Run mypy on CI, fix or ignore typing issues (#987)

* Run mypy on CI

* Rename, add mypy to test deps

* Fix typing jupyter-ai codebase (mostly)

* Three more cases

* update deepmerge version specifier

---------

Co-authored-by: David L. Qiu <[email protected]>

.github/workflows/unit-tests.yml

@@ -1,4 +1,4 @@
-name: Python Unit Tests
+name: Python Tests
 
 # suppress warning raised by https://github.com/jupyter/jupyter_core/pull/292
 env:
@@ -12,7 +12,7 @@ on:
 
 jobs:
   unit-tests:
-    name: Linux
+    name: Unit tests
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -28,3 +28,22 @@ jobs:
         run: |
           set -eux
           pytest -vv -r ap --cov jupyter_ai
+
+  typing-tests:
+    name: Typing test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Base Setup
+        uses: jupyterlab/maintainer-tools/.github/actions/base-setup@v1
+
+      - name: Install extension dependencies and build the extension
+        run: ./scripts/install.sh
+
+      - name: Run mypy
+        run: |
+          set -eux
+          mypy --version
+          mypy packages/jupyter-ai

packages/jupyter-ai-magics/jupyter_ai_magics/models/completion.py

@@ -43,6 +43,7 @@ class InlineCompletionItem(BaseModel):
 
 class CompletionError(BaseModel):
     type: str
+    title: str
     traceback: str
 
 

packages/jupyter-ai/jupyter_ai/chat_handlers/ask.py

@@ -72,6 +72,7 @@ async def process_message(self, message: HumanChatMessage):
 
         try:
             with self.pending("Searching learned documents", message):
+                assert self.llm_chain
                 result = await self.llm_chain.acall({"question": query})
                 response = result["answer"]
             self.reply(response, message)

packages/jupyter-ai/jupyter_ai/chat_handlers/base.py

@@ -13,6 +13,7 @@
     Optional,
     Type,
     Union,
+    cast,
 )
 from uuid import uuid4
 
@@ -28,6 +29,7 @@
 )
 from jupyter_ai_magics import Persona
 from jupyter_ai_magics.providers import BaseProvider
+from langchain.chains import LLMChain
 from langchain.pydantic_v1 import BaseModel
 
 if TYPE_CHECKING:
@@ -36,8 +38,8 @@
     from langchain_core.chat_history import BaseChatMessageHistory
 
 
-def get_preferred_dir(root_dir: str, preferred_dir: str) -> Optional[str]:
-    if preferred_dir != "":
+def get_preferred_dir(root_dir: str, preferred_dir: Optional[str]) -> Optional[str]:
+    if preferred_dir is not None and preferred_dir != "":
         preferred_dir = os.path.expanduser(preferred_dir)
         if not preferred_dir.startswith(root_dir):
             preferred_dir = os.path.join(root_dir, preferred_dir)
@@ -47,7 +49,7 @@ def get_preferred_dir(root_dir: str, preferred_dir: str) -> Optional[str]:
 
 # Chat handler type, with specific attributes for each
 class HandlerRoutingType(BaseModel):
-    routing_method: ClassVar[Union[Literal["slash_command"]]] = ...
+    routing_method: ClassVar[Union[Literal["slash_command"]]]
     """The routing method that sends commands to this handler."""
 
 
@@ -83,17 +85,17 @@ class BaseChatHandler:
     multiple chat handler classes."""
 
     # Class attributes
-    id: ClassVar[str] = ...
+    id: ClassVar[str]
     """ID for this chat handler; should be unique"""
 
-    name: ClassVar[str] = ...
+    name: ClassVar[str]
     """User-facing name of this handler"""
 
-    help: ClassVar[str] = ...
+    help: ClassVar[str]
     """What this chat handler does, which third-party models it contacts,
     the data it returns to the user, and so on, for display in the UI."""
 
