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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • GitHub issue templates for bug reports, feature requests, documentation, performance, questions, and bioinformatics issues
  • GitHub pull request template with comprehensive checklist
  • GitHub Actions workflows for CI/CD, release management, and dependabot auto-merge
  • Security policy and vulnerability reporting guidelines
  • Contributing guidelines and code of conduct
  • Repository settings configuration
  • Dependabot configuration for automated dependency updates

Changed

  • Enhanced project documentation structure

Fixed

  • Improved issue and PR management workflows

[0.1.0] - 2024-01-01

Added

  • Initial release of DeepCritical
  • Core workflow engine with Pydantic Graph integration
  • PRIME flow for protein engineering workflows
  • Bioinformatics flow for data fusion and reasoning
  • DeepSearch flow for web research
  • Challenge flow for experimental workflows
  • Tool registry with 65+ specialized tools
  • Agent system with Pydantic AI integration
  • Hydra configuration management
  • Comprehensive documentation and examples

Features

  • PRIME Architecture: Three-stage workflow (Parse → Plan → Execute)
  • Bioinformatics Integration: Multi-source data fusion with GO, PubMed, and other databases
  • Adaptive Re-planning: Strategic and tactical recovery mechanisms
  • Scientific Grounding: Verifiable results from validated tools
  • Configuration Management: Flexible Hydra-based configuration system
  • Agent Orchestration: Multi-agent coordination for complex workflows

Components

  • Core Workflow Engine: Pydantic Graph-based stateful workflow execution
  • PRIME Flow: Protein engineering with specialized tools and scientific intent detection
  • Bioinformatics Flow: Data fusion, reasoning, and quality assessment
  • DeepSearch Flow: Web research and information gathering
  • Tool Registry: Comprehensive tool management and validation system
  • Agent System: Pydantic AI-based agent communication and coordination

Installation

# Using uv (recommended)
uv add deepcritical

# Using pip
pip install deepcritical

Usage

# Basic usage
uv run deepresearch question="Your research question"

# PRIME flow
uv run deepresearch flows.prime.enabled=true question="Design a therapeutic antibody"

# Bioinformatics flow
uv run deepresearch flows.bioinformatics.enabled=true question="Analyze gene function"

Version History

  • 0.1.0: Initial release with core functionality
  • 0.2.0: Enhanced bioinformatics workflows (planned)
  • 0.3.0: Advanced PRIME flow improvements (planned)
  • 1.0.0: Production-ready release (planned)

Contributing

See CONTRIBUTING.md for guidelines on contributing to this project.

Security

See SECURITY.md for security policy and vulnerability reporting.

License

This project is licensed under the MIT License - see the LICENSE file for details.
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