Pulling in latest fhaviary, mypy, ruff (#647)

Co-authored-by: Andrew White <[email protected]>

.github/renovate.json5

@@ -9,17 +9,18 @@
   prHourlyLimit: 4,
   timezone: "America/Los_Angeles",
   rangeStrategy: "widen",
-  lockFileMaintenance: {
-    enabled: true,
-  },
-  "pre-commit": {
-    enabled: true,
-  },
+  lockFileMaintenance: { enabled: true },
+  "pre-commit": { enabled: true },
   packageRules: [
     {
       // Allow 'widen' range strategy while matching aviary_internal pyproject.toml
       matchPackageNames: ["openai"],
       allowedVersions: "<1.47",
     },
+    {
+      // TODO: remove after fhaviary supports Python 3.13
+      matchPackageNames: ["python"],
+      allowedVersions: "<=3.12",
+    },
   ],
 }

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
       - id: mixed-line-ending
       - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.7.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -55,36 +55,37 @@ repos:
     hooks:
       - id: check-mailmap
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.20.2
+    rev: v0.22
     hooks:
       - id: validate-pyproject
         additional_dependencies:
           - "validate-pyproject-schema-store[all]>=2024.06.24" # Pin for Ruff's FURB154
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.4.21
+    rev: 0.4.27
     hooks:
       - id: uv-lock
   - repo: https://github.com/renovatebot/pre-commit-hooks
-    rev: 38.122.0
+    rev: 38.131.1
     hooks:
       - id: renovate-config-validator
+        args: [--strict]
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.19.0
+    rev: 1.19.1
     hooks:
       - id: blacken-docs
   - repo: https://github.com/jsh9/markdown-toc-creator
     rev: 0.0.8
     hooks:
       - id: markdown-toc-creator
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.13.0
     hooks:
       - id: mypy
         args: [--pretty, --ignore-missing-imports]
         additional_dependencies:
           - aiohttp
           - coredis
-          - fhaviary[llm]>=0.6 # Match pyproject.toml
+          - fhaviary[llm]>=0.8.2 # Match pyproject.toml
           - ldp>=0.9 # Match pyproject.toml
           - html2text
           - httpx

paperqa/agents/env.py

@@ -2,9 +2,14 @@
 from copy import deepcopy
 from typing import Any, Self, cast
 
-from aviary.env import Environment, Frame
-from aviary.message import Message
-from aviary.tools import Tool, ToolRequestMessage, ToolResponseMessage
+from aviary.core import (
+    Environment,
+    Frame,
+    Message,
+    Tool,
+    ToolRequestMessage,
+    ToolResponseMessage,
+)
 
 from paperqa.docs import Docs
 from paperqa.llms import EmbeddingModel, LiteLLMModel

paperqa/agents/main.py

@@ -3,8 +3,9 @@
 from collections.abc import Awaitable, Callable
 from typing import TYPE_CHECKING, Any
 
-from aviary.message import MalformedMessageError, Message
-from aviary.tools import (
+from aviary.core import (
+    MalformedMessageError,
+    Message,
     Tool,
     ToolCall,
     ToolRequestMessage,
@@ -40,7 +41,7 @@ class Callback:  # type: ignore[no-redef]
 from .tools import EnvironmentState, GatherEvidence, GenerateAnswer, PaperSearch
 
 if TYPE_CHECKING:
-    from aviary.env import Environment
+    from aviary.core import Environment
     from ldp.agent import Agent, SimpleAgentState
     from ldp.graph.ops import OpResult
 
@@ -234,7 +235,8 @@ async def run_aviary_agent(
             while not done:
                 if max_timesteps is not None and timestep >= max_timesteps:
                     logger.warning(
-                        f"Agent didn't finish within {max_timesteps} timesteps, just answering."
+                        f"Agent didn't finish within {max_timesteps} timesteps, just"
+                        " answering."
                     )
                     generate_answer_tool = next(
                         filter(

paperqa/agents/search.py

@@ -428,7 +428,7 @@ async def maybe_get_manifest(
             }
             if not file_loc_to_records:
                 raise ValueError(  # noqa: TRY301
-                    f"No mapping of file location to details extracted from manifest"
+                    "No mapping of file location to details extracted from manifest"
                     f" file {filename}."
                 )
             logger.debug(
@@ -593,11 +593,9 @@ async def get_directory_index(  # noqa: PLR0912
     index_settings = _settings.agent.index
     if index_name:
         warnings.warn(
-            (
-                f"The index_name argument has been moved to"
-                f" {type(_settings.agent.index).__name__},"
-                " this deprecation will conclude in version 6."
-            ),
+            "The index_name argument has been moved to"
+            f" {type(_settings.agent.index).__name__},"
+            " this deprecation will conclude in version 6.",
             category=DeprecationWarning,
             stacklevel=2,
         )
@@ -620,11 +618,9 @@ async def get_directory_index(  # noqa: PLR0912
 
