From 84a6956f6dd23c93a613aeb3d02f6de5461ccdc4 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 10 Mar 2026 15:52:44 -0400
Subject: [PATCH 1/3] chore(ci): Add `python -m pytest` test

---
 .github/workflows/test.yml | 24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 774c509e0..b3a86a5ea 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -105,7 +105,7 @@ jobs:
       - name: Run tests
         run: pytest --doctest-modules --doctest-plus -v --pyargs nibabel -n auto
 
-  test:
+  tox:
     # Check each OS, all supported Python, minimum versions and latest releases
     runs-on: ${{ matrix.os }}
     strategy:
@@ -227,6 +227,26 @@ jobs:
           path: test-results.xml
         if: ${{ always() }}
 
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.14']
+    steps:
+      - name: Shallow checkout
+        uses: actions/checkout@v6
+      - name: Setup uv and Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: true
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install with pytest
+        run: uv sync --extra=test --extra=all
+      - name: Run test suite
+        run: python -m pytest
+
   checks:
     runs-on: 'ubuntu-slim'
     continue-on-error: true
@@ -255,7 +275,7 @@ jobs:
   publish:
     runs-on: ubuntu-slim
     environment: "Package deployment"
-    needs: [test, test-package]
+    needs: [tox, pytest, test-package]
     permissions:
       # Required for trusted publishing
       id-token: write

From 719b5f9ec2ae4b8b67be91df80f64428a614009e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 10 Mar 2026 15:54:23 -0400
Subject: [PATCH 2/3] fix: Ignore executable name in checking for usage output

---
 nibabel/cmdline/tests/test_roi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nibabel/cmdline/tests/test_roi.py b/nibabel/cmdline/tests/test_roi.py
index bc8d11d62..0b8caa96a 100644
--- a/nibabel/cmdline/tests/test_roi.py
+++ b/nibabel/cmdline/tests/test_roi.py
@@ -147,7 +147,7 @@ def test_entrypoint(capsys):
         with pytest.raises(SystemExit):
             main()
     captured = capsys.readouterr()
-    assert captured.out.startswith('usage: nib-roi')
+    assert captured.out.startswith('usage: ')
 
 
 def test_nib_roi_unknown_axes(capsys):

From d8653ec9ec1c6dc5c9241ae016b586815add96ac Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Tue, 10 Mar 2026 16:04:33 -0400
Subject: [PATCH 3/3] test: Skip removalschedule tests on shallow checkouts

---
 nibabel/tests/test_removalschedule.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/nibabel/tests/test_removalschedule.py b/nibabel/tests/test_removalschedule.py
index d2bc7da2f..f08d3b65b 100644
--- a/nibabel/tests/test_removalschedule.py
+++ b/nibabel/tests/test_removalschedule.py
@@ -173,3 +173,7 @@ def test_unremoved_object():
 def test_unremoved_attr():
     with pytest.raises(AssertionError):
         test_attribute_removal()
+
+
+if cmp_pkg_version('1.0.0') > -1:
+    pytest.skip('Shallow checkout, version unavailable', allow_module_level=True)