#!/usr/bin/env python3
"""
Interactive setup script for biomni environment configuration.
This script helps users set up:
1. Conda environment with required dependencies
2. API keys for LLM providers
3. Data lake directory configuration
4. MCP server setup (optional)
Usage:
python setup_environment.py
"""
import os
import sys
import subprocess
from pathlib import Path
from typing import Dict, Optional
def check_conda_installed() -> bool:
"""Check if conda is available in the system."""
try:
subprocess.run(
['conda', '--version'],
capture_output=True,
check=True
)
return True
except (subprocess.CalledProcessError, FileNotFoundError):
return False
def setup_conda_environment():
"""Guide user through conda environment setup."""
print("\n=== Conda Environment Setup ===")
if not check_conda_installed():
print("❌ Conda not found. Please install Miniconda or Anaconda:")
print(" https://docs.conda.io/en/latest/miniconda.html")
return False
print("✓ Conda is installed")
# Check if biomni_e1 environment exists
result = subprocess.run(
['conda', 'env', 'list'],
capture_output=True,
text=True
)
if 'biomni_e1' in result.stdout:
print("✓ biomni_e1 environment already exists")
return True
print("\nCreating biomni_e1 conda environment...")
print("This will install Python 3.10 and required dependencies.")
response = input("Proceed? [y/N]: ").strip().lower()
if response != 'y':
print("Skipping conda environment setup")
return False
try:
# Create conda environment
subprocess.run(
['conda', 'create', '-n', 'biomni_e1', 'python=3.10', '-y'],
check=True
)
print("\n✓ Conda environment created successfully")
print("\nTo activate: conda activate biomni_e1")
print("Then install biomni: pip install biomni --upgrade")
return True
except subprocess.CalledProcessError as e:
print(f"❌ Failed to create conda environment: {e}")
return False
def setup_api_keys() -> Dict[str, str]:
"""Interactive API key configuration."""
print("\n=== API Key Configuration ===")
print("Biomni supports multiple LLM providers.")
print("At minimum, configure one provider.")
api_keys = {}
# Anthropic (recommended)
print("\n1. Anthropic Claude (Recommended)")
print(" Get your API key from: https://console.anthropic.com/")
anthropic_key = input(" Enter ANTHROPIC_API_KEY (or press Enter to skip): ").strip()
if anthropic_key:
api_keys['ANTHROPIC_API_KEY'] = anthropic_key
# OpenAI
print("\n2. OpenAI")
print(" Get your API key from: https://platform.openai.com/api-keys")
openai_key = input(" Enter OPENAI_API_KEY (or press Enter to skip): ").strip()
if openai_key:
api_keys['OPENAI_API_KEY'] = openai_key
# Google Gemini
print("\n3. Google Gemini")
print(" Get your API key from: https://makersuite.google.com/app/apikey")
google_key = input(" Enter GOOGLE_API_KEY (or press Enter to skip): ").strip()
if google_key:
api_keys['GOOGLE_API_KEY'] = google_key
# Groq
print("\n4. Groq")
print(" Get your API key from: https://console.groq.com/keys")
groq_key = input(" Enter GROQ_API_KEY (or press Enter to skip): ").strip()
if groq_key:
api_keys['GROQ_API_KEY'] = groq_key
if not api_keys:
print("\n⚠️ No API keys configured. You'll need at least one to use biomni.")
return {}
return api_keys
def save_api_keys(api_keys: Dict[str, str], method: str = 'env_file'):
"""Save API keys using specified method."""
if method == 'env_file':
env_file = Path.cwd() / '.env'
# Read existing .env if present
existing_vars = {}
if env_file.exists():
with open(env_file, 'r') as f:
for line in f:
line = line.strip()
if line and not line.startswith('#'):
if '=' in line:
key, val = line.split('=', 1)
existing_vars[key.strip()] = val.strip()
# Update with new keys
existing_vars.update(api_keys)
# Write to .env
with open(env_file, 'w') as f:
f.write("# Biomni API Keys\n")
f.write(f"# Generated by setup_environment.py\n\n")
for key, value in existing_vars.items():
f.write(f"{key}={value}\n")
print(f"\n✓ API keys saved to {env_file}")
print(" Keys will be loaded automatically when biomni runs in this directory")
elif method == 'shell_export':
shell_file = Path.home() / '.bashrc' # or .zshrc for zsh users
print("\n📋 Add these lines to your shell configuration:")
for key, value in api_keys.items():
print(f" export {key}=\"{value}\"")
print(f"\nThen run: source {shell_file}")
def setup_data_directory() -> Optional[Path]:
"""Configure biomni data lake directory."""
print("\n=== Data Lake Configuration ===")
print("Biomni requires ~11GB for integrated biomedical databases.")
