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370
skills/biomni/scripts/generate_report.py Executable file
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#!/usr/bin/env python3
"""
Enhanced PDF report generation for biomni conversation histories.
This script provides additional customization options for biomni reports:
- Custom styling and branding
- Formatted code blocks
- Section organization
- Metadata inclusion
- Export format options (PDF, HTML, Markdown)
Usage:
python generate_report.py --input conversation.json --output report.pdf
python generate_report.py --agent-object agent --output report.pdf --format html
"""
import argparse
import json
from pathlib import Path
from typing import Dict, List, Optional, Any
from datetime import datetime
def format_conversation_history(
messages: List[Dict[str, Any]],
include_metadata: bool = True,
include_code: bool = True,
include_timestamps: bool = False
) -> str:
"""
Format conversation history into structured markdown.
Args:
messages: List of conversation message dictionaries
include_metadata: Include metadata section
include_code: Include code blocks
include_timestamps: Include message timestamps
Returns:
Formatted markdown string
"""
sections = []
# Header
sections.append("# Biomni Analysis Report\n")
# Metadata
if include_metadata:
sections.append("## Metadata\n")
sections.append(f"- **Generated**: {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}")
sections.append(f"- **Number of interactions**: {len(messages)}")
sections.append("\n---\n")
# Process messages
sections.append("## Analysis\n")
for i, msg in enumerate(messages, 1):
role = msg.get('role', 'unknown')
content = msg.get('content', '')
if role == 'user':
sections.append(f"### Task {i // 2 + 1}\n")
sections.append(f"**Query:**\n```\n{content}\n```\n")
elif role == 'assistant':
sections.append(f"**Response:**\n")
# Check if content contains code
if include_code and ('```' in content or 'import ' in content):
# Attempt to separate text and code
parts = content.split('```')
for j, part in enumerate(parts):
if j % 2 == 0:
# Text content
if part.strip():
sections.append(f"{part.strip()}\n")
else:
# Code content
# Check if language is specified
lines = part.split('\n', 1)
if len(lines) > 1 and lines[0].strip() in ['python', 'r', 'bash', 'sql']:
lang = lines[0].strip()
code = lines[1]
else:
lang = 'python' # Default to python
code = part
sections.append(f"```{lang}\n{code}\n```\n")
else:
sections.append(f"{content}\n")
sections.append("\n---\n")
return '\n'.join(sections)
def markdown_to_html(markdown_content: str, title: str = "Biomni Report") -> str:
"""
Convert markdown to styled HTML.
Args:
markdown_content: Markdown string
title: HTML page title
Returns:
HTML string
"""
# Simple markdown to HTML conversion
# For production use, consider using a library like markdown or mistune
html_template = f"""
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>{title}</title>
<style>
body {{
font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, sans-serif;
line-height: 1.6;
max-width: 900px;
margin: 0 auto;
padding: 20px;
color: #333;
}}
h1 {{
color: #2c3e50;
border-bottom: 3px solid #3498db;
padding-bottom: 10px;
}}
h2 {{
color: #34495e;
margin-top: 30px;
border-bottom: 2px solid #95a5a6;
padding-bottom: 5px;
}}
h3 {{
color: #555;
}}
code {{
background-color: #f4f4f4;
padding: 2px 6px;
border-radius: 3px;
font-family: 'Monaco', 'Menlo', 'Courier New', monospace;
}}
pre {{
background-color: #f8f8f8;
border: 1px solid #ddd;
border-radius: 5px;
padding: 15px;
overflow-x: auto;
}}
pre code {{
background-color: transparent;
padding: 0;
}}
hr {{
border: none;
border-top: 1px solid #ddd;
margin: 30px 0;
}}
.metadata {{
background-color: #ecf0f1;
padding: 15px;
border-radius: 5px;
margin-bottom: 20px;
}}
.task {{
background-color: #e8f4f8;
padding: 10px;
border-left: 4px solid #3498db;
margin: 20px 0;
}}
.footer {{
margin-top: 50px;
text-align: center;
color: #7f8c8d;
font-size: 0.9em;
}}
</style>
</head>
<body>
<div class="content">
{markdown_to_html_simple(markdown_content)}
</div>
<div class="footer">
<p>Generated with Biomni | Stanford SNAP Lab</p>
<p><a href="https://github.com/snap-stanford/biomni">github.com/snap-stanford/biomni</a></p>
</div>
</body>
</html>
"""
return html_template
def markdown_to_html_simple(md: str) -> str:
"""Simple markdown to HTML converter (basic implementation)."""
