# dagztagz/dagztagz-hypothesis-engine architecture

> Architecture diagram of the GitHub repository dagztagz/dagztagz-hypothesis-engine, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-25). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/dagztagz/dagztagz-hypothesis-engine
- Repository: https://github.com/dagztagz/dagztagz-hypothesis-engine

## Overview

DagzTagz Hypothesis Engine is a single-workflow scientific research aid. A researcher submits a topic through the CLI; the workflow optionally retrieves passages from local files, builds a background brief, generates hypotheses, checks each adversarially, and suggests experiments or simulations. Results are structured and displayed or saved, with optional local audit records. The README documents these capabilities; sampled workflow excerpts are incomplete, so internal links are limited to the documented flow and visible retrieval behavior.

Main entry points: [`src/hypothesis_engine/workflow.py`](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py) (Workflow orchestration), [`src/hypothesis_engine/cli.py`](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/cli.py) (Command-line interface), [`src/hypothesis_engine/llm.py`](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/llm.py) (Grok API client), [`src/hypothesis_engine/audit.py`](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/audit.py) (Audit logging)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_interface["User interface"]
  node_cli["Command-line interface<br/>[cli.py]"]
end

subgraph group_research["Research workflow"]
  node_workflow["Workflow orchestration<br/>[workflow.py]"]
  node_background["Background brief<br/>[workflow.py]"]
  node_generation["Hypothesis generation<br/>[workflow.py]"]
  node_verification["Multi-check verification<br/>[workflow.py]"]
  node_testdesign["Test suggestions<br/>[workflow.py]"]
  node_prompts["Scientific prompts<br/>[prompts.py]"]
  node_models["Structured results<br/>[models.py]"]
end

subgraph group_integration["Model and retrieval"]
  node_settings["Runtime settings<br/>[config.py]"]
  node_llm["Grok API client<br/>[llm.py]"]
  node_retrieval["Local retrieval<br/>[retrieval.py]"]
end

subgraph group_privacy["Local records"]
  node_audit["Audit logging<br/>[audit.py]"]
  node_crypto["Topic encryption<br/>[audit_crypto.py]"]
  node_localfiles["Local output and logs"]
end

node_researcher(("Researcher"))
node_xai["xAI Grok API"]
node_corpus["Research files"]

node_researcher -->|"submits topic"| node_cli
node_cli -->|"loads settings"| node_settings
node_cli -->|"runs workflow"| node_workflow
node_workflow -->|"retrieves passages"| node_retrieval
node_corpus -->|"provides files"| node_retrieval
node_workflow -->|"builds brief"| node_background
node_workflow -->|"generates hypotheses"| node_generation
node_workflow -->|"checks hypotheses"| node_verification
node_workflow -->|"suggests tests"| node_testdesign
node_workflow -->|"uses templates"| node_prompts
node_workflow -->|"requests completions"| node_llm
node_llm -->|"reads credentials"| node_settings
node_llm -->|"sends prompts"| node_xai
node_xai -->|"returns responses"| node_llm
node_workflow -->|"validates results"| node_models
node_workflow -.->|"creates mock passages"| node_retrieval
node_cli -->|"records run"| node_audit
node_audit -.->|"encrypts topic"| node_crypto
node_audit -->|"writes audit log"| node_localfiles
node_cli -->|"writes output"| node_localfiles
node_cli -->|"displays results"| node_researcher

click node_cli "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/cli.py"
click node_workflow "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py"
click node_background "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py"
click node_generation "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py"
click node_verification "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py"
click node_testdesign "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py"
click node_prompts "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/prompts.py"
click node_models "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/models.py"
click node_settings "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/config.py"
click node_llm "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/llm.py"
click node_retrieval "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/retrieval.py"
click node_audit "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/audit.py"
click node_crypto "https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/audit_crypto.py"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_cli toneBlue
class node_workflow,node_background,node_generation,node_verification,node_testdesign,node_prompts,node_models toneAmber
class node_settings,node_llm,node_retrieval,node_xai toneMint
class node_audit,node_crypto,node_localfiles toneRose
class node_researcher,node_corpus toneIndigo
```

## Components

### User interface

- [Command-line interface](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/cli.py): `src/hypothesis_engine/cli.py`

### Research workflow

- [Workflow orchestration](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py): `src/hypothesis_engine/workflow.py`
- [Background brief](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py): `src/hypothesis_engine/workflow.py`
- [Hypothesis generation](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py): `src/hypothesis_engine/workflow.py`
- [Multi-check verification](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py): `src/hypothesis_engine/workflow.py`
- [Test suggestions](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/workflow.py): `src/hypothesis_engine/workflow.py`
- [Scientific prompts](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/prompts.py): `src/hypothesis_engine/prompts.py`
- [Structured results](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/models.py): `src/hypothesis_engine/models.py`

### Model and retrieval

- [Runtime settings](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/config.py): `src/hypothesis_engine/config.py`
- [Grok API client](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/llm.py): `src/hypothesis_engine/llm.py`
- [Local retrieval](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/retrieval.py): `src/hypothesis_engine/retrieval.py`

### Local records

- [Audit logging](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/audit.py): `src/hypothesis_engine/audit.py`
- [Topic encryption](https://github.com/dagztagz/dagztagz-hypothesis-engine/blob/main/src/hypothesis_engine/audit_crypto.py): `src/hypothesis_engine/audit_crypto.py`
- **Local output and logs**

### Other components

- **Researcher**
- **xAI Grok API**
- **Research files**

## Connections

- Researcher → Command-line interface: submits topic
- Command-line interface → Runtime settings: loads settings
- Command-line interface → Workflow orchestration: runs workflow
- Workflow orchestration → Local retrieval: retrieves passages
- Research files → Local retrieval: provides files
- Workflow orchestration → Background brief: builds brief
- Workflow orchestration → Hypothesis generation: generates hypotheses
- Workflow orchestration → Multi-check verification: checks hypotheses
- Workflow orchestration → Test suggestions: suggests tests
- Workflow orchestration → Scientific prompts: uses templates
- Workflow orchestration → Grok API client: requests completions
- Grok API client → Runtime settings: reads credentials
- Grok API client → xAI Grok API: sends prompts
- xAI Grok API → Grok API client: returns responses
- Workflow orchestration → Structured results: validates results
- Workflow orchestration → Local retrieval: creates mock passages
- Command-line interface → Audit logging: records run
- Audit logging → Topic encryption: encrypts topic
- Audit logging → Local output and logs: writes audit log
- Command-line interface → Local output and logs: writes output
- Command-line interface → Researcher: displays results