Network Plot Error Using Python / iPython - numpy

Question

The following starter code errors out (AttributeError: incompatible shape for a non-contiguous array) when I try to use networkx on OSX 10.8.2, in an IPython notebook.
import networkx as nx
g = nx.Graph()
g.add_node(1)
g.add_node(2)
g.add_edge(1,2) # no error if this line is omitted
nx.draw(g)
I do not see the error if I do not add the edge to this graph. Matplotlib, Numpy, and Scipy were all installed as suggested here.
Below is the error message:
AttributeError Traceback (most recent call last)
<ipython-input-33-df7dfeff6452> in <module>()
----> 1 nx.draw(g)
/usr/local/lib/python2.7/site-packages/networkx/drawing/nx_pylab.pyc in draw(G, pos, ax, hold, **kwds)
131 pylab.hold(h)
132 try:
--> 133 draw_networkx(G,pos=pos,ax=ax,**kwds)
134 ax.set_axis_off()
135 pylab.draw_if_interactive()
/usr/local/lib/python2.7/site-packages/networkx/drawing/nx_pylab.pyc in draw_networkx(G, pos, with_labels, **kwds)
265
266 node_collection=draw_networkx_nodes(G, pos, **kwds)
--> 267 edge_collection=draw_networkx_edges(G, pos, **kwds)
268 if with_labels:
269 draw_networkx_labels(G, pos, **kwds)
/usr/local/lib/python2.7/site-packages/networkx/drawing/nx_pylab.pyc in draw_networkx_edges(G, pos, edgelist, width, edge_color, style, alpha, edge_cmap, edge_vmin, edge_vmax, ax, arrows, label, **kwds)
544 edge_collection.set_zorder(1) # edges go behind nodes
545 edge_collection.set_label(label)
--> 546 ax.add_collection(edge_collection)
547
548 # Note: there was a bug in mpl regarding the handling of alpha values for
/usr/local/lib/python2.7/site-packages/matplotlib/axes.pyc in add_collection(self, collection, autolim)
1443 if autolim:
1444 if collection._paths and len(collection._paths):
-> 1445 self.update_datalim(collection.get_datalim(self.transData))
1446
1447 collection._remove_method = lambda h: self.collections.remove(h)
/usr/local/lib/python2.7/site-packages/matplotlib/collections.pyc in get_datalim(self, transData)
165 offsets = offsets.filled(np.nan)
166 # get_path_collection_extents handles nan but not masked arrays
--> 167 offsets.shape = (-1, 2) # Make it Nx2
168
169 result = mpath.get_path_collection_extents(
AttributeError: incompatible shape for a non-contiguous array
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/usr/local/lib/python2.7/site-packages/IPython/zmq/pylab/backend_inline.pyc in show(close)
100 try:
101 for figure_manager in Gcf.get_all_fig_managers():
--> 102 send_figure(figure_manager.canvas.figure)
103 finally:
104 show._to_draw = []
/usr/local/lib/python2.7/site-packages/IPython/zmq/pylab/backend_inline.pyc in send_figure(fig)
209 """
210 fmt = InlineBackend.instance().figure_format
--> 211 data = print_figure(fig, fmt)
212 # print_figure will return None if there's nothing to draw:
213 if data is None:
/usr/local/lib/python2.7/site-packages/IPython/core/pylabtools.pyc in print_figure(fig, fmt)
102 try:
103 bytes_io = BytesIO()
--> 104 fig.canvas.print_figure(bytes_io, format=fmt, bbox_inches='tight')
105 data = bytes_io.getvalue()
106 finally:
/usr/local/lib/python2.7/site-packages/matplotlib/backend_bases.pyc in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, **kwargs)
1981 orientation=orientation,
1982 dryrun=True,
-> 1983 **kwargs)
1984 renderer = self.figure._cachedRenderer
1985 bbox_inches = self.figure.get_tightbbox(renderer)
/usr/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.pyc in print_png(self, filename_or_obj, *args, **kwargs)
467
468 def print_png(self, filename_or_obj, *args, **kwargs):
--> 469 FigureCanvasAgg.draw(self)
470 renderer = self.get_renderer()
471 original_dpi = renderer.dpi
/usr/local/lib/python2.7/site-packages/matplotlib/backends/backend_agg.pyc in draw(self)
419
420 try:
--> 421 self.figure.draw(self.renderer)
422 finally:
423 RendererAgg.lock.release()
/usr/local/lib/python2.7/site-packages/matplotlib/artist.pyc in draw_wrapper(artist, renderer, *args, **kwargs)
53 def draw_wrapper(artist, renderer, *args, **kwargs):
54 before(artist, renderer)
---> 55 draw(artist, renderer, *args, **kwargs)
56 after(artist, renderer)
57
/usr/local/lib/python2.7/site-packages/matplotlib/figure.pyc in draw(self, renderer)
896 dsu.sort(key=itemgetter(0))
897 for zorder, a, func, args in dsu:
--> 898 func(*args)
899
900 renderer.close_group('figure')
/usr/local/lib/python2.7/site-packages/matplotlib/artist.pyc in draw_wrapper(artist, renderer, *args, **kwargs)
53 def draw_wrapper(artist, renderer, *args, **kwargs):
54 before(artist, renderer)
---> 55 draw(artist, renderer, *args, **kwargs)
56 after(artist, renderer)
57
/usr/local/lib/python2.7/site-packages/matplotlib/axes.pyc in draw(self, renderer, inframe)
1995
1996 for zorder, a in dsu:
-> 1997 a.draw(renderer)
1998
1999 renderer.close_group('axes')
/usr/local/lib/python2.7/site-packages/matplotlib/artist.pyc in draw_wrapper(artist, renderer, *args, **kwargs)
53 def draw_wrapper(artist, renderer, *args, **kwargs):
54 before(artist, renderer)
---> 55 draw(artist, renderer, *args, **kwargs)
56 after(artist, renderer)
57
/usr/local/lib/python2.7/site-packages/matplotlib/collections.pyc in draw(self, renderer)
227 self.update_scalarmappable()
228
--> 229 transform, transOffset, offsets, paths = self._prepare_points()
230
231 gc = renderer.new_gc()
/usr/local/lib/python2.7/site-packages/matplotlib/collections.pyc in _prepare_points(self)
203
204 offsets = np.asanyarray(offsets, np.float_)
--> 205 offsets.shape = (-1, 2) # Make it Nx2
206
207 if not transform.is_affine:
AttributeError: incompatible shape for a non-contiguous array

Answer 1

This was reported earlier in Draw a graph with edges using Networkx. It likely is a bug/feature in the NumPy library development version as mentioned above (numpy issue 2700).