Merge pull request #1 from nipy/master

update to nipy/nipype master

Author: William Triplett

.coveragerc

@@ -4,6 +4,5 @@ source = nipype
 include = */nipype/*
 omit =
     */nipype/external/*
-    */nipype/workflows/*
     */nipype/fixes/*
     */setup.py

.travis.yml

@@ -36,15 +36,10 @@ install:
   conda install -y nipype &&
   rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* &&
   pip install -r requirements.txt &&
-  pip install -e .[$NIPYPE_EXTRAS] &&
-  export COVERAGE_PROCESS_START=$(pwd)/.coveragerc &&
-  export COVERAGE_DATA_FILE=$(pwd)/.coverage &&
-  echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START}; }
+  pip install -e .[$NIPYPE_EXTRAS]; }
 - travis_retry inst
 script:
-- py.test --doctest-modules --cov=nipype nipype
-after_success:
-- bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
+- py.test --doctest-modules nipype
 deploy:
   provider: pypi
   user: satra

circle.yml

@@ -49,8 +49,7 @@ test:
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
         timeout: 1600
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
-    # Disabled until https://github.com/nipy/nipype/issues/1692 is resolved
-    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
     - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
     - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
 

doc/users/config_file.rst

@@ -134,7 +134,7 @@ Execution
 *poll_sleep_duration*
     This controls how long the job submission loop will sleep between submitting
     all pending jobs and checking for job completion. To be nice to cluster
-    schedulers the default is set to 60 seconds.
+    schedulers the default is set to 2 seconds.
 
 *xvfb_max_wait*
     Maximum time (in seconds) to wait for Xvfb to start, if the _redirect_x parameter of an Interface is True.

nipype/__init__.py

@@ -11,9 +11,9 @@
                    STATUS as __status__,
                    __version__)
 from .utils.config import NipypeConfig
-from .fixes.numpy.testing import nosetester
 from .utils.logger import Logging
 from .refs import due
+from .pkg_info import get_pkg_info as _get_pkg_info
 
 try:
     import faulthandler
@@ -25,48 +25,26 @@
 logging = Logging(config)
 
 
-class _NoseTester(nosetester.NoseTester):
-    """ Subclass numpy's NoseTester to add doctests by default
-    """
-
-    def _get_custom_doctester(self):
-        return None
-
-    def test(self, label='fast', verbose=1, extra_argv=['--exe'],
-             doctests=True, coverage=False):
-        """Run the full test suite
+class NipypeTester(object):
+    def __call__(self, doctests=True):
+        try:
+            import pytest
+        except:
+            raise RuntimeError('py.test not installed, run: pip install pytest')
+        params = {'args': []}
+        if doctests:
+            params['args'].append('--doctest-modules')
+        nipype_path = os.path.dirname(__file__)
+        params['args'].extend(['-x', '--ignore={}/external'.format(nipype_path),
+                               nipype_path])
+        pytest.main(**params)
 
-        Examples
-        --------
-        This will run the test suite and stop at the first failing
-        example
-        >>> from nipype import test
-        >>> test(extra_argv=['--exe', '-sx'])  # doctest: +SKIP
-        """
-        return super(_NoseTester, self).test(label=label,
-                                             verbose=verbose,
-                                             extra_argv=extra_argv,
-                                             doctests=doctests,
-                                             coverage=coverage)
-
-try:
-    test = _NoseTester(raise_warnings="release").test
-except TypeError:
-    # Older versions of numpy do not have a raise_warnings argument
-    test = _NoseTester().test
-del nosetester
+test = NipypeTester()
 
-# Set up package information function
-from .pkg_info import get_pkg_info as _get_pkg_info
-get_info = lambda: _get_pkg_info(os.path.dirname(__file__))
-
-# If this file is exec after being imported, the following lines will
-# fail
-try:
-    del Tester
-except:
-    pass
 
+def get_info():
+    """Returns package information"""
+    return _get_pkg_info(os.path.dirname(__file__))
 
 from .pipeline import Node, MapNode, JoinNode, Workflow
 from .interfaces import (DataGrabber, DataSink, SelectFiles,

nipype/algorithms/confounds.py

@@ -668,7 +668,7 @@ def compute_dvars(in_file, in_mask, remove_zerovariance=False):
         warnings.filterwarnings('error')
 
