High accuracy RAG for answering questions from scientific documents with citations
This report summarizes scanner evidence for Future-House/paper-qa, a Python project with 9,345 GitHub stars. SynthScan examined 79,463 lines of code across 146 source files, recording 368 pattern matches distributed across 15 syntactic categories. The legacy adjusted pattern signal is 5.1 (Moderate pattern signal); it is not an authorship estimate.
Use the findings to ask whether maintainers can explain intent, verify dependencies, simplify unnecessary scaffolding, and focus review effort. Risk Payload v1 adds ownership, supply-chain, over-engineering, and review-effort vectors when available. These are prompts for human verification, not probabilities, security findings, or measured maintenance costs.
Use each vector to guide manual verification of the underlying findings.
Can maintainers explain intent, assumptions, and trade-offs? 217 finding(s).
Are imports declared and package/API names verified? 104 finding(s).
Are wrappers, guards, and repeated structures necessary? 227 finding(s).
Which changes need focused human review? 368 finding(s).
This chart tracks the legacy adjusted pattern score across scan runs. Changes can reflect source changes, scan coverage, or detector/scoring versions; they do not measure AI adoption or prove that a team refactored code. Compare runs only when their scoring versions are compatible. The dashed line tracks the raw pattern-hit count.
Groups findings by configured severity weight. Severity is not a confidence estimate, security rating, or proof that a package is missing. Verify imports against the project's manifests and inspect each finding in its local design context.
This horizontal bar chart shows where configured pattern scores accumulate across directories. Treat the bars as locations to inspect, not as evidence of authorship or code quality. Use the file-level findings to decide whether a directory needs a focused ownership, dependency, complexity, or review check.
The scanner identified 368 distinct pattern matches across 15 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a detector match to inspect in context. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.
Reading the findings table: The Severity column indicates the configured finding weight (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — legacy comment-context matches receive a ×1.5 score weight. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier under the legacy scoring model.
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tests/test_configs.py | 27 | def test_prompt_settings_validation() -> None: | CODE |
| LOW | tests/test_configs.py | 40 | def test_get_formatted_variables() -> None: | CODE |
| LOW | tests/test_configs.py | 53 | def test_get_settings_with_valid_config(value: MaybeSettings) -> None: | CODE |
| LOW | tests/test_configs.py | 58 | def test_get_settings_missing_file() -> None: | CODE |
| LOW | tests/test_configs.py | 69 | def test_settings_default_instantiation(tmpdir, subtests: SubTests) -> None: | CODE |
| LOW | tests/test_configs.py | 106 | def test_router_kwargs_present_in_models() -> None: | CODE |
| LOW⚡ | tests/test_configs.py | 204 | def test_matches_filter_criteria(doc_class, doc_data, filter_criteria, expected_result): | CODE |
| LOW⚡ | tests/test_configs.py | 209 | def test_citation_prompt_current_year(): | CODE |
| LOW⚡ | tests/test_configs.py | 218 | def test_validity_of_bundled_configs(subtests: SubTests) -> None: | CODE |
