feat: add mypy type checking to pre-commit

- Add mypy configuration to pyproject.toml
- Add mypy hook to pre-commit with type stubs
- Start with lenient settings, strict checking for content_registry
- All other modules excluded until fully typed (gradual adoption)

Addresses #1266.

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Author: dimitri-yatsenko

.pre-commit-config.yaml

@@ -36,6 +36,15 @@ repos:
   hooks:
   # lint github actions workflow yaml
   - id: actionlint
-
-## Suggest to add pytest hook that runs unit test | Prerequisite: split unit/integration test
-## https://github.com/datajoint/datajoint-python/issues/1211
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v1.14.1
+  hooks:
+    - id: mypy
+      files: ^src/datajoint/
+      additional_dependencies:
+        - pydantic
+        - pydantic-settings
+        - types-PyMySQL
+        - types-tqdm
+        - pandas-stubs
+        - numpy

pyproject.toml

@@ -152,6 +152,60 @@ quote-style = "double"
 indent-style = "space"
 line-ending = "auto"
 
+[tool.mypy]
+python_version = "3.10"
+ignore_missing_imports = true
+# Start with lenient settings, gradually enable stricter checks
+warn_return_any = false
+warn_unused_ignores = false
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+check_untyped_defs = true
+
+# Modules with complete type coverage - strict checking enabled
+[[tool.mypy.overrides]]
+module = [
+    "datajoint.content_registry",
+]
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+warn_return_any = true
+
+# Modules excluded from type checking until fully typed
+[[tool.mypy.overrides]]
+module = [
+    "datajoint.admin",
+    "datajoint.autopopulate",
+    "datajoint.blob",
+    "datajoint.builtin_codecs",
+    "datajoint.cli",
+    "datajoint.codecs",
+    "datajoint.condition",
+    "datajoint.connection",
+    "datajoint.declare",
+    "datajoint.dependencies",
+    "datajoint.diagram",
+    "datajoint.errors",
+    "datajoint.expression",
+    "datajoint.gc",
+    "datajoint.hash",
+    "datajoint.heading",
+    "datajoint.jobs",
+    "datajoint.lineage",
+    "datajoint.logging",
+    "datajoint.migrate",
+    "datajoint.objectref",
+    "datajoint.preview",
+    "datajoint.schemas",
+    "datajoint.settings",
+    "datajoint.staged_insert",
+    "datajoint.storage",
+    "datajoint.table",
+    "datajoint.user_tables",
+    "datajoint.utils",
+]
+ignore_errors = true
+
 [tool.setuptools]
 packages = ["datajoint"]
 package-dir = {"" = "src"}