Graphify Docs

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Export & Output Formats ​

Fresh

Standard Output Structure ​

Every graphify run produces:

graphify-out/
├── graph.html           # Interactive vis.js visualization
├── GRAPH_REPORT.md      # Human-readable audit
├── graph.json           # Persistent queryable graph
└── cache/               # SHA256 change detection
    ├── <file-hash>.json
    └── ...

graph.html — Interactive Visualization ​

The HTML visualization uses vis.js and runs entirely in the browser with no server required.

Features:

  • Click any node to see its relationships
  • Filter by Leiden community cluster
  • Search for specific nodes by name
  • Zoom, pan, and rearrange
  • Node size reflects degree (more connections = bigger node)
  • Edge color reflects type: EXTRACTED (solid), INFERRED (dashed), AMBIGUOUS (dotted)

Open it:

bash
open graphify-out/graph.html      # macOS
start graphify-out/graph.html     # Windows
xdg-open graphify-out/graph.html  # Linux

GRAPH_REPORT.md — Audit Report ​

Structured Markdown report containing:

SectionContent
God NodesHighest-degree nodes — the hubs of your system
Community ClustersLeiden-detected semantic groupings with member nodes
Surprising ConnectionsCross-community edges that suggest unexpected coupling
Suggested QuestionsPre-generated query strings for rich graph traversal
StatisticsNode count, edge count, confidence breakdown

graph.json — Queryable Persistent Graph ​

The JSON graph persists between sessions. Structure:

json
{
  "nodes": [
    {
      "id": "AuthService",
      "type": "class",
      "file": "src/auth/service.py",
      "community": 2,
      "degree": 14
    }
  ],
  "edges": [
    {
      "source": "AuthService",
      "target": "Database",
      "type": "EXTRACTED",
      "confidence": 0.95,
      "relationship": "calls"
    }
  ],
  "metadata": {
    "built_at": "2025-01-15T10:30:00Z",
    "file_count": 52,
    "mode": "standard"
  }
}

Optional Export Formats ​

Wiki Export (--wiki) ​

bash
/graphify . --wiki

Produces graphify-out/wiki/ with one Markdown file per Leiden community cluster. Each file is a Wikipedia-style article summarizing the cluster's concepts and relationships.

graphify-out/wiki/
├── authentication-cluster.md
├── data-layer-cluster.md
├── api-routing-cluster.md
└── ...

Obsidian Export (--obsidian) ​

bash
/graphify . --obsidian

Produces graphify-out/obsidian/ as a full Obsidian vault with:

  • Bidirectional wiki-links between concepts
  • Tags for community clusters
  • Frontmatter with node metadata

GraphML Export (--graphml) ​

bash
/graphify . --graphml

Produces graphify-out/graph.graphml for import into Gephi, yEd, or other graph visualization tools.

Neo4j Export (--neo4j) ​

bash
/graphify . --neo4j                              # Generate cypher.txt
/graphify . --neo4j-push bolt://localhost:7687   # Push to live Neo4j

Generates Cypher CREATE statements for all nodes and edges.

SVG Export (--svg) ​

bash
/graphify . --svg

Static SVG snapshot of the graph at build time.

Cache Directory ​

Do Not Delete Cache

The cache/ directory contains SHA256 hashes of every processed file. Deleting it forces a full rebuild on the next --update run, which re-triggers LLM extraction for all prose/doc files.

To commit the graph but not the cache (recommended for large teams):

gitignore
# .gitignore
graphify-out/cache/

This forces each team member to rebuild the cache locally on first pull, but keeps the committed graph small.