Merge pull request #1221 from alexsavio/enh/py3k

Apply python-future for Python 3.4 support

Author: chrisgorgo

.gitignore

@@ -5,6 +5,7 @@
 /nipype/build
 /nipype/nipype.egg-info
 /doc/_build
+/doc/preproc
 /doc/users/examples
 /doc/api/generated
 *.pyc
@@ -17,3 +18,6 @@
 .DS_Store
 nipype/testing/data/von-ray_errmap.nii.gz
 nipype/testing/data/von_errmap.nii.gz
+crash*.pklz
+.coverage
+htmlcov/

.travis.yml

@@ -3,16 +3,17 @@ cache:
 language: python
 python:
 - 2.7
+- 3.4
 env:
 - INSTALL_DEB_DEPENDECIES=true
 - INSTALL_DEB_DEPENDECIES=false
 before_install:
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
-  -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh
+  -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
   -O miniconda.sh; fi
 - chmod +x miniconda.sh
 - "./miniconda.sh -b"
-- export PATH=/home/travis/miniconda/bin:$PATH
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then export PATH=/home/travis/miniconda/bin:$PATH; else export PATH=/home/travis/miniconda3/bin:$PATH; fi
 - if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi
 - if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi
 - if $INSTALL_DEB_DEPENDECIES; then bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh);
@@ -27,15 +28,16 @@ install:
 - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
 - source activate testenv
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
-- conda install --yes numpy scipy nose traits networkx dateutil
-- pip install nibabel
+- conda install --yes numpy scipy nose networkx dateutil
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes traits; else pip install traits; fi
 - pip install python-coveralls
 - pip install nose-cov
+- pip install -r requirements.txt  # finish remaining requirements
 - pip install https://github.com/RDFLib/rdflib/archive/master.zip
 - pip install https://github.com/trungdong/prov/archive/rdf.zip
 - python setup.py install
 script:
-- nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
+- python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-cov --cover-package nipype --cov-config .coveragerc --logging-level=INFO
 after_success:
 - coveralls --config_file .coveragerc
 deploy:

THANKS.rst

@@ -10,9 +10,11 @@ Contributors to Nipype include but are not limited to:
   * Aimi Watanabe
   * Alexander Schaefer
   * Alexandre Gramfort
+  * Alexandre Savio
   * Anisha Keshavan
   * Ariel Rokem
   * Ben Acland
+  * Ben Cipollini
   * Basile Pinsard
   * Brendan Moloney
   * Brian Cheung

build_docs.py

@@ -8,6 +8,8 @@
     python setup.py build_sphinx
 """
 
+from __future__ import print_function
+
 # Standard library imports
 import sys
 import os
@@ -43,7 +45,7 @@ def run(self):
         install.run()
 
         # Horrible trick to reload nipype with our temporary instal
-        for key in sys.modules.keys():
+        for key in list(sys.modules.keys()):
             if key.startswith('nipype'):
                 sys.modules.pop(key, None)
         sys.path.append(os.path.abspath(self.temp_install_dir))
@@ -131,7 +133,7 @@ def run(self):
 
         def zip_docs(self):
             if not os.path.exists(DOC_BUILD_DIR):
-                raise OSError, 'Doc directory does not exist.'
+                raise OSError('Doc directory does not exist.')
             target_file = os.path.join('doc', 'documentation.zip')
             # ZIP_DEFLATED actually compresses the archive. However, there
             # will be a RuntimeError if zlib is not installed, so we check
@@ -170,17 +172,17 @@ def run(self):
         clean.run(self)
         api_path = os.path.join('doc', 'api', 'generated')
         if os.path.exists(api_path):
-            print "Removing %s" % api_path
+            print("Removing %s" % api_path)
             shutil.rmtree(api_path)
         interface_path = os.path.join('doc', 'interfaces', 'generated')
         if os.path.exists(interface_path):
-            print "Removing %s" % interface_path
+            print("Removing %s" % interface_path)
             shutil.rmtree(interface_path)
         if os.path.exists(DOC_BUILD_DIR):
-            print "Removing %s" % DOC_BUILD_DIR
+            print("Removing %s" % DOC_BUILD_DIR)
             shutil.rmtree(DOC_BUILD_DIR)
         if os.path.exists(DOC_DOCTREES_DIR):
-            print "Removing %s" % DOC_DOCTREES_DIR
+            print("Removing %s" % DOC_DOCTREES_DIR)
             shutil.rmtree(DOC_DOCTREES_DIR)
 
