Merge branch 'ref/interface-base' of github.com:oesteban/nipype into ref/interface-base

Author: oesteban

.zenodo.json

@@ -1,4 +1,4 @@
-Upcoming release
+Upcoming release (0.14.1)
 ================
 
 

CHANGES

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "0.14.0-rc1"
+release = "0.14.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/conf.py

@@ -10,7 +10,7 @@
 # full release.  '.dev' as a version_extra string means this is a development
 # version
 # Remove -dev for release
-__version__ = '0.14.0-rc1'
+__version__ = '0.14.1-dev'
 
 
 def get_nipype_gitversion():

nipype/info.py

@@ -26,7 +26,9 @@ def test_ANTS_inputs():
     ),
     metric=dict(mandatory=True,
     ),
-    metric_weight=dict(requires=['metric'],
+    metric_weight=dict(mandatory=True,
+    requires=['metric'],
+    usedefault=True,
     ),
     mi_option=dict(argstr='--MI-option %s',
     sep='x',
@@ -49,7 +51,8 @@ def test_ANTS_inputs():
     mandatory=True,
     usedefault=True,
     ),
-    radius=dict(requires=['metric'],
+    radius=dict(mandatory=True,
+    requires=['metric'],
     ),
     regularization=dict(argstr='%s',
     ),

nipype/interfaces/ants/tests/test_auto_ANTS.py

@@ -252,30 +252,30 @@ def get_hashval(self, hash_method=None):
 
         Returns
         -------
-        dict_withhash : dict
+        list_withhash : dict
             Copy of our dictionary with the new file hashes included
             with each file.
         hashvalue : str
             The md5 hash value of the traited spec
 
         """
 
-        dict_withhash = []
-        dict_nofilename = []
+        list_withhash = []
+        list_nofilename = []
         for name, val in sorted(self.get().items()):
             if not isdefined(val) or self.has_metadata(name, "nohash", True):
                 # skip undefined traits and traits with nohash=True
                 continue
 
             hash_files = (not self.has_metadata(name, "hash_files", False) and not
                           self.has_metadata(name, "name_source"))
-            dict_nofilename.append((name,
+            list_nofilename.append((name,
                                     self._get_sorteddict(val, hash_method=hash_method,
                                                          hash_files=hash_files)))
-            dict_withhash.append((name,
+            list_withhash.append((name,
                                   self._get_sorteddict(val, True, hash_method=hash_method,
                                                        hash_files=hash_files)))
-        return dict_withhash, md5(to_str(dict_nofilename).encode()).hexdigest()
+        return list_withhash, md5(to_str(list_nofilename).encode()).hexdigest()
 
     def _get_sorteddict(self, objekt, dictwithhash=False, hash_method=None,
                         hash_files=True):

nipype/interfaces/base/specs.py

@@ -49,7 +49,6 @@ class Bunch(object):
     >>> inputs
     Bunch(fwhm=6.0, infile='subj.nii', register_to_mean=False)
 
-
     Notes
     -----
     The Bunch pattern came from the Python Cookbook:

nipype/interfaces/base/support.py

@@ -2173,7 +2173,7 @@ def _list_outputs(self):
 
 
 def load_template(name):
-    """Load a template from the script_templates directory
+    """Load a template from the model_templates directory
 
     Parameters
     ----------
@@ -2186,8 +2186,8 @@ def load_template(name):
 
     """
     from pkg_resources import resource_filename as pkgrf
-    full_fname = pkgrf('nipype',
-                       os.path.join('script_templates', name))
+    full_fname = pkgrf(
+        'nipype', os.path.join('interfaces', 'fsl', 'model_templates', name))
     with open(full_fname) as template_file:
         template = Template(template_file.read())
 

nipype/interfaces/fsl/model.py

@@ -4,15 +4,11 @@
 
 import pytest
 
-from ....utils.filemanip import which
 from ....testing import example_data
 from ...niftyreg import get_custom_path
 
 from ..asl import FitAsl
-
-
-def no_nifty_tool(cmd=None):
-    return which(cmd) is None
+from ...niftyreg.tests.test_regutils import no_nifty_tool
 
