Examples

Explore complete working examples in the examples/ directory of the repository.

Available Examples

Example	Description
evolution_harmonypy/	Code evolution example: optimizing the Harmony batch correction algorithm
evolution_agent/	Agent-guided code evolution workflow
fastq_processing/	FASTQ file processing pipeline
paper_reporter/	Academic paper analysis and summarization
paper_reporter_v2/	Enhanced multi-agent paper analysis
single_cell_spatial_analysis/	Single-cell and spatial genomics analysis

Running Examples

Each example directory contains a README with specific instructions. General pattern:

cd examples/<example_name>

# Read the README
cat README.md

# Run the example
python run.py  # or main.py, depending on the example

Evolution Example

The evolution_harmonypy example demonstrates code evolution:

cd examples/evolution_harmonypy

# Test the evaluator
python evaluator.py

# Run evolution (quick test)
python run_evolution.py --iterations 10

See Evolution System for detailed documentation on the Evolution System.