From 2ecccbabb9b7e43be895a093f45884b88281052c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 3 Oct 2024 10:00:42 -0400
Subject: [PATCH 1/2] TEST: Clear registry before and after every doctest

---
 sdcflows/conftest.py | 34 ++++++++++++++++++++++------------
 1 file changed, 22 insertions(+), 12 deletions(-)

diff --git a/sdcflows/conftest.py b/sdcflows/conftest.py
index c0d03c1535..e8f2e709be 100644
--- a/sdcflows/conftest.py
+++ b/sdcflows/conftest.py
@@ -27,6 +27,7 @@
 import nibabel
 import pytest
 from bids.layout import BIDSLayout
+from .fieldmaps import clear_registry
 
 # disable ET
 os.environ['NO_ET'] = '1'
@@ -59,18 +60,27 @@ def pytest_report_header(config):
 
 
 @pytest.fixture(autouse=True)
-def add_np(doctest_namespace):
-    doctest_namespace["np"] = numpy
-    doctest_namespace["nb"] = nibabel
-    doctest_namespace["os"] = os
-    doctest_namespace["Path"] = Path
-    doctest_namespace["layouts"] = layouts
-    for key, val in list(layouts.items()):
-        doctest_namespace[key] = Path(val.root)
-
-    doctest_namespace["dsA_dir"] = data_dir / "dsA"
-    doctest_namespace["dsB_dir"] = data_dir / "dsB"
-    doctest_namespace["dsC_dir"] = data_dir / "dsC"
+def doctest_fixture(doctest_namespace, request):
+    doctest_plugin = request.config.pluginmanager.getplugin("doctest")
+    if isinstance(request.node, doctest_plugin.DoctestItem):
+        doctest_namespace.update(
+            np=numpy,
+            nb=nibabel,
+            os=os,
+            Path=Path,
+            layouts=layouts,
+            dsA_dir=data_dir / "dsA",
+            dsB_dir=data_dir / "dsB",
+            dsC_dir=data_dir / "dsC",
+        )
+        doctest_namespace.update((key, Path(val.root)) for key, val in layouts.items())
+
+        # Start every doctest clean, and clean up after ourselves
+        clear_registry()
+        yield
+        clear_registry()
+    else:
+        yield
 
 
 @pytest.fixture

From aee2c921efe6a863dd8cd12b19d9644c77aaa7af Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 3 Oct 2024 10:01:13 -0400
Subject: [PATCH 2/2] TEST: Remove redundant raises check, autoclear registry

---
 sdcflows/tests/test_fieldmaps.py | 30 +++++++++++-------------------
 1 file changed, 11 insertions(+), 19 deletions(-)

diff --git a/sdcflows/tests/test_fieldmaps.py b/sdcflows/tests/test_fieldmaps.py
index e4f0db155f..1cd1073219 100644
--- a/sdcflows/tests/test_fieldmaps.py
+++ b/sdcflows/tests/test_fieldmaps.py
@@ -28,6 +28,13 @@
 from .. import fieldmaps as fm
 
 
+@pytest.fixture(autouse=True)
+def clear_registry():
+    fm.clear_registry()
+    yield
+    fm.clear_registry()
+
+
 def test_FieldmapFile(dsA_dir):
     """Test one existing file."""
     f1 = fm.FieldmapFile(dsA_dir / "sub-01" / "anat" / "sub-01_T1w.nii.gz")
@@ -45,13 +52,12 @@ def test_FieldmapFile(dsA_dir):
 
 
 @pytest.mark.parametrize(
-    "inputfiles,method,nsources,raises",
+    "inputfiles,method,nsources",
     [
         (
             ("fmap/sub-01_fieldmap.nii.gz", "fmap/sub-01_magnitude.nii.gz"),
             fm.EstimatorType.MAPPED,
             2,
-            False,
         ),
         (
             (
@@ -62,51 +68,37 @@ def test_FieldmapFile(dsA_dir):
             ),
             fm.EstimatorType.PHASEDIFF,
             4,
-            False,
         ),
         (
             ("fmap/sub-01_phase1.nii.gz", "fmap/sub-01_phase2.nii.gz"),
             fm.EstimatorType.PHASEDIFF,
             4,
-            True,
         ),
-        (("fmap/sub-01_phase2.nii.gz",), fm.EstimatorType.PHASEDIFF, 4, True),
-        (("fmap/sub-01_phase1.nii.gz",), fm.EstimatorType.PHASEDIFF, 4, True),
+        (("fmap/sub-01_phase2.nii.gz",), fm.EstimatorType.PHASEDIFF, 4),
+        (("fmap/sub-01_phase1.nii.gz",), fm.EstimatorType.PHASEDIFF, 4),
         (
             ("fmap/sub-01_dir-LR_epi.nii.gz", "fmap/sub-01_dir-RL_epi.nii.gz"),
             fm.EstimatorType.PEPOLAR,
             2,
-            False,
         ),
         (
             ("fmap/sub-01_dir-LR_epi.nii.gz", "dwi/sub-01_dir-RL_sbref.nii.gz"),
             fm.EstimatorType.PEPOLAR,
             2,
-            False,
         ),
         (
             ("anat/sub-01_T1w.nii.gz", "dwi/sub-01_dir-RL_sbref.nii.gz"),
             fm.EstimatorType.ANAT,
             2,
-            False,
         ),
     ],
 )
-def test_FieldmapEstimation(dsA_dir, inputfiles, method, nsources, raises):
+def test_FieldmapEstimation(dsA_dir, inputfiles, method, nsources):
     """Test errors."""
     sub_dir = dsA_dir / "sub-01"
 
     sources = [sub_dir / f for f in inputfiles]
 
-    if raises is True:
-        # Ensure that _estimators is still holding values from previous
-        # parameter set of this parametrized execution.
-        with pytest.raises(ValueError):
-            fm.FieldmapEstimation(sources)
-
-        # Clean up so this parameter set can be tested.
-        fm.clear_registry()
-
     fe = fm.FieldmapEstimation(sources)
     assert fe.method == method
     assert len(fe.sources) == nsources