     if not sync_index_w_directory:
         warnings.warn(
-            (
-                f"The sync_index_w_directory argument has been moved to"
-                f" {type(_settings.agent.index).__name__},"
-                " this deprecation will conclude in version 6."
-            ),
+            "The sync_index_w_directory argument has been moved to"
+            f" {type(_settings.agent.index).__name__},"
+            " this deprecation will conclude in version 6.",
             category=DeprecationWarning,
             stacklevel=2,
         )
@@ -686,7 +682,8 @@ async def get_directory_index(  # noqa: PLR0912
                     )
                 else:
                     logger.debug(
-                        f"File {rel_file_path} found in paper directory {paper_directory}."
+                        f"File {rel_file_path} found in paper directory"
+                        f" {paper_directory}."
                     )
 
     if search_index.changed:

paperqa/agents/task.py

@@ -15,9 +15,15 @@
 from enum import StrEnum
 from typing import TYPE_CHECKING, Any, Self, assert_never
 
-from aviary.env import ENV_REGISTRY, TASK_DATASET_REGISTRY, Frame, TaskDataset
-from aviary.message import Message
-from aviary.tools import ToolRequestMessage, ToolResponseMessage
+from aviary.core import (
+    TASK_DATASET_REGISTRY,
+    Frame,
+    Message,
+    TaskDataset,
+    ToolRequestMessage,
+    ToolResponseMessage,
+)
+from aviary.env import ENV_REGISTRY
 
 from paperqa.types import DocDetails
 

paperqa/clients/semantic_scholar.py

@@ -256,7 +256,7 @@ async def s2_title_search(
     # need to check if nested under a 'data' key or not (depends on filtering)
     if (
         strings_similarity(
-            data.get("title") if "data" not in data else data["data"][0]["title"],
+            data.get("title", "") if "data" not in data else data["data"][0]["title"],
             title,
         )
         < title_similarity_threshold

paperqa/llms.py

@@ -216,7 +216,8 @@ def __init__(self, **kwargs):
             from sentence_transformers import SentenceTransformer
         except ImportError as exc:
             raise ImportError(
-                "Please install paper-qa[local] to use SentenceTransformerEmbeddingModel."
+                "Please install paper-qa[local] to use"
+                " SentenceTransformerEmbeddingModel."
             ) from exc
 
         self._model = SentenceTransformer(self.name)

paperqa/rate_limiter.py

@@ -330,9 +330,6 @@ async def try_acquire(
             raise_impossible_limits (:obj:`bool`, optional): flag will raise a
                 ValueError for weights that exceed the rate.
 
-        Returns:
-            None if the rate limit is satisfied.
-
         Raises:
             TimeoutError: if the acquire_timeout is exceeded.
             ValueError: if the weight exceeds the rate limit and raise_impossible_limits is True.
@@ -352,7 +349,8 @@ async def try_acquire(
 
         if rate_limit.amount < weight and raise_impossible_limits:
             raise ValueError(
-                f"Weight ({weight}) > RateLimit ({rate_limit}), cannot satisfy rate limit."
+                f"Weight ({weight}) > RateLimit ({rate_limit}), cannot satisfy rate"
+                " limit."
             )
         while True:
             elapsed = 0.0

paperqa/readers.py

@@ -3,7 +3,7 @@
 import os
 from math import ceil
 from pathlib import Path
-from typing import Literal, overload
+from typing import Literal, cast, overload
 
 import pymupdf
 import tiktoken
@@ -172,7 +172,9 @@ def chunk_text(
             f"ParsedText.content must be a `str`, not {type(parsed_text.content)}."
         )
 
