Merge remote-tracking branch 'upstream/master' into enh/restingconn

* upstream/master:
  tiny typo
  another attempt at fixing bash conditionals
  fixed bash conditionals
  added no dep install version. we'll be testing on both.
  Added xor option in Camino connectivity for robustness
  Conmat test function
  Added more connectivity matrix options in Camino interface
  Fixed tests.
  remove deb packages installation
  added apt caching
  switched to six.string_types for string type checks
  added external package: 'six'
  Removed unnecessary positional parameters as well as args argument
  Added whitespaces
  Dcm2nii and related tests
  Added input options to dcm2nii
  replaced str with basestring in instance checks to support unicode strings

Author: satra

.travis.yml

@@ -1,20 +1,24 @@
+cache:
+  - apt
 language: python
 python:
   - 2.6
   - 2.7
+env:
+  - INSTALL_DEB_DEPENDECIES=true
+  - INSTALL_DEB_DEPENDECIES=false
 # Setup anaconda
 before_install:
   - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh -O miniconda.sh; fi
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda/bin:$PATH
-  # The next couple lines fix a crash with multiprocessing on Travis
-  - sudo rm -rf /dev/shm
-  - sudo ln -s /run/shm /dev/shm
-  - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-  - travis_retry sudo apt-get install -qq --no-install-recommends fsl afni elastix
-  - travis_retry sudo apt-get install -qq fsl-atlases
-  - source /etc/fsl/fsl.sh
+  - 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); fi
+  - if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq --no-install-recommends fsl afni elastix; fi
+  - if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq fsl-atlases; fi
+  - if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
 
 # Install packages
 install:

doc/sphinxext/numpy_ext/docscrape_sphinx.py

@@ -1,6 +1,7 @@
 import re, inspect, textwrap, pydoc
 import sphinx
 from docscrape import NumpyDocString, FunctionDoc, ClassDoc
+from nipype.external import six
 
 class SphinxDocString(NumpyDocString):
     def __init__(self, docstring, config={}):
@@ -140,7 +141,7 @@ def _str_references(self):
         out = []
         if self['References']:
             out += self._str_header('References')
-            if isinstance(self['References'], str):
+            if isinstance(self['References'], six.string_types):
                 self['References'] = [self['References']]
             out.extend(self['References'])
             out += ['']

examples/fmri_ants_openfmri.py

@@ -14,6 +14,8 @@
 
 from nipype import config
 config.enable_provenance()
+from nipype.external import six
+
 
 from glob import glob
 import os
@@ -443,7 +445,7 @@ def get_contrasts(contrast_file, task_id, conds):
 
     def check_behav_list(behav):
         out_behav = []
-        if isinstance(behav, basestring):
+        if isinstance(behav, six.string_types):
             behav = [behav]
         for val in behav:
             if not isinstance(val, list):

examples/fmri_openfmri.py

@@ -14,6 +14,7 @@
 
 from nipype import config
 config.enable_provenance()
+from nipype.external import six
 
 from glob import glob
 import os
@@ -237,7 +238,7 @@ def get_contrasts(contrast_file, task_id, conds):
 
     def check_behav_list(behav):
         out_behav = []
-        if isinstance(behav, basestring):
+        if isinstance(behav, six.string_types):
             behav = [behav]
         for val in behav:
             if not isinstance(val, list):

nipype/algorithms/modelgen.py

@@ -30,6 +30,7 @@
                                     isdefined)
 from nipype.utils.filemanip import filename_to_list
 from .. import config, logging
+from nipype.external import six
 iflogger = logging.getLogger('interface')
 
 def gcd(a, b):
@@ -422,7 +423,7 @@ def _concatenate_info(self, infolist):
         for i, f in enumerate(self.inputs.functional_runs):
             if isinstance(f, list):
                 numscans = len(f)
-            elif isinstance(f, str):
+            elif isinstance(f, six.string_types):
                 img = load(f)
                 numscans = img.get_shape()[3]
             else:

nipype/algorithms/rapidart.py

@@ -26,6 +26,7 @@
 import numpy as np
 from scipy import signal
 import scipy.io as sio
+from nipype.external import six
 
 from ..interfaces.base import (BaseInterface, traits, InputMultiPath,
                                     OutputMultiPath, TraitedSpec, File,
@@ -279,7 +280,7 @@ def _get_output_filenames(self, motionfile, output_dir):
         output_dir: string
             output directory in which the files will be generated
         """
-        if isinstance(motionfile, str):
+        if isinstance(motionfile, six.string_types):
             infile = motionfile
         elif isinstance(motionfile, list):
             infile = motionfile[0]
@@ -350,7 +351,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
             cwd = os.getcwd()
 
         # read in functional image
-        if isinstance(imgfile, str):
+        if isinstance(imgfile, six.string_types):
             nim = load(imgfile)
         elif isinstance(imgfile, list):
             if len(imgfile) == 1:

nipype/external/provcopy.py

@@ -17,6 +17,7 @@
 import dateutil.parser
 import collections
 from collections import defaultdict
+import six
 
 try:
     from rdflib.term import URIRef, BNode
@@ -187,7 +188,7 @@ def _parse_xsd_dateTime(s):
 
 
 def _ensure_datetime(time):
-    if isinstance(time, basestring):
+    if isinstance(time, six.string_types):
         return _parse_xsd_dateTime(time)
     else:
         return time
@@ -232,12 +233,12 @@ def parse_xsd_types(value, datatype):
 
 
 def _ensure_multiline_string_triple_quoted(s):
-    format_str = u'"""%s"""' if isinstance(s, basestring) and '\n' in s else u'"%s"'
+    format_str = u'"""%s"""' if isinstance(s, six.string_types) and '\n' in s else u'"%s"'
     return format_str % s
 
 
 def encoding_PROV_N_value(value):
-    if isinstance(value, basestring):
+    if isinstance(value, six.string_types):
         return _ensure_multiline_string_triple_quoted(value)
     elif isinstance(value, datetime.datetime):
         return value.isoformat()
@@ -536,7 +537,7 @@ def _auto_literal_conversion(self, literal):
         if isinstance(literal, URIRef):
             return literal
 
-        if isinstance(literal, basestring):
+        if isinstance(literal, six.string_types):
             return unicode(literal)
 
         if isinstance(literal, Literal) and literal.has_no_langtag():
@@ -1568,7 +1569,7 @@ def _decode_JSON_container(self, jc):
                          key=lambda tuple_rec: tuple_rec[0])
 
         record_map = {}
-        _parse_attr_value = lambda value: record_map[value] if (isinstance(value, basestring) and value in record_map) else self._decode_json_representation(value)
+        _parse_attr_value = lambda value: record_map[value] if (isinstance(value, six.string_types) and value in record_map) else self._decode_json_representation(value)
         #  Create all the records before setting their attributes
         for (record_type, identifier, content) in records:
             if record_type == PROV_REC_BUNDLE: