Replace validate_stubs scripts with stubtest

.github/workflows/test.yml

@@ -6,15 +6,20 @@ jobs:
   test:
     runs-on: ubuntu-latest
     timeout-minutes: 10
+    strategy:
+      matrix:
+        # Oldest non-EOL and newest released
+        python-version: ["3.9", "3.13"]
+      fail-fast: false
 
     steps:
       - name: Check out code
         uses: actions/checkout@v2
 
-      - name: Setup Python
+      - name: Setup Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
-          python-version: "3.11"
+          python-version: ${{ matrix.python-version }}
 
       - name: Cache pip
         uses: actions/cache@v4
@@ -35,6 +40,9 @@ jobs:
       - name: Run mypy tests
         run: python -m mypy .
 
+      - name: Run stubtest
+        run: python tests/run_stubtests.py
+
   hygiene:
     runs-on: ubuntu-latest
     timeout-minutes: 10
@@ -45,4 +53,5 @@ jobs:
 
       - name: Run Ruff Linter
         uses: astral-sh/ruff-action@v3
-      - run: ruff format --check
+      - name: Run Ruff Formatter
+        run: ruff format --check

.gitignore

@@ -357,6 +357,9 @@ MigrationBackup/
 # Python virtual environment
 .venv
 
+# Lock files (like uv.lock)
+*.lock
+
 # Build files from utils
 .eggs
 *.egg-info

pyproject.toml

@@ -11,24 +11,29 @@ hygiene = ["ruff ==0.11.*"]
 tests = [
     # Tools used for testing
     "docopt-ng",
-    "mypy ==1.13.*",
+    "mypy ==1.15.*",
     "pyright",
 
     # Typed libraries and stubs
     "matplotlib >=3.8",
+    "numpy >=2",
     "pandas-stubs",
     "pytest",
     "scipy-stubs",
     "typing_extensions",
 
-    # Untyped libraries, used to prevent "reportMissingImports" and get inferred typing
+    # Untyped libraries. Used to prevent "reportMissingImports" and get inferred typing
     "joblib",
-    "networkx",
     "PyOpenGL",
-    "scikit-learn",
-    "sympy",
     "traitlets",
     "transformers",
+
+    # The libraries we're stubbing. Needed for stubtest
+    "networkx",
+    "scikit-image",
+    "scikit-learn",
+    "sympy",
+    "vispy",
 ]
 dev = [{ include-group = "hygiene" }, { include-group = "tests" }]
 
@@ -57,6 +62,7 @@ target-version = "py39"
 extend-select = [
     "FA", # flake8-future-annotations
     "I", # isort
+    "ICN", # flake8-import-conventions
     "PYI", # flake8-pyi
     "UP", # pyupgrade
     "W", # pycodestyle Warning
@@ -100,12 +106,22 @@ ignore = [
 # We keep docstrings in sklearn
 "stubs/sklearn/**" = ["PYI021"]
 
+[tool.ruff.lint.flake8-import-conventions.aliases]
+# Prevent aliasing these, as it causes false-negatives for certain rules
+typing_extensions = "typing_extensions"
+typing = "typing"
+
 [tool.ruff.lint.isort]
 combine-as-imports = true
 extra-standard-library = [
     # Group these with stdlib
     "typing_extensions",
     "_typeshed",
+    # Extra modules not recognized by Ruff
+    # Added in Python 3.9
+    "zoneinfo",
+    # Added in Python 3.14
+    "compression",
 ]
 
 [tool.pyright]