From 8baa17c8e8f73a8b88c54c13a709bd530801e78c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?=
 <jon.haitz.legarreta@gmail.com>
Date: Fri, 20 Dec 2024 10:19:11 -0500
Subject: [PATCH] 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, including the spell checking.

Documentation:
https://mypy.readthedocs.io/en/stable/index.html
---
 .github/workflows/test.yml | 25 +++++++++++++++++++++++++
 pyproject.toml             | 16 ++++++++++++++++
 tox.ini                    |  9 +++++++++
 3 files changed, 50 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 0293c50..1aa2ca5 100644
--- a/.github/workflows/test.yml
+++ b/.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 }}
diff --git a/pyproject.toml b/pyproject.toml
index 7cefdca..4c9c7a0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -73,6 +73,12 @@ test = [
     "pytest-env",
     "pytest-xdist >= 1.28"
 ]
+types = [
+    "pandas-stubs",
+    "scipy-stubs",
+    "pytest",
+    "microsoft-python-type-stubs @ git+https://github.com/microsoft/python-type-stubs.git",
+]
 
 antsopt = [
     "ConfigSpace",
@@ -122,6 +128,16 @@ version-file = "src/nifreeze/_version.py"
 # Developer tool configurations
 #
 
+[[tool.mypy.overrides]]
+module = [
+  "nipype.*",
+  "nilearn.*",
+  "nireports.*",
+  "nitransforms.*",
+  "seaborn",
+]
+ignore_missing_imports = true
+
 [tool.ruff]
 line-length = 99
 target-version = "py310"
diff --git a/tox.ini b/tox.ini
index 77371e1..a7c652e 100644
--- a/tox.ini
+++ b/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 nireports
+
 [testenv:spellcheck]
 description = Check spelling
 labels = check