All Ruff ANN autofixes (#341)

Author: jamesbraza

paperqa/agents/__init__.py

@@ -163,7 +163,7 @@ def save_settings(
         logger.info(f"Settings saved to: {full_settings_path}")
 
 
-def main():
+def main() -> None:
     parser = argparse.ArgumentParser(description="PaperQA CLI")
 
     parser.add_argument(

paperqa/agents/models.py

@@ -166,7 +166,7 @@ def start(self, name: str) -> None:
         except RuntimeError:  # No running event loop (not in async)
             self.running_timers[name] = TimerData(start_time=time.time())
 
-    def stop(self, name: str):
+    def stop(self, name: str) -> None:
         timer_data = self.running_timers.pop(name, None)
         if timer_data:
             try:

paperqa/agents/search.py

@@ -193,7 +193,7 @@ async def filecheck(self, filename: str, body: str | None = None):
 
     async def add_document(
         self, index_doc: dict, document: Any | None = None, max_retries: int = 1000
-    ):
+    ) -> None:
         @retry(
             stop=stop_after_attempt(max_retries),
             wait=wait_random_exponential(multiplier=0.25, max=60),

paperqa/clients/exceptions.py

@@ -1,4 +1,4 @@
 class DOINotFoundError(Exception):
-    def __init__(self, message="DOI not found"):
+    def __init__(self, message="DOI not found") -> None:
         self.message = message
         super().__init__(self.message)

paperqa/docs.py

@@ -54,11 +54,11 @@
 
 
 # this is just to reduce None checks/type checks
-async def empty_callback(result: LLMResult):
+async def empty_callback(result: LLMResult) -> None:
     pass
 
 
-async def print_callback(result: LLMResult):
+async def print_callback(result: LLMResult) -> None:
     pass
 
 
@@ -85,7 +85,7 @@ def handle_default(cls, value: Path | None, info: ValidationInfo) -> Path | None
             return PAPERQA_DIR / info.data["name"]
         return value
 
-    def clear_docs(self):
+    def clear_docs(self) -> None:
         self.texts = []
         self.docs = {}
         self.docnames = set()
@@ -451,7 +451,7 @@ def delete(
         self.deleted_dockeys.add(dockey)
         self.texts = list(filter(lambda x: x.doc.dockey != dockey, self.texts))
 
-    def _build_texts_index(self):
+    def _build_texts_index(self) -> None:
         texts = [t for t in self.texts if t not in self.texts_index]
         self.texts_index.add_texts_and_embeddings(texts)
 

paperqa/llms.py

@@ -488,10 +488,10 @@ class VectorStore(BaseModel, ABC):
     model_config = ConfigDict(extra="forbid")
     texts_hashes: set[int] = Field(default_factory=set)
 
-    def __contains__(self, item):
+    def __contains__(self, item) -> bool:
         return hash(item) in self.texts_hashes
 
-    def __len__(self):
+    def __len__(self) -> int:
         return len(self.texts_hashes)
 
     @abstractmethod
@@ -614,7 +614,7 @@ class LangchainVectorStore(VectorStore):
     class_type: type[Embeddable] = Field(default=Embeddable)
     model_config = ConfigDict(extra="forbid")
 
-    def __init__(self, **data):
+    def __init__(self, **data) -> None:
         raise NotImplementedError(
             "Langchain has updated vectorstore internals and this is not yet supported"
         )

paperqa/types.py

@@ -89,7 +89,7 @@ class LLMResult(BaseModel):
         default=0.0, description="Delta time (sec) to last response token's arrival."
     )
 
-    def __str__(self):
+    def __str__(self) -> str:
         return self.text
 
     @computed_field  # type: ignore[prop-decorator]
@@ -198,7 +198,7 @@ def get_citation(self, name: str) -> str:
             raise ValueError(f"Could not find docname {name} in contexts.") from exc
         return doc.citation
 
-    def add_tokens(self, result: LLMResult):
+    def add_tokens(self, result: LLMResult) -> None:
         """Update the token counts for the given result."""
         if result.model not in self.token_counts:
             self.token_counts[result.model] = [

tests/conftest.py

@@ -20,12 +20,12 @@
 
 
 @pytest.fixture(autouse=True, scope="session")
-def _load_env():
+def _load_env() -> None:
     load_dotenv()
 
 
 @pytest.fixture(autouse=True)
-def _setup_default_logs():
+def _setup_default_logs() -> None:
     setup_default_logs()
 
 

tests/test_agents.py

@@ -48,7 +48,7 @@ async def test_get_directory_index(agent_test_settings) -> None:
 @pytest.mark.asyncio
 async def test_get_directory_index_w_manifest(
     agent_test_settings, reset_log_levels, caplog  # noqa: ARG001
-):
+) -> None:
     agent_test_settings.manifest_file = "stub_manifest.csv"
     index = await get_directory_index(settings=agent_test_settings)
     assert index.fields == [
@@ -71,7 +71,7 @@ async def test_get_directory_index_w_manifest(
 @pytest.mark.flaky(reruns=2, only_rerun=["AssertionError", "httpx.RemoteProtocolError"])
 @pytest.mark.parametrize("agent_type", ["fake", "OpenAIFunctionsAgent"])
 @pytest.mark.asyncio
-async def test_agent_types(agent_test_settings, agent_type):
+async def test_agent_types(agent_test_settings, agent_type) -> None:
 
     question = "How can you use XAI for chemical property prediction?"
 