| LOW | tests/test_configs.py | 230 | def test_readme_settings_cheatsheet_accuracy(subtests: SubTests) -> None: | CODE |
| LOW | tests/test_utils.py | 4 | def test_citation_to_docname_acronym_title() -> None: | CODE |
| LOW | tests/test_utils.py | 9 | def test_citation_to_docname_non_text_fallback_is_deterministic() -> None: | CODE |
| LOW | tests/conftest.py | 56 | def _defeat_litellm_callbacks() -> None: | CODE |
| LOW | tests/conftest.py | 61 | def _patch_litellm_logging_worker_for_race_condition() -> Iterator[None]: | CODE |
| LOW | tests/conftest.py | 92 | def ensure_initialized_and_enqueue(self, async_coroutine: Coroutine) -> None: | CODE |
| LOW | tests/conftest.py | 184 | def stub_data_dir_w_near_dupes(stub_data_dir: Path, tmp_path: Path) -> Iterator[Path]: | CODE |
| LOW | tests/conftest.py | 219 | async def _vcr_handle_async_request( | CODE |
| LOW | tests/conftest.py | 245 | def _build_response_with_raw_headers(vcr_request, vcr_response, history): | CODE |
| LOW⚡ | tests/test_paperqa.py | 146 | def test_citations_with_pages() -> None: | CODE |
| LOW⚡ | tests/test_paperqa.py | 151 | def test_citations_without_space() -> None: | CODE |
| LOW⚡ | tests/test_paperqa.py | 156 | def test_citations_with_commas() -> None: | CODE |
| LOW⚡ | tests/test_paperqa.py | 3197 | def test_basic_json_extraction(self, input_text: str) -> None: | CODE |
| LOW⚡ | tests/test_paperqa.py | 3260 | def test_relevance_score_parsing(self, input_text: str) -> None: | CODE |
| LOW⚡ | tests/test_paperqa.py | 3338 | def test_json_broken_formatting(self, input_text: str) -> None: | CODE |
| LOW⚡ | tests/test_paperqa.py | 3366 | def test_llm_parse_json_with_escaped_characters(self, input_text, expected_output): | CODE |
| LOW | tests/test_paperqa.py | 181 | def test_citations_with_special_characters() -> None: | CODE |
| LOW | tests/test_paperqa.py | 186 | def test_citations_with_nonstandard_chars() -> None: | CODE |
| LOW | tests/test_paperqa.py | 816 | async def acompletion_that_breaks_first_context(*args, **kwargs): | CODE |
| LOW | tests/test_paperqa.py | 844 | async def test_nonduplicate_contexts() -> None: | CODE |
| LOW | tests/test_paperqa.py | 899 | async def acompletion_that_breaks_first_context(*args, **kwargs): | CODE |
| LOW | tests/test_paperqa.py | 1018 | async def test_custom_context_str_fn(docs_fixture) -> None: | CODE |
| LOW | tests/test_paperqa.py | 1043 | async def test_aquery_groups_contexts_by_question(docs_fixture) -> None: | CODE |
| LOW | tests/test_paperqa.py | 1118 | async def test_query_with_iteration(docs_fixture) -> None: | CODE |
| LOW | tests/test_paperqa.py | 1253 | async def test_docs_with_custom_embedding( | CODE |
| LOW | tests/test_paperqa.py | 1386 | async def test_custom_llm_custom_media(stub_data_dir: Path) -> None: | CODE |
| LOW | tests/test_paperqa.py | 1565 | async def test_pdf_reader_w_no_match_doc_details(stub_data_dir: Path) -> None: | CODE |
| LOW | tests/test_paperqa.py | 1584 | async def test_pdf_reader_w_no_chunks(stub_data_dir: Path) -> None: | CODE |
| LOW | tests/test_paperqa.py | 1605 | async def test_partly_embedded_texts(defer_embeddings: bool) -> None: | CODE |
| LOW | tests/test_paperqa.py | 1651 | async def test_pdf_reader_match_doc_details(stub_data_dir: Path) -> None: | CODE |
| LOW | tests/test_paperqa.py | 1793 | async def test_chunk_metadata_reader( | CODE |
| LOW | tests/test_paperqa.py | 1916 | def test_parsed_media_data_or_url() -> None: | CODE |
| LOW | tests/test_paperqa.py | 1942 | def test_parsed_media_url_only_hash_eq() -> None: | CODE |
