paper-siphon 0.3.0

Extract clean Markdown from academic PDFs - like drinking through a straw

Paper Siphon

Extract clean Markdown from academic PDFs - like drinking through a straw.

Academic papers come with artifacts: awkward page breaks, mangled tables, or even line numbers. Paper Siphon filters them out, leaving you with clean, readable Markdown.

paper-siphon paper.pdf

That's it. Your paper is now paper.md.

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Features

• Smart whitespace - Collapses excessive blank lines, normalizes spacing
• Table preservation - Keeps your data tables intact and formatted
• Formula support - Optional enrichment for mathematical expressions
• Line number removal - Automatically strips the margin numbers (when present)
• VLM pipeline - Use vision-language models for complex layouts
• Apple Silicon acceleration - MLX support for fast processing on M-series Macs

Installation

# With uv (recommended)
uv pip install paper-siphon

# With pip
pip install paper-siphon

For Apple Silicon acceleration (optional):

uv pip install paper-siphon[mlx]

Usage

Quick start (no install)

uvx paper-siphon paper.pdf                # Run directly with uvx

Basic

paper-siphon paper.pdf                    # Creates paper.md
paper-siphon paper.pdf -o notes.md        # Custom output path

From URL (including arXiv)

paper-siphon https://arxiv.org/pdf/1706.03762.pdf

Tip: For arXiv papers, just change /abs/ to /pdf/ in the URL:

https://arxiv.org/abs/1706.03762  →  https://arxiv.org/pdf/1706.03762.pdf

(That's "Attention Is All You Need" - the Transformer paper)

Advanced

paper-siphon --vlm paper.pdf              # Use VLM for complex layouts
paper-siphon --enrich-formula paper.pdf   # Enable formula enrichment
paper-siphon --no-mlx --vlm paper.pdf     # VLM without MLX acceleration
paper-siphon -v paper.pdf                 # Verbose logging

How It Works

Paper Siphon uses Docling for PDF parsing, then applies post-processing to clean up common academic paper artifacts:

1. PDF parsing - Extracts structure, text, and tables
2. Line number filtering - Removes standalone 1-4 digit numbers (common in journal formats)
3. Whitespace normalization - Collapses multiple blank lines

Options

Flag	Description
-o, --output	Output file path (default: input with .md extension)
--vlm	Use VLM pipeline for complex layouts
--mlx/--no-mlx	Toggle MLX acceleration (Apple Silicon, default: on)
--enrich-formula	Enable formula enrichment (slow, CPU-bound)
-v, --verbose	Enable debug logging

Development

# Clone and install
git clone https://github.com/mrshu/paper-siphon.git
cd paper-siphon
uv sync --dev

# Run tests
uv run pytest

# Run tests with coverage
uv run pytest --cov=paper_siphon

License

MIT

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Stop wrestling with PDFs. Just siphon the good stuff.