Merge branch 'py3-fixes' into main-master

* py3-fixes: (25 commits)
  RF - refactored 2 to 3 doctest markup with more comprehensive tests
  RF - guard against syntax errors parsing input for strings
  DOC+RF - reorganizing comments and tests for python 2 skipping
  DOC - more py3builder doctest processor docstring
  BF - clear up remaining test and doctest failures in python 3
  NF - added fancy syntax tree string find /replace
  DOC - mini-language doctest markup in action
  BF - more doctest 3 fixes
  BF - merge Stephans py3 port changes
  BF - add gifti data files to data files; continue to try to fix python3 doc tests
  NF - add doctest search replace and markup parser
  RF - add doctest conversion to 2to3
  DOC - revert doc for reverted __eq__ to __cmp__ change
  RF+BF - non-doctests now all pass on py3k
  RF+BF - gradual cleanup of py3k test errors; still 10 E 15 F to fix
  RF - updated netcdf file from scipy distribution, adding py3k port stuff
  BF - further python 3k fixes
  RF+BF - trying to get strings, bytes, logs working
  RF - attempting to deal with string vs byte for python 3
  RF - removed parametric testing patch, some test cleanup
  ...

Conflicts:
	nibabel/tests/test_nifti1.py

Author: matthew-brett

doc/sphinxext/docscrape.py

@@ -112,8 +112,8 @@ def __init__(self,docstring):
     def __getitem__(self,key):
         return self._parsed_data[key]
 
-    def __setitem__(self,key,val):
-        if not self._parsed_data.has_key(key):
+    def __setitem__(self,key,val)
+        if not key in self._parsed_data:
             warn("Unknown section %s" % key)
         else:
             self._parsed_data[key] = val
@@ -451,7 +451,7 @@ def __str__(self):
                  'meth': 'method'}
 
         if self._role:
-            if not roles.has_key(self._role):
+            if not self._role in roles:
                 print "Warning: invalid role %s" % self._role
             out += '.. %s:: %s\n    \n\n' % (roles.get(self._role,''),
                                              func_name)

nibabel/analyze.py

@@ -141,8 +141,8 @@
      array_to_file, array_from_file, can_cast, \
      floating_point_types
 
-from .spatialimages import HeaderDataError, HeaderTypeError, \
-    ImageDataError, SpatialImage
+from .spatialimages import (HeaderDataError, HeaderTypeError,
+                            ImageDataError, SpatialImage)
 
 from . import imageglobals as imageglobals
 from .fileholders import FileHolderError, copy_file_map
@@ -395,10 +395,10 @@ def from_fileobj(klass, fileobj, endianness=None, check=True):
 
         Examples
         --------
-        >>> import StringIO
+        >>> from StringIO import StringIO #23dt : BytesIO
         >>> hdr = AnalyzeHeader()
-        >>> fileobj = StringIO.StringIO(hdr.binaryblock)
-        >>> fileobj.seek(0)
+        >>> fileobj = StringIO(hdr.binaryblock) #23dt : BytesIO
+        >>> _ = fileobj.seek(0) # returns 0 in python 3
         >>> hdr2 = AnalyzeHeader.from_fileobj(fileobj)
         >>> hdr2.binaryblock == hdr.binaryblock
         True
@@ -445,8 +445,8 @@ def write_to(self, fileobj):
         Examples
         --------
         >>> hdr = AnalyzeHeader()
-        >>> import StringIO
-        >>> str_io = StringIO.StringIO()
+        >>> from StringIO import StringIO #23dt : BytesIO
+        >>> str_io = StringIO() #23dt : BytesIO
         >>> hdr.write_to(str_io)
         >>> hdr.binaryblock == str_io.getvalue()
         True
@@ -523,10 +523,6 @@ def __eq__(self, other):
         return this_bb == other_bb
 
     def __ne__(self, other):
-        ''' equality between two headers defined by ``header_data``
-
-        For examples, see ``__eq__`` method docstring
-        '''
         return not self == other
 