 

doc/devel/matlab_interface_devel.rst

@@ -93,7 +93,7 @@ By subclassing **MatlabCommand** for your main class, and **MatlabInputSpec** fo
             >>> hello = HelloWorld()
             >>> hello.inputs.name = 'hello_world'
             >>> out = hello.run()
-            >>> print out.outputs.matlab_output
+            >>> print(out.outputs.matlab_output)
             """
             input_spec = HelloWorldInputSpec
             output_spec = HelloWorldOutputSpec

doc/sphinxext/autosummary_generate.py

@@ -16,6 +16,8 @@
             ./ext/autosummary_generate.py -o source/generated source/*.rst
 
 """
+
+from __future__ import print_function
 import glob, re, inspect, os, optparse, pydoc
 from autosummary import import_by_name
 
@@ -44,7 +46,7 @@ def main():
 
     # read
     names = {}
-    for name, loc in get_documented(args).items():
+    for name, loc in list(get_documented(args).items()):
         for (filename, sec_title, keyword, toctree) in loc:
             if toctree is not None:
                 path = os.path.join(os.path.dirname(filename), toctree)
@@ -60,8 +62,8 @@ def main():
 
         try:
             obj, name = import_by_name(name)
-        except ImportError, e:
-            print "Failed to import '%s': %s" % (name, e)
+        except ImportError as e:
+            print("Failed to import '%s': %s" % (name, e))
             continue
 
         fn = os.path.join(path, '%s.rst' % name)
@@ -129,8 +131,8 @@ def get_documented_in_docstring(name, module=None, filename=None):
         return get_documented_in_lines(lines, module=name, filename=filename)
     except AttributeError:
         pass
-    except ImportError, e:
-        print "Failed to import '%s': %s" % (name, e)
+    except ImportError as e:
+        print("Failed to import '%s': %s" % (name, e))
     return {}
 
 def get_documented_in_lines(lines, module=None, filename=None):

doc/sphinxext/numpy_ext/docscrape.py

@@ -2,13 +2,20 @@
 
 """
 
+from __future__ import print_function
+from future import standard_library
+standard_library.install_aliases()
+from builtins import object
+
 import inspect
 import textwrap
 import re
 import pydoc
-from StringIO import StringIO
 from warnings import warn
 
+from nipype.external.six import StringIO
+
+
 class Reader(object):
     """A line-based string reader.
 
@@ -113,7 +120,7 @@ def __getitem__(self,key):
         return self._parsed_data[key]
 
     def __setitem__(self,key,val):
-        if not self._parsed_data.has_key(key):
+        if key not in self._parsed_data:
             warn("Unknown section %s" % key)
         else:
             self._parsed_data[key] = val
@@ -370,7 +377,7 @@ def _str_index(self):
         idx = self['index']
         out = []
         out += ['.. index:: %s' % idx.get('default','')]
-        for section, references in idx.iteritems():
+        for section, references in list(idx.items()):
             if section == 'default':
                 continue
             out += ['   :%s: %s' % (section, ', '.join(references))]
@@ -428,7 +435,7 @@ def __init__(self, func, role='func', doc=None, config={}):
                 argspec = inspect.formatargspec(*argspec)
                 argspec = argspec.replace('*','\*')
                 signature = '%s%s' % (func_name, argspec)
-            except TypeError, e:
+            except TypeError as e:
                 signature = '%s()' % func_name
             self['Signature'] = signature
 
@@ -450,8 +457,8 @@ def __str__(self):
                  'meth': 'method'}
 
         if self._role:
-            if not roles.has_key(self._role):
-                print "Warning: invalid role %s" % self._role
+            if self._role not in roles:
+                print("Warning: invalid role %s" % self._role)
             out += '.. %s:: %s\n    \n\n' % (roles.get(self._role,''),
                                              func_name)
 

doc/sphinxext/numpy_ext/docscrape_sphinx.py

@@ -1,7 +1,10 @@
+from __future__ import absolute_import
 import re, inspect, textwrap, pydoc
 import sphinx
-from docscrape import NumpyDocString, FunctionDoc, ClassDoc
-from nipype.external import six
+from .docscrape import NumpyDocString, FunctionDoc, ClassDoc
+from nipype.external.six import string_types
+
+
 
 class SphinxDocString(NumpyDocString):
     def __init__(self, docstring, config={}):
@@ -128,7 +131,7 @@ def _str_index(self):
             return out
 
         out += ['.. index:: %s' % idx.get('default','')]
-        for section, references in idx.iteritems():
+        for section, references in list(idx.items()):
             if section == 'default':
                 continue
             elif section == 'refguide':
@@ -141,7 +144,7 @@ def _str_references(self):
         out = []
         if self['References']:
             out += self._str_header('References')
-            if isinstance(self['References'], six.string_types):
+            if isinstance(self['References'], string_types):
                 self['References'] = [self['References']]
             out.extend(self['References'])
             out += ['']

doc/sphinxext/numpy_ext/numpydoc.py

@@ -16,13 +16,16 @@
 
 """
 