-    routing_type: ClassVar[HandlerRoutingType] = ...
+    routing_type: ClassVar[HandlerRoutingType]
 
     uses_llm: ClassVar[bool] = True
     """Class attribute specifying whether this chat handler uses the LLM
@@ -153,9 +155,9 @@ def __init__(
         self.help_message_template = help_message_template
         self.chat_handlers = chat_handlers
 
-        self.llm = None
-        self.llm_params = None
-        self.llm_chain = None
+        self.llm: Optional[BaseProvider] = None
+        self.llm_params: Optional[dict] = None
+        self.llm_chain: Optional[LLMChain] = None
 
     async def on_message(self, message: HumanChatMessage):
         """
@@ -168,9 +170,8 @@ async def on_message(self, message: HumanChatMessage):
 
         # ensure the current slash command is supported
         if self.routing_type.routing_method == "slash_command":
-            slash_command = (
-                "/" + self.routing_type.slash_id if self.routing_type.slash_id else ""
-            )
+            routing_type = cast(SlashCommandRoutingType, self.routing_type)
+            slash_command = "/" + routing_type.slash_id if routing_type.slash_id else ""
             if slash_command in lm_provider_klass.unsupported_slash_commands:
                 self.reply(
                     "Sorry, the selected language model does not support this slash command."

packages/jupyter-ai/jupyter_ai/chat_handlers/default.py

@@ -41,10 +41,10 @@ def create_llm_chain(
         prompt_template = llm.get_chat_prompt_template()
         self.llm = llm
 
-        runnable = prompt_template | llm
+        runnable = prompt_template | llm  # type:ignore
         if not llm.manages_history:
             runnable = RunnableWithMessageHistory(
-                runnable=runnable,
+                runnable=runnable,  #  type:ignore[arg-type]
                 get_session_history=self.get_llm_chat_memory,
                 input_messages_key="input",
                 history_messages_key="history",
@@ -106,6 +106,7 @@ async def process_message(self, message: HumanChatMessage):
             # stream response in chunks. this works even if a provider does not
             # implement streaming, as `astream()` defaults to yielding `_call()`
             # when `_stream()` is not implemented on the LLM class.
+            assert self.llm_chain
             async for chunk in self.llm_chain.astream(
                 {"input": message.body},
                 config={"configurable": {"last_human_msg": message}},
@@ -117,7 +118,7 @@ async def process_message(self, message: HumanChatMessage):
                     stream_id = self._start_stream(human_msg=message)
                     received_first_chunk = True
 
-                if isinstance(chunk, AIMessageChunk):
+                if isinstance(chunk, AIMessageChunk) and isinstance(chunk.content, str):
                     self._send_stream_chunk(stream_id, chunk.content)
                 elif isinstance(chunk, str):
                     self._send_stream_chunk(stream_id, chunk)

packages/jupyter-ai/jupyter_ai/chat_handlers/fix.py

@@ -93,6 +93,7 @@ async def process_message(self, message: HumanChatMessage):
 
         self.get_llm_chain()
         with self.pending("Analyzing error", message):
+            assert self.llm_chain
             response = await self.llm_chain.apredict(
                 extra_instructions=extra_instructions,
                 stop=["\nHuman:"],

packages/jupyter-ai/jupyter_ai/chat_handlers/generate.py

@@ -226,7 +226,7 @@ class GenerateChatHandler(BaseChatHandler):
     def __init__(self, log_dir: Optional[str], *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.log_dir = Path(log_dir) if log_dir else None
-        self.llm = None
+        self.llm: Optional[BaseProvider] = None
 
     def create_llm_chain(
         self, provider: Type[BaseProvider], provider_params: Dict[str, str]
@@ -248,6 +248,7 @@ async def _generate_notebook(self, prompt: str):
         # Save the user input prompt, the description property is now LLM generated.
         outline["prompt"] = prompt
 
+        assert self.llm
         if self.llm.allows_concurrency:
             # fill the outline concurrently
             await afill_outline(outline, llm=self.llm, verbose=True)

packages/jupyter-ai/jupyter_ai/chat_handlers/learn.py

@@ -223,7 +223,9 @@ async def learn_dir(
         }
         splitter = ExtensionSplitter(
             splitters=splitters,
-            default_splitter=RecursiveCharacterTextSplitter(**splitter_kwargs),
+            default_splitter=RecursiveCharacterTextSplitter(
+                **splitter_kwargs  # type:ignore[arg-type]
+            ),
         )
 
         delayed = split(path, all_files, splitter=splitter)
@@ -352,7 +354,7 @@ async def aget_relevant_documents(
         self, query: str
     ) -> Coroutine[Any, Any, List[Document]]:
         if not self.index:
-            return []
+            return []  # type:ignore[return-value]
 
         await self.delete_and_relearn()
         docs = self.index.similarity_search(query)
@@ -370,12 +372,14 @@ def get_embedding_model(self):
 
 
 class Retriever(BaseRetriever):
-    learn_chat_handler: LearnChatHandler = None
+    learn_chat_handler: LearnChatHandler = None  # type:ignore[assignment]
 
-    def _get_relevant_documents(self, query: str) -> List[Document]:
+    def _get_relevant_documents(  # type:ignore[override]
+        self, query: str
+    ) -> List[Document]:
         raise NotImplementedError()
 
-    async def _aget_relevant_documents(
+    async def _aget_relevant_documents(  # type:ignore[override]
         self, query: str
     ) -> Coroutine[Any, Any, List[Document]]:
         docs = await self.learn_chat_handler.aget_relevant_documents(query)

packages/jupyter-ai/jupyter_ai/config_manager.py

@@ -3,7 +3,7 @@
 import os
 import shutil
 import time
-from typing import List, Optional, Union
+from typing import List, Optional, Type, Union
 
 from deepmerge import always_merger as Merger
 from jsonschema import Draft202012Validator as Validator
@@ -60,7 +60,7 @@ class BlockedModelError(Exception):
     pass
 
 
-def _validate_provider_authn(config: GlobalConfig, provider: AnyProvider):
+def _validate_provider_authn(config: GlobalConfig, provider: Type[AnyProvider]):
     # TODO: handle non-env auth strategies
     if not provider.auth_strategy or provider.auth_strategy.type != "env":
         return
@@ -147,7 +147,7 @@ def _init_config_schema(self):
             os.makedirs(os.path.dirname(self.schema_path), exist_ok=True)
             shutil.copy(OUR_SCHEMA_PATH, self.schema_path)
 
-    def _init_validator(self) -> Validator:
+    def _init_validator(self) -> None:
         with open(OUR_SCHEMA_PATH, encoding="utf-8") as f:
             schema = json.loads(f.read())
             Validator.check_schema(schema)
@@ -364,7 +364,7 @@ def delete_api_key(self, key_name: str):
         config_dict["api_keys"].pop(key_name, None)
         self._write_config(GlobalConfig(**config_dict))
 
-    def update_config(self, config_update: UpdateConfigRequest):
+    def update_config(self, config_update: UpdateConfigRequest):  # type:ignore
         last_write = os.stat(self.config_path).st_mtime_ns
         if config_update.last_read and config_update.last_read < last_write:
             raise WriteConflictError(

packages/jupyter-ai/jupyter_ai/document_loaders/directory.py

@@ -30,7 +30,7 @@ def arxiv_to_text(id: str, output_dir: str) -> str:
         output path to the downloaded TeX file
     """
 