@@ -87,7 +87,7 @@ async def test_agent_types(agent_test_settings, agent_type):
 
 
 @pytest.mark.asyncio
-async def test_timeout(agent_test_settings):
+async def test_timeout(agent_test_settings) -> None:
     agent_test_settings.prompts.pre = None
     agent_test_settings.agent.timeout = 0.001
     agent_test_settings.llm = "gpt-4o-mini"
@@ -287,7 +287,7 @@ def test_functions() -> None:
     ]
 
 
-def test_query_request_docs_name_serialized():
+def test_query_request_docs_name_serialized() -> None:
     """Test that the query request has a docs_name property."""
     request = QueryRequest(query="Are COVID-19 vaccines effective?")
     request_data = json.loads(request.model_dump_json())
@@ -298,7 +298,7 @@ def test_query_request_docs_name_serialized():
     assert request_data["docs_name"] == "my_doc"
 
 
-def test_answers_are_striped():
+def test_answers_are_striped() -> None:
     """Test that answers are striped."""
     answer = Answer(
         question="What is the meaning of life?",

tests/test_cli.py

@@ -15,7 +15,7 @@
     pytest.skip("agents module is not installed", allow_module_level=True)
 
 
-def test_can_modify_settings():
+def test_can_modify_settings() -> None:
     old_argv = sys.argv
     old_stdout = sys.stdout
     captured_output = io.StringIO()
@@ -37,7 +37,7 @@ def test_can_modify_settings():
         os.unlink(pqa_directory("settings") / "unit_test.json")
 
 
-def test_cli_ask(agent_index_dir: Path, stub_data_dir: Path):
+def test_cli_ask(agent_index_dir: Path, stub_data_dir: Path) -> None:
     settings = Settings.from_name("debug")
     settings.index_directory = agent_index_dir
     settings.paper_directory = stub_data_dir
@@ -56,7 +56,9 @@ def test_cli_ask(agent_index_dir: Path, stub_data_dir: Path):
     assert found_answer.model_dump_json() == response.model_dump_json()
 
 
-def test_cli_can_build_and_search_index(agent_index_dir: Path, stub_data_dir: Path):
+def test_cli_can_build_and_search_index(
+    agent_index_dir: Path, stub_data_dir: Path
+) -> None:
     settings = Settings.from_name("debug")
     settings.index_directory = agent_index_dir
     index_name = "test"

tests/test_clients.py

@@ -96,7 +96,7 @@
     ],
 )
 @pytest.mark.asyncio
-async def test_title_search(paper_attributes: dict[str, str]):
+async def test_title_search(paper_attributes: dict[str, str]) -> None:
     async with aiohttp.ClientSession() as session:
         client = DocMetadataClient(session, clients=ALL_CLIENTS)
         details = await client.query(title=paper_attributes["title"])
@@ -192,7 +192,7 @@ async def test_title_search(paper_attributes: dict[str, str]):
     ],
 )
 @pytest.mark.asyncio
-async def test_doi_search(paper_attributes: dict[str, str]):
+async def test_doi_search(paper_attributes: dict[str, str]) -> None:
     async with aiohttp.ClientSession() as session:
         client = DocMetadataClient(session, clients=ALL_CLIENTS)
         details = await client.query(doi=paper_attributes["doi"])
@@ -210,7 +210,7 @@ async def test_doi_search(paper_attributes: dict[str, str]):
 
 @pytest.mark.vcr
 @pytest.mark.asyncio
-async def test_bulk_doi_search():
+async def test_bulk_doi_search() -> None:
     dois = [
         "10.1063/1.4938384",
         "10.48550/arxiv.2312.07559",
@@ -228,7 +228,7 @@ async def test_bulk_doi_search():
 
 @pytest.mark.vcr
 @pytest.mark.asyncio
-async def test_bulk_title_search():
+async def test_bulk_title_search() -> None:
     titles = [
         (
             "Effect of native oxide layers on copper thin-film tensile properties: A"
@@ -253,7 +253,7 @@ async def test_bulk_title_search():
 
 @pytest.mark.vcr
 @pytest.mark.asyncio
-async def test_bad_titles():
+async def test_bad_titles() -> None:
     async with aiohttp.ClientSession() as session:
         client = DocMetadataClient(session)
         details = await client.query(title="askldjrq3rjaw938h")
@@ -269,7 +269,7 @@ async def test_bad_titles():
 