         # voxelwise standardization
-        diff_vx_stdz = func_diff / np.array([diff_sdhat] * func_diff.shape[-1]).T            
+        diff_vx_stdz = func_diff / np.array([diff_sdhat] * func_diff.shape[-1]).T
         dvars_vx_stdz = diff_vx_stdz.std(axis=0, ddof=1)
 
     return (dvars_stdz, dvars_nstd, dvars_vx_stdz)

nipype/algorithms/tests/test_auto_ACompCor.py

@@ -0,0 +1,36 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..confounds import ACompCor
+
+
+def test_ACompCor_inputs():
+    input_map = dict(components_file=dict(usedefault=True,
+    ),
+    header=dict(),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    mask_file=dict(),
+    num_components=dict(usedefault=True,
+    ),
+    realigned_file=dict(mandatory=True,
+    ),
+    regress_poly_degree=dict(usedefault=True,
+    ),
+    use_regress_poly=dict(usedefault=True,
+    ),
+    )
+    inputs = ACompCor.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_ACompCor_outputs():
+    output_map = dict(components_file=dict(),
+    )
+    outputs = ACompCor.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/algorithms/tests/test_auto_TCompCor.py

@@ -29,8 +29,22 @@ def test_TCompCor_inputs():
 
 
 def test_TCompCor_outputs():
-    output_map = dict(components_file=dict(),
-                      high_variance_mask=dict()
+    output_map = dict(components_file=dict(usedefault=True,
+    ),
+    header=dict(),
+    high_variance_mask=dict(),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    mask_file=dict(),
+    num_components=dict(usedefault=True,
+    ),
+    realigned_file=dict(mandatory=True,
+    ),
+    regress_poly_degree=dict(usedefault=True,
+    ),
+    use_regress_poly=dict(usedefault=True,
+    ),
     )
     outputs = TCompCor.output_spec()
 

nipype/algorithms/tests/test_compcor.py

@@ -16,7 +16,7 @@ class TestCompCor():
     filenames = {'functionalnii': 'compcorfunc.nii',
                  'masknii': 'compcormask.nii',
                  'components_file': None}
-    
+
     @pytest.fixture(autouse=True)
     def setup_class(self, tmpdir):
         # setup
@@ -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_icc_anova.py

@@ -19,4 +19,4 @@ def test_ICC_rep_anova():
     assert round(icc, 2) == 0.71
     assert dfc == 3
     assert dfe == 15
-    assert r_var / (r_var + e_var) == icc
+    assert np.isclose(r_var / (r_var + e_var), icc)

nipype/algorithms/tests/test_mesh_ops.py

@@ -25,7 +25,7 @@ def test_ident_distances(tmpdir):
     dist_ident.inputs.out_file = os.path.join(tempdir, 'distance.npy')
     res = dist_ident.run()
     assert res.outputs.distance == 0.0
-    
+
     dist_ident.inputs.weighting = 'area'
     res = dist_ident.run()
     assert res.outputs.distance == 0.0
@@ -34,33 +34,31 @@ 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')
     warped_surf = os.path.join(tempdir, 'warped.vtk')
-    
+
     inc = np.array([0.7, 0.3, -0.2])
-    
+
     r1 = tvtk.PolyDataReader(file_name=in_surf)
     vtk1 = VTKInfo.vtk_output(r1)
     r1.update()
     vtk1.points = np.array(vtk1.points) + inc
-    
+
     writer = tvtk.PolyDataWriter(file_name=warped_surf)
     VTKInfo.configure_input_data(writer, vtk1)
     writer.write()
-    
+
     dist = m.ComputeMeshWarp()
     dist.inputs.surface1 = in_surf
     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")
@@ -79,10 +77,10 @@ def test_meshwarpmaths(tmpdir):
 
 @pytest.mark.skipif(not VTKInfo.no_tvtk(), reason="tvtk is installed")
 def test_importerror():
-    with pytest.raises(ImportError): 
+    with pytest.raises(ImportError):
         m.ComputeMeshWarp()
 
-    with pytest.raises(ImportError): 
+    with pytest.raises(ImportError):
         m.WarpPoints()
 
     with pytest.raises(ImportError):

nipype/algorithms/tests/test_modelgen.py

@@ -152,8 +152,8 @@ def test_modelgen_sparse(tmpdir):
     assert len(res.outputs.session_info[0]['regress']) == 1
     s.inputs.use_temporal_deriv = True
     res = s.run()
-    
+
     assert len(res.outputs.session_info[0]['regress']) == 2
     npt.assert_almost_equal(res.outputs.session_info[0]['regress'][0]['val'][0], 0.016675298129743384)
     npt.assert_almost_equal(res.outputs.session_info[1]['regress'][1]['val'][5], 0.007671459162258378)
-    
+

nipype/algorithms/tests/test_overlap.py

@@ -26,7 +26,7 @@ def check_close(val1, val2):
     overlap.inputs.volume2 = in1
     res = overlap.run()
     check_close(res.outputs.jaccard, 1.0)
-    
+
     overlap = Overlap()
     overlap.inputs.volume1 = in1
     overlap.inputs.volume2 = in2