Update docstring and fix flake8 errors

theano/d3viz/d3viz.py

@@ -8,20 +8,35 @@ import shutil
 import re
 from six import iteritems
 
-from .formatting import PyDotFormatter
+from theano.d3viz.formatting import PyDotFormatter
 
 __path__ = os.path.dirname(os.path.realpath(__file__))
 
 
 def replace_patterns(x, replace):
-    """Replace patterns `replace` in x."""
+    """Replace `replace` in string `x`.
+
+    Parameters
+    ----------
+    s: str
+        String on which function is applied
+    replace: dict
+        `key`, `value` pairs where key is a regular expression and `value` a
+        string by which `key` is replaced
+    """
     for from_, to in iteritems(replace):
         x = x.replace(str(from_), str(to))
     return x
 
 
 def escape_quotes(s):
-    """Escape quotes in string."""
+    """Escape quotes in string.
+
+    Parameters
+    ----------
+    s: str
+        String on which function is applied
+    """
     s = re.sub(r'''(['"])''', r'\\\1', s)
     return s
 
@@ -29,17 +44,6 @@ def escape_quotes(s):
 def d3viz(fct, outfile, copy_deps=True, *args, **kwargs):
     """Create HTML file with dynamic visualizing of a Theano function graph.
 
-    Parameters
-    ----------
-    fct -- theano.compile.function_module.Function
-        A compiled Theano function, variable, apply or a list of variables.
-    outfile -- str
-        Path to output HTML file.
-    copy_deps -- bool, optional
-        Copy javascript and CSS dependencies to output directory.
-    *args, **kwargs -- dict, optional
-        Arguments passed to PyDotFormatter.
-
     In the HTML file, the whole graph or single nodes can be moved by drag and
     drop. Zooming is possible via the mouse wheel. Detailed information about
     nodes and edges are displayed via mouse-over events. Node labels can be
@@ -53,6 +57,19 @@ def d3viz(fct, outfile, copy_deps=True, *args, **kwargs):
     Edges are black by default. If a node returns a view of an
     input, the input edge will be blue. If it returns a destroyed input, the
     edge will be red.
+
+    Parameters
+    ----------
+    fct : theano.compile.function_module.Function
+        A compiled Theano function, variable, apply or a list of variables.
+    outfile : str
+        Path to output HTML file.
+    copy_deps : bool, optional
+        Copy javascript and CSS dependencies to output directory.
+    *args : tuple, optional
+        Arguments passed to PyDotFormatter.
+    *kwargs : dict, optional
+        Arguments passed to PyDotFormatter.
     """
 
     # Create DOT graph
@@ -96,7 +113,20 @@ def d3viz(fct, outfile, copy_deps=True, *args, **kwargs):
 
 
 def d3write(fct, path, *args, **kwargs):
-    """Convert Theano graph to pydot graph and write to file."""
+    """Convert Theano graph to pydot graph and write to dot file.
+
+    Parameters
+    ----------
+    fct : theano.compile.function_module.Function
+        A compiled Theano function, variable, apply or a list of variables.
+    path: str
+        Path to output file
+    *args : tuple, optional
+        Arguments passed to PyDotFormatter.
+    *kwargs : dict, optional
+        Arguments passed to PyDotFormatter.
+    """
+
     formatter = PyDotFormatter(*args, **kwargs)
     graph = formatter(fct)
     graph.write_dot(path)

theano/d3viz/formatting.py

@@ -28,14 +28,25 @@ _logger = logging.getLogger("theano.printing")
 
 
 class PyDotFormatter(object):
+    """Create `pydot` graph object from Theano function.
+
+    Parameters
+    ----------
+    compact : bool
+        if True, will remove intermediate variables without name.
+
+    Attributes
+    ----------
+    node_colors : dict
+        Color table of node types.
+    apply_colors : dict
+        Color table of apply nodes.
+    shapes : dict
+        Shape table of node types.
+    """
 
     def __init__(self, compact=True):
-        """Converts compute to to `pydot` object.
-
-        :param compact: if True, will remove intermediate variables without
-                        name.
-        """
-
+        """Construct PyDotFormatter object."""
         if not pydot_imported:
             raise RuntimeError("Failed to import pydot. Please install pydot!")
 
@@ -59,14 +70,36 @@ class PyDotFormatter(object):
         self.__node_prefix = 'n'
 
     def __add_node(self, node):
-        """Add new node to node list and return unique id."""
+        """Add new node to node list and return unique id.
+
+        Parameters
+        ----------
+        node : Theano graph node
+            Apply node, tensor variable, or shared variable in compute graph.
+
+        Returns
+        -------
+        str
+            Unique node id.
+        """
         assert node not in self.__nodes
         _id = '%s%d' % (self.__node_prefix, len(self.__nodes) + 1)
         self.__nodes[node] = _id
         return _id
 
     def __node_id(self, node):
-        """Return unique node id."""
+        """Return unique node id.
+
+        Parameters
+        ----------
+        node : Theano graph node
+            Apply node, tensor variable, or shared variable in compute graph.
+
+        Returns
+        -------
+        str
+            Unique node id.
+        """
         if node in self.__nodes:
             return self.__nodes[node]
         else:
@@ -75,10 +108,18 @@ class PyDotFormatter(object):
     def __call__(self, fct, graph=None):
         """Create pydot graph from function.
 
-        :param fct: a compiled Theano function, a Variable, an Apply or
-                    a list of Variable.
-        :param graph: `pydot` graph to which nodes are added. Creates new one
-                      if not given.
+        Parameters
+        ----------
+        fct : theano.compile.function_module.Function
+            A compiled Theano function, variable, apply or a list of variables.
+        graph: pydot.Dot
+            `pydot` graph to which nodes are added. Creates new one if
+            undefined.
+
+        Returns
+        -------
+        pydot.Dot
+            Pydot graph of `fct`
         """
         if graph is None:
             graph = pd.Dot()
@@ -287,6 +328,7 @@ def apply_profile(node, profile):
 
 
 def broadcastable_to_str(b):
+    """Return string representation of broadcastable."""
     named_broadcastable = {(): 'scalar',
                            (False,): 'vector',
                            (False, True): 'col',
@@ -300,6 +342,7 @@ def broadcastable_to_str(b):
 
 
 def dtype_to_char(dtype):
+    """Return character that represents data type."""
     dtype_char = {
         'complex64': 'c',
         'complex128': 'z',

theano/d3viz/tests/test_d3viz.py

@@ -3,7 +3,6 @@ import os.path as pt
 import tempfile
 import unittest
 import filecmp
-import sys
 
 import theano as th
 import theano.d3viz as d3v

theano/tests/test_flake8.py

@@ -216,6 +216,7 @@ whitelist_flake8 = [
     "gof/tests/test_cc.py",
     "gof/tests/test_compute_test_value.py",
     "gof/sandbox/equilibrium.py",
+    "d3viz/__init__.py"
 ]