 
 @pytest.mark.skipif(no_nifty_tool(cmd='fit_asl'),

nipype/script_templates/feat_contrast_element.tcl renamed to nipype/interfaces/fsl/model_templates/feat_contrast_element.tcl

@@ -3,15 +3,11 @@
 
 import pytest
 
-from ....utils.filemanip import which
 from ....testing import example_data
 from ...niftyreg import get_custom_path
 
 from ..dwi import FitDwi, DwiTool
-
-
-def no_nifty_tool(cmd=None):
-    return which(cmd) is None
+from ...niftyreg.tests.test_regutils import no_nifty_tool
 
 
 @pytest.mark.skipif(no_nifty_tool(cmd='fit_dwi'),

nipype/script_templates/feat_contrast_ftest_element.tcl renamed to nipype/interfaces/fsl/model_templates/feat_contrast_ftest_element.tcl

@@ -4,17 +4,12 @@
 
 import pytest
 
-from ....utils.filemanip import which
 from ....testing import example_data
 from ...niftyreg import get_custom_path
-
+from ...niftyreg.tests.test_regutils import no_nifty_tool
 from ..qt1 import FitQt1
 
 
-def no_nifty_tool(cmd=None):
-    return which(cmd) is None
-
-
 @pytest.mark.skipif(no_nifty_tool(cmd='fit_qt1'),
                     reason="niftyfit is not installed")
 def test_fit_qt1():

nipype/script_templates/feat_contrast_header.tcl renamed to nipype/interfaces/fsl/model_templates/feat_contrast_header.tcl

@@ -4,13 +4,9 @@
 
 import pytest
 
-from ....utils.filemanip import which
 from ....testing import example_data
 from .. import (get_custom_path, RegAladin, RegF3D)
-
-
-def no_nifty_tool(cmd=None):
-    return which(cmd) is None
+from .test_regutils import no_nifty_tool
 
 
 @pytest.mark.skipif(

nipype/script_templates/feat_contrast_prolog.tcl renamed to nipype/interfaces/fsl/model_templates/feat_contrast_prolog.tcl

@@ -3,16 +3,12 @@
 
 import pytest
 
-from ....utils.filemanip import which
 from ....testing import example_data
 from ...niftyreg import get_custom_path
+from ...niftyreg.tests.test_regutils import no_nifty_tool
 from .. import EM
 
 
-def no_nifty_tool(cmd=None):
-    return which(cmd) is None
-
-
 @pytest.mark.skipif(no_nifty_tool(cmd='seg_EM'),
                     reason="niftyseg is not installed")
 def test_seg_em():

nipype/script_templates/feat_contrastmask_element.tcl renamed to nipype/interfaces/fsl/model_templates/feat_contrastmask_element.tcl

@@ -3,16 +3,12 @@
 
 import pytest
 
-from ....utils.filemanip import which
 from ....testing import example_data
 from ...niftyreg import get_custom_path
+from ...niftyreg.tests.test_regutils import no_nifty_tool
 from .. import LabelFusion, CalcTopNCC
 
 
-def no_nifty_tool(cmd=None):
-    return which(cmd) is None
-
-
 @pytest.mark.skipif(no_nifty_tool(cmd='seg_LabFusion'),
                     reason="niftyseg is not installed")
 def test_seg_lab_fusion():

nipype/script_templates/feat_contrastmask_footer.tcl renamed to nipype/interfaces/fsl/model_templates/feat_contrastmask_footer.tcl

@@ -3,16 +3,12 @@
 
 import pytest
 
-from ....utils.filemanip import which
 from ....testing import example_data
 from ...niftyreg import get_custom_path
+from ...niftyreg.tests.test_regutils import no_nifty_tool
 from .. import FillLesions
 
 
-def no_nifty_tool(cmd=None):
-    return which(cmd) is None
-
-
 @pytest.mark.skipif(no_nifty_tool(cmd='seg_FillLesions'),
                     reason="niftyseg is not installed")
 def test_seg_filllesions():

nipype/script_templates/feat_contrastmask_header.tcl renamed to nipype/interfaces/fsl/model_templates/feat_contrastmask_header.tcl

@@ -3,18 +3,14 @@
 
 import pytest
 
-from ....utils.filemanip import which
 from ....testing import example_data
 from ...niftyreg import get_custom_path
+from ...niftyreg.tests.test_regutils import no_nifty_tool
 from .. import (UnaryMaths, BinaryMaths,
                 BinaryMathsInteger, TupleMaths,
                 Merge)
 
