docnest-ai 0.4.0a3

The document normalisation engine RAG has always needed

DOCNEST

The document normalization engine RAG has always needed.

Parse any document. Understand its structure. Build RAG that actually works.

Why DOCNEST • Installation • Quick Start • Python API • PDF Parsing • How It Works • CLI Reference • Providers • Roadmap

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The Problem with RAG Today

Every RAG pipeline ingests documents the same broken way:

PDF → extract text → split every 512 chars → embed → store → hope

What gets silently destroyed:

Source	What blind chunking loses
Financial report	Table row 45.2% | Q3 | Europe has no column headers
Legal contract	Clause split mid-sentence across two chunks
API documentation	Code example separated from its description
Research paper	Figure caption disconnected from its analysis

The LLM receives noise and returns approximate answers. This is not a retrieval problem — it is an ingestion problem.

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✨ Why DOCNEST

DOCNEST reads the structure of a document before touching the content. Every heading becomes a navigable §section. Every table is preserved as { caption, headers, rows[] }. Every section gets a one-sentence summary, a keyword index, and a quantized embedding — computed once at ingest, used forever.

The output is a .udf file — a self-contained portable knowledge base you can share by email, copy to USB, or upload to S3.

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📦 Installation

pip install docnest-ai

Optional extras

# Fast PDF parsing (no ML, no downloads) — recommended for most PDFs
pip install pymupdf

# ML-quality PDF parsing (tables, scanned docs) — requires more RAM
pip install docling

# Fast approximate nearest-neighbour search (large document sets)
pip install faiss-cpu

# Persistent cross-session vector store
pip install chromadb

# Everything at once
pip install docnest-ai pymupdf docling faiss-cpu chromadb

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🚀 Quick Start

Convert a document

# Fastest — PyMuPDF parser, local embeddings, no LLM required
docnest convert report.pdf --pdf-engine pymupdf --fast

# Full quality — Docling parser + LLM enrichment (Groq is free-tier friendly)
docnest convert report.pdf --llm-provider groq --llm-model llama-3.3-70b-versatile

# Large PDF (>30 pages) — auto page-chunked, full ML quality, bounded RAM
docnest convert big-report.pdf --llm-provider openai --llm-model gpt-4o-mini

# With metadata tags
docnest convert report.pdf \
  --owner "Alice Smith" \
  --department "Finance" \
  --tags "q4,2024,revenue"

Query a document

docnest query report.udf "What was Q3 revenue?"
docnest query report.udf "What are the key risks?" --layers 0,1,2

Inspect a document

docnest inspect report.udf

View as HTML

docnest view report.udf           # opens browser
docnest view report.udf --out report.html

Library — multi-document search

docnest library init ./docs/
docnest library add  ./docs/ report.udf
docnest library add  ./docs/ contract.udf
docnest library list ./docs/
docnest library search ./docs/ "revenue forecast"
docnest library remove ./docs/ old-report.udf

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🐍 Python API

Converting a document

from docnest.pipeline import DocNestPipeline

# ── Option 1: Fully local — no API keys, no internet after first download ──
pipeline = DocNestPipeline(
    llm_provider="ollama",
    llm_model="llama3.2",          # ollama pull llama3.2
    emb_provider="huggingface",
    emb_model="all-MiniLM-L6-v2",  # downloaded automatically on first run
)
pipeline.convert("report.pdf")     # → report.udf

# ── Option 2: Groq LLM + local HuggingFace embeddings (recommended) ──
pipeline = DocNestPipeline(
    llm_provider="groq",
    llm_model="llama-3.3-70b-versatile",
    llm_api_key="gsk_...",          # or set GROQ_API_KEY env var
    emb_provider="huggingface",
    emb_model="all-MiniLM-L6-v2",
)
pipeline.convert("report.pdf")

# ── Option 3: OpenAI for both LLM and embeddings ──
pipeline = DocNestPipeline(
    llm_provider="openai",
    llm_model="gpt-4o-mini",
    llm_api_key="sk-...",
    emb_provider="openai",
    emb_model="text-embedding-3-small",
    emb_api_key="sk-...",
)
pipeline.convert("report.pdf")