-    content = parsed_text.content if not use_tiktoken else parsed_text.encode_content()
+    content: str | list[int] = (
+        parsed_text.content if not use_tiktoken else parsed_text.encode_content()
+    )
     if not content:  # Avoid div0 in token calculations
         raise ImpossibleParsingError(
             f"No text was parsed from the document named {doc.docname!r} with ID"
@@ -195,7 +197,11 @@ def chunk_text(
         ]
         texts.append(
             Text(
-                text=enc.decode(split) if use_tiktoken else split,
+                text=(
+                    enc.decode(cast(list[int], split))
+                    if use_tiktoken
+                    else cast(str, split)
+                ),
                 name=f"{doc.docname} chunk {i + 1}",
                 doc=doc,
             )

paperqa/settings.py

@@ -9,7 +9,7 @@
 from typing import TYPE_CHECKING, Any, ClassVar, Self, assert_never, cast
 
 import anyio
-from aviary.tools import ToolSelector
+from aviary.core import ToolSelector
 from pydantic import (
     BaseModel,
     ConfigDict,
@@ -99,11 +99,9 @@ def _deprecated_field(self) -> Self:
         # default is True, so we only warn if it's False
         if not self.evidence_detailed_citations:
             warnings.warn(
-                (
-                    "The 'evidence_detailed_citations' field is deprecated and will be"
-                    " removed in version 6. Adjust 'PromptSettings.context_inner' to remove"
-                    " detailed citations."
-                ),
+                "The 'evidence_detailed_citations' field is deprecated and will be"
+                " removed in version 6. Adjust 'PromptSettings.context_inner' to remove"
+                " detailed citations.",
                 category=DeprecationWarning,
                 stacklevel=2,
             )
@@ -259,8 +257,10 @@ class PromptSettings(BaseModel):
     )
     context_inner: str = Field(
         default=CONTEXT_INNER_PROMPT,
-        description="Prompt for how to format a single context in generate answer. "
-        "This should at least contain key and name.",
+        description=(
+            "Prompt for how to format a single context in generate answer. "
+            "This should at least contain key and name."
+        ),
     )
 
     @field_validator("summary")
@@ -380,7 +380,8 @@ class IndexSettings(BaseModel):
         default=True,
         description=(
             "Whether to sync the index with the paper directory when loading an index."
-            " Setting to True will add or delete index files to match the source paper directory."
+            " Setting to True will add or delete index files to match the source paper"
+            " directory."
         ),
     )
 
@@ -537,11 +538,9 @@ def _deprecated_field(self) -> Self:
             value = getattr(self, deprecated_field_name)
             if value != type(self).model_fields[deprecated_field_name].default:
                 warnings.warn(
-                    (
-                        f"The {deprecated_field_name!r} field has been moved to"
-                        f" {AgentSettings.__name__},"
-                        " this deprecation will conclude in version 6."
-                    ),
+                    f"The {deprecated_field_name!r} field has been moved to"
+                    f" {AgentSettings.__name__},"
+                    " this deprecation will conclude in version 6.",
                     category=DeprecationWarning,
                     stacklevel=2,
                 )
@@ -667,11 +666,9 @@ def _deprecated_field(self) -> Self:
             value = getattr(self, deprecated_field_name)
             if value != type(self).model_fields[deprecated_field_name].default:
                 warnings.warn(
-                    (
-                        f"The {deprecated_field_name!r} field has been moved to"
-                        f" {AgentSettings.__name__},"
-                        " this deprecation will conclude in version 6."
-                    ),
+                    f"The {deprecated_field_name!r} field has been moved to"
+                    f" {AgentSettings.__name__},"
+                    " this deprecation will conclude in version 6.",
                     category=DeprecationWarning,
                     stacklevel=2,
                 )

paperqa/types.py

@@ -12,7 +12,7 @@
 
 import litellm  # for cost
 import tiktoken
-from aviary.message import Message
+from aviary.core import Message
 from pybtex.database import BibliographyData, Entry, Person
 from pybtex.database.input.bibtex import Parser
 from pybtex.scanner import PybtexSyntaxError
@@ -360,8 +360,10 @@ class DocDetails(Doc):
     file_location: str | os.PathLike | None = None
     license: str | None = Field(
         default=None,
-        description="string indicating license."
-        " Should refer specifically to pdf_url (since that could be preprint). None means unknown/unset.",
+        description=(
+            "string indicating license. Should refer specifically to pdf_url (since"
+            " that could be preprint). None means unknown/unset."
+        ),
     )
     pdf_url: str | None = None
     other: dict[str, Any] = Field(
@@ -612,8 +614,8 @@ def formatted_citation(self) -> str:
 
         if self.source_quality_message:
             return (
-                f"{self.citation} This article has {self.citation_count} citations and is"
-                f" from a {self.source_quality_message}."
+                f"{self.citation} This article has {self.citation_count} citations and"
+                f" is from a {self.source_quality_message}."
             )
         return f"{self.citation} This article has {self.citation_count} citations."