Context id updates

[mskarlin]

We had some scenarios where our formatted answer could miss context-ids. This implements a more universal matching solution along with tests.

[dosubot]

Related Documentation

Checked 1 published document(s). No updates required.

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[Copilot]

Pull Request Overview

This PR implements a more robust solution for handling context ID parsing and replacement in formatted answers. It addresses scenarios where context IDs could be missed in the previous implementation.

• Replaces regex-based parenthetical matching with a proper parser
• Updates get_citation_ids to preserve order and handle duplicates
• Adds comprehensive test coverage for various edge cases in context ID parsing

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
src/paperqa/utils.py	Adds get_parenthetical_substrings function and updates get_citation_ids to return list with preserved order
src/paperqa/types.py	Updates context ID replacement logic to use new parsing functions and fix parenthetical replacement
tests/test_paperqa.py	Adds comprehensive test cases for context ID parsing edge cases

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[jamesbraza]

Nice work

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[dosubot]

Documentation Updates

Checked 1 published document(s). No updates required.

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