# ── Option 4: Skip intelligence (no LLM, fastest) ──
pipeline = DocNestPipeline(skip_intelligence=True)
pipeline.convert("report.pdf")     # embeddings only, no section summaries

# ── Option 5: Custom output path + progress callback ──
pipeline = DocNestPipeline(
    llm_provider="groq",
    llm_api_key="gsk_...",
)
pipeline.convert(
    "report.pdf",
    output_path="./output/report.udf",
    on_stage_complete=lambda stage, _: print(f"✓ {stage}"),
)

Querying a document

from docnest.reader import UDFIndex

# Load the .udf file (instant — no LLM needed to load)
idx = UDFIndex.load("report.udf")

# ── Simple query — escalates through layers automatically ──
result = idx.query(
    "What was Q3 revenue?",
    llm_provider="groq",
    llm_model="llama-3.3-70b-versatile",
    llm_api_key="gsk_...",
)

print(result.answer)       # "Q3 revenue was $38M, up 22% YoY."
print(result.citations)    # ["§3.1"]
print(result.layer_used)   # 1  (BM25+cosine, 0 tokens!)
print(result.tokens_used)  # 0

# ── Use FAISS for faster search on large documents ──
idx = UDFIndex.load("report.udf", vector="faiss")

# ── ChromaDB — persists across sessions ──
idx = UDFIndex.load("report.udf", vector="chroma", persist_dir="./chroma_store")

# ── Multiple queries on same index (load once, reuse) ──
questions = [
    "What were the key risks?",
    "What is the revenue forecast for 2025?",
    "Who are the main competitors?",
]
for q in questions:
    r = idx.query(q, llm_provider="groq", llm_api_key="gsk_...")
    print(f"[L{r.layer_used}] {r.answer[:120]}")

Parsing PDFs directly

from docnest.parsers.pdf import DoclingPDFParser
from docnest.parsers.pymupdf_pdf import PyMuPDFParser
from docnest.parsers.factory import ParserFactory

# ── DoclingPDFParser — full ML quality (tables, headings, scanned pages) ──

# Small PDF (≤30 pages) — runs Docling directly
parser = DoclingPDFParser()
raw = parser.parse("report.pdf")

# Large PDF — auto page-chunked in 30-page pieces, same full ML quality
raw = DoclingPDFParser().parse("600-page-annual-report.pdf")

# Explicit chunk size — tune to your RAM
raw = DoclingPDFParser(chunk_pages=10).parse("large.pdf")   # low RAM machine
raw = DoclingPDFParser(chunk_pages=50).parse("large.pdf")   # high RAM machine

# Scanned PDF (OCR) — requires Docling's Tesseract integration
raw = DoclingPDFParser(ocr=True).parse("scanned-contract.pdf")

# ── PyMuPDFParser — fast, zero ML, works on any machine ──
parser = PyMuPDFParser()
raw = parser.parse("report.pdf")

# ── ParserFactory — auto-selects the right parser by file extension ──
factory = ParserFactory()                          # default: Docling for PDF
factory = ParserFactory(pdf_engine="pymupdf")      # lightweight: PyMuPDF for PDF

raw = factory.get("report.pdf").parse("report.pdf")
raw = factory.get("report.docx").parse("report.docx")
raw = factory.get("data.xlsx").parse("data.xlsx")
raw = factory.get("page.html").parse("page.html")
raw = factory.get("notes.md").parse("notes.md")

# Inspect what was parsed
print(f"Sections: {len(raw.sections)}")
for s in raw.sections:
    print(f"  L{s.level}  {s.title}  ({len(s.tables)} tables)")

Custom PDF engine at runtime

from docnest.parsers.factory import ParserFactory

factory = ParserFactory()

# Switch to PyMuPDF for this session
factory.set_pdf_engine("pymupdf")

# Switch back to Docling
factory.set_pdf_engine("docling")

# Register a completely custom parser
from docnest.parsers.base import IParser

class MyParser(IParser):
    def supports(self, path: str) -> bool:
        return path.endswith(".myformat")
    def parse(self, path: str):
        ...

factory.register(MyParser())

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📄 PDF Parsing & Memory Guide

DOCNEST gives you two PDF parsers. Choose based on your document type and available RAM:

