uv workspace layout, broke out PyMuPDF

[jamesbraza]

As a prerequisite for PyPDF support, this PR:

1. Adopts uv workspace layout: https://docs.astral.sh/uv/concepts/projects/workspaces/#workspace-layouts
2. Moves PyMuPDF to a separate package paper-qa-pymupdf, so in a future PR a PyPDF one can be made

[Copilot]

Pull Request Overview

This PR restructures the codebase to adopt the uv workspace layout and extracts PyMuPDF functionality into a separate package as preparation for PyPDF support.

• Migrates the project structure to use uv workspace layout with packages under packages/ directory
• Extracts PyMuPDF-related functionality into a separate paper-qa-pymupdf package
• Updates import statements and configuration files to reflect the new package structure

Reviewed Changes

Copilot reviewed 15 out of 61 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
pyproject.toml	Configures uv workspace, updates package structure, adds dependency on paper-qa-pymupdf
packages/paper-qa-pymupdf/*	New separate package containing PyMuPDF PDF parsing functionality
src/paperqa/readers.py	Removes PyMuPDF code that was moved to separate package
src/paperqa/settings.py	Updates imports to use paperqa_pymupdf package
tests/test_paperqa.py	Updates imports and moves test to new package
.github/workflows/*	Updates CI to build both packages

[cursor]

Bug: Circular Dependency Blocks Package Installation

A circular dependency exists between the paper-qa and paper-qa-pymupdf packages. paper-qa-pymupdf declares paper-qa as a dependency, while paper-qa also declares paper-qa-pymupdf as a dependency. This prevents proper installation, packaging, and dependency resolution. The paper-qa-pymupdf package further reinforces this circular dependency by importing modules from paperqa.

packages/paper-qa-pymupdf/pyproject.toml#L19-L23

paper-qa/packages/paper-qa-pymupdf/pyproject.toml

Lines 19 to 23 in 154042d

	]
	dependencies = [
	"PyMuPDF>=1.24.12", # For pymupdf.set_messages addition
	"paper-qa",
	]

pyproject.toml#L33-L34

paper-qa/pyproject.toml

Lines 33 to 34 in 154042d

	"numpy",
	"paper-qa-pymupdf",

Fix in Cursor • Fix in Web

---

Bug: Apache-AGPL License Conflict

License incompatibility: The paper-qa package, licensed under Apache Software License, depends on paper-qa-pymupdf, which is licensed under GNU Affero General Public License v3. This dependency on a more restrictively licensed package creates a conflict, potentially making the entire paper-qa distribution subject to AGPLv3 terms.

packages/paper-qa-pymupdf/pyproject.toml#L10-L11

paper-qa/packages/paper-qa-pymupdf/pyproject.toml

Lines 10 to 11 in 154042d

	"Intended Audience :: Developers",
	"License :: OSI Approved :: GNU Affero General Public License v3",

Fix in Cursor • Fix in Web

---

Comment bugbot run to trigger another review on this PR
Was this report helpful? Give feedback by reacting with 👍 or 👎