Merge pull request #1171 from satra/fix/setup

fix: cleaned up setup and several tests

Author: satra

MANIFEST.in

@@ -10,5 +10,4 @@ include doc/documentation.zip
 include nipype/COMMIT_INFO.txt
 
 recursive-include doc *
-recursive-include matlabscripts *
 recursive-include tools *

nipype/algorithms/setup.py

@@ -0,0 +1,2 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:

nipype/algorithms/tests/__init__.py

@@ -6,12 +6,10 @@
 from shutil import rmtree
 from tempfile import mkdtemp
 
-from nipype.testing import (assert_equal, assert_raises, skipif,
+from nipype.testing import (assert_equal, skipif,
                             assert_almost_equal, example_data)
 
 import numpy as np
-import nibabel as nb
-import nipype.testing as nit
 
 from nipype.algorithms import mesh as m
 

nipype/algorithms/tests/test_mesh_ops.py

@@ -7,11 +7,9 @@
 from shutil import rmtree
 from tempfile import mkdtemp
 
-from nipype.testing import (assert_equal, assert_raises,
-                            assert_almost_equal, example_data)
+from nipype.testing import (example_data)
 
 import numpy as np
-import nibabel as nb
 
 
 def test_overlap():
@@ -25,6 +23,7 @@ def check_close(val1, val2):
     in1 = example_data('segmentation0.nii.gz')
     in2 = example_data('segmentation1.nii.gz')
 
+    cwd = os.getcwd()
     os.chdir(tempdir)
     overlap = Overlap()
     overlap.inputs.volume1 = in1
@@ -48,4 +47,5 @@ def check_close(val1, val2):
     yield (check_close, res.outputs.roi_voldiff,
            np.array([0.0063086, -0.0025506, 0.0]))
 
+    os.chdir(cwd)
     rmtree(tempdir)

nipype/algorithms/tests/test_overlap.py

@@ -1,11 +1,12 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-from nipype.testing import (assert_equal, assert_false, assert_true,
-                            assert_almost_equal)
-import nipype.algorithms.rapidart as ra
-from nipype.interfaces.base import Bunch
 import numpy as np
 
+from ...testing import (assert_equal, assert_false, assert_true,
+                        assert_almost_equal)
+from .. import rapidart as ra
+from ...interfaces.base import Bunch
+
 
 def test_ad_init():
     ad = ra.ArtifactDetect(use_differences=[True, False])

nipype/algorithms/tests/test_rapidart.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import os
 from shutil import rmtree
 from tempfile import mkdtemp
 from nipype.testing import (assert_equal, example_data)
@@ -11,6 +10,9 @@ def test_split_and_merge():
     import numpy as np
     import nibabel as nb
     import os.path as op
+    import os
+    cwd = os.getcwd()
+
     from nipype.algorithms.misc import split_rois, merge_rois
     tmpdir = mkdtemp()
 
@@ -21,7 +23,6 @@ def test_split_and_merge():
 
     dwshape = (mskdata.shape[0], mskdata.shape[1], mskdata.shape[2], 6)
     dwdata = np.random.normal(size=dwshape)
-
     os.chdir(tmpdir)
     nb.Nifti1Image(dwdata.astype(np.float32),
                    aff, None).to_filename(dwfile)
@@ -30,8 +31,8 @@ def test_split_and_merge():
     merged = merge_rois(resdw, resid, in_mask)
     dwmerged = nb.load(merged).get_data()
 
-    dwmasked = np.zeros_like(dwdata)
     dwmasked = dwdata * mskdata[:, :, :, np.newaxis]
+    os.chdir(cwd)
     rmtree(tmpdir)
 
     yield assert_equal, np.allclose(dwmasked, dwmerged), True

nipype/algorithms/tests/test_splitmerge.py

@@ -6,10 +6,10 @@
 
 from nose.tools import assert_equal
 
-from nipype.caching import Memory
-from nipype.pipeline.tests.test_engine import TestInterface
-from nipype.utils.config import NipypeConfig
-config = NipypeConfig()
+from .. import Memory
+from ...pipeline.tests.test_engine import TestInterface
+
+from ... import config
 config.set_default_config()
 
 nb_runs = 0