STY, DOC: linting, documentation.

Author: Ben Cipollini

nibabel/gifti/gifti.py

@@ -28,7 +28,7 @@ class GiftiMetaData(xml.XmlSerializable):
     the list self.data """
     def __init__(self, nvpair=None):
         self.data = []
-        if not nvpair is None:
+        if nvpair is not None:
             self.data.append(nvpair)
 
     @classmethod
@@ -295,7 +295,7 @@ def from_array(klass,
         cda.intent = intent_codes.code[intent]
         cda.encoding = gifti_encoding_codes.code[encoding]
         cda.endian = gifti_endian_codes.code[endian]
-        if not coordsys is None:
+        if coordsys is not None:
             cda.coordsys = coordsys
         cda.ind_ord = array_index_order_codes.code[ordering]
         cda.meta = GiftiMetaData.from_dict(meta)
@@ -370,7 +370,7 @@ def print_summary(self):
         print('Endian: ', gifti_endian_codes.specs[self.endian])
         print('ExternalFileName: ', self.ext_fname)
         print('ExternalFileOffset: ', self.ext_offset)
-        if not self.coordsys is None:
+        if self.coordsys is not None:
             print('----')
             print('Coordinate System:')
             print(self.coordsys.print_summary())

nibabel/gifti/parse_gifti_fast.py

@@ -338,4 +338,4 @@ def __init__(self, *args, **kwargs):
 
 @np.deprecate_with_doc("Use GiftiImageParser.parse() instead.")
 def parse_gifti_file(fname=None, fptr=None, buffer_size=None):
-    GiftiImageParser().parse(fname=fname, fptr=fptr, buffer_size=buffer_size)
+    GiftiImageParser(buffer_size=buffer_size).parse(fname=fname, fptr=fptr)

nibabel/gifti/tests/test_parse_gifti_fast.py

@@ -317,8 +317,8 @@ def test_parse_dataarrays():
             assert_equal(len(w), 1)
             assert_equal(img.numDA, 0)
 
-def test_parse_deprecated():
 
+def test_parse_deprecated():
 
     # Test deprecation
     with clear_and_catch_warnings() as w:

nibabel/xmlbasedimages.py

@@ -34,14 +34,33 @@ class XmlBasedHeader(FileBasedHeader, XmlSerializable):
 
 
 class XmlImageParser(object):
-    """ Base class for defining how to parse xml-based images."""
+    """ Base class for defining how to parse xml-based images.
+
+    Image-specific parsers should define:
+        StartElementHandler
+        EndElementHandler
+        CharacterDataHandler
+    """
 
     HANDLER_NAMES = ['StartElementHandler',
                      'EndElementHandler',
                      'CharacterDataHandler']
 
     def __init__(self, encoding=None, buffer_size=35000000, verbose=0):
-        self.encoding = encoding
+        """
+        Parameters
+        ----------
+        encoding : str
+            string containing xml document
+
+        buffer_size: None or int, optional
+            size of read buffer. None uses default buffer_size
+            from xml.parsers.expat.
+
+        verbose : int, optional
+            amount of output during parsing (0=silent, by default).
+        """
+        self.encoding=encoding
         self.buffer_size = buffer_size
         self.verbose = verbose
         self.img = None
@@ -55,7 +74,7 @@ def _create_parser(self):
         parser.buffer_size = self.buffer_size
         return parser
 
-    def parse(self, string=None, fname=None, fptr=None, buffer_size=None):
+    def parse(self, string=None, fname=None, fptr=None):
         """
         Parameters
         ----------
@@ -68,11 +87,6 @@ def parse(self, string=None, fname=None, fptr=None, buffer_size=None):
         fptr : file pointer
             open file pointer to an xml document
 
-        buffer_size: None or int, optional
-            size of read buffer. None gives default of 35000000 unless on python <
-            2.6, in which case it is read only in the parser.  In that case values
-            other than None cause a ValueError on execution
-
         Returns
         -------
         img : XmlBasedImage
@@ -107,7 +121,16 @@ def CharacterDataHandler(self, data):
 
 
 class XmlBasedImage(FileBasedImage, XmlSerializable):
+    """Basic convenience wrapper around FileBasedImage and XmlSerializable.
+
+        Properties
+        ----------
+        parser : XmlImageParser
+            class name of the XML parser associated with this image type.
+    """
+
     parser = XmlImageParser
+    header = XmlBasedHeader
 
     def to_file_map(self, file_map=None):
         """ Save the current image to the specified file_map