| LOW | tests/test_paperqa.py | 2000 | async def test_read_doc_images_metadata(stub_data_dir: Path) -> None: | CODE |
| LOW | tests/test_paperqa.py | 2052 | async def test_read_doc_images_concurrency(stub_data_dir: Path) -> None: | CODE |
| LOW | tests/test_paperqa.py | 2114 | def test_should_parse_and_enrich_media( | CODE |
| LOW | tests/test_paperqa.py | 2136 | async def test_image_enrichment_normal_use(stub_data_dir: Path) -> None: | CODE |
| LOW | tests/test_paperqa.py | 2266 | async def test_image_enrichment_invalid_image(caplog) -> None: | CODE |
| LOW | tests/test_paperqa.py | 2287 | async def test_image_enrichment_with_oversized_image(caplog) -> None: | CODE |
| LOW | tests/test_paperqa.py | 2425 | async def test_duplicate_media_context_creation(stub_data_dir: Path) -> None: | CODE |
| LOW | tests/test_paperqa.py | 2563 | def test_missing_page_doesnt_crash_us() -> None: | CODE |
| LOW | tests/test_paperqa.py | 2676 | async def test_context_inner_outer_prompt(stub_data_dir: Path) -> None: | CODE |
| LOW | tests/test_paperqa.py | 2717 | def test_get_index_name_uniqueness( | CODE |
| LOW | tests/test_paperqa.py | 2731 | def test_case_insensitive_matching(): | CODE |
| LOW | tests/test_paperqa.py | 2752 | def test_dois_resolve_to_correct_journals(doi_journals): | CODE |
| LOW | tests/test_paperqa.py | 2765 | def test_docdetails_merge_with_non_list_fields() -> None: | CODE |
| LOW | tests/test_paperqa.py | 2799 | def test_docdetails_merge_with_list_fields() -> None: | CODE |
| LOW | tests/test_paperqa.py | 2833 | def test_docdetails_deserialization(tmp_path) -> None: | CODE |
| LOW | tests/test_paperqa.py | 2892 | def test_docdetails_doc_id_roundtrip() -> None: | CODE |
| LOW | tests/test_paperqa.py | 3048 | async def test_partitioning_fn_docs(use_partition: bool) -> None: | CODE |
| LOW | tests/test_paperqa.py | 3378 | def test_llm_subquotes_and_newlines(self, input_text: str) -> None: | CODE |
| 115 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tests/conftest.py | 1 | CODE | |
| LOW | tests/test_paperqa.py | 12 | CODE | |
| LOW | tests/test_clients.py | 1 | CODE | |
| LOW | tests/test_clients.py | 7 | CODE | |
| LOW | tests/test_clients.py | 7 | CODE | |
| LOW | tests/test_clients.py | 24 | CODE | |
| LOW | tests/test_clients.py | 24 | CODE | |
| LOW | tests/test_agents.py | 1 | CODE | |
| LOW | …kages/paper-qa-docling/src/paperqa_docling/__init__.py | 3 | CODE | |
| LOW | packages/paper-qa-docling/src/paperqa_docling/reader.py | 30 | CODE | |
| LOW | …kages/paper-qa-pymupdf/src/paperqa_pymupdf/__init__.py | 1 | CODE | |
| LOW | …kages/paper-qa-pymupdf/src/paperqa_pymupdf/__init__.py | 1 | CODE | |
| LOW | …kages/paper-qa-pymupdf/src/paperqa_pymupdf/__init__.py | 1 | CODE | |
| LOW | packages/paper-qa-pypdf/src/paperqa_pypdf/__init__.py | 1 | CODE | |
| LOW | packages/paper-qa-pypdf/src/paperqa_pypdf/reader.py | 27 | CODE | |
| LOW | …ges/paper-qa-nemotron/src/paperqa_nemotron/__init__.py | 3 | CODE | |
| LOW | packages/paper-qa-nemotron/src/paperqa_nemotron/api.py | 59 | CODE | |
| LOW | packages/paper-qa-nemotron/src/paperqa_nemotron/api.py | 60 | CODE | |
| LOW | src/paperqa/readers.py | 1 | CODE | |
| LOW | src/paperqa/__init__.py | 1 | CODE | |
| LOW | src/paperqa/__init__.py | 1 | CODE | |
| LOW | src/paperqa/__init__.py | 1 | CODE | |
| LOW | src/paperqa/__init__.py | 1 | CODE | |
| LOW | src/paperqa/__init__.py | 1 | CODE | |
| LOW | src/paperqa/__init__.py | 1 | CODE | |
| LOW | src/paperqa/__init__.py | 1 | CODE | |
| LOW | src/paperqa/__init__.py | 1 | CODE | |
| LOW | src/paperqa/__init__.py | 1 | CODE | |
