Add more scientific skills

scientific-packages/biomni/scripts/setup_environment.py

@@ -0,0 +1,230 @@
+#!/usr/bin/env python3
+"""
+Biomni Environment Setup and Validation Script
+
+This script helps users set up and validate their Biomni environment,
+including checking dependencies, API keys, and data availability.
+"""
+
+import os
+import sys
+import subprocess
+from pathlib import Path
+from typing import Dict, List, Tuple
+
+
+def check_python_version() -> Tuple[bool, str]:
+    """Check if Python version is compatible."""
+    version = sys.version_info
+    if version.major == 3 and version.minor >= 8:
+        return True, f"Python {version.major}.{version.minor}.{version.micro} ✓"
+    else:
+        return False, f"Python {version.major}.{version.minor} - requires Python 3.8+"
+
+
+def check_conda_env() -> Tuple[bool, str]:
+    """Check if running in biomni conda environment."""
+    conda_env = os.environ.get('CONDA_DEFAULT_ENV', None)
+    if conda_env == 'biomni_e1':
+        return True, f"Conda environment: {conda_env} ✓"
+    else:
+        return False, f"Not in biomni_e1 environment (current: {conda_env})"
+
+
+def check_package_installed(package: str) -> bool:
+    """Check if a Python package is installed."""
+    try:
+        __import__(package)
+        return True
+    except ImportError:
+        return False
+
+
+def check_dependencies() -> Tuple[bool, List[str]]:
+    """Check for required and optional dependencies."""
+    required = ['biomni']
+    optional = ['weasyprint', 'markdown2pdf']
+
+    missing_required = [pkg for pkg in required if not check_package_installed(pkg)]
+    missing_optional = [pkg for pkg in optional if not check_package_installed(pkg)]
+
+    messages = []
+    success = len(missing_required) == 0
+
+    if missing_required:
+        messages.append(f"Missing required packages: {', '.join(missing_required)}")
+        messages.append("Install with: pip install biomni --upgrade")
+    else:
+        messages.append("Required packages: ✓")
+
+    if missing_optional:
+        messages.append(f"Missing optional packages: {', '.join(missing_optional)}")
+        messages.append("For PDF reports, install: pip install weasyprint")
+
+    return success, messages
+
+
+def check_api_keys() -> Tuple[bool, Dict[str, bool]]:
+    """Check which API keys are configured."""
+    api_keys = {
+        'ANTHROPIC_API_KEY': os.environ.get('ANTHROPIC_API_KEY'),
+        'OPENAI_API_KEY': os.environ.get('OPENAI_API_KEY'),
+        'GEMINI_API_KEY': os.environ.get('GEMINI_API_KEY'),
+        'GROQ_API_KEY': os.environ.get('GROQ_API_KEY'),
+    }
+
+    configured = {key: bool(value) for key, value in api_keys.items()}
+    has_any = any(configured.values())
+
+    return has_any, configured
+
+
+def check_data_directory(data_path: str = './data') -> Tuple[bool, str]:
+    """Check if Biomni data directory exists and has content."""
+    path = Path(data_path)
+
+    if not path.exists():
+        return False, f"Data directory not found at {data_path}"
+
+    # Check if directory has files (data has been downloaded)
+    files = list(path.glob('*'))
+    if len(files) == 0:
+        return False, f"Data directory exists but is empty. Run agent once to download."
+
+    # Rough size check (should be ~11GB)
+    total_size = sum(f.stat().st_size for f in path.rglob('*') if f.is_file())
+    size_gb = total_size / (1024**3)
+
+    if size_gb < 1:
+        return False, f"Data directory exists but seems incomplete ({size_gb:.1f} GB)"
+
+    return True, f"Data directory: {data_path} ({size_gb:.1f} GB) ✓"
+
+
+def check_disk_space(required_gb: float = 20) -> Tuple[bool, str]:
+    """Check if sufficient disk space is available."""
+    try:
+        import shutil
+        stat = shutil.disk_usage('.')
+        free_gb = stat.free / (1024**3)
+
+        if free_gb >= required_gb:
+            return True, f"Disk space: {free_gb:.1f} GB available ✓"
+        else:
+            return False, f"Low disk space: {free_gb:.1f} GB (need {required_gb} GB)"
+    except Exception as e:
+        return False, f"Could not check disk space: {e}"
+
+
+def test_biomni_import() -> Tuple[bool, str]:
+    """Test if Biomni can be imported and initialized."""
+    try:
+        from biomni.agent import A1
+        from biomni.config import default_config
+        return True, "Biomni import successful ✓"
+    except ImportError as e:
+        return False, f"Cannot import Biomni: {e}"
+    except Exception as e:
+        return False, f"Biomni import error: {e}"
+
+
+def suggest_fixes(results: Dict[str, Tuple[bool, any]]) -> List[str]:
+    """Generate suggestions for fixing issues."""
+    suggestions = []
+
+    if not results['python'][0]:
+        suggestions.append("➜ Upgrade Python to 3.8 or higher")
+
+    if not results['conda'][0]:
+        suggestions.append("➜ Activate biomni environment: conda activate biomni_e1")
+
+    if not results['dependencies'][0]:
+        suggestions.append("➜ Install Biomni: pip install biomni --upgrade")
+
+    if not results['api_keys'][0]:
+        suggestions.append("➜ Set API key: export ANTHROPIC_API_KEY='your-key'")
+        suggestions.append("   Or create .env file with API keys")
+
+    if not results['data'][0]:
+        suggestions.append("➜ Data will auto-download on first agent.go() call")
+
+    if not results['disk_space'][0]:
+        suggestions.append("➜ Free up disk space (need ~20GB total)")
+
+    return suggestions
+
+
+def main():
+    """Run all environment checks and display results."""
+    print("=" * 60)
+    print("Biomni Environment Validation")
+    print("=" * 60)
+    print()
+
+    # Run all checks
+    results = {}
+
+    print("Checking Python version...")
+    results['python'] = check_python_version()
+    print(f"  {results['python'][1]}")
+    print()
+
+    print("Checking conda environment...")
+    results['conda'] = check_conda_env()
+    print(f"  {results['conda'][1]}")
+    print()
+
+    print("Checking dependencies...")
+    results['dependencies'] = check_dependencies()
+    for msg in results['dependencies'][1]:
+        print(f"  {msg}")
+    print()
+
+    print("Checking API keys...")
+    results['api_keys'] = check_api_keys()
+    has_keys, key_status = results['api_keys']
+    for key, configured in key_status.items():
+        status = "✓" if configured else "✗"
+        print(f"  {key}: {status}")
+    print()
+
+    print("Checking Biomni data directory...")
+    results['data'] = check_data_directory()
+    print(f"  {results['data'][1]}")
+    print()
+
+    print("Checking disk space...")
+    results['disk_space'] = check_disk_space()
+    print(f"  {results['disk_space'][1]}")
+    print()
+
+    print("Testing Biomni import...")
+    results['biomni_import'] = test_biomni_import()
+    print(f"  {results['biomni_import'][1]}")
+    print()
+
+    # Summary
+    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')")
+    else:
+        print("⚠ Some checks failed. See suggestions below:")
+        print()
+        suggestions = suggest_fixes(results)
+        for suggestion in suggestions:
+            print(suggestion)
+
+    print("=" * 60)
+
+    return 0 if all_passed else 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())