 
-def no_nifty_tool(cmd=None):
-    return which(cmd) is None
-
-
 @pytest.mark.skipif(no_nifty_tool(cmd='seg_maths'),
                     reason="niftyseg is not installed")
 def test_unary_maths():

nipype/script_templates/feat_contrasts.tcl renamed to nipype/interfaces/fsl/model_templates/feat_contrasts.tcl

@@ -3,16 +3,12 @@
 
 import pytest
 
-from ....utils.filemanip import which
 from ....testing import example_data
 from ...niftyreg import get_custom_path
+from ...niftyreg.tests.test_regutils import no_nifty_tool
 from .. import PatchMatch
 
 
-def no_nifty_tool(cmd=None):
-    return which(cmd) is None
-
-
 @pytest.mark.skipif(no_nifty_tool(cmd='seg_PatchMatch'),
                     reason="niftyseg is not installed")
 def test_seg_patchmatch():

nipype/script_templates/feat_ev_custom.tcl renamed to nipype/interfaces/fsl/model_templates/feat_ev_custom.tcl

@@ -3,16 +3,12 @@
 
 import pytest
 
-from ....utils.filemanip import which
 from ....testing import example_data
 from ...niftyreg import get_custom_path
+from ...niftyreg.tests.test_regutils import no_nifty_tool
 from .. import UnaryStats, BinaryStats
 
 
-def no_nifty_tool(cmd=None):
-    return which(cmd) is None
-
-
 @pytest.mark.skipif(no_nifty_tool(cmd='seg_stats'),
                     reason="niftyseg is not installed")
 def test_unary_stats():

nipype/script_templates/feat_ev_gamma.tcl renamed to nipype/interfaces/fsl/model_templates/feat_ev_gamma.tcl

@@ -72,7 +72,7 @@ def test_callback_multiproc_normal(tmpdir):
     tmpdir.chdir()
 
     so = Status()
-    wf = pe.Workflow(name='test')
+    wf = pe.Workflow(name='test', base_dir=tmpdir.strpath)
     f_node = pe.Node(niu.Function(function=func, input_names=[],
                                   output_names=[]),
                      name='f_node')
@@ -90,7 +90,7 @@ def test_callback_multiproc_exception(tmpdir):
     tmpdir.chdir()
 
     so = Status()
-    wf = pe.Workflow(name='test')
+    wf = pe.Workflow(name='test', base_dir=tmpdir.strpath)
     f_node = pe.Node(niu.Function(function=bad_func, input_names=[],
                                   output_names=[]),
                      name='f_node')

nipype/script_templates/feat_ev_hrf.tcl renamed to nipype/interfaces/fsl/model_templates/feat_ev_hrf.tcl

@@ -684,7 +684,7 @@ def which(cmd, env=None, pathext=None):
     """
 
     if pathext is None:
-        pathext = os.environ.get("PATHEXT", "").split(os.pathsep)
+        pathext = os.getenv('PATHEXT', '').split(os.pathsep)
         pathext.insert(0, '')
 
     path = os.getenv("PATH", os.defpath)
@@ -751,10 +751,10 @@ def canonicalize_env(env):
         return env
 
     out_env = {}
-    for key, val in env:
+    for key, val in env.items():
         if not isinstance(key, bytes):
             key = key.encode('utf-8')
         if not isinstance(val, bytes):
-            val = key.encode('utf-8')
+            val = val.encode('utf-8')
         out_env[key] = val
     return out_env

nipype/script_templates/feat_ev_none.tcl renamed to nipype/interfaces/fsl/model_templates/feat_ev_none.tcl

@@ -106,7 +106,7 @@ def main():
         pjoin('workflows', 'data', '*'),
         pjoin('pipeline', 'engine', 'report_template.html'),
         pjoin('external', 'd3.js'),
-        pjoin('script_templates', '*'),
+        pjoin('interfaces', 'fsl', 'model_templates', '*'),
         pjoin('interfaces', 'tests', 'realign_json.json'),
         pjoin('interfaces', 'tests', 'use_resources'),
         'pytest.ini',