| LOW | src/paperqa/__init__.py | 13 | CODE | |
| LOW | src/paperqa/__init__.py | 14 | CODE | |
| LOW | src/paperqa/__init__.py | 15 | CODE | |
| LOW | src/paperqa/__init__.py | 15 | CODE | |
| LOW | src/paperqa/__init__.py | 16 | CODE | |
| LOW | src/paperqa/__init__.py | 16 | CODE | |
| LOW | src/paperqa/__init__.py | 16 | CODE | |
| LOW | src/paperqa/__init__.py | 21 | CODE | |
| LOW | src/paperqa/__init__.py | 21 | CODE | |
| LOW | src/paperqa/__init__.py | 22 | CODE | |
| LOW | src/paperqa/__init__.py | 22 | CODE | |
| LOW | src/paperqa/__init__.py | 22 | CODE | |
| LOW | src/paperqa/__init__.py | 22 | CODE | |
| LOW | src/paperqa/__init__.py | 23 | CODE | |
| LOW | src/paperqa/docs.py | 1 | CODE | |
| LOW | src/paperqa/types.py | 1 | CODE | |
| LOW | src/paperqa/_ldp_shims.py | 33 | CODE | |
| LOW | src/paperqa/_ldp_shims.py | 33 | CODE | |
| LOW | src/paperqa/settings.py | 49 | CODE | |
| LOW | src/paperqa/llms.py | 7 | CODE | |
| LOW | src/paperqa/clients/unpaywall.py | 1 | CODE | |
| LOW | src/paperqa/clients/journal_quality.py | 1 | CODE | |
| LOW | src/paperqa/clients/retractions.py | 1 | CODE | |
| LOW | src/paperqa/clients/__init__.py | 1 | CODE | |
| LOW | src/paperqa/clients/__init__.py | 5 | CODE | |
| LOW | src/paperqa/clients/client_models.py | 1 | CODE | |
| LOW | src/paperqa/clients/semantic_scholar.py | 1 | CODE | |
| LOW | src/paperqa/clients/openalex.py | 1 | CODE | |
| LOW | src/paperqa/clients/crossref.py | 1 | CODE | |
| LOW | src/paperqa/agents/models.py | 1 | CODE | |
| LOW | src/paperqa/agents/__init__.py | 1 | CODE | |
| LOW | src/paperqa/agents/search.py | 1 | CODE | |
| 6 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW⚡ | tests/test_paperqa.py | 3168 | '{\n"summary": "Lorem Ipsum",\n"relevance_score": 8\n}' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3174 | '```json\n{\n"summary": "Lorem Ipsum",\n"relevance_score": 8\n}\n```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3180 | '```json { "summary": "Lorem Ipsum", "relevance_ score": 8 } ```', | CODE |
| LOW⚡ | tests/test_paperqa.py | 3185 | '{ "summary": "Lorem Ipsum", "relevance_score": 8 }' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3191 | '{\n "summary": "Lorem Ipsum",\n "relevance_score": "8" \n}' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3198 | output = {"summary": "Lorem Ipsum", "relevance_score": 8} | CODE |
| LOW⚡ | tests/test_paperqa.py | 3206 | ' Ipsum\n\ndolor sit amet",\n"relevance_score": 8\n}\nHope this helps!', | CODE |
| LOW⚡ | tests/test_paperqa.py | 3212 | output = {"summary": "Lorem Ipsum\n\ndolor sit amet", "relevance_score": 8} | CODE |
| LOW⚡ | tests/test_paperqa.py | 3212 | output = {"summary": "Lorem Ipsum\n\ndolor sit amet", "relevance_score": 8} | CODE |
| LOW⚡ | tests/test_paperqa.py | 3221 | '```json { "summary": "Lorem Ipsum", "relevance_score": 7.6 } ```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3228 | '```json { "summary": "Lorem Ipsum", "relevance_score": "8" } ```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3234 | ' "Lorem Ipsum", "relevance_score": "8/10" } ```Hope this helps!', | CODE |
| LOW⚡ | tests/test_paperqa.py | 3240 | '```json { "summary": "Lorem Ipsum", "relevance_score": "4/5" } ```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3247 | '```json { "summary": "Lorem Ipsum", "relevance_score": 8/10 } ```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3254 | '```json { "summary": "Lorem Ipsum", "relevance_score": 4/5 } ```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3261 | output = {"summary": "Lorem Ipsum", "relevance_score": 8} | CODE |
