Initial commit
This commit is contained in:
Zhongwei Li
355
skills/biomni/scripts/setup_environment.py
Executable file
355
skills/biomni/scripts/setup_environment.py
Executable file
@@ -0,0 +1,355 @@
|
||||
#!/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)
|
||||
Reference in New Issue
Block a user