-    import arxiv
+    import arxiv  # type:ignore[import-not-found,import-untyped]
 
     outfile = f"{id}-{datetime.now():%Y-%m-%d-%H-%M}.tex"
     download_filename = "downloaded-paper.tar.gz"

packages/jupyter-ai/jupyter_ai/extension.py

@@ -52,7 +52,7 @@
 
 class AiExtension(ExtensionApp):
     name = "jupyter_ai"
-    handlers = [
+    handlers = [  # type:ignore[assignment]
         (r"api/ai/api_keys/(?P<api_key_name>\w+)", ApiKeysHandler),
         (r"api/ai/config/?", GlobalConfigHandler),
         (r"api/ai/chats/?", RootChatHandler),

packages/jupyter-ai/jupyter_ai/handlers.py

@@ -4,7 +4,7 @@
 import uuid
 from asyncio import AbstractEventLoop
 from dataclasses import asdict
-from typing import TYPE_CHECKING, Dict, List, Optional
+from typing import TYPE_CHECKING, Dict, List, Optional, cast
 
 import tornado
 from jupyter_ai.chat_handlers import BaseChatHandler, SlashCommandRoutingType
@@ -42,14 +42,12 @@
     from jupyter_ai_magics.embedding_providers import BaseEmbeddingsProvider
     from jupyter_ai_magics.providers import BaseProvider
 
-    from .history import BoundChatHistory
+    from .history import BoundedChatHistory
 
 
 class ChatHistoryHandler(BaseAPIHandler):
     """Handler to return message history"""
 
-    _messages = []
-
     @property
     def chat_history(self) -> List[ChatMessage]:
         return self.settings["chat_history"]
@@ -103,7 +101,7 @@ def chat_history(self, new_history):
         self.settings["chat_history"] = new_history
 
     @property
-    def llm_chat_memory(self) -> "BoundChatHistory":
+    def llm_chat_memory(self) -> "BoundedChatHistory":
         return self.settings["llm_chat_memory"]
 
     @property
@@ -145,6 +143,7 @@ def get_chat_user(self) -> ChatUser:
         environment."""
         # Get a dictionary of all loaded extensions.
         # (`serverapp` is a property on all `JupyterHandler` subclasses)
+        assert self.serverapp
         extensions = self.serverapp.extension_manager.extensions
         collaborative = (
             "jupyter_collaboration" in extensions
@@ -401,7 +400,7 @@ def filter_predicate(local_model_id: str):
             if self.blocked_models:
                 return model_id not in self.blocked_models
             else:
-                return model_id in self.allowed_models
+                return model_id in cast(List, self.allowed_models)
 
         # filter out every model w/ model ID according to allow/blocklist
         for provider in providers:
@@ -514,7 +513,7 @@ def post(self):
 
 class ApiKeysHandler(BaseAPIHandler):
     @property
-    def config_manager(self) -> ConfigManager:
+    def config_manager(self) -> ConfigManager:  # type:ignore[override]
         return self.settings["jai_config_manager"]
 
     @web.authenticated
@@ -529,7 +528,7 @@ class SlashCommandsInfoHandler(BaseAPIHandler):
     """List slash commands that are currently available to the user."""
 
     @property
-    def config_manager(self) -> ConfigManager:
+    def config_manager(self) -> ConfigManager:  # type:ignore[override]
         return self.settings["jai_config_manager"]
 
     @property

packages/jupyter-ai/jupyter_ai/history.py

@@ -25,7 +25,7 @@ class BoundedChatHistory(BaseChatMessageHistory, BaseModel):
     _all_messages: List[BaseMessage] = PrivateAttr(default_factory=list)
 
     @property
-    def messages(self) -> List[BaseMessage]:
+    def messages(self) -> List[BaseMessage]:  # type:ignore[override]
         if self.k is None:
             return self._all_messages
         return self._all_messages[-self.k * 2 :]
@@ -92,7 +92,7 @@ class WrappedBoundedChatHistory(BaseChatMessageHistory, BaseModel):
     last_human_msg: HumanChatMessage
 
     @property
-    def messages(self) -> List[BaseMessage]:
+    def messages(self) -> List[BaseMessage]:  # type:ignore[override]
         return self.history.messages
 
     def add_message(self, message: BaseMessage) -> None: