MNT: Execute slowest tests on schedule

Execute slowest tests on schedule.

Co-authored-by: Chris Markiewicz <[email protected]>

Author: jhlegarreta

.github/workflows/tox.yml

@@ -62,6 +62,7 @@ jobs:
           datalad get -J 2 -d $TEST_DATA_HOME
 
   test:
+    if: github.event_name != 'schedule'
     runs-on: ubuntu-latest
     needs: [cache-test-data]
     strategy:
@@ -110,6 +111,53 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
 
+
+  slow-tests:
+    if: github.event_name == 'schedule'
+    runs-on: ubuntu-latest
+    needs: [cache-test-data]
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        dependencies: [latest, pre]
+        include:
+          - python-version: "3.9"
+            dependencies: min
+        exclude:
+          # Do not test pre-releases for versions out of SPEC0
+          - python-version: "3.9"
+            dependencies: pre
+          - python-version: "3.10"
+            dependencies: pre
+
+    env:
+      DEPENDS: ${{ matrix.dependencies }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - uses: actions/cache/restore@v4
+        with:
+          path: ${{ env.TEST_DATA_HOME }}
+          key: data-cache-v2-${{ needs.cache-test-data.outputs.SHA }}
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install tox
+        run: |
+          uv tool install tox --with=tox-uv --with=tox-gh-actions
+      - name: Show tox config
+        run: tox c
+      - name: Run tox
+        run: tox -v -e slow-tests --exit-and-dump-after 1200
+
   checks:
     runs-on: 'ubuntu-latest'
     continue-on-error: true

nitransforms/tests/test_resampling.py

@@ -286,6 +286,7 @@ def test_displacements_field2(tmp_path, testdata_path, sw_tool):
     assert np.sqrt((diff**2).mean()) < RMSE_TOL_LINEAR
 
 
+@pytest.mark.slow
 def test_apply_transformchain(tmp_path, testdata_path):
     """Check a translation-only field on one or more axes, different image orientations."""
     os.chdir(str(tmp_path))

nitransforms/tests/test_surface.py

@@ -138,6 +138,7 @@ def test_SurfaceCoordinateTransformIO(testdata_path, tmpdir):
     assert sct == sct2
 
 
+@pytest.mark.slow
 def test_ProjectUnproject(testdata_path):
     sphere_reg_path = (
         testdata_path
@@ -165,6 +166,7 @@ def test_ProjectUnproject(testdata_path):
     assert np.all(transformed._triangles == projunproj_ref.agg_data()[1])
 
 
+@pytest.mark.slow
 def test_SurfaceResampler(testdata_path, tmpdir):
     dif_tol = 0.001
     fslr_sphere_path = testdata_path / "tpl-fsLR_hemi-R_den-32k_sphere.surf.gii"

pyproject.toml

@@ -83,6 +83,9 @@ doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
 filterwarnings = ["ignore::DeprecationWarning"]
 junit_family = "xunit2"
+ markers = [
+   "slow: marks tests as slow (deselect with '-m \"not slow\"')"
+]
 
 [tool.coverage.run]
 branch = true

tox.ini

@@ -51,7 +51,39 @@ uv_resolution =
 
 commands =
   python -c "import nitransforms; print(nitransforms.__version__)"
-  pytest --durations=20 --durations-min=1.0 --cov-report term-missing {posargs:-n auto}
+  pytest --durations=20 --durations-min=1.0 --cov-report term-missing {posargs:-n auto -m "not slow"}
+
+[testenv:slow-tests]
+description = Pytest with coverage
+labels = test
+pip_pre =
+  pre: true
+pass_env =
+  # Overrides default location for finding test data
+  TEST_DATA_HOME
+  # getpass.getuser() sources for Windows:
+  LOGNAME
+  USER
+  LNAME
+  USERNAME
+  # Pass user color preferences through
+  PY_COLORS
+  FORCE_COLOR
+  NO_COLOR
+  CLICOLOR
+  CLICOLOR_FORCE
+  PYTHON_GIL
+extras = tests
+setenv =
+  FSLOUTPUTTYPE=NIFTI_GZ
+  pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  pre: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+uv_resolution =
+  min: lowest-direct
+
+commands =
+  python -c "import nitransforms; print(nitransforms.__version__)"
+  pytest --durations=20 --durations-min=1.0 --cov-report term-missing {posargs:-n auto -m slow}
 
 [testenv:style]
 description = Check our style guide