chore: update pre-commit hooks (#1508)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: pre-commit-ci[bot]

.github/workflows/ci.yml

@@ -106,6 +106,9 @@ jobs:
       - uses: actions/checkout@v6
 
       - uses: jupyterlab/maintainer-tools/.github/actions/base-setup@v1
+      - name: Check mypy deps are in sync with project deps
+        run: hatch run typing:check
+
       - name: Run Linters
         run: |
           hatch run typing:test

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.37.0
+    rev: 0.37.2
     hooks:
       - id: check-github-workflows
 
@@ -39,28 +39,50 @@ repos:
         types_or: [yaml, html, json]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.19.1"
+    rev: "v2.1.0"
     hooks:
       - id: mypy
         files: ipykernel
         stages: [manual]
         args: ["--install-types", "--non-interactive"]
         additional_dependencies:
           [
-            "traitlets>=5.13",
-            "ipython>=8.16.1",
-            "jupyter_client>=8.5",
-            "appnope",
+            "appnope>=0.1.2",
+            "comm>=0.1.1",
+            "debugpy>=1.6.5",
+            "ipython>=7.23.1",
+            "jupyter_client>=8.9.0",
+            "jupyter_core>=5.1",
+            "matplotlib-inline>=0.1",
+            "nest_asyncio2>=1.7.0",
+            "packaging>=22",
+            "psutil>=5.7",
+            "pyzmq>=25",
+            "tornado>=6.4.1",
+            "traitlets>=5.4.0",
           ]
 
+  - repo: local
+    hooks:
+      - id: check-mypy-deps
+        name: mypy deps in sync with project deps
+        entry: python scripts/check_mypy_deps.py
+        language: python
+        pass_filenames: false
+        always_run: true
+        additional_dependencies:
+          - "pyyaml"
+          - "packaging"
+          - "tomli; python_version < '3.11'"
+
   - repo: https://github.com/adamchainz/blacken-docs
     rev: "1.20.0"
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==23.7.0]
 
   - repo: https://github.com/codespell-project/codespell
-    rev: "v2.4.1"
+    rev: "v2.4.2"
     hooks:
       - id: codespell
         args: ["-L", "sur,nd"]
@@ -73,7 +95,7 @@ repos:
       - id: rst-inline-touching-normal
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.4
+    rev: v0.15.16
     hooks:
       - id: ruff-check
         types_or: [python, jupyter]
@@ -82,7 +104,7 @@ repos:
         types_or: [python, jupyter]
 
   - repo: https://github.com/scientific-python/cookie
-    rev: "2026.03.02"
+    rev: "2026.04.04"
     hooks:
       - id: sp-repo-review
         additional_dependencies: ["repo-review[cli]"]

ipykernel/comm/comm.py

@@ -16,7 +16,7 @@
 
 
 # this is the class that will be created if we do comm.create_comm
-class BaseComm(comm.base_comm.BaseComm):  # type:ignore[misc]
+class BaseComm(comm.base_comm.BaseComm):
     """The base class for comms."""
 
     kernel: Optional["Kernel"] = None
@@ -90,7 +90,7 @@ def __init__(
         kernel = kwargs.pop("kernel", None)
         if target_name:
             kwargs["target_name"] = target_name
-        BaseComm.__init__(self, data=data, metadata=metadata, buffers=buffers, **kwargs)  # type:ignore[call-arg]
+        BaseComm.__init__(self, data=data, metadata=metadata, buffers=buffers, **kwargs)
         # only re-add kernel if explicitly provided
         if had_kernel:
             kwargs["kernel"] = kernel

ipykernel/comm/manager.py

@@ -14,7 +14,7 @@
 logger = logging.getLogger("ipykernel.comm")
 
 
-class CommManager(comm.base_comm.CommManager, traitlets.config.LoggingConfigurable):  # type:ignore[misc]
+class CommManager(comm.base_comm.CommManager, traitlets.config.LoggingConfigurable):
     """A comm manager."""
 
     kernel = traitlets.Instance("ipykernel.kernelbase.Kernel")

ipykernel/eventloops.py

@@ -301,7 +301,7 @@ def _schedule_exit(delay):
     else:
         import asyncio
 
-        import nest_asyncio2
+        import nest_asyncio2  # type: ignore[import-untyped]
 
         nest_asyncio2.apply()
 

ipykernel/kernelbase.py

@@ -441,7 +441,7 @@ async def dispatch_shell(self, msg, /, subshell_id: str | None = None):
         # Only abort execute requests
         if msg_type == "execute_request":
             if subshell_id is None:
-                aborting = self._aborting  # type:ignore[unreachable]
+                aborting = self._aborting
             else:
                 aborting = self.shell_channel_thread.manager.get_subshell_aborting(subshell_id)
             if aborting:

pyproject.toml

@@ -113,14 +113,16 @@ dependencies = ["pre-commit"]
 detached = true
 [tool.hatch.envs.typing.scripts]
 test = "pre-commit run --all-files --hook-stage manual mypy"
+check = "pre-commit run --all-files check-mypy-deps"
 
 [tool.hatch.envs.lint]
 dependencies = ["pre-commit"]
 detached = true
 [tool.hatch.envs.lint.scripts]
 build = [
   "pre-commit run --all-files ruff-check",
-  "pre-commit run --all-files ruff-format"
+  "pre-commit run --all-files ruff-format",
+  "pre-commit run --all-files check-mypy-deps",
 ]
 
 [tool.mypy]

scripts/check_mypy_deps.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+"""Verify that the mypy hook's additional_dependencies in .pre-commit-config.yaml
+includes all runtime dependencies declared in pyproject.toml.
+
+Run directly or via pre-commit (check-mypy-deps hook).
+"""
+
+from __future__ import annotations
+
+import sys
+
+try:
+    import tomllib
+except ImportError:
+    import tomli as tomllib  # type: ignore[no-reuse-def]
+
+import yaml
+from packaging.requirements import Requirement
+
+
+def normalize(name: str) -> str:
+    return name.lower().replace("-", "_").replace(".", "_")
+
+
+def main() -> int:
+    with open("pyproject.toml", "rb") as f:
+        pyproject = tomllib.load(f)
+
+    with open(".pre-commit-config.yaml") as f:
+        pre_commit = yaml.safe_load(f)
+
+    project_deps: list[str] = pyproject["project"]["dependencies"]
+    project_packages = {normalize(Requirement(dep).name) for dep in project_deps}
+
+    mypy_additional: list[str] | None = None
+    for repo in pre_commit["repos"]:
+        for hook in repo.get("hooks", []):
+            if hook["id"] == "mypy":
+                mypy_additional = hook.get("additional_dependencies", [])
+                break
+        if mypy_additional is not None:
+            break
+
+    if mypy_additional is None:
+        print("ERROR: mypy hook not found in .pre-commit-config.yaml")
+        return 1
+
+    mypy_packages = {normalize(Requirement(dep).name) for dep in mypy_additional}
+
+    missing = project_packages - mypy_packages
+    if missing:
+        print(
+            "ERROR: The following project dependencies are missing from the mypy\n"
+            "hook's additional_dependencies in .pre-commit-config.yaml:\n"
+        )
+        for pkg in sorted(missing):
+            print(f"  {pkg}")
+        print("\nAdd them to the `additional_dependencies` list of the mypy hook.")
+        return 1
+
+    print("OK: mypy additional_dependencies covers all project runtime dependencies.")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())