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

Author: oesteban

nipype/interfaces/base/support.py

@@ -3,12 +3,12 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
 
-Miscelanous tools to support Interface functionality
-....................................................
+Miscellaneous tools to support Interface functionality
+......................................................
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import range, object, open, str
+from builtins import range, object, str
 
 import os
 from copy import deepcopy
@@ -18,7 +18,7 @@
 
 from ... import logging
 from ...utils.misc import is_container
-from ...utils.filemanip import md5, to_str
+from ...utils.filemanip import md5, to_str, hash_infile
 iflogger = logging.getLogger('interface')
 
 
@@ -116,27 +116,6 @@ def __repr__(self):
         outstr.append(')')
         return ''.join(outstr)
 
-    def _hash_infile(self, adict, key):
-        # Inject file hashes into adict[key]
-        stuff = adict[key]
-        if not is_container(stuff):
-            stuff = [stuff]
-        file_list = []
-        for afile in stuff:
-            if os.path.isfile(afile):
-                md5obj = md5()
-                with open(afile, 'rb') as fp:
-                    while True:
-                        data = fp.read(8192)
-                        if not data:
-                            break
-                        md5obj.update(data)
-                md5hex = md5obj.hexdigest()
-            else:
-                md5hex = None
-            file_list.append((afile, md5hex))
-        return file_list
-
     def _get_bunch_hash(self):
         """Return a dictionary of our items with hashes for each file.
 
@@ -181,7 +160,7 @@ def _get_bunch_hash(self):
         dict_withhash = self.dictcopy()
         dict_nofilename = self.dictcopy()
         for item in infile_list:
-            dict_withhash[item] = self._hash_infile(dict_withhash, item)
+            dict_withhash[item] = _hash_bunch_dict(dict_withhash, item)
             dict_nofilename[item] = [val[1] for val in dict_withhash[item]]
         # Sort the items of the dictionary, before hashing the string
         # representation so we get a predictable order of the
@@ -208,6 +187,15 @@ def __pretty__(self, p, cycle):
             p.end_group(6, ')')
 
 
+def _hash_bunch_dict(adict, key):
+    """Inject file hashes into adict[key]"""
+    stuff = adict[key]
+    if not is_container(stuff):
+        stuff = [stuff]
+    return [(afile, hash_infile(afile))
+            for afile in stuff]
+
+
 class InterfaceResult(object):
     """Object that contains the results of running a particular Interface.
 
@@ -307,7 +295,7 @@ def load_template(name):
     please use nipype.interfaces.fsl.model.load_template
 
     """
-    from .fsl.model import load_template
+    from ..fsl.model import load_template
     iflogger.warning(
         'Deprecated in 1.0.0, and will be removed in 1.1.0, '
         'please use nipype.interfaces.fsl.model.load_template instead.'

nipype/interfaces/base/traits_extension.py

@@ -2,7 +2,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
-Traits extention
+Traits extension
 ................
 
 This module contains Trait classes that we've pulled from the