 @pytest.mark.vcr
 @pytest.mark.asyncio
-async def test_bad_dois():
+async def test_bad_dois() -> None:
     async with aiohttp.ClientSession() as session:
         client = DocMetadataClient(session)
         details = await client.query(title="abs12032jsdafn")
@@ -278,7 +278,7 @@ async def test_bad_dois():
 
 @pytest.mark.vcr
 @pytest.mark.asyncio
-async def test_minimal_fields_filtering():
+async def test_minimal_fields_filtering() -> None:
     async with aiohttp.ClientSession() as session:
         client = DocMetadataClient(session)
         details = await client.query(
@@ -303,7 +303,7 @@ async def test_minimal_fields_filtering():
 
 @pytest.mark.vcr
 @pytest.mark.asyncio
-async def test_s2_only_fields_filtering():
+async def test_s2_only_fields_filtering() -> None:
     async with aiohttp.ClientSession() as session:
         # now get with authors just from one source
         s2_client = DocMetadataClient(session, clients=[SemanticScholarProvider])
@@ -373,7 +373,7 @@ async def test_crossref_journalquality_fields_filtering() -> None:
 
 @pytest.mark.vcr
 @pytest.mark.asyncio
-async def test_author_matching():
+async def test_author_matching() -> None:
     async with aiohttp.ClientSession() as session:
         crossref_client = DocMetadataClient(session, clients=[CrossrefProvider])
         s2_client = DocMetadataClient(session, clients=[SemanticScholarProvider])
@@ -402,7 +402,7 @@ async def test_author_matching():
 
 @pytest.mark.vcr
 @pytest.mark.asyncio
-async def test_odd_client_requests():
+async def test_odd_client_requests() -> None:
     # try querying using an authors match, but not requesting authors back
     async with aiohttp.ClientSession() as session:
         client = DocMetadataClient(session)
@@ -449,7 +449,7 @@ async def test_odd_client_requests():
 
 
 @pytest.mark.asyncio
-async def test_ensure_robust_to_timeouts(monkeypatch):
+async def test_ensure_robust_to_timeouts(monkeypatch) -> None:
     # 0.15 should be short enough to not get a response in time.
     monkeypatch.setattr(paperqa.clients.crossref, "CROSSREF_API_REQUEST_TIMEOUT", 0.05)
     monkeypatch.setattr(
@@ -466,7 +466,7 @@ async def test_ensure_robust_to_timeouts(monkeypatch):
 
 
 @pytest.mark.asyncio
-async def test_bad_init():
+async def test_bad_init() -> None:
     with pytest.raises(
         ValueError, match="At least one MetadataProvider must be provided."
     ):
@@ -475,7 +475,7 @@ async def test_bad_init():
 
 @pytest.mark.vcr
 @pytest.mark.asyncio
-async def test_ensure_sequential_run(caplog, reset_log_levels):  # noqa: ARG001
+async def test_ensure_sequential_run(caplog, reset_log_levels) -> None:  # noqa: ARG001
     caplog.set_level(logging.DEBUG)
     # were using a DOI that is NOT in crossref, but running the crossref client first
     # we will ensure that both are run sequentially
@@ -512,7 +512,7 @@ async def test_ensure_sequential_run(caplog, reset_log_levels):  # noqa: ARG001
 @pytest.mark.asyncio
 async def test_ensure_sequential_run_early_stop(
     caplog, reset_log_levels  # noqa: ARG001
-):
+) -> None:
     caplog.set_level(logging.DEBUG)
     # now we should stop after hitting s2
     async with aiohttp.ClientSession() as session:

tests/test_configs.py

@@ -11,7 +11,7 @@
 )
 
 
-def test_prompt_settings_validation():
+def test_prompt_settings_validation() -> None:
     with pytest.raises(ValidationError):
         PromptSettings(summary="Invalid {variable}")
 
@@ -27,13 +27,13 @@ def test_prompt_settings_validation():
     assert valid_pre_settings.pre == "{question}"
 
 
-def test_get_formatted_variables():
+def test_get_formatted_variables() -> None:
     template = "This is a test {variable} with {another_variable}"
     variables = get_formatted_variables(template)
     assert variables == {"variable", "another_variable"}
 
 
-def test_get_settings_with_valid_config():
+def test_get_settings_with_valid_config() -> None:
     settings = get_settings("fast")
     assert not settings.parsing.use_doc_details
 
@@ -46,7 +46,7 @@ def test_get_settings_missing_file() -> None:
         get_settings("missing_config")
 
 
-def test_settings_default_instantiation():
+def test_settings_default_instantiation() -> None:
     settings = Settings()
     assert "gpt-" in settings.llm
     assert settings.answer.evidence_k == 10