From 9596bdc813046effde2f38f78a52d48f2fe9923e Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 21:10:32 -0400
Subject: [PATCH] TEST: Mark slow tests and run in their own jobs

---
 .github/workflows/unittests.yml              | 10 +++++++++-
 sdcflows/workflows/fit/tests/test_pepolar.py |  1 +
 sdcflows/workflows/fit/tests/test_phdiff.py  |  1 +
 sdcflows/workflows/fit/tests/test_syn.py     |  1 +
 sdcflows/workflows/tests/test_ancillary.py   |  1 +
 sdcflows/workflows/tests/test_base.py        |  1 +
 6 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 89ce32bde5..be3f82f4e4 100644
--- a/.github/workflows/unittests.yml
+++ b/.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:
diff --git a/sdcflows/workflows/fit/tests/test_pepolar.py b/sdcflows/workflows/fit/tests/test_pepolar.py
index f7dc970d5b..e95128d153 100644
--- a/sdcflows/workflows/fit/tests/test_pepolar.py
+++ b/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."""
diff --git a/sdcflows/workflows/fit/tests/test_phdiff.py b/sdcflows/workflows/fit/tests/test_phdiff.py
index ef278fbe8b..94932f6243 100644
--- a/sdcflows/workflows/fit/tests/test_phdiff.py
+++ b/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",
     [
diff --git a/sdcflows/workflows/fit/tests/test_syn.py b/sdcflows/workflows/fit/tests/test_syn.py
index 065a594265..905c1d808b 100644
--- a/sdcflows/workflows/fit/tests/test_syn.py
+++ b/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"
diff --git a/sdcflows/workflows/tests/test_ancillary.py b/sdcflows/workflows/tests/test_ancillary.py
index 50f01c87bc..7e407d86e3 100644
--- a/sdcflows/workflows/tests/test_ancillary.py
+++ b/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."""
diff --git a/sdcflows/workflows/tests/test_base.py b/sdcflows/workflows/tests/test_base.py
index 39f37348f2..8b74ac9ddf 100644
--- a/sdcflows/workflows/tests/test_base.py
+++ b/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")]
 )