mirror of
https://github.com/K-Dense-AI/claude-scientific-skills.git
synced 2026-03-28 07:33:45 +08:00
Improved Biomni support
This commit is contained in:
Timothy Kassis
457
scientific-packages/biomni/scripts/setup_environment.py
Normal file → Executable file
457
scientific-packages/biomni/scripts/setup_environment.py
Normal file → Executable file
@@ -1,230 +1,355 @@
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#!/usr/bin/env python3
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"""
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Biomni Environment Setup and Validation Script
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Interactive setup script for biomni environment configuration.
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This script helps users set up and validate their Biomni environment,
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including checking dependencies, API keys, and data availability.
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This script helps users set up:
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1. Conda environment with required dependencies
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2. API keys for LLM providers
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3. Data lake directory configuration
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4. MCP server setup (optional)
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Usage:
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python setup_environment.py
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"""
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import os
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import sys
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import subprocess
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from pathlib import Path
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from typing import Dict, List, Tuple
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from typing import Dict, Optional
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def check_python_version() -> Tuple[bool, str]:
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"""Check if Python version is compatible."""
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version = sys.version_info
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if version.major == 3 and version.minor >= 8:
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return True, f"Python {version.major}.{version.minor}.{version.micro} ✓"
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else:
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return False, f"Python {version.major}.{version.minor} - requires Python 3.8+"
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def check_conda_env() -> Tuple[bool, str]:
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"""Check if running in biomni conda environment."""
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conda_env = os.environ.get('CONDA_DEFAULT_ENV', None)
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if conda_env == 'biomni_e1':
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return True, f"Conda environment: {conda_env} ✓"
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else:
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return False, f"Not in biomni_e1 environment (current: {conda_env})"
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def check_package_installed(package: str) -> bool:
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"""Check if a Python package is installed."""
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def check_conda_installed() -> bool:
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"""Check if conda is available in the system."""
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try:
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__import__(package)
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subprocess.run(
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['conda', '--version'],
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capture_output=True,
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check=True
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)
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return True
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except ImportError:
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except (subprocess.CalledProcessError, FileNotFoundError):
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return False
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def check_dependencies() -> Tuple[bool, List[str]]:
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"""Check for required and optional dependencies."""
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required = ['biomni']
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optional = ['weasyprint', 'markdown2pdf']
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def setup_conda_environment():
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"""Guide user through conda environment setup."""
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print("\n=== Conda Environment Setup ===")
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missing_required = [pkg for pkg in required if not check_package_installed(pkg)]
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missing_optional = [pkg for pkg in optional if not check_package_installed(pkg)]
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if not check_conda_installed():
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print("❌ Conda not found. Please install Miniconda or Anaconda:")
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print(" https://docs.conda.io/en/latest/miniconda.html")
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return False
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messages = []
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success = len(missing_required) == 0
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print("✓ Conda is installed")
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if missing_required:
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messages.append(f"Missing required packages: {', '.join(missing_required)}")
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messages.append("Install with: pip install biomni --upgrade")
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# Check if biomni_e1 environment exists
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result = subprocess.run(
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['conda', 'env', 'list'],
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capture_output=True,
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text=True
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)
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if 'biomni_e1' in result.stdout:
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print("✓ biomni_e1 environment already exists")
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return True
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print("\nCreating biomni_e1 conda environment...")
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print("This will install Python 3.10 and required dependencies.")
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response = input("Proceed? [y/N]: ").strip().lower()
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if response != 'y':
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print("Skipping conda environment setup")
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return False
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try:
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# Create conda environment
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subprocess.run(
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['conda', 'create', '-n', 'biomni_e1', 'python=3.10', '-y'],
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check=True
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)
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print("\n✓ Conda environment created successfully")
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print("\nTo activate: conda activate biomni_e1")
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print("Then install biomni: pip install biomni --upgrade")
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return True
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except subprocess.CalledProcessError as e:
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print(f"❌ Failed to create conda environment: {e}")
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return False
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def setup_api_keys() -> Dict[str, str]:
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"""Interactive API key configuration."""
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print("\n=== API Key Configuration ===")
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print("Biomni supports multiple LLM providers.")
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print("At minimum, configure one provider.")
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api_keys = {}
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# Anthropic (recommended)
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print("\n1. Anthropic Claude (Recommended)")
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print(" Get your API key from: https://console.anthropic.com/")
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anthropic_key = input(" Enter ANTHROPIC_API_KEY (or press Enter to skip): ").strip()
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if anthropic_key:
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api_keys['ANTHROPIC_API_KEY'] = anthropic_key
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# OpenAI
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print("\n2. OpenAI")
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print(" Get your API key from: https://platform.openai.com/api-keys")
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openai_key = input(" Enter OPENAI_API_KEY (or press Enter to skip): ").strip()
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if openai_key:
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api_keys['OPENAI_API_KEY'] = openai_key
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# Google Gemini
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print("\n3. Google Gemini")
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print(" Get your API key from: https://makersuite.google.com/app/apikey")
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google_key = input(" Enter GOOGLE_API_KEY (or press Enter to skip): ").strip()
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if google_key:
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api_keys['GOOGLE_API_KEY'] = google_key
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# Groq
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print("\n4. Groq")
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print(" Get your API key from: https://console.groq.com/keys")
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groq_key = input(" Enter GROQ_API_KEY (or press Enter to skip): ").strip()
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if groq_key:
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api_keys['GROQ_API_KEY'] = groq_key
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if not api_keys:
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print("\n⚠️ No API keys configured. You'll need at least one to use biomni.")
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return {}
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return api_keys
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def save_api_keys(api_keys: Dict[str, str], method: str = 'env_file'):
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"""Save API keys using specified method."""
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if method == 'env_file':
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env_file = Path.cwd() / '.env'
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# Read existing .env if present
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existing_vars = {}
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if env_file.exists():
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with open(env_file, 'r') as f:
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for line in f:
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line = line.strip()
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if line and not line.startswith('#'):
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if '=' in line:
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key, val = line.split('=', 1)
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existing_vars[key.strip()] = val.strip()
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# Update with new keys
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existing_vars.update(api_keys)
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# Write to .env
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with open(env_file, 'w') as f:
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f.write("# Biomni API Keys\n")
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f.write(f"# Generated by setup_environment.py\n\n")
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for key, value in existing_vars.items():
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f.write(f"{key}={value}\n")
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print(f"\n✓ API keys saved to {env_file}")
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print(" Keys will be loaded automatically when biomni runs in this directory")
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elif method == 'shell_export':
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shell_file = Path.home() / '.bashrc' # or .zshrc for zsh users
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print("\n📋 Add these lines to your shell configuration:")
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for key, value in api_keys.items():
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print(f" export {key}=\"{value}\"")
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print(f"\nThen run: source {shell_file}")
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def setup_data_directory() -> Optional[Path]:
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"""Configure biomni data lake directory."""
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print("\n=== Data Lake Configuration ===")
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print("Biomni requires ~11GB for integrated biomedical databases.")
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default_path = Path.cwd() / 'biomni_data'
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print(f"\nDefault location: {default_path}")
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response = input("Use default location? [Y/n]: ").strip().lower()
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if response == 'n':
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custom_path = input("Enter custom path: ").strip()
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data_path = Path(custom_path).expanduser().resolve()
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else:
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messages.append("Required packages: ✓")
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data_path = default_path
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if missing_optional:
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messages.append(f"Missing optional packages: {', '.join(missing_optional)}")
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messages.append("For PDF reports, install: pip install weasyprint")
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# Create directory if it doesn't exist
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data_path.mkdir(parents=True, exist_ok=True)
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return success, messages
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print(f"\n✓ Data directory configured: {data_path}")
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print(" Data will be downloaded automatically on first use")
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return data_path
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def check_api_keys() -> Tuple[bool, Dict[str, bool]]:
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"""Check which API keys are configured."""
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api_keys = {
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'ANTHROPIC_API_KEY': os.environ.get('ANTHROPIC_API_KEY'),
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'OPENAI_API_KEY': os.environ.get('OPENAI_API_KEY'),
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'GEMINI_API_KEY': os.environ.get('GEMINI_API_KEY'),
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'GROQ_API_KEY': os.environ.get('GROQ_API_KEY'),
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}
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def test_installation(data_path: Path):
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"""Test biomni installation with a simple query."""
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print("\n=== Installation Test ===")
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print("Testing biomni installation with a simple query...")
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configured = {key: bool(value) for key, value in api_keys.items()}
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has_any = any(configured.values())
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response = input("Run test? [Y/n]: ").strip().lower()
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if response == 'n':
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print("Skipping test")
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return
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return has_any, configured
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test_code = f'''
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import os
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from biomni.agent import A1
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# Use environment variables for API keys
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agent = A1(path='{data_path}', llm='claude-sonnet-4-20250514')
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def check_data_directory(data_path: str = './data') -> Tuple[bool, str]:
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"""Check if Biomni data directory exists and has content."""
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path = Path(data_path)
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# Simple test query
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result = agent.go("What is the primary function of the TP53 gene?")
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print("Test result:", result)
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'''
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if not path.exists():
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return False, f"Data directory not found at {data_path}"
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test_file = Path('test_biomni.py')
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with open(test_file, 'w') as f:
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f.write(test_code)
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# Check if directory has files (data has been downloaded)
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files = list(path.glob('*'))
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if len(files) == 0:
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return False, f"Data directory exists but is empty. Run agent once to download."
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print(f"\nTest script created: {test_file}")
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print("Running test...")
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# Rough size check (should be ~11GB)
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total_size = sum(f.stat().st_size for f in path.rglob('*') if f.is_file())
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size_gb = total_size / (1024**3)
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if size_gb < 1:
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return False, f"Data directory exists but seems incomplete ({size_gb:.1f} GB)"
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return True, f"Data directory: {data_path} ({size_gb:.1f} GB) ✓"
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def check_disk_space(required_gb: float = 20) -> Tuple[bool, str]:
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"""Check if sufficient disk space is available."""
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try:
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import shutil
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stat = shutil.disk_usage('.')
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free_gb = stat.free / (1024**3)
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if free_gb >= required_gb:
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return True, f"Disk space: {free_gb:.1f} GB available ✓"
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else:
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return False, f"Low disk space: {free_gb:.1f} GB (need {required_gb} GB)"
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except Exception as e:
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return False, f"Could not check disk space: {e}"
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subprocess.run([sys.executable, str(test_file)], check=True)
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print("\n✓ Test completed successfully!")
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test_file.unlink() # Clean up test file
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except subprocess.CalledProcessError:
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print("\n❌ Test failed. Check your configuration.")
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print(f" Test script saved as {test_file} for debugging")
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def test_biomni_import() -> Tuple[bool, str]:
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"""Test if Biomni can be imported and initialized."""
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try:
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from biomni.agent import A1
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from biomni.config import default_config
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return True, "Biomni import successful ✓"
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except ImportError as e:
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return False, f"Cannot import Biomni: {e}"
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except Exception as e:
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return False, f"Biomni import error: {e}"
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def generate_example_script(data_path: Path):
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"""Generate example usage script."""
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example_code = f'''#!/usr/bin/env python3
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"""
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Example biomni usage script
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This demonstrates basic biomni usage patterns.
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Modify this script for your research tasks.
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"""
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def suggest_fixes(results: Dict[str, Tuple[bool, any]]) -> List[str]:
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"""Generate suggestions for fixing issues."""
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suggestions = []
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from biomni.agent import A1
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if not results['python'][0]:
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suggestions.append("➜ Upgrade Python to 3.8 or higher")
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# Initialize agent
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agent = A1(
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path='{data_path}',
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llm='claude-sonnet-4-20250514' # or your preferred LLM
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)
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if not results['conda'][0]:
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suggestions.append("➜ Activate biomni environment: conda activate biomni_e1")
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# Example 1: Simple gene query
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print("Example 1: Gene function query")
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result = agent.go("""
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What are the main functions of the BRCA1 gene?