+from __future__ import absolute_import
+from builtins import object
+
 import sphinx
 
 if sphinx.__version__ < '1.0.1':
     raise RuntimeError("Sphinx 1.0.1 or newer is required")
 
 import os, re, pydoc
-from docscrape_sphinx import get_doc_object, SphinxDocString
+from .docscrape_sphinx import get_doc_object, SphinxDocString
 from sphinx.util.compat import Directive
 import inspect
 
@@ -39,7 +42,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,
         lines[:] = title_re.sub(u'', u"\n".join(lines)).split(u"\n")
     else:
         doc = get_doc_object(obj, what, u"\n".join(lines), config=cfg)
-        lines[:] = unicode(doc).split(u"\n")
+        lines[:] = str(doc).split(u"\n")
 
     if app.config.numpydoc_edit_link and hasattr(obj, '__name__') and \
            obj.__name__:
@@ -120,7 +123,7 @@ def __init__(self, *a, **kw):
         self.wrap_mangling_directives()
 
     def wrap_mangling_directives(self):
-        for name, objtype in self.directive_mangling_map.items():
+        for name, objtype in list(self.directive_mangling_map.items()):
             self.directives[name] = wrap_mangling_directive(
                 self.directives[name], objtype)
 

examples/dmri_camino_dti.py

@@ -91,7 +91,7 @@ def get_affine(volume):
 """
 
 datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
-                                               outfields=info.keys()),
+                                               outfields=list(info.keys())),
                      name = 'datasource')
 
 datasource.inputs.template = "%s/%s"

examples/dmri_connectivity.py

@@ -146,7 +146,7 @@ def select_aparc_annot(list_of_files):
 """
 
 datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
-                                               outfields=info.keys()),
+                                               outfields=list(info.keys())),
                      name = 'datasource')
 
 datasource.inputs.template = "%s/%s"

examples/dmri_connectivity_advanced.py

@@ -66,7 +66,7 @@
 
 try:
     package_check('cmp')
-except Exception, e:
+except Exception as e:
     warnings.warn('cmp not installed')
 else:
     import cmp
@@ -114,7 +114,7 @@
 """
 
 datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
-                                               outfields=info.keys()),
+                                               outfields=list(info.keys())),
                      name = 'datasource')
 
 datasource.inputs.template = "%s/%s"

examples/dmri_dtk_dti.py

@@ -98,7 +98,7 @@
 """
 
 datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
-                                               outfields=info.keys()),
+                                               outfields=list(info.keys())),
                      name = 'datasource')
 
 datasource.inputs.template = "%s/%s"

examples/dmri_dtk_odf.py

@@ -98,7 +98,7 @@
 """
 
 datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
-                                               outfields=info.keys()),
+                                               outfields=list(info.keys())),
                      name = 'datasource')
 
 datasource.inputs.template = "%s/%s"

examples/dmri_fsl_dti.py

@@ -107,7 +107,7 @@
 """
 
 datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
-                                               outfields=info.keys()),
+                                               outfields=list(info.keys())),
                      name = 'datasource')
 
 datasource.inputs.template = "%s/%s"

examples/dmri_group_connectivity_camino.py

@@ -126,7 +126,7 @@
 title = ''
 for idx, group_id in enumerate(group_list.keys()):
     title += group_id
-    if not idx == len(group_list.keys()) - 1:
+    if not idx == len(list(group_list.keys())) - 1:
         title += '-'
 
     info = dict(dwi=[['subject_id', 'dti']],

examples/dmri_group_connectivity_mrtrix.py

@@ -131,7 +131,7 @@
 title = ''
 for idx, group_id in enumerate(group_list.keys()):
     title += group_id
-    if not idx == len(group_list.keys()) - 1:
+    if not idx == len(list(group_list.keys())) - 1:
         title += '-'
 
     info = dict(dwi=[['subject_id', 'dti']],

examples/dmri_mrtrix_dti.py

@@ -57,7 +57,7 @@
 """
 
 datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
-                                               outfields=info.keys()),
+                                               outfields=list(info.keys())),
                      name = 'datasource')
 
 datasource.inputs.template = "%s/%s"

examples/dmri_preprocessing.py

@@ -81,7 +81,7 @@
 """
 
 datasource = pe.Node(nio.DataGrabber(infields=['subject_id'],
-                     outfields=info.keys()), name='datasource')
+                     outfields=list(info.keys())), name='datasource')
 
 datasource.inputs.template = "%s/%s"