Merge pull request #4505 from kmike/d3viz

.travis.yml

@@ -35,7 +35,7 @@ install:
   - if [[ $TRAVIS_PYTHON_VERSION == '2.6' ]]; then conda create --yes -q -n pyenv mkl python=2.6 numpy=1.7.1 scipy=0.11 nose=1.3.0 pyparsing=1.5 pip flake8=2.3 six=1.9.0 pep8=1.6.2 pyflakes=0.8.1 sphinx; fi
   - if [[ $TRAVIS_PYTHON_VERSION == '3.3' ]]; then conda create --yes -q -n pyenv mkl python=3.3 numpy=1.9.1 scipy=0.14.0 nose=1.3.4 pyparsing=1.5 pip flake8=2.3 six=1.9.0 pep8=1.6.2 pyflakes=0.8.1 sphinx; fi
   - source activate pyenv
-  - if [[ $TRAVIS_PYTHON_VERSION == '2.6' ]]; then pip install pydot; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == '2.6' ]]; then pip install pydot; else pip install pydot-ng; fi
   - pip install . --no-deps
   - pip install flake8-future-import nose-parameterized==0.5.0
 

doc/cifarSC2011/advanced_theano.txt

@@ -464,7 +464,7 @@ The graph after optimization:
 
 Picture Printing of Graphs
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
-``pydotprint`` requires graphviz and pydot.
+``pydotprint`` requires graphviz and either pydot or pydot-ng.
 
 The graph before optimization:
 

doc/crei2013/advanced_theano.txt

@@ -202,7 +202,7 @@ The graph after optimization:
 Picture Printing of Graphs
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-``pydotprint`` requires graphviz and pydot.
+``pydotprint`` requires graphviz and either pydot or pydot-ng.
 
 The graph before optimization:
 

doc/install.txt

@@ -59,7 +59,7 @@ The following libraries and software are optional:
     `Git <http://git-scm.com>`_
         To download bleeding-edge versions of Theano.
 
-    `pydot-ng <https://github.com/pydot/pydot-ng>`_ or `pydot <https://code.google.com/p/pydot/>`_
+    `graphiz <http://www.graphviz.org/>`__ and either `pydot-ng <https://github.com/pydot/pydot-ng>`__ or `pydot <https://code.google.com/p/pydot/>`__
         To be able to make picture of Theano computation graph.
 	pydot-ng is a pydot compatible replacement that support newer Python.
 
@@ -613,7 +613,7 @@ To install the missing Theano optional dependency (pydot):
 
 .. code-block:: bash
 
-    $ conda install pydot
+    $ conda install pydot-ng
 
 If you want the bleeding edge version instead execute this command:
 

doc/library/d3viz/index.txt

@@ -17,11 +17,14 @@ Requirements
 ------------
 
 ``d3viz`` requires the `pydot <https://pypi.python.org/pypi/pydot>`__
-package, which can be installed with ``pip``:
+package. `pydot-ng <https://github.com/pydot/pydot-ng>`__ fork is better
+maintained, and it works both in Python 2.x and 3.x. Install it with pip::
 
-::
+    pip install pydot-ng
 
-    pip install pydot
+Like Theano’s `printing module
+<http://deeplearning.net/software/theano/library/printing.html>`__, ``d3viz``
+requires `graphviz <http://www.graphviz.org/>`__ binary to be available.
 
 Overview
 --------
@@ -123,6 +126,19 @@ may not be perfect. In this case, you can press the ``Release node``
 button in the top-left corner to automatically arrange nodes. To reset
 nodes to their default position, press the ``Reset nodes`` button.
 
+You can also display the interactive graph inline in
+IPython using ``IPython.display.IFrame``:
+
+.. code:: python
+
+    from IPython.display import IFrame
+    d3v.d3viz(predict, 'examples/mlp.html')
+    IFrame('examples/mlp.html', width=700, height=500)
+
+Currently if you use display.IFrame you still have to create a file,
+and this file can't be outside notebooks root (e.g. usually it can't be
+in /tmp/).
+
 Profiling
 ---------
 

theano/d3viz/d3viz.py

@@ -7,6 +7,7 @@ from __future__ import absolute_import, print_function, division
 import os
 import shutil
 import re
+import six
 from six import iteritems
 
 from theano.d3viz.formatting import PyDotFormatter
@@ -78,7 +79,10 @@ def d3viz(fct, outfile, copy_deps=True, *args, **kwargs):
     # Create DOT graph
     formatter = PyDotFormatter(*args, **kwargs)
     graph = formatter(fct)
-    dot_graph = escape_quotes(str(graph.create_dot())).replace('\n', '').replace('\r', '')
+    dot_graph_raw = graph.create_dot()
+    if not six.PY2:
+        dot_graph_raw = dot_graph_raw.decode('utf8')
+    dot_graph = escape_quotes(dot_graph_raw).replace('\n', '').replace('\r', '')
 
     # Create output directory if not existing
     outdir = os.path.dirname(outfile)

theano/d3viz/formatting.py

@@ -52,8 +52,9 @@ class PyDotFormatter(object):
     def __init__(self, compact=True):
         """Construct PyDotFormatter object."""
         if not pydot_imported:
-            raise ImportError('Failed to import pydot. You must install pydot'
-                              ' and graphviz for `PyDotFormatter` to work.')
+            raise ImportError('Failed to import pydot. You must install '
+                              'graphviz and either pydot or pydot-ng for '
+                              '`PyDotFormatter` to work.')
 
         self.compact = compact
         self.node_colors = {'input': 'limegreen',

theano/printing.py

@@ -747,8 +747,9 @@ def pydotprint(fct, outfile=None,
         outputs = fct.outputs
         topo = fct.toposort()
     if not pydot_imported:
-        raise RuntimeError("Failed to import pydot. You must install pydot"
-                           " and graphviz for `pydotprint` to work.",
+        raise RuntimeError("Failed to import pydot. You must install graphviz"
+                           " and either pydot or pydot-ng for "
+                           "`pydotprint` to work.",
                            pydot_imported_msg)
 
     g = pd.Dot()