fix: clean up some tests and remove dependency on raises_regexp

Author: satra

nipype/algorithms/tests/test_compcor.py

@@ -83,13 +83,13 @@ def test_compcor_bad_input_shapes(self):
         for data_shape in (shape_less_than, shape_more_than):
             data_file = utils.save_toy_nii(np.zeros(data_shape), 'temp.nii')
             interface = CompCor(realigned_file=data_file, mask_file=self.mask_file)
-            with pytest.raises_regexp(ValueError, "dimensions"): interface.run()
+            with pytest.raises(ValueError, message="Dimension mismatch"): interface.run()
 
     def test_tcompcor_bad_input_dim(self):
         bad_dims = (2, 2, 2)
         data_file = utils.save_toy_nii(np.zeros(bad_dims), 'temp.nii')
         interface = TCompCor(realigned_file=data_file)
-        with pytest.raises_regexp(ValueError, '4-D'): interface.run()
+        with pytest.raises(ValueError, message='Not a 4D file'): interface.run()
 
     def run_cc(self, ccinterface, expected_components, expected_header='CompCor'):
         # run

nipype/algorithms/tests/test_mesh_ops.py

@@ -34,8 +34,6 @@ def test_ident_distances(tmpdir):
 @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed")
 def test_trans_distances(tmpdir):
     tempdir = str(tmpdir)
-    os.chdir(tempdir)
-
     from ...interfaces.vtkbase import tvtk
 
     in_surf = example_data('surf01.vtk')
@@ -57,10 +55,10 @@ def test_trans_distances(tmpdir):
     dist.inputs.surface2 = warped_surf
     dist.inputs.out_file = os.path.join(tempdir, 'distance.npy')
     res = dist.run()
-    npt.assert_almost_equal(res.outputs.distance, np.linalg.norm(inc), 4)
+    assert np.allclose(res.outputs.distance, np.linalg.norm(inc), 4)
     dist.inputs.weighting = 'area'
     res = dist.run()
-    npt.assert_almost_equal(res.outputs.distance, np.linalg.norm(inc), 4)
+    assert np.allclose(res.outputs.distance, np.linalg.norm(inc), 4)
 
 
 @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed")

nipype/interfaces/freesurfer/tests/test_model.py

@@ -3,8 +3,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
 import os
-import tempfile
-import shutil
 import numpy as np
 import nibabel as nib
 
@@ -14,12 +12,11 @@
 
 
 @pytest.mark.skipif(no_freesurfer(), reason="freesurfer is not installed")
-def test_concatenate():
-    tmp_dir = os.path.realpath(tempfile.mkdtemp())
-    cwd = os.getcwd()
-    os.chdir(tmp_dir)
-    in1 = os.path.join(tmp_dir, 'cont1.nii')
-    in2 = os.path.join(tmp_dir, 'cont2.nii')
+def test_concatenate(tmpdir):
+    tempdir = str(tmpdir)
+    os.chdir(tempdir)
+    in1 = os.path.join(tempdir, 'cont1.nii')
+    in2 = os.path.join(tempdir, 'cont2.nii')
     out = 'bar.nii'
 
     data1 = np.zeros((3, 3, 3, 1), dtype=np.float32)
@@ -32,27 +29,27 @@ def test_concatenate():
 
     # Test default behavior
     res = model.Concatenate(in_files=[in1, in2]).run()
-    assert res.outputs.concatenated_file == os.path.join(tmp_dir, 'concat_output.nii.gz')
-    assert nib.load('concat_output.nii.gz').get_data() == out_data
+    assert res.outputs.concatenated_file == os.path.join(tempdir, 'concat_output.nii.gz')
+    assert np.allclose(nib.load('concat_output.nii.gz').get_data(), out_data)
 
     # Test specified concatenated_file
     res = model.Concatenate(in_files=[in1, in2], concatenated_file=out).run()
-    assert res.outputs.concatenated_file == os.path.join(tmp_dir, out)
-    assert nib.load(out).get_data() == out_data
+    assert res.outputs.concatenated_file == os.path.join(tempdir, out)
+    assert np.allclose(nib.load(out).get_data(), out_data)
 
     # Test in workflow
-    wf = pe.Workflow('test_concatenate', base_dir=tmp_dir)
+    wf = pe.Workflow('test_concatenate', base_dir=tempdir)
     concat = pe.Node(model.Concatenate(in_files=[in1, in2],
                                        concatenated_file=out),
                      name='concat')
     wf.add_nodes([concat])
     wf.run()
-    assert nib.load(os.path.join(tmp_dir, 'test_concatenate','concat', out)).get_data()== out_data
+    assert np.allclose(nib.load(os.path.join(tempdir,
+                                             'test_concatenate',
+                                             'concat', out)).get_data(),
+                       out_data)
 
     # Test a simple statistic
     res = model.Concatenate(in_files=[in1, in2], concatenated_file=out,
                             stats='mean').run()
-    assert nib.load(out).get_data() == mean_data
-
-    os.chdir(cwd)
-    shutil.rmtree(tmp_dir)
+    assert np.allclose(nib.load(out).get_data(), mean_data)

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -169,10 +169,9 @@ def test_fast_list_outputs(setup_infile):
     def _run_and_test(opts, output_base):
         outputs = fsl.FAST(**opts)._list_outputs()
         for output in outputs.values():
-            filenames = filename_to_list(output)
-            if filenames is not None:
-                for filename in filenames:
-                    assert filename[:len(output_base)] == output_base
+            if output:
+                for filename in filename_to_list(output):
+                    assert os.path.realpath(filename).startswith(os.path.realpath(output_base))
 
     # set up
     tmp_infile, indir = setup_infile