	DoclingPDFParser	PyMuPDFParser
Table quality	✅ ML-grade (TableFormer)	⚠️ Heuristic (basic grids)
Scanned PDFs	✅ OCR support	❌ Text-only
Heading detection	✅ Semantic (Docling layout)	⚠️ Font-size heuristic
RAM usage	~1–2 GB (ML models)	~50 MB
First-run download	~1 GB models	None
Speed	Slower	Very fast
Best for	Financial reports, contracts, research papers	Resumes, simple reports, fast prototyping

Memory management for large PDFs

DoclingPDFParser auto-chunks large PDFs — no quality loss, bounded RAM:

# Auto-chunking kicks in for PDFs > 30 pages
# Peak RAM ≈ RAM_per_chunk, not RAM_for_whole_file
raw = DoclingPDFParser().parse("600-page-report.pdf")

# Tune chunk size to your machine
raw = DoclingPDFParser(chunk_pages=10).parse("report.pdf")   # 8 GB RAM
raw = DoclingPDFParser(chunk_pages=30).parse("report.pdf")   # 16 GB RAM (default)
raw = DoclingPDFParser(chunk_pages=60).parse("report.pdf")   # 32 GB+ RAM

# Page images are disabled by default (saves 50-200 MB per page)
# Only enable if you specifically need image assets
raw = DoclingPDFParser(generate_images=True).parse("report.pdf")

How chunking works:

1. PyMuPDF splits the PDF into N-page temp files
2. Docling runs with full ML quality on each chunk
3. Sections are merged — output is identical to processing the whole file at once
4. Temp files are deleted immediately after each chunk

If you hit std::bad_alloc or OSError: paging file too small, fall back to PyMuPDF:

from docnest.parsers.pymupdf_pdf import PyMuPDFParser
raw = PyMuPDFParser().parse("huge.pdf")  # Zero ML, always succeeds

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🧠 How It Works

DOCNEST runs a 6-stage normalization pipeline on every document:

Stage 1  Structure Extraction    (Docling / PyMuPDF)   headings, tables, lists, hierarchy
Stage 2  Section Assignment      (rule-based)           §1, §1.1, §1.2 … every heading = §id
Stage 3  Table Normalization     (normaliser)           { caption, headers, rows[] } JSON
Stage 4  Section Summarization   (LLM)                  one sentence per section
Stage 5  Document Intelligence   (LLM)                  summary, insights[], key_numbers[]
Stage 6  Embedding + Quantize    (local)                BM25 keywords + float16 vectors

Stages 1, 2, 3, and 6 run locally — zero LLM cost.
Stages 4–5 call an LLM once per document. Every future query benefits for free.

The result is a .udf file — a self-contained, portable knowledge base:

document.udf  (zip)
├── manifest.json      format version, embedding model, quantization, DocMeta
├── catalogue.json     section index + BM25 keywords + intelligence
├── content.json       full section text (loaded on demand)
├── embeddings.bin     flat float16 binary blob (~87% smaller than base64)
└── assets/            images, structured tables

embeddings.bin is a flat binary blob: N × D × 2 bytes (float16).
Legacy base64-per-section format is still read for backward compatibility.

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⚡ Query Resolution — Five Layers

DOCNEST resolves queries without sending full documents to the LLM:

Layer	Mechanism	Tokens	Latency
0	Pre-computed (summary, insights, key_numbers)	0	< 1 ms
1	BM25 + cosine → navigate to §section	0	< 20 ms
2	Section-scoped LLM (~300 tokens)	~300	1–3 s
3	Multi-section synthesis (~900 tokens)	~900	2–5 s
4	Full document fallback	~4000+	5–15 s
—	Naive RAG (blind chunking)	~4000–8000	5–15 s

Layers 0 and 1 answer ~70% of real-world questions with zero LLM cost.

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📂 Supported Formats

Format	Parser	Notes
PDF (text-based)	DoclingPDFParser / PyMuPDFParser	Full heading hierarchy, table extraction
PDF (scanned)	DoclingPDFParser(ocr=True)	OCR via Docling's Tesseract integration
DOCX	DocxParser	Word documents with styles and heading levels
XLSX	ExcelParser	Each sheet → section, all tables preserved
HTML	HTMLParser	h1–h6 hierarchy via BeautifulSoup
Markdown	MarkdownParser	ATX and Setext headings via mistletoe

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🔌 Provider Interfaces

All external dependencies sit behind swappable interfaces. Change the string — no other code changes.

