From e94ecbc3c7993f33da096c839ea9225fa47c1691 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 19 Dec 2024 09:25:43 -0500
Subject: [PATCH 1/5] chore: Configure mypy

---
 pyproject.toml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index b132bccc..df238198 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -66,6 +66,14 @@ test = [
     "pytest-xdist >= 2.5",
     "sphinx >= 6",
 ]
+types = [
+    "pandas-stubs",
+    "scipy-stubs",
+    "types-jinja2",
+    "types-pyyaml",
+    "pytest",
+    "microsoft-python-type-stubs @ git+https://github.com/microsoft/python-type-stubs.git",
+]
 
 # Aliases
 docs = ["nireports[doc]"]
@@ -198,3 +206,19 @@ ignore-words-list = "objekt"
 ignore = [
   "W002",
 ]
+
+[[tool.mypy.overrides]]
+module = [
+  "nipype.*",
+  "seaborn",
+  "nilearn.*",
+  "templateflow.*",
+  "bids.*",
+  "svgutils",
+  "svgutils.*",
+  "pylab",
+  "mpl_toolkits.*",
+  "nitransforms.*",
+  "IPython.*",
+]
+ignore_missing_imports = true

From 1a7c206e363b058f49cbf15f6941aa07ca9b40a3 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 19 Dec 2024 09:40:59 -0500
Subject: [PATCH 2/5] typ: Resolve mypy complaint

---
 nireports/interfaces/reporting/registration.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nireports/interfaces/reporting/registration.py b/nireports/interfaces/reporting/registration.py
index 2d0fe983..871250f7 100644
--- a/nireports/interfaces/reporting/registration.py
+++ b/nireports/interfaces/reporting/registration.py
@@ -30,6 +30,7 @@
 from nipype.interfaces import fsl
 from nipype.interfaces.base import (
     File,
+    TraitedSpec,
     isdefined,
     traits,
 )
@@ -131,10 +132,9 @@ class ApplyXFMRPT(FLIRTRPT, fsl.ApplyXFM):
     output_spec = _FLIRTOutputSpecRPT
 
 
+_BBRegisterInputSpec: type[TraitedSpec] = fs.preprocess.BBRegisterInputSpec6
 if LooseVersion("0.0.0") < fs.Info.looseversion() < LooseVersion("6.0.0"):
     _BBRegisterInputSpec = fs.preprocess.BBRegisterInputSpec
-else:
-    _BBRegisterInputSpec = fs.preprocess.BBRegisterInputSpec6
 
 
 class _BBRegisterInputSpecRPT(nrb._SVGReportCapableInputSpec, _BBRegisterInputSpec):

From 23ac12f47cf30157e720a93bd232c31eec9ee4f7 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 19 Dec 2024 09:44:37 -0500
Subject: [PATCH 3/5] chore(tox): Add typecheck environment

---
 tox.ini | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/tox.ini b/tox.ini
index 92f00deb..2cfbeae1 100644
--- a/tox.ini
+++ b/tox.ini
@@ -90,6 +90,15 @@ commands =
   ruff format
   ruff check --select ISC001
 
+[testenv:typecheck]
+description = "Run mypy type checking"
+labels = check
+deps =
+  mypy
+extras = types
+commands =
+  mypy nireports
+
 [testenv:spellcheck]
 description = Check spelling
 labels = check

From 475ee5074b2d80ae40884dc1b5e831f87e7dbd49 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 19 Dec 2024 09:47:51 -0500
Subject: [PATCH 4/5] chore(ci): Run tox checks in CI

---
 .github/workflows/build_test_deploy.yml | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/.github/workflows/build_test_deploy.yml b/.github/workflows/build_test_deploy.yml
index 95cdb726..65ba2f4e 100644
--- a/.github/workflows/build_test_deploy.yml
+++ b/.github/workflows/build_test_deploy.yml
@@ -150,3 +150,28 @@ jobs:
         # Remove once OIDC is set up
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}
+
+  checks:
+    runs-on: 'ubuntu-latest'
+    continue-on-error: true
+    strategy:
+      matrix:
+        check: ['style', '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 3.12
+        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 }}

From cccd528c57c65b135f332e27e916c0f4d344d08f Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 19 Dec 2024 10:46:47 -0500
Subject: [PATCH 5/5] Remove redundant svgutils ignore

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index df238198..c67379a9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -214,7 +214,6 @@ module = [
   "nilearn.*",
   "templateflow.*",
   "bids.*",
-  "svgutils",
   "svgutils.*",
   "pylab",
   "mpl_toolkits.*",