| LOW⚡ | tests/test_paperqa.py | 3270 | '```json { "summary": "Lorem Ipsum", "relevance-score": 8 } ```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3277 | '```json { "summary": "Lorem Ipsum", "relevance_ score": 8 } ```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3284 | '```json { "summary": "Lorem Ipsum", "score": 8 } ```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3291 | '```json { "summary": "Lorem Ipsum", "relevance score": 8 } ```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3298 | '```json { "summary": "Lorem Ipsum", "relevance": 8 } ```' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3305 | output = {"summary": "Lorem Ipsum", "relevance_score": 8} | CODE |
| LOW⚡ | tests/test_paperqa.py | 3314 | '{ "summary": "Lorem Ipsum", "relevance_score": 8, }' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3321 | '{ "summary": "Lorem Ipsum", , "relevance_score": 8 }' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3328 | '{ , "summary": "Lorem Ipsum", "relevance_score": 8 }' | CODE |
| LOW⚡ | tests/test_paperqa.py | 3333 | '{ "summary": "Lorem Ipsum" "relevance_score": 8 }', | CODE |
| LOW⚡ | tests/test_paperqa.py | 3339 | output = {"summary": "Lorem Ipsum", "relevance_score": 8} | CODE |
| LOW⚡ | tests/test_paperqa.py | 3346 | "<think> Thinking </think>Lorem Ipsum. Hope this helps!", | CODE |
| LOW⚡ | tests/test_paperqa.py | 3350 | "Lorem Ipsum. Hope this helps!", | CODE |
| LOW⚡ | tests/test_paperqa.py | 3356 | output = {"summary": "Lorem Ipsum. Hope this helps!"} | CODE |
| LOW | tests/test_paperqa.py | 3894 | author_name="John Doe", | CODE |
| LOW | tests/test_paperqa.py | 3902 | author_name="John Doe", | CODE |
| LOW | tests/test_paperqa.py | 3940 | author_name="John Doe", | CODE |
| LOW | tests/test_paperqa.py | 3957 | author_name="John Doe", # Reversed order from context_with_extras | CODE |
| LOW | tests/test_clients.py | 380 | assert not await client.query(doi="placeholder") | CODE |
| LOW⚡ | tests/test_clients.py | 759 | ("Doe, John", "John Doe"), | CODE |
| LOW⚡ | tests/test_clients.py | 762 | ("Doe, Jane", "Jane Doe"), | CODE |
| LOW⚡ | tests/test_clients.py | 767 | ("Jane Doe", "Jane Doe"), | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tests/conftest.py | 43 | def _setup_default_logs() -> None: | CODE |
| LOW | …kages/paper-qa-docling/src/paperqa_docling/__init__.py | 5 | __all__ = ["parse_pdf_to_pages"] | CODE |
| LOW | …kages/paper-qa-pymupdf/src/paperqa_pymupdf/__init__.py | 3 | __all__ = [ | CODE |
| LOW | packages/paper-qa-pypdf/src/paperqa_pypdf/__init__.py | 3 | __all__ = [ | CODE |
| LOW | …ges/paper-qa-nemotron/src/paperqa_nemotron/__init__.py | 5 | __all__ = ["parse_pdf_to_pages"] | CODE |
| LOW | packages/paper-qa-nemotron/src/paperqa_nemotron/api.py | 62 | logger = logging.getLogger(__name__) | CODE |
| LOW | …kages/paper-qa-nemotron/src/paperqa_nemotron/reader.py | 36 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/__init__.py | 25 | __all__ = [ | CODE |
| LOW | src/paperqa/docs.py | 42 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/core.py | 16 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/types.py | 56 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/_ldp_shims.py | 3 | __all__ = [ | CODE |
