paper2mdviallm

paper2mdviallm is a Python CLI for converting digital academic PDFs into Obsidian-friendly Markdown.

It is the external conversion backend used by the Scholia Obsidian plugin, but it can also be installed and run on its own.

Install

When paper2mdviallm is published to PyPI, install it into a dedicated environment:

conda create -n scholia python=3.11
conda activate scholia
pip install paper2mdviallm

For local development from this repository:

python -m venv .venv
.venv/bin/pip install -r requirements-dev.txt
.venv/bin/pip install -e .

Requirements

• Python 3.10+
• An OpenAI or Anthropic API key
• Digital PDFs with a text layer

The CLI reads API keys from the environment:

• OPENAI_API_KEY
• ANTHROPIC_API_KEY

Usage

Inspect a PDF before conversion:

paper2mdviallm inspect paper.pdf

Convert a PDF to Markdown:

paper2mdviallm convert paper.pdf -o out/

Override the model or concurrency when needed:

paper2mdviallm convert paper.pdf -o out/ --model claude-sonnet-4-6 --concurrency 3

With Scholia

After installing into a conda environment, point Scholia at either:

• the environment root, such as /Users/me/miniconda3/envs/scholia, or
• the concrete executable, such as /Users/me/miniconda3/envs/scholia/bin/paper2mdviallm

Scholia resolves the binary and executes it directly.

Development

Run tests:

python -m pytest tests

Bootstrap from the repo root:

tools/paper2mdviallm/bootstrap.sh

Boundaries

• The current target is digital PDFs, not OCR-heavy scanned documents.
• Formula-heavy papers still need manual inspection after conversion.
• The output is optimized for Obsidian reading workflows rather than general document fidelity.