default_path = Path.cwd() / 'biomni_data'
print(f"\nDefault location: {default_path}")
response = input("Use default location? [Y/n]: ").strip().lower()
if response == 'n':
custom_path = input("Enter custom path: ").strip()
data_path = Path(custom_path).expanduser().resolve()
else:
data_path = default_path
# Create directory if it doesn't exist
data_path.mkdir(parents=True, exist_ok=True)
print(f"\n✓ Data directory configured: {data_path}")
print(" Data will be downloaded automatically on first use")
return data_path
def test_installation(data_path: Path):
"""Test biomni installation with a simple query."""
print("\n=== Installation Test ===")
print("Testing biomni installation with a simple query...")
response = input("Run test? [Y/n]: ").strip().lower()
if response == 'n':
print("Skipping test")
return
test_code = f'''
import os
from biomni.agent import A1
# Use environment variables for API keys
agent = A1(path='{data_path}', llm='claude-sonnet-4-20250514')
# Simple test query
result = agent.go("What is the primary function of the TP53 gene?")
print("Test result:", result)
'''
test_file = Path('test_biomni.py')
with open(test_file, 'w') as f:
f.write(test_code)
print(f"\nTest script created: {test_file}")
print("Running test...")
try:
subprocess.run([sys.executable, str(test_file)], check=True)
print("\n✓ Test completed successfully!")
test_file.unlink() # Clean up test file
except subprocess.CalledProcessError:
print("\n❌ Test failed. Check your configuration.")
print(f" Test script saved as {test_file} for debugging")
def generate_example_script(data_path: Path):
"""Generate example usage script."""
example_code = f'''#!/usr/bin/env python3
"""
Example biomni usage script
This demonstrates basic biomni usage patterns.
Modify this script for your research tasks.
"""
from biomni.agent import A1
# Initialize agent
agent = A1(
path='{data_path}',
llm='claude-sonnet-4-20250514' # or your preferred LLM
)
# Example 1: Simple gene query
print("Example 1: Gene function query")
result = agent.go("""
What are the main functions of the BRCA1 gene?
Include information about:
- Molecular function
- Associated diseases
- Protein interactions
""")
print(result)
print("-" * 80)
# Example 2: Data analysis
print("\\nExample 2: GWAS analysis")
result = agent.go("""
Explain how to analyze GWAS summary statistics for:
1. Identifying genome-wide significant variants
2. Mapping variants to genes
3. Pathway enrichment analysis
""")
print(result)
# Save conversation history
agent.save_conversation_history("example_results.pdf")
print("\\nResults saved to example_results.pdf")
'''
example_file = Path('example_biomni_usage.py')
with open(example_file, 'w') as f:
f.write(example_code)
print(f"\n✓ Example script created: {example_file}")
def main():
"""Main setup workflow."""
print("=" * 60)
print("Biomni Environment Setup")
print("=" * 60)
# Step 1: Conda environment
conda_success = setup_conda_environment()
if conda_success:
print("\n⚠️ Remember to activate the environment:")
print(" conda activate biomni_e1")
print(" pip install biomni --upgrade")
# Step 2: API keys
api_keys = setup_api_keys()
if api_keys:
print("\nHow would you like to store API keys?")
print("1. .env file (recommended, local to this directory)")
print("2. Shell export (add to .bashrc/.zshrc)")
choice = input("Choose [1/2]: ").strip()
if choice == '2':
save_api_keys(api_keys, method='shell_export')
else:
save_api_keys(api_keys, method='env_file')
# Step 3: Data directory
data_path = setup_data_directory()
# Step 4: Generate example script
if data_path:
generate_example_script(data_path)
# Step 5: Test installation (optional)
if api_keys and data_path:
test_installation(data_path)
# Summary
print("\n" + "=" * 60)
print("Setup Complete!")
print("=" * 60)
if conda_success:
print("✓ Conda environment: biomni_e1")
if api_keys:
print(f"✓ API keys configured: {', '.join(api_keys.keys())}")
if data_path:
print(f"✓ Data directory: {data_path}")
print("\nNext steps:")
if conda_success:
print("1. conda activate biomni_e1")
print("2. pip install biomni --upgrade")
print("3. Run example_biomni_usage.py to test")
else:
print("1. Install conda/miniconda")
print("2. Run this script again")
print("\nFor documentation, see:")
print(" - GitHub: https://github.com/snap-stanford/biomni")
print(" - Paper: https://www.biorxiv.org/content/10.1101/2025.05.30.656746v1")
if __name__ == "__main__":
try:
main()
except KeyboardInterrupt:
print("\n\nSetup interrupted by user")
sys.exit(1)
except Exception as e:
print(f"\n❌ Error during setup: {e}")
sys.exit(1)