permission issues with the setup script:

chmod +x scripts/setup_venv.sh
bash scripts/setup_venv.sh

Dependency Installation Issues

If some dependencies fail to install:

Update pip: pip install --upgrade pip

Try installing dependencies individually:

pip install numpy scipy pandas
pip install jax jaxlib
pip install numba

Environment Not Found

If the virtual environment is not found:

Ensure you’re in the project root directory
Check if the neurological_env/ directory exists

Recreate the environment if necessary:

rm -rf neurological_env
bash scripts/setup_venv.sh

Development Workflow

Activate environment: source neurological_env/bin/activate
Make changes to the code
Run tests: python -m pytest tests/ -v
Test functionality: python scripts/biomedical_scenarios_demo.py
Deactivate when done: deactivate

IDE Integration

VS Code

Open the project in VS Code
Press Ctrl+Shift+P (or Cmd+Shift+P on macOS)
Type “Python: Select Interpreter”
Choose the interpreter from ./neurological_env/bin/python

PyCharm

Open the project in PyCharm
Go to File → Settings → Project → Python Interpreter
Click the gear icon → Add
Choose “Existing environment”
Select ./neurological_env/bin/python

Notes

The virtual environment name neurological_env is appropriate for this project
All dependencies are specified in pyproject.toml
The project uses Python 3.11+ for compatibility with advanced ML and JAX libraries
Lazy imports are implemented to reduce startup time and memory usage