├── .gitattributes ├── .github ├── renovate.json5 └── workflows │ ├── build.yml │ └── tests.yml ├── .gitignore ├── .mailmap ├── .pre-commit-config.yaml ├── .python-version ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docs ├── 2024-10-16_litqa2-splits.json5 └── tutorials │ ├── querying_with_clinical_trials.md │ ├── running_on_lfrqa.ipynb │ ├── running_on_lfrqa.md │ ├── settings_tutorial.ipynb │ ├── settings_tutorial.md │ └── where_do_I_get_papers.md ├── packages ├── paper-qa-docling │ ├── LICENSE │ ├── README.md │ ├── pyproject.toml │ ├── src │ │ └── paperqa_docling │ │ │ ├── __init__.py │ │ │ ├── py.typed │ │ │ └── reader.py │ └── tests │ │ └── test_paperqa_docling.py ├── paper-qa-nemotron │ ├── LICENSE │ ├── README.md │ ├── pyproject.toml │ ├── src │ │ └── paperqa_nemotron │ │ │ ├── __init__.py │ │ │ ├── api.py │ │ │ ├── py.typed │ │ │ └── reader.py │ └── tests │ │ ├── cassettes │ │ ├── TestNvidiaAPI.test_detection_only[0].yaml │ │ ├── TestNvidiaAPI.test_detection_only[1].yaml │ │ ├── TestNvidiaAPI.test_markdown_bbox[0].yaml │ │ ├── TestNvidiaAPI.test_markdown_bbox[1].yaml │ │ ├── TestNvidiaAPI.test_markdown_no_bbox[0].yaml │ │ └── TestNvidiaAPI.test_markdown_no_bbox[1].yaml │ │ ├── conftest.py │ │ ├── test_api.py │ │ └── test_paperqa_nemotron.py ├── paper-qa-pymupdf │ ├── LICENSE │ ├── README.md │ ├── pyproject.toml │ ├── src │ │ └── paperqa_pymupdf │ │ │ ├── __init__.py │ │ │ ├── py.typed │ │ │ └── reader.py │ └── tests │ │ └── test_paperqa_pymupdf.py └── paper-qa-pypdf │ ├── LICENSE │ ├── README.md │ ├── pyproject.toml │ ├── src │ └── paperqa_pypdf │ │ ├── __init__.py │ │ ├── py.typed │ │ └── reader.py │ └── tests │ └── test_paperqa_pypdf.py ├── pyproject.toml ├── src └── paperqa │ ├── __init__.py │ ├── _ldp_shims.py │ ├── agents │ ├── __init__.py │ ├── env.py │ ├── helpers.py │ ├── main.py │ ├── models.py │ ├── search.py │ └── tools.py │ ├── clients │ ├── __init__.py │ ├── client_data │ │ └── journal_quality.csv │ ├── client_models.py │ ├── crossref.py │ ├── exceptions.py │ ├── journal_quality.py │ ├── openalex.py │ ├── retractions.py │ ├── semantic_scholar.py │ └── unpaywall.py │ ├── configs │ ├── clinical_trials.json │ ├── contracrow.json │ ├── debug.json │ ├── fast.json │ ├── high_quality.json │ ├── openreview.json │ ├── search_only_clinical_trials.json │ ├── tier1_limits.json │ ├── tier2_limits.json │ ├── tier3_limits.json │ ├── tier4_limits.json │ ├── tier5_limits.json │ └── wikicrow.json │ ├── contrib │ ├── __init__.py │ ├── openreview_paper_helper.py │ └── zotero.py │ ├── core.py │ ├── docs.py │ ├── llms.py │ ├── paths.py │ ├── prompts.py │ ├── py.typed │ ├── readers.py │ ├── settings.py │ ├── sources │ ├── __init__.py │ └── clinical_trials.py │ ├── types.py │ └── utils.py ├── tests ├── __init__.py ├── cassettes │ ├── test_arxiv_doi_is_used_when_available.yaml │ ├── test_author_matching.yaml │ ├── test_bad_dois.yaml │ ├── test_bad_titles.yaml │ ├── test_bulk_doi_search.yaml │ ├── test_bulk_title_search.yaml │ ├── test_crossref_journalquality_fields_filtering.yaml │ ├── test_crossref_retraction_status.yaml │ ├── test_docs_lifecycle.yaml │ ├── test_does_openalex_work[not-in-openalex].yaml │ ├── test_does_openalex_work[not-oa-in-openalex].yaml │ ├── test_does_openalex_work[oa-in-openalex1].yaml │ ├── test_does_openalex_work[oa-in-openalex2].yaml │ ├── test_doi_search[paper_attributes0].yaml │ ├── test_doi_search[paper_attributes1].yaml │ ├── test_doi_search[paper_attributes2].yaml │ ├── test_doi_search[paper_attributes3].yaml │ ├── test_doi_search[paper_attributes4].yaml │ ├── test_ensure_sequential_run.yaml │ ├── test_ensure_sequential_run_early_stop.yaml │ ├── test_equations[parse_pdf_to_pages0].yaml │ ├── test_equations[parse_pdf_to_pages1].yaml │ ├── test_equations[parse_pdf_to_pages2].yaml │ ├── test_get_reasoning[deepseek-reasoner].yaml │ ├── test_get_reasoning[openrouter-deepseek].yaml │ ├── test_image_enrichment_invalid_image.yaml │ ├── test_image_enrichment_normal_use.yaml │ ├── test_maybe_is_text.yaml │ ├── test_minimal_fields_filtering.yaml │ ├── test_nonduplicate_contexts.yaml │ ├── test_odd_client_requests.yaml │ ├── test_partitioning_fn_docs[False].yaml │ ├── test_partitioning_fn_docs[True].yaml │ ├── test_partly_embedded_texts[False].yaml │ ├── test_partly_embedded_texts[True].yaml │ ├── test_pdf_reader_match_doc_details.yaml │ ├── test_s2_only_fields_filtering.yaml │ ├── test_title_search[paper_attributes0].yaml │ ├── test_title_search[paper_attributes1].yaml │ ├── test_title_search[paper_attributes2].yaml │ ├── test_tricky_journal_quality_results[10.1016-j.bbcan.2023.188947-1].yaml │ ├── test_tricky_journal_quality_results[10.1016-j.semcdb.2016.08.024-1].yaml │ ├── test_tricky_journal_quality_results[10.1038-s41598-018-27044-6-1].yaml │ ├── test_tricky_journal_quality_results[10.1073-pnas.1205508109-3].yaml │ ├── test_tricky_journal_quality_results[10.1146-annurev.pathol.4.110807.092311-2].yaml │ └── 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