Modernizing bundled configs

[jamesbraza]

#1054 missed updating the bundled configs. This PR:

1. Adds a test that bundled configs load
2. Modernizes configs as needed

Closes #1250

[dosubot]

Related Documentation

Checked 1 published document(s) in 1 knowledge base(s). No updates required.

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[Copilot]

Pull request overview

This PR modernizes bundled configuration files to align with the new parsing settings structure introduced in PR #1054, and adds a test to ensure all bundled configs can be loaded successfully.

Key Changes:

• Adds a test that validates all bundled JSON configs can be loaded via get_settings()
• Migrates parsing configuration from old flat structure (chunk_size, overlap) to new nested structure (reader_config.chunk_chars, reader_config.overlap)
• Removes deprecated chunking_algorithm field from configs

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/test_configs.py	Adds test to validate all bundled configs load successfully using subtests for each config file
src/paperqa/configs/wikicrow.json	Modernizes parsing config: moves chunk_size/overlap to reader_config dict, removes chunking_algorithm
src/paperqa/configs/tier5_limits.json	Modernizes parsing config: moves chunk_size/overlap to reader_config dict
src/paperqa/configs/tier4_limits.json	Modernizes parsing config: moves chunk_size/overlap to reader_config dict
src/paperqa/configs/tier3_limits.json	Modernizes parsing config: moves chunk_size/overlap to reader_config dict
src/paperqa/configs/tier2_limits.json	Modernizes parsing config: moves chunk_size/overlap to reader_config dict
src/paperqa/configs/search_only_clinical_trials.json	Modernizes parsing config: moves chunk_size/overlap to reader_config dict
src/paperqa/configs/openreview.json	Modernizes parsing config: moves chunk_size to reader_config.chunk_chars
src/paperqa/configs/high_quality.json	Modernizes parsing config: moves chunk_size/overlap to reader_config dict
src/paperqa/configs/contracrow.json	Modernizes parsing config: moves chunk_size/overlap to reader_config dict, removes chunking_algorithm
src/paperqa/configs/clinical_trials.json	Modernizes parsing config: moves chunk_size/overlap to reader_config dict

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[kirillkoncha]

Hi! Thank you for fixes, now importing filename from config name works fine. However, another issue is raised, when I am trying to set myself a custom config. For example:

from paperqa.settings import (
    AgentSettings,
    AnswerSettings,
    IndexSettings,
    ParsingSettings,
    PromptSettings,
    Settings,
)
settings=Settings(
    AnswerSettings(
        evidence_k=10,
        evidence_detailed_citations=True,
        evidence_retrieval=True,
        evidence_summary_length="about 100 words",
        evidence_skip_summary=False,
        answer_max_sources=5,
        max_answer_attempts=None,
        answer_length="must not exceed 1000 words, but sometimes can be longer",
        max_concurrent_requests=10,
    )
)

Raises this pydantic error:

ValidationError: 1 validation error for AnswerSettings
evidence_detailed_citations
  Extra inputs are not permitted [type=extra_forbidden, input_value=True, input_type=bool]
    For further information visit https://errors.pydantic.dev/2.12/v/extra_forbidden