feat : adds rag

[Josephrp]

Pull Request

Description

Type of Change

• 🐛 Bug fix (non-breaking change which fixes an issue)
• ✨ New feature (non-breaking change which adds functionality)
• 💥 Breaking change (fix or feature that would cause existing functionality to not work as expected)
• 📚 Documentation update
• ⚡ Performance improvement
• 🧹 Code refactoring
• 🧪 Test addition or update
• 🔧 Configuration change
• 🧬 Bioinformatics enhancement
• 🔄 Workflow improvement

Component

• Core Workflow Engine
• PRIME Flow (Protein Engineering)
• Bioinformatics Flow (Data Fusion)
• DeepSearch Flow (Web Research)
• Challenge Flow (Experimental)
• Tool Registry
• Agent System
• Configuration (Hydra)
• Pydantic Graph
• Documentation
• Tests
• Other:

Related Issues

• Fixes #
• Closes #
• Related to #

Changes Made

Testing

• I have tested these changes locally
• I have added/updated tests for my changes
• All existing tests pass
• I have tested with different configurations
• I have tested with different flows (PRIME, Bioinformatics, DeepSearch, etc.)

Test Configuration

# Example test command
uv run deepresearch question="..." app_mode=single_react

Configuration Changes

• No configuration changes
• Added new configuration options
• Modified existing configuration
• Removed configuration options

Configuration Details

# Example configuration changes
flows:
  new_flow:
    enabled: true
    params:
      new_param: "value"

Documentation

• No documentation changes needed
• Updated README
• Updated API documentation
• Updated configuration documentation
• Added code comments
• Updated examples

Performance Impact

• No performance impact
• Performance improvement
• Performance regression (explain below)

Performance Details

• Execution time:
• Memory usage:
• Other metrics:

Breaking Changes

• No breaking changes
• Breaking change (describe below)

Migration Guide

Checklist

• My code follows the project's style guidelines
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published

Additional Notes

Screenshots/Output

Before

After

Reviewer Notes