Installation

Installation Guide

This guide will help you install and configure Scribe2FHIR in your development environment.

Prerequisites

Before installing Scribe2FHIR, ensure you have the following prerequisites:

• Python: Version 3.8 or higher
• pip: Python package installer
• Virtual Environment: Recommended for isolation (venv, conda, or similar)

Installation Methods

Using pip (Recommended)

Install Scribe2FHIR directly from PyPI:

pip install scribe2fhir

From Source

For development or to get the latest features:

# Clone the repository
git clone https://github.com/MedScribeAlliance/scribe2fhir.git
cd scribe2fhir

# Install in development mode
pip install -e .

Using Poetry

If you prefer Poetry for dependency management:

poetry add scribe2fhir

Virtual Environment Setup

We strongly recommend using a virtual environment to avoid dependency conflicts:

Using venv

# Create virtual environment
python -m venv scribe2fhir-env

# Activate virtual environment
# On macOS/Linux:
source scribe2fhir-env/bin/activate
# On Windows:
scribe2fhir-env\Scripts\activate

# Install Scribe2FHIR
pip install scribe2fhir

Using conda

# Create conda environment
conda create -n scribe2fhir python=3.10

# Activate environment
conda activate scribe2fhir

# Install Scribe2FHIR
pip install scribe2fhir

Dependencies

Scribe2FHIR automatically installs the following key dependencies:

• fhir.resources: FHIR resource models and validation
• pydantic: Data validation and parsing
• python-dateutil: Date parsing utilities
• typing-extensions: Enhanced type hints

For a complete list, see the requirements.txt file in the repository.

Verification

Verify your installation by importing Scribe2FHIR in Python:

import scribe2fhir
from scribe2fhir.core import DocumentBuilder

# Check version
print(f"Scribe2FHIR version: {scribe2fhir.__version__}")

# Create a simple document builder to test installation
builder = DocumentBuilder()
print("Installation successful!")

Development Setup

For contributors or advanced users who want to modify the source code:

Clone and Setup Development Environment

# Clone the repository
git clone https://github.com/MedScribeAlliance/scribe2fhir.git
cd scribe2fhir

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

# Install development dependencies
pip install -e ".[dev]"

# Run tests to verify setup
python -m pytest tests/

Development Dependencies

Additional packages for development:

• pytest: Testing framework
• black: Code formatting
• isort: Import sorting
• mypy: Type checking
• pre-commit: Git hooks for code quality

Configuration

Scribe2FHIR works out of the box with default settings, but you can customize behavior through configuration files or environment variables.

Environment Variables

Set these optional environment variables:

# FHIR server endpoint (if using external FHIR server)
export FHIR_SERVER_URL="https://your-fhir-server.com"

# Logging level
export SCRIBE2FHIR_LOG_LEVEL="INFO"

Configuration File

Create a config.yaml file for custom settings:

fhir:
  version: "R5"
  base_url: "https://your-fhir-server.com"

logging:
  level: "INFO"
  format: "%(asctime)s - %(name)s - %(levelname)s - %(message)s"

processing:
  batch_size: 100
  timeout: 30

Troubleshooting

Common Installation Issues

Python Version Compatibility

Ensure you’re using Python 3.8+:

python --version

Dependency Conflicts

If you encounter dependency conflicts:

# Create a fresh virtual environment
python -m venv fresh-env
source fresh-env/bin/activate
pip install --upgrade pip
pip install scribe2fhir

Network Issues

If installation fails due to network issues:

# Try with increased timeout
pip install --timeout 60 scribe2fhir

# Or use a different index
pip install -i https://pypi.org/simple/ scribe2fhir

Getting Help

If you encounter issues:

1. Check the troubleshooting section in the documentation
2. Search existing GitHub issues
3. Create a new issue with detailed error information

Next Steps

Now that you have Scribe2FHIR installed, you can:

1. Explore the Python SDK - Learn core concepts and API
2. Check out examples - See practical implementations
3. Understand FHIR specification - Learn about FHIR standards

Ready to build your first FHIR resource? Head to the Python SDK documentation to get started!