| LOW | src/paperqa/utils.py | 33 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/settings.py | 86 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/llms.py | 47 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/clients/journal_quality.py | 28 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/clients/retractions.py | 15 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/clients/__init__.py | 23 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/clients/client_models.py | 24 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/clients/semantic_scholar.py | 30 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/clients/openalex.py | 31 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/clients/crossref.py | 38 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/agents/env.py | 42 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/agents/models.py | 18 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/agents/tools.py | 24 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/agents/__init__.py | 22 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/agents/search.py | 56 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/agents/main.py | 48 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/agents/helpers.py | 17 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/contrib/openreview_paper_helper.py | 21 | logger = logging.getLogger(__name__) | CODE |
| LOW | src/paperqa/contrib/__init__.py | 3 | __all__ = ["ZoteroDB"] | CODE |
| LOW | src/paperqa/sources/clinical_trials.py | 23 | logger = logging.getLogger(__name__) | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | packages/paper-qa-docling/tests/test_paperqa_docling.py | 0 | <html> <head><title>404 not found</title></head> <body> <center><h1>404 not found</h1></center> <hr><center>nginx</cente | STRING |
| HIGH | packages/paper-qa-pymupdf/tests/test_paperqa_pymupdf.py | 0 | <html> <head><title>404 not found</title></head> <body> <center><h1>404 not found</h1></center> <hr><center>nginx</cente | STRING |
| HIGH | packages/paper-qa-pypdf/tests/test_paperqa_pypdf.py | 0 | <html> <head><title>404 not found</title></head> <body> <center><h1>404 not found</h1></center> <hr><center>nginx</cente | STRING |
| HIGH | …kages/paper-qa-nemotron/tests/test_paperqa_nemotron.py | 0 | <html> <head><title>404 not found</title></head> <body> <center><h1>404 not found</h1></center> <hr><center>nginx</cente | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tests/test_agents.py | 68 | CODE | |
| LOW | packages/paper-qa-docling/src/paperqa_docling/reader.py | 38 | CODE | |
| LOW | packages/paper-qa-pymupdf/src/paperqa_pymupdf/reader.py | 127 | CODE | |
| LOW | packages/paper-qa-pypdf/src/paperqa_pypdf/reader.py | 56 | CODE | |
| LOW | packages/paper-qa-nemotron/src/paperqa_nemotron/api.py | 464 | CODE | |
| LOW | packages/paper-qa-nemotron/src/paperqa_nemotron/api.py | 603 | CODE | |
| LOW | src/paperqa/readers.py | 203 | CODE | |
| LOW | src/paperqa/readers.py | 426 | CODE | |
| LOW | src/paperqa/core.py | 178 | CODE | |
| LOW | src/paperqa/types.py | 474 | CODE | |
| LOW | src/paperqa/types.py | 983 | CODE | |
| LOW | src/paperqa/types.py | 1267 | CODE | |
| LOW | src/paperqa/utils.py | 314 | CODE | |
| LOW | src/paperqa/utils.py | 589 | CODE | |
| LOW | src/paperqa/clients/crossref.py | 167 | CODE | |
| LOW | src/paperqa/agents/env.py | 47 | CODE | |
| LOW | src/paperqa/agents/search.py | 186 | CODE | |
| LOW | src/paperqa/contrib/zotero.py | 147 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | README.md | 36 | - [Agentic Adding/Querying Documents](#agentic-addingquerying-documents) | CODE |
| MEDIUM | tests/test_paperqa.py | 1590 | settings.summary_llm = "gpt-4o-mini" # context window needs to fit our one chunk | CODE |
| MEDIUM | tests/test_agents.py | 463 | # https://docs.anthropic.com/en/docs/build-with-claude/tool-use#chain-of-thought | COMMENT |
| MEDIUM | docs/tutorials/where_do_I_get_papers.md | 20 | # 1Mil context window helps to suggest papers. These settings are not required, but useful for an initial setup. | COMMENT |
| MEDIUM | src/paperqa/llms.py | 551 | # Recursively create each component embedding model | COMMENT |
| MEDIUM | src/paperqa/sources/clinical_trials.py | 294 | # for embedding model context windows, we truncate at TRIAL_CHAR_TRUNCATION_SIZE | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | packages/paper-qa-pymupdf/src/paperqa_pymupdf/reader.py | 49 | Load a PDF page and extract its text. Args: file: An open (assumed) PyMuPDF document. page_num: Zer | STRING |
| HIGH | src/paperqa/clients/openalex.py | 74 | Get paper details from OpenAlex given a DOI or paper title. Args: client: Async HTTP client for any request | STRING |
| HIGH | src/paperqa/agents/tools.py | 474 | Search for clinical trials, with support for repeated calls and concurrent execution. Will add new clinical tri | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | src/paperqa/readers.py | 77 | except Exception as exc: | CODE |
| LOW | src/paperqa/types.py | 1128 | except Exception: | CODE |
| LOW | src/paperqa/utils.py | 328 | except Exception: | CODE |
| MEDIUM | src/paperqa/utils.py | 227 | def get_loop() -> asyncio.AbstractEventLoop: | CODE |
| LOW | src/paperqa/llms.py | 297 | except Exception as e: | CODE |
| LOW | src/paperqa/agents/search.py | 252 | except Exception: | CODE |
| LOW | src/paperqa/agents/search.py | 477 | except Exception: | CODE |
| LOW | src/paperqa/agents/search.py | 531 | except Exception as e: | CODE |
| MEDIUM | src/paperqa/agents/search.py | 367 | def save_index(self) -> None: | CODE |
| LOW | src/paperqa/agents/main.py | 164 | except Exception: | CODE |
| LOW | src/paperqa/sources/clinical_trials.py | 275 | except Exception as e: | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | src/paperqa/readers.py | 228 | # Create a ParsedMedia object | COMMENT |
| MEDIUM | src/paperqa/settings.py | 1248 | # Create a section with a question heading | COMMENT |
| MEDIUM | src/paperqa/llms.py | 346 | # Create a new event loop in a new thread to avoid nested loop issues | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | packages/paper-qa-pymupdf/src/paperqa_pymupdf/reader.py | 127 | CODE | |
| LOW | …kages/paper-qa-nemotron/src/paperqa_nemotron/reader.py | 136 | CODE | |
| LOW | src/paperqa/docs.py | 93 | CODE | |
| LOW | src/paperqa/docs.py | 156 | CODE | |
| LOW | src/paperqa/contrib/zotero.py | 147 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | packages/paper-qa-nemotron/src/paperqa_nemotron/api.py | 635 | # We just use aiobotocore directly here | COMMENT |
| LOW | src/paperqa/clients/__init__.py | 253 | # if we can't get metadata, just return the doc, but don't overwrite any fields | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | pyproject.toml | 324 | # Set true to activate the evaluation score. | COMMENT |
| LOW | src/paperqa/utils.py | 89 | # Check if the entropy is within a reasonable range for text | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | pyproject.toml | 181 | mypy_path = "$MYPY_CONFIG_FILE_DIR/src,$MYPY_CONFIG_FILE_DIR/packages/paper-qa-pypdf/src,$MYPY_CONFIG_FILE_DIR/packages/ | COMMENT |
| LOW | src/paperqa/settings.py | 1141 | media.info["is_irrelevant"], | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tests/test_paperqa.py | 1304 | # For QdrantVectorStore, we need to check if collection exists and has points | COMMENT |