changed from numpy raises to pytest.raises and skipif

Author: orduek

nibabel/freesurfer/tests/test_io.py

@@ -12,15 +12,15 @@
 
 import pytest
 import numpy as np
-from numpy.testing import assert_equal, assert_raises, dec, assert_allclose, assert_array_equal
+from numpy.testing import assert_allclose, assert_array_equal
 
 from .. import (read_geometry, read_morph_data, read_annot, read_label,
                 write_geometry, write_morph_data, write_annot)
 from ..io import _pack_rgb
 
 from ...tests.nibabel_data import get_nibabel_data, needs_nibabel_data
 from ...fileslice import strided_scalar
-from ...testing import clear_and_catch_warnings
+from ...testing_pytest import clear_and_catch_warnings
 
 DATA_SDIR = 'fsaverage'
 
@@ -36,10 +36,7 @@
         data_path = pjoin(nib_data, 'nitest-freesurfer', DATA_SDIR)
         have_freesurfer = isdir(data_path)
 
-freesurfer_test = dec.skipif(
-    not have_freesurfer,
-    'cannot find freesurfer {0} directory'.format(DATA_SDIR))
-
+freesurfer_test = pytest.mark.skipif(not have_freesurfer, reason='cannot find freesurfer {0} directory'.format(DATA_SDIR))
 
 def _hash_file_content(fname):
     hasher = hashlib.md5()
@@ -54,19 +51,18 @@ def test_geometry():
     """Test IO of .surf"""
     surf_path = pjoin(data_path, "surf", "%s.%s" % ("lh", "inflated"))
     coords, faces = read_geometry(surf_path)
-    assert_equal(0, faces.min())
-    assert_equal(coords.shape[0], faces.max() + 1)
+    assert 0==faces.min()
+    assert coords.shape[0]== faces.max() + 1
 
     surf_path = pjoin(data_path, "surf", "%s.%s" % ("lh", "sphere"))
     coords, faces, volume_info, create_stamp = read_geometry(
         surf_path, read_metadata=True, read_stamp=True)
 
-    assert_equal(0, faces.min())
-    assert_equal(coords.shape[0], faces.max() + 1)
-    assert_equal(9, len(volume_info))
-    assert_equal([2, 0, 20], volume_info['head'])
-    assert_equal(u'created by greve on Thu Jun  8 19:17:51 2006',
-                 create_stamp)
+    assert 0 == faces.min()
+    assert coords.shape[0] == faces.max() + 1
+    assert 9 == len(volume_info)
+    assert [2, 0, 20] == volume_info['head']
+    assert 'created by greve on Thu Jun  8 19:17:51 2006' == create_stamp
 
     # Test equivalence of freesurfer- and nibabel-generated triangular files
     # with respect to read_geometry()
@@ -83,7 +79,7 @@ def test_geometry():
         for key in ('xras', 'yras', 'zras', 'cras'):
             assert_allclose(volume_info2[key], volume_info[key],
                             rtol=1e-7, atol=1e-30)
-        assert_equal(volume_info2['cras'], volume_info['cras'])
+        assert volume_info2['cras'] == volume_info['cras']
         with open(surf_path, 'rb') as fobj:
             np.fromfile(fobj, ">u1", 3)
             read_create_stamp = fobj.readline().decode().rstrip('\n')
@@ -101,10 +97,11 @@ def test_geometry():
             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
-        assert_raises(ValueError, write_geometry, surf_path, coords,
-                      faces, create_stamp, volume_info)
+        with pytest.raises(ValueError):
+            write_geometry(surf_path, coords, faces, create_stamp, volume_info)
+        
 
-    assert_equal(create_stamp, read_create_stamp)
+    assert create_stamp == read_create_stamp
 
     np.testing.assert_array_equal(coords, coords2)
     np.testing.assert_array_equal(faces, faces2)
@@ -123,14 +120,14 @@ def test_quad_geometry():
     new_quad = pjoin(get_nibabel_data(), 'nitest-freesurfer', 'subjects',
                      'bert', 'surf', 'lh.inflated.nofix')
     coords, faces = read_geometry(new_quad)
-    assert_equal(0, faces.min())
-    assert_equal(coords.shape[0], faces.max() + 1)
+    assert 0 == faces.min()
+    assert coords.shape[0] == faces.max() + 1
     with InTemporaryDirectory():
         new_path = 'test'
         write_geometry(new_path, coords, faces)
         coords2, faces2 = read_geometry(new_path)
-        assert_equal(coords, coords2)
-        assert_equal(faces, faces2)
+        assert coords == coords2
+        assert faces == faces2
 
 
 @freesurfer_test
@@ -144,7 +141,7 @@ def test_morph_data():
         new_path = 'test'
         write_morph_data(new_path, curv)
         curv2 = read_morph_data(new_path)
-        assert_equal(curv2, curv)
+        assert curv2 == curv
 
 
 def test_write_morph_data():
@@ -157,17 +154,17 @@ def test_write_morph_data():
         for shape in okay_shapes:
             write_morph_data('test.curv', values.reshape(shape))
             # Check ordering is preserved, regardless of shape
-            assert_equal(values, read_morph_data('test.curv'))
-        assert_raises(ValueError, write_morph_data, 'test.curv',
-                      np.zeros(shape), big_num)
-        # Windows 32-bit overflows Python int
+            assert values == read_morph_data('test.curv')
+        with pytest.raises(ValueError):
+            write_morph_data('test.curv', np.zeros(shape), big_num)
+                # Windows 32-bit overflows Python int
         if np.dtype(np.int) != np.dtype(np.int32):
-            assert_raises(ValueError, write_morph_data, 'test.curv',
-                          strided_scalar((big_num,)))
+            with pytest.raises(ValueError):
+                write_morph_data('test.curv',  strided_scalar((big_num,)))
         for shape in bad_shapes:
-            assert_raises(ValueError, write_morph_data, 'test.curv',
-                          values.reshape(shape))
-
+            with pytest.raises(ValueError):
+                write_morph_data('test.curv', values.reshape(shape))
+            
 
 @freesurfer_test
 def test_annot():
@@ -208,7 +205,7 @@ def test_annot():
         if labels_orig is not None:
             np.testing.assert_array_equal(labels_orig, labels_orig_2)
         np.testing.assert_array_equal(ctab, ctab2)
-        assert_equal(names, names2)
+        assert names == names2
 
 
 def test_read_write_annot():
@@ -374,4 +371,4 @@ def test_write_annot_maxstruct():
         # Check round-trip
         assert_array_equal(labels, rt_labels)
         assert_array_equal(rgba, rt_ctab[:, :4])
-        assert_equal(names, [n.decode('ascii') for n in rt_names])
+        assert names == [n.decode('ascii') for n in rt_names]