site_name: DeepCritical

site_description: Hydra-configured, Pydantic Graph-based deep research workflow

site_author: DeepCritical Team

site_url: https://deepcritical.github.io/DeepCritical/

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nav:

- Home: index.md

- Getting Started:

- Installation: getting-started/installation.md

- Quick Start: getting-started/quickstart.md

- Configuration: getting-started/configuration.md

- User Guide:

- Architecture Overview: architecture/overview.md

- Configuration: user-guide/configuration.md

- LLM Models: user-guide/llm-models.md

- Flows:

- PRIME Flow: user-guide/flows/prime.md

- Bioinformatics Flow: user-guide/flows/bioinformatics.md

- DeepSearch Flow: user-guide/flows/deepsearch.md

- Challenge Flow: user-guide/flows/challenge.md

- Code Execution Flow: user-guide/flows/code-execution.md

- Flow Overview: flows/index.md

- Tools:

- Tool Registry: api/tools.md

- Tool Registry Guide: user-guide/tools/registry.md

- Bioinformatics Tools: user-guide/tools/bioinformatics.md

- Search Tools: user-guide/tools/search.md

- RAG Tools: user-guide/tools/rag.md

- Neo4j Integration: user-guide/tools/neo4j-integration.md

- Knowledge Query Tools: user-guide/tools/knowledge-query.md

- API Reference:

- Overview: api/index.md

- Agents: api/agents.md

- Tools: api/tools.md

- Data Types: api/datatypes.md

- Configuration: api/configuration.md

- Core Modules: core/index.md

- Utilities: utilities/index.md

- Flows: flows/index.md

- Tool Overview: tools/index.md

- Development:

- Setup: development/setup.md

- Contributing: development/contributing.md

- Testing: development/testing.md

- CI/CD: development/ci-cd.md

- Scripts: development/scripts.md

- Makefile Usage: development/makefile-usage.md

- Pre-commit Hooks: development/pre-commit-hooks.md

- Tool Development: development/tool-development.md

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- Basic Usage: examples/basic.md

- Advanced Workflows: examples/advanced.md