TEST: Mark slow tests and run in their own jobs

Author: effigies

.github/workflows/unittests.yml

@@ -34,6 +34,12 @@ jobs:
       max-parallel: 5
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
+        marks: ["not slow"]
+        include:
+          - python-version: "3.9"
+            marks: "slow"
+          - python-version: "3.12"
+            marks: "slow"
 
     steps:
     - uses: actions/cache@v4
@@ -176,7 +182,9 @@ jobs:
         export PATH=${AFNI_HOME}:$PATH
         export FSLDIR=${CONDA_PREFIX}
         pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows \
-          --durations=20 --durations-min=10
+          --durations=20 --durations-min=10 -m "$MARKS"
+      env:
+        MARKS: ${{ matrix.marks }}
 
     - uses: codecov/codecov-action@v4
       with:

pyproject.toml

@@ -165,6 +165,9 @@ 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]

sdcflows/workflows/fit/tests/test_pepolar.py

@@ -27,6 +27,7 @@
 from ..pepolar import init_topup_wf
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize("ds", ("ds001771", "HCP101006"))
 def test_topup_wf(tmpdir, bids_layouts, workdir, outdir, ds):
     """Test preparation workflow."""

sdcflows/workflows/fit/tests/test_phdiff.py

@@ -29,6 +29,7 @@
 from ..fieldmap import init_fmap_wf, Workflow
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize(
     "fmap_file",
     [

sdcflows/workflows/fit/tests/test_syn.py

@@ -28,6 +28,7 @@
 from ..syn import init_syn_sdc_wf, init_syn_preprocessing_wf, _adjust_zooms, _set_dtype
 
 
+@pytest.mark.slow
 def test_syn_wf(tmpdir, datadir, workdir, outdir, sloppy_mode):
     """Build and run an SDC-SyN workflow."""
     derivs_path = datadir / "ds000054" / "derivatives"

sdcflows/workflows/tests/test_ancillary.py

@@ -28,6 +28,7 @@
 from ..ancillary import init_brainextraction_wf
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize("folder", ["magnitude/ds000054", "magnitude/ds000217"])
 def test_brainmasker(tmpdir, datadir, workdir, outdir, folder):
     """Exercise the brain masking tool."""

sdcflows/workflows/tests/test_base.py

@@ -28,6 +28,7 @@
 from sdcflows.workflows.base import init_fmap_preproc_wf
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize(
     "dataset,subject", [("ds000054", "100185"), ("HCP101006", "101006")]
 )