lines = md.split('\n')
html_lines = []
in_code_block = False
in_list = False
for line in lines:
# Code blocks
if line.startswith('```'):
if in_code_block:
html_lines.append('</code></pre>')
in_code_block = False
else:
lang = line[3:].strip()
html_lines.append(f'<pre><code class="language-{lang}">')
in_code_block = True
continue
if in_code_block:
html_lines.append(line)
continue
# Headers
if line.startswith('# '):
html_lines.append(f'<h1>{line[2:]}</h1>')
elif line.startswith('## '):
html_lines.append(f'<h2>{line[3:]}</h2>')
elif line.startswith('### '):
html_lines.append(f'<h3>{line[4:]}</h3>')
# Lists
elif line.startswith('- '):
if not in_list:
html_lines.append('<ul>')
in_list = True
html_lines.append(f'<li>{line[2:]}</li>')
else:
if in_list:
html_lines.append('</ul>')
in_list = False
# Horizontal rule
if line.strip() == '---':
html_lines.append('<hr>')
# Bold
elif '**' in line:
line = line.replace('**', '<strong>', 1).replace('**', '</strong>', 1)
html_lines.append(f'<p>{line}</p>')
# Regular paragraph
elif line.strip():
html_lines.append(f'<p>{line}</p>')
else:
html_lines.append('<br>')
if in_list:
html_lines.append('</ul>')
return '\n'.join(html_lines)
def generate_report(
conversation_data: Dict[str, Any],
output_path: Path,
format: str = 'markdown',
title: Optional[str] = None
):
"""
Generate formatted report from conversation data.
Args:
conversation_data: Conversation history dictionary
output_path: Output file path
format: Output format ('markdown', 'html', or 'pdf')
title: Report title
"""
messages = conversation_data.get('messages', [])
if not title:
title = f"Biomni Analysis - {datetime.now().strftime('%Y-%m-%d')}"
# Generate markdown
markdown_content = format_conversation_history(messages)
if format == 'markdown':
output_path.write_text(markdown_content)
print(f"✓ Markdown report saved to {output_path}")
elif format == 'html':
html_content = markdown_to_html(markdown_content, title)
output_path.write_text(html_content)
print(f"✓ HTML report saved to {output_path}")
elif format == 'pdf':
# For PDF generation, we'd typically use a library like weasyprint or reportlab
# This is a placeholder implementation
print("PDF generation requires additional dependencies (weasyprint or reportlab)")
print("Falling back to HTML format...")
html_path = output_path.with_suffix('.html')
html_content = markdown_to_html(markdown_content, title)
html_path.write_text(html_content)
print(f"✓ HTML report saved to {html_path}")
print(" To convert to PDF:")
print(f" 1. Install weasyprint: pip install weasyprint")
print(f" 2. Run: weasyprint {html_path} {output_path}")
else:
raise ValueError(f"Unsupported format: {format}")
def main():
"""Main entry point for CLI usage."""
parser = argparse.ArgumentParser(
description="Generate enhanced reports from biomni conversation histories"
)
parser.add_argument(
'--input',
type=Path,
required=True,
help='Input conversation history JSON file'
)
parser.add_argument(
'--output',
type=Path,
required=True,
help='Output report file path'
)
parser.add_argument(
'--format',
choices=['markdown', 'html', 'pdf'],
default='markdown',
help='Output format (default: markdown)'
)
parser.add_argument(
'--title',
type=str,
help='Report title (optional)'
)
args = parser.parse_args()
# Load conversation data
try:
with open(args.input, 'r') as f:
conversation_data = json.load(f)
except FileNotFoundError:
print(f"❌ Input file not found: {args.input}")
return 1
except json.JSONDecodeError:
print(f"❌ Invalid JSON in input file: {args.input}")
return 1
# Generate report
try:
generate_report(
conversation_data,
args.output,
format=args.format,
title=args.title
)
return 0
except Exception as e:
print(f"❌ Error generating report: {e}")
return 1
if __name__ == '__main__':
import sys
sys.exit(main())

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skills/biomni/scripts/setup_environment.py Executable file
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#!/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)