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Include information about:
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- Molecular function
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- Associated diseases
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- Protein interactions
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""")
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print(result)
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print("-" * 80)
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if not results['dependencies'][0]:
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suggestions.append("➜ Install Biomni: pip install biomni --upgrade")
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# Example 2: Data analysis
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print("\\nExample 2: GWAS analysis")
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result = agent.go("""
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Explain how to analyze GWAS summary statistics for:
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1. Identifying genome-wide significant variants
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2. Mapping variants to genes
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3. Pathway enrichment analysis
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""")
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print(result)
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if not results['api_keys'][0]:
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suggestions.append("➜ Set API key: export ANTHROPIC_API_KEY='your-key'")
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suggestions.append(" Or create .env file with API keys")
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# Save conversation history
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agent.save_conversation_history("example_results.pdf")
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print("\\nResults saved to example_results.pdf")
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'''
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if not results['data'][0]:
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suggestions.append("➜ Data will auto-download on first agent.go() call")
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example_file = Path('example_biomni_usage.py')
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with open(example_file, 'w') as f:
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f.write(example_code)
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if not results['disk_space'][0]:
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suggestions.append("➜ Free up disk space (need ~20GB total)")
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return suggestions
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print(f"\n✓ Example script created: {example_file}")
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||||
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def main():
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"""Run all environment checks and display results."""
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"""Main setup workflow."""
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print("=" * 60)
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print("Biomni Environment Validation")
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||||
print("Biomni Environment Setup")
|
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print("=" * 60)
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print()
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# Run all checks
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results = {}
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# Step 1: Conda environment
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conda_success = setup_conda_environment()
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||||
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print("Checking Python version...")
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results['python'] = check_python_version()
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print(f" {results['python'][1]}")
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print()
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if conda_success:
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print("\n⚠️ Remember to activate the environment:")
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print(" conda activate biomni_e1")
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print(" pip install biomni --upgrade")
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||||
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print("Checking conda environment...")
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results['conda'] = check_conda_env()
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print(f" {results['conda'][1]}")
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print()
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||||
# Step 2: API keys
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api_keys = setup_api_keys()
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||||
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||||
print("Checking dependencies...")
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||||
results['dependencies'] = check_dependencies()
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for msg in results['dependencies'][1]:
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print(f" {msg}")
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print()
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if api_keys:
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print("\nHow would you like to store API keys?")
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print("1. .env file (recommended, local to this directory)")
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print("2. Shell export (add to .bashrc/.zshrc)")
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||||
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||||
print("Checking API keys...")
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||||
results['api_keys'] = check_api_keys()
|
||||
has_keys, key_status = results['api_keys']
|
||||
for key, configured in key_status.items():
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status = "✓" if configured else "✗"
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||||
print(f" {key}: {status}")
|
||||
print()
|
||||
choice = input("Choose [1/2]: ").strip()
|
||||
|
||||
print("Checking Biomni data directory...")
|
||||
results['data'] = check_data_directory()
|
||||
print(f" {results['data'][1]}")
|
||||
print()
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if choice == '2':
|
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save_api_keys(api_keys, method='shell_export')
|
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else:
|
||||
save_api_keys(api_keys, method='env_file')
|
||||
|
||||
print("Checking disk space...")
|
||||
results['disk_space'] = check_disk_space()
|
||||
print(f" {results['disk_space'][1]}")
|
||||
print()
|
||||
# Step 3: Data directory
|
||||
data_path = setup_data_directory()
|
||||
|
||||
print("Testing Biomni import...")
|
||||
results['biomni_import'] = test_biomni_import()
|
||||
print(f" {results['biomni_import'][1]}")
|
||||
print()
|
||||
# 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)
|
||||
all_passed = all(result[0] for result in results.values())
|
||||
|
||||
if all_passed:
|
||||
print("✓ All checks passed! Environment is ready.")
|
||||
print()
|
||||
print("Quick start:")
|
||||
print(" from biomni.agent import A1")
|
||||
print(" agent = A1(path='./data', llm='claude-sonnet-4-20250514')")
|
||||
print(" agent.go('Your biomedical task')")
|
||||
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("⚠ Some checks failed. See suggestions below:")
|
||||
print()
|
||||
suggestions = suggest_fixes(results)
|
||||
for suggestion in suggestions:
|
||||
print(suggestion)
|
||||
print("1. Install conda/miniconda")
|
||||
print("2. Run this script again")
|
||||
|
||||
print("=" * 60)
|
||||
|
||||
return 0 if all_passed else 1
|
||||
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__":
|
||||
sys.exit(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