CHANGELOG.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
bmlib/__init__.py
bmlib/py.typed
bmlib.egg-info/PKG-INFO
bmlib.egg-info/SOURCES.txt
bmlib.egg-info/dependency_links.txt
bmlib.egg-info/requires.txt
bmlib.egg-info/top_level.txt
bmlib/agents/__init__.py
bmlib/agents/base.py
bmlib/db/__init__.py
bmlib/db/connection.py
bmlib/db/migrations.py
bmlib/db/operations.py
bmlib/db/transactions.py
bmlib/fulltext/__init__.py
bmlib/fulltext/cache.py
bmlib/fulltext/jats_parser.py
bmlib/fulltext/models.py
bmlib/fulltext/pdf_converter.py
bmlib/fulltext/service.py
bmlib/llm/__init__.py
bmlib/llm/client.py
bmlib/llm/data_types.py
bmlib/llm/json_repair.py
bmlib/llm/text_utils.py
bmlib/llm/token_tracker.py
bmlib/llm/utils.py
bmlib/llm/providers/__init__.py
bmlib/llm/providers/anthropic.py
bmlib/llm/providers/base.py
bmlib/llm/providers/deepseek.py
bmlib/llm/providers/gemini.py
bmlib/llm/providers/mistral.py
bmlib/llm/providers/ollama.py
bmlib/llm/providers/openai_compat.py
bmlib/llm/providers/openai_provider.py
bmlib/publications/__init__.py
bmlib/publications/models.py
bmlib/publications/schema.py
bmlib/publications/storage.py
bmlib/publications/sync.py
bmlib/publications/fetchers/__init__.py
bmlib/publications/fetchers/biorxiv.py
bmlib/publications/fetchers/openalex.py
bmlib/publications/fetchers/pubmed.py
bmlib/publications/fetchers/registry.py
bmlib/quality/__init__.py
bmlib/quality/cochrane_formatter.py
bmlib/quality/cochrane_models.py
bmlib/quality/data_models.py
bmlib/quality/extractors.py
bmlib/quality/manager.py
bmlib/quality/metadata_filter.py
bmlib/quality/quality_agent.py
bmlib/quality/scoring_models.py
bmlib/quality/study_classifier.py
bmlib/templates/__init__.py
bmlib/templates/engine.py
bmlib/transparency/__init__.py
bmlib/transparency/analyzer.py
bmlib/transparency/models.py
tests/test_agents.py
tests/test_cochrane.py
tests/test_db.py
tests/test_extractors.py
tests/test_fulltext_cache.py
tests/test_fulltext_models.py
tests/test_fulltext_service.py
tests/test_jats_parser.py
tests/test_json_repair.py
tests/test_llm.py
tests/test_llm_tools.py
tests/test_migrations.py
tests/test_openai_compat.py
tests/test_openalex_fetcher.py
tests/test_pdf_converter.py
tests/test_publications.py
tests/test_pubmed_fetcher.py
tests/test_quality.py
tests/test_registry.py
tests/test_sync.py
tests/test_templates.py
tests/test_text_utils.py
tests/test_transparency.py