LLM Providers (llm_provider=)

Value	Notes
"groq"	Fast, generous free tier — recommended for getting started
"openai"	GPT-4o-mini, GPT-4o
"ollama"	Fully local — ollama pull llama3.2
"anthropic"	Claude Haiku, Claude Sonnet
"google"	Gemini Flash, Gemini Pro
"mistral"	Mistral Large, Mixtral
"together"	Together AI hosted models
"cohere"	Command R+
"bedrock"	AWS Bedrock (boto3 required)

Embedding Providers (emb_provider=)

Value	Notes
"huggingface"	Local — downloads model once, then offline. Default.
"openai"	text-embedding-3-small / text-embedding-3-large
"ollama"	Local via Ollama (nomic-embed-text, etc.)
"google"	Vertex AI / Gemini embeddings
"cohere"	embed-english-v3.0
"bedrock"	AWS Bedrock Titan embeddings
"nvidia"	NVIDIA NIM embeddings
"mistral"	Mistral embeddings

Vector Backends (vector=)

Value	Install	Best for
"numpy" (default)	built-in	Small docs, zero extra deps
"faiss"	pip install faiss-cpu	Fast ANN on large collections
"chroma"	pip install chromadb	Persistent cross-session store

from docnest.reader import UDFIndex

idx = UDFIndex.load("report.udf")                               # numpy (default)
idx = UDFIndex.load("report.udf", vector="faiss")              # FAISS
idx = UDFIndex.load("report.udf", vector="chroma",             # ChromaDB
                    persist_dir="./store")

Search Providers

Value	Notes
"auto"	Picks best available — bm25 → tfidf → keyword
"bm25"	BM25Okapi — best keyword recall
"tfidf"	TF-IDF — good fallback
"keyword"	Simple term overlap — zero deps

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🗺 Roadmap

Phase	Description	Status
1	Core parsers — PDF (Docling + PyMuPDF), DOCX, XLSX, HTML, MD	✅ Done
2	Embedding + quantization (10+ providers via LangChain)	✅ Done
3	Intelligence engine (summary, insights, key_numbers)	✅ Done
4	UDF writer + reader + five-layer query engine	✅ Done
5	Large PDF chunking — full ML quality, bounded RAM	✅ Done
6	Library mode — multi-document cross-search	✅ Done
7	PyPI release pip install docnest-ai	✅ Done
8	Connectors: GitHub, Confluence, Notion, Jira	📋 Planned
9	Hierarchical supervisor+worker for datasets > 200 MB	📋 Planned

Track detailed progress: ROADMAP.md

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🤝 Contributing

DOCNEST is community-first. We are building this in the open and want contributors at every level.

Area	Good for
🧩 New parser (PPTX, EPUB, RST)	Familiar with Docling or document formats
🔌 New vector backend (Qdrant, Weaviate)	Vector database experience
🔌 New connector (SharePoint, Linear)	API integration experience
🧪 Test fixtures	Any skill level — add sample documents for testing
📖 Documentation	Any skill level — improve examples, fix typos
🐛 Bug reports	Any skill level — try it, break it, report it
💡 Architecture discussion	Senior engineers — open a Discussion

See CONTRIBUTING.md for the full guide.

Give us a ⭐ if DOCNEST solves a problem you have — it helps others find the project.

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📐 Technical Specification

Full implementation spec: SPEC_DOCNEST_PYPI.md

Covers: architecture, SOLID compliance, design patterns, interfaces, concrete classes, code snippets, test plan, dependency costs.

Open format spec: github.com/tailorgunjan93/udf-spec

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📄 License

MIT — free for commercial use. See LICENSE.

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🔗 Ecosystem

Product	Description
DOCNESTd	This library — document normalization engine
udf-spec	Open specification for the .udf format
synapse-local	Desktop RAG app (Tauri) powered by DOCNEST
udf-reader-vscode	VS Code extension for .udf files

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Built with ❤️ for the RAG community · github.com/tailorgunjan93/DOCNESTd