Updating tooling for jupytext + black break

[jamesbraza]

This PR updates tooling to work around mwouts/jupytext#1467

It also starts using black-jupyter to run black on our notebooks.

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Note

Updates tooling (pre-commit, ruff/pylint) to support jupytext+black, adds black-jupyter and markdown TOC, and tweaks code to satisfy new lint rules.

• Tooling:
  • Pre-commit: Bump multiple hooks; switch to black-jupyter; pin black<25.11.0 for jupytext; update jupytext and markdown-toc-creator hooks.
  • Linting: Extend Ruff rules (e.g., ASYNC240, B912, DOC102, RUF065); update Pylint disables and per-file ignores; add PLC2701 ignore for tests; add # noqa: ASYNC240 in code.
  • Config: Add [tool.markdown_toc_creator] in pyproject.toml.
• Docs:
  • README.md: Add visible Table of Contents section with horizontal rules.
  • docs/tutorials/running_on_lfrqa.ipynb: Minor formatting/signature tweaks.
• Code:
  • src/paperqa/agents/search.py: Adjust path construction and formatting for lint compliance.
  • src/paperqa/clients/crossref.py, src/paperqa/contrib/openreview_paper_helper.py: Minor lint-related changes.
• Tests:
  • tests/test_paperqa.py: Remove inline # noqa now covered by config.

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Related Documentation

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Pull Request Overview

This PR updates the project's tooling configuration to work around a compatibility issue between jupytext and black version 25.11.0. The main changes include switching to black-jupyter for notebook formatting, downpinning black in the jupytext pre-commit hook, and updating various linting rules and tool versions.

Key Changes

• Switched from black to black-jupyter in pre-commit configuration for better notebook support
• Added temporary workaround by downpinning black to version <25.11.0 in the jupytext hook due to upstream issue
• Enabled new linting rules (ASYNC240, B912, DOC102, RUF065) and added corresponding noqa comments where needed

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
.pre-commit-config.yaml	Updated tool versions and switched to black-jupyter; added black downpin workaround for jupytext
pyproject.toml	Added new linting rules, updated pylint configuration, and added markdown-toc-creator settings
tests/test_paperqa.py	Removed obsolete PLC2701 noqa comment (now handled by per-file-ignores)
src/paperqa/contrib/openreview_paper_helper.py	Added ASYNC240 noqa comments to suppress blocking path operations warnings
src/paperqa/clients/crossref.py	Added ASYNC240 noqa comment to suppress blocking path operation warning
src/paperqa/agents/search.py	Added ASYNC240 noqa comment to suppress blocking path operation warning
docs/tutorials/running_on_lfrqa.ipynb	Reformatted function signatures and removed trailing newlines per black-jupyter
README.md	Updated table of contents formatting with horizontal rules

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