From 5502c51e59d9d768f40e5a87d19def48397765d7 Mon Sep 17 00:00:00 2001
From: James Braza <jamesbraza@gmail.com>
Date: Fri, 13 Sep 2024 16:16:26 -0700
Subject: [PATCH 1/2] Fixing mutable `BaseModel` defaults and removing extra
 `BaseModel` (#400)

---
 paperqa/agents/main.py   | 17 ++---------------
 paperqa/agents/models.py |  4 ++--
 paperqa/docs.py          |  8 ++++----
 paperqa/types.py         |  2 +-
 4 files changed, 9 insertions(+), 22 deletions(-)

diff --git a/paperqa/agents/main.py b/paperqa/agents/main.py
index 31fdcb44..fa1d4fd3 100644
--- a/paperqa/agents/main.py
+++ b/paperqa/agents/main.py
@@ -10,10 +10,10 @@
     Tool,
     ToolCall,
     ToolRequestMessage,
-    ToolResponseMessage,
     ToolSelector,
+    ToolSelectorLedger,
 )
-from pydantic import BaseModel, Field, TypeAdapter
+from pydantic import BaseModel, TypeAdapter
 from tenacity import (
     Retrying,
     before_sleep_log,
@@ -268,19 +268,6 @@ async def step(tool: Tool, **call_kwargs) -> None:
     return env.state.answer, AgentStatus.SUCCESS
 
 
-class ToolSelectorLedger(BaseModel):
-    """
-    Simple ledger to record tools and messages.
-
-    TODO: remove this after it's upstreamed into aviary.
-    """
-
-    tools: list[Tool] = Field(default_factory=list)
-    messages: list[ToolRequestMessage | ToolResponseMessage | Message] = Field(
-        default_factory=list
-    )
-
-
 async def run_aviary_agent(
     query: QueryRequest,
     docs: Docs,
diff --git a/paperqa/agents/models.py b/paperqa/agents/models.py
index 12567393..e35c92fa 100644
--- a/paperqa/agents/models.py
+++ b/paperqa/agents/models.py
@@ -130,8 +130,8 @@ class SimpleProfiler(BaseModel):
     # [Profiling] {**name** of timer} | {**elapsed** time of function} | {**__version__** of PaperQA}
     """
 
-    timers: dict[str, list[float]] = {}
-    running_timers: dict[str, TimerData] = {}
+    timers: dict[str, list[float]] = Field(default_factory=dict)
+    running_timers: dict[str, TimerData] = Field(default_factory=dict)
     uid: UUID = Field(default_factory=uuid4)
 
     @asynccontextmanager
diff --git a/paperqa/docs.py b/paperqa/docs.py
index ad2fc595..2fb5b466 100644
--- a/paperqa/docs.py
+++ b/paperqa/docs.py
@@ -68,15 +68,15 @@ class Docs(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     id: UUID = Field(default_factory=uuid4)
-    docs: dict[DocKey, Doc | DocDetails] = {}
-    texts: list[Text] = []
-    docnames: set[str] = set()
+    docs: dict[DocKey, Doc | DocDetails] = Field(default_factory=dict)
+    texts: list[Text] = Field(default_factory=list)
+    docnames: set[str] = Field(default_factory=set)
     texts_index: VectorStore = Field(default_factory=NumpyVectorStore)
     name: str = Field(default="default", description="Name of this docs collection")
     index_path: Path | None = Field(
         default=PAPERQA_DIR, description="Path to save index", validate_default=True
     )
-    deleted_dockeys: set[DocKey] = set()
+    deleted_dockeys: set[DocKey] = Field(default_factory=set)
 
     @field_validator("index_path")
     @classmethod
diff --git a/paperqa/types.py b/paperqa/types.py
index 2aee291e..036a8116 100644
--- a/paperqa/types.py
+++ b/paperqa/types.py
@@ -155,7 +155,7 @@ class Answer(BaseModel):
     question: str
     answer: str = ""
     context: str = ""
-    contexts: list[Context] = []
+    contexts: list[Context] = Field(default_factory=list)
     references: str = ""
     formatted_answer: str = ""
     cost: float = 0.0

From be173caf3feafdef9bb928f3f81e311c30d1d21a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci-lite[bot]"
 <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
Date: Fri, 13 Sep 2024 23:45:59 +0000
Subject: [PATCH 2/2] [pre-commit.ci lite] apply automatic fixes

---
 paperqa/readers.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/paperqa/readers.py b/paperqa/readers.py
index faca366f..10498777 100644
--- a/paperqa/readers.py
+++ b/paperqa/readers.py
@@ -34,6 +34,7 @@ def parse_pdf_to_pages(path: Path) -> ParsedText:
     )
     return ParsedText(content=pages, metadata=metadata)
 
+
 def parse_docx_to_text(path: Path) -> ParsedText:
     doc = docx.Document(path)
     text = "\n".join([para.text for para in doc.paragraphs])