     def raw_data_from_fileobj(self, fileobj):
@@ -616,8 +612,8 @@ def data_to_fileobj(self, data, fileobj):
         >>> hdr = AnalyzeHeader()
         >>> hdr.set_data_shape((1, 2, 3))
         >>> hdr.set_data_dtype(np.float64)
-        >>> from StringIO import StringIO
-        >>> str_io = StringIO()
+        >>> from StringIO import StringIO #23dt : BytesIO
+        >>> str_io = StringIO() #23dt : BytesIO
         >>> data = np.arange(6).reshape(1,2,3)
         >>> hdr.data_to_fileobj(data, str_io)
         >>> data.astype(np.float64).tostring('F') == str_io.getvalue()
@@ -659,7 +655,7 @@ def __setitem__(self, item, value):
         --------
         >>> hdr = AnalyzeHeader()
         >>> hdr['descrip'] = 'description'
-        >>> str(hdr['descrip'])
+        >>> np.asscalar(hdr['descrip']) #23dt next : bytes
         'description'
         '''
         self._header_data[item] = value
@@ -834,15 +830,15 @@ def set_data_dtype(self, datatype):
         >>> hdr.set_data_dtype(np.dtype(np.uint8))
         >>> hdr.get_data_dtype()
         dtype('uint8')
-        >>> hdr.set_data_dtype('implausible')
+        >>> hdr.set_data_dtype('implausible') #doctest: +IGNORE_EXCEPTION_DETAIL
         Traceback (most recent call last):
            ...
         HeaderDataError: data dtype "implausible" not recognized
-        >>> hdr.set_data_dtype('none')
+        >>> hdr.set_data_dtype('none') #doctest: +IGNORE_EXCEPTION_DETAIL
         Traceback (most recent call last):
            ...
         HeaderDataError: data dtype "none" known but not supported
-        >>> hdr.set_data_dtype(np.void)
+        >>> hdr.set_data_dtype(np.void) #doctest: +IGNORE_EXCEPTION_DETAIL
         Traceback (most recent call last):
            ...
         HeaderDataError: data dtype "<type 'numpy.void'>" known but not supported

nibabel/batteryrunners.py

@@ -211,8 +211,17 @@ def __init__(self,
         self.problem_msg = problem_msg
         self.fix_msg = fix_msg
 
+    def __getstate__(self):
+        """ State that defines object
+
+        Returns
+        -------
+        tup : tuple
+        """
+        return self.error, self.problem_level, self.problem_msg, self.fix_msg
+
     def __eq__(self, other):
-        ''' Test for equality
+        ''' are two BatteryRunner-like objects equal?
 
         Parameters
         ----------
@@ -229,19 +238,14 @@ def __eq__(self, other):
         >>> rep == rep3
         False
         '''
-        return (self.__dict__ == other.__dict__)
+        return self.__getstate__() == other.__getstate__()
 
     def __ne__(self, other):
-        ''' Test for equality
-
-        Parameters
-        ----------
-        other : object
-           report-like object to test equality
+        """ are two BatteryRunner-like objects not equal?
 
-        See __eq__ docstring for examples
-        '''
-        return (self.__dict__ != other.__dict__)
+        See docstring for __eq__
+        """
+        return not self == other
 
     def __str__(self):
         ''' Printable string for object '''

nibabel/data.py

@@ -279,7 +279,8 @@ def make_datasource(pkg_def, **kwargs):
     names = unix_relpath.split('/')
     try:
         pth = find_data_dir(data_path, *names)
-    except DataError, exception:
+    except DataError:
+        exception = sys.exc_info()[1] # Python 2 and 3 compatibility
         pth = [pjoin(this_data_path, *names)
                 for this_data_path in data_path]
         pkg_hint = pkg_def.get('install hint', DEFAULT_INSTALL_HINT)
@@ -337,7 +338,8 @@ def datasource_or_bomber(pkg_def, **options):
     sys_relpath = os.path.sep.join(names)
     try:
         ds = make_datasource(pkg_def, **options)
-    except DataError, exception:
+    except DataError:
+        exception = sys.exc_info()[1] # python 2 and 3 compatibility
         return Bomber(sys_relpath, exception)
     # check version
     if (version is None or

nibabel/eulerangles.py

@@ -84,6 +84,8 @@
 '''
 
 import math
+from functools import reduce
+
 import numpy as np