ENH: Add static type checking

Add static type checking: use `mypy` to ensure that variable and
function calls are using the appropriate types.

Configure and run `mypy` checks in CI.

Take advantage of the commit to include running the spell checker in the
check matrix.

Documentation:
https://mypy.readthedocs.io/en/stable/index.html

Author: jhlegarreta

.github/workflows/test.yml

@@ -84,3 +84,28 @@ jobs:
         with:
           files: cov.xml
           token: ${{ secrets.CODECOV_TOKEN }}
+
+  checks:
+    runs-on: 'ubuntu-latest'
+    continue-on-error: true
+    strategy:
+      matrix:
+        check: ['spellcheck', 'typecheck']
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
+      # Can remove this once there is a traits release that supports 3.13
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - name: Install tox
+        run: uv tool install tox --with=tox-uv
+      - name: Show tox config
+        run: tox c
+      - name: Show tox config (this call)
+        run: tox c -e ${{ matrix.check }}
+      - name: Run check
+        run: tox -e ${{ matrix.check }}

pyproject.toml

@@ -73,6 +73,15 @@ test = [
     "pytest-env",
     "pytest-xdist >= 1.28"
 ]
+types = [
+  "pandas-stubs",
+  "types-setuptools",
+  "scipy-stubs",
+  "types-PyYAML",
+  "types-tqdm",
+  "pytest",
+  "microsoft-python-type-stubs @ git+https://github.com/microsoft/python-type-stubs.git",
+]
 
 antsopt = [
     "ConfigSpace",
@@ -122,6 +131,15 @@ version-file = "src/nifreeze/_version.py"
 # Developer tool configurations
 #
 
+[[tool.mypy.overrides]]
+module = [
+  "nipype.*",
+  "nilearn.*",
+  "nitransforms.*",
+  "seaborn",
+]
+ignore_missing_imports = true
+
 [tool.ruff]
 line-length = 99
 target-version = "py310"

tox.ini

@@ -46,6 +46,15 @@ extras = doc
 commands =
   make -C docs/ SPHINXOPTS="-W -v" BUILDDIR="$HOME/docs" OUTDIR="${CURBRANCH:-html}" html
 
+[testenv:typecheck]
+description = Run mypy type checking
+labels = check
+deps =
+  mypy
+extras = types
+commands =
+  mypy nifreeze
+
 [testenv:spellcheck]
 description = Check spelling
 labels = check