TEST: Suppress warnings in freesurfer

Author: effigies

nibabel/freesurfer/tests/test_io.py

@@ -86,14 +86,14 @@ def test_geometry():
 
         # now write an incomplete file
         write_geometry(surf_path, coords, faces)
-        with clear_and_catch_warnings() as w:
+        with pytest.warns(Warning) as w:
             warnings.filterwarnings('always', category=DeprecationWarning)
             read_geometry(surf_path, read_metadata=True)
 
         assert any('volume information contained' in str(ww.message) for ww in w)
         assert any('extension code' in str(ww.message) for ww in w)
         volume_info['head'] = [1, 2]
-        with clear_and_catch_warnings() as w:
+        with pytest.warns(Warning) as w:
             write_geometry(surf_path, coords, faces, create_stamp, volume_info)
         assert any('Unknown extension' in str(ww.message) for ww in w)
         volume_info['a'] = 0
@@ -266,7 +266,7 @@ def test_write_annot_fill_ctab():
         # values back.
         badannot = (10 * np.arange(nlabels, dtype=np.int32)).reshape(-1, 1)
         rgbal = np.hstack((rgba, badannot))
-        with clear_and_catch_warnings() as w:
+        with pytest.warns(Warning) as w:
             write_annot(annot_path, labels, rgbal, names, fill_ctab=False)
         assert any(f'Annotation values in {annot_path} will be incorrect' == str(ww.message)
                    for ww in w)

nibabel/freesurfer/tests/test_mghformat.py

@@ -345,11 +345,14 @@ def test_deprecated_fields():
 
     # mrparams is the only deprecated field at the moment
     # Accessing hdr_data is equivalent to accessing hdr, so double all checks
-    assert_array_equal(hdr['mrparams'], 0)
+    with pytest.deprecated_call():
+        assert_array_equal(hdr['mrparams'], 0)
     assert_array_equal(hdr_data['mrparams'], 0)
 
-    hdr['mrparams'] = [1, 2, 3, 4]
-    assert_array_almost_equal(hdr['mrparams'], [1, 2, 3, 4])
+    with pytest.deprecated_call():
+        hdr['mrparams'] = [1, 2, 3, 4]
+    with pytest.deprecated_call():
+        assert_array_almost_equal(hdr['mrparams'], [1, 2, 3, 4])
     assert hdr['tr'] == 1
     assert hdr['flip_angle'] == 2
     assert hdr['te'] == 3
@@ -366,14 +369,16 @@ def test_deprecated_fields():
     hdr['flip_angle'] = 6
     hdr['te'] = 7
     hdr['ti'] = 8
-    assert_array_almost_equal(hdr['mrparams'], [5, 6, 7, 8])
+    with pytest.deprecated_call():
+        assert_array_almost_equal(hdr['mrparams'], [5, 6, 7, 8])
     assert_array_almost_equal(hdr_data['mrparams'], [5, 6, 7, 8])
 
     hdr_data['tr'] = 9
     hdr_data['flip_angle'] = 10
     hdr_data['te'] = 11
     hdr_data['ti'] = 12
-    assert_array_almost_equal(hdr['mrparams'], [9, 10, 11, 12])
+    with pytest.deprecated_call():
+        assert_array_almost_equal(hdr['mrparams'], [9, 10, 11, 12])
     assert_array_almost_equal(hdr_data['mrparams'], [9, 10, 11, 12])