Hi,
I'm trying to plot a graph in an interactive window using the graph_draw command with no output, and I get an error that says "interactive_window is not defined". The same thing happens when I run from a notebook with the kwarg inline=False.
I assume that this is an installation issue? I installed on a Mac via Homebrew, roughly following the recommended tutorial, and I'm pretty sure I have all the listed dependencies – boost, boost-python, cairo, cairomm, py2cairo, graphviz and many others are all installed via Homebrew.
This problem is independent of MatPlotLib; in any case the backend is set to MacOSX in my matplotlibrc file.
Please can you help me narrow it down?
The error trace is below.
Thanks!
Charlie
--------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-18-450166b22c69> in <module>() ----> 1 gt.graph_draw(g) #, inline=False)
/usr/local/lib/python2.7/site-packages/graph_tool/draw/cairo_draw.pyc in graph_draw(g, pos, vprops, eprops, vorder, eorder, nodesfirst, output_size, fit_view, inline, output, fmt, **kwargs) 875 eprops[p] = _convert(edge_attrs.__dict__[p], val, 876 kwargs.get("ecmap", default_cm)) --> 877 return interactive_window(g, pos, vprops, eprops, vorder, eorder, 878 nodesfirst, **kwargs) 879 else:
NameError: global name 'interactive_window' is not defined
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On 17.11.2014 15:55, charlie wrote:
Hi,
I'm trying to plot a graph in an interactive window using the graph_draw command with no output, and I get an error that says "interactive_window is not defined". The same thing happens when I run from a notebook with the kwarg inline=False.
I assume that this is an installation issue? I installed on a Mac via Homebrew, roughly following the recommended tutorial, and I'm pretty sure I have all the listed dependencies – boost, boost-python, cairo, cairomm, py2cairo, graphviz and many others are all installed via Homebrew.
This problem is independent of MatPlotLib; in any case the backend is set to MacOSX in my matplotlibrc file.
Please can you help me narrow it down?
Do you have Gtk+ and gobject installed?
Best, Tiago
Thank you very much for the reply Tiago.
Apparently I did not have GTK installed. I have now installed gtk+3 via homebrew, and it has included several dependencies including gobject-introspection.
Do I also need pygobject, or pygobject3?
And will I need to reinstall graph-tool (using make or make configure)?
Cheers,
Charlie
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On 18.11.2014 15:58, charlie wrote:
Thank you very much for the reply Tiago.
Apparently I did not have GTK installed. I have now installed gtk+3 via homebrew, and it has included several dependencies including gobject-introspection.
Do I also need pygobject, or pygobject3?
Yes, I think so.
And will I need to reinstall graph-tool (using make or make configure)?
No, this is not necessary.
Best, Tiago
Thanks.
I have installed gtk+3 and pygobject , and have definite progress. Import graph_tool now launches an X11 session, so that's promising. But the command that should produce an interactive plot now gives a different error. Traceback below.
Thank you very much for your ongoing help Tiago, you are a forum hero!
Best,
Charlie
gt.graph_draw(g, inline=False)
--------------------------------------------------------------------------- Error Traceback (most recent call last) <ipython-input-21-bd72d1c9116d> in <module>() ----> 1 gt.graph_draw(g, inline=False)
/usr/local/lib/python2.7/site-packages/graph_tool/draw/cairo_draw.pyc in graph_draw(g, pos, vprops, eprops, vorder, eorder, nodesfirst, output_size, fit_view, inline, output, fmt, **kwargs) 876 kwargs.get("ecmap", default_cm)) 877 return interactive_window(g, pos, vprops, eprops, vorder, eorder, --> 878 nodesfirst, **kwargs) 879 else: 880 if isinstance(output, str):
/usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.pyc in interactive_window(g, pos, vprops, eprops, vorder, eorder, nodesfirst, geometry, update_layout, async, **kwargs) 954 pos = sfdp_layout(g) 955 win = GraphWindow(g, pos, geometry, vprops, eprops, vorder, eorder, --> 956 nodesfirst, update_layout, **kwargs) 957 win.show_all() 958 if async:
/usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.pyc in __init__(self, g, pos, geometry, vprops, eprops, vorder, eorder, nodesfirst, update_layout, **kwargs) 884 Gtk.Window.__init__(self, title="graph-tool's interactive window™") 885 icon = GdkPixbuf.Pixbuf.new_from_file('%s/graph-tool-logo.svg' % --> 886 os.path.dirname(__file__)) 887 self.set_icon(icon) 888 self.set_default_size(geometry[0], geometry[1])
Error: gdk-pixbuf-error-quark: Couldn't recognise the image file format for file '/usr/local/lib/python2.7/site-packages/graph_tool/draw/graph-tool-logo.svg' (3)
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I’ve just installed libsvg and libsvg-cairo but neither one removes the error.
Cheers,
Charlie
On 18 Nov 2014, at 15:16, charlie charliejharrison@gmail.com wrote:
Thanks.
I have installed gtk+3 and pygobject , and have definite progress. Import graph_tool now launches an X11 session, so that's promising. But the command that should produce an interactive plot now gives a different error. Traceback below.
Thank you very much for your ongoing help Tiago, you are a forum hero!
Best,
Charlie
gt.graph_draw(g, inline=False)
Error Traceback (most recent call last) <ipython-input-21-bd72d1c9116d> in <module>() ----> 1 gt.graph_draw(g, inline=False)
/usr/local/lib/python2.7/site-packages/graph_tool/draw/cairo_draw.pyc in graph_draw(g, pos, vprops, eprops, vorder, eorder, nodesfirst, output_size, fit_view, inline, output, fmt, **kwargs) 876 kwargs.get("ecmap", default_cm)) 877 return interactive_window(g, pos, vprops, eprops, vorder, eorder, --> 878 nodesfirst, **kwargs) 879 else: 880 if isinstance(output, str):
/usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.pyc in interactive_window(g, pos, vprops, eprops, vorder, eorder, nodesfirst, geometry, update_layout, async, **kwargs) 954 pos = sfdp_layout(g) 955 win = GraphWindow(g, pos, geometry, vprops, eprops, vorder, eorder, --> 956 nodesfirst, update_layout, **kwargs) 957 win.show_all() 958 if async:
/usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.pyc in __init__(self, g, pos, geometry, vprops, eprops, vorder, eorder, nodesfirst, update_layout, **kwargs) 884 Gtk.Window.__init__(self, title="graph-tool's interactive window™") 885 icon = GdkPixbuf.Pixbuf.new_from_file('%s/graph-tool-logo.svg' % --> 886 os.path.dirname(__file__)) 887 self.set_icon(icon) 888 self.set_default_size(geometry[0], geometry[1])
Error: gdk-pixbuf-error-quark: Couldn't recognise the image file format for file '/usr/local/lib/python2.7/site-packages/graph_tool/draw/graph-tool-logo.svg' (3)
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On 18.11.2014 16:35, Charlie Harrison wrote:
I’ve just installed libsvg and libsvg-cairo but neither one removes the error.
You need to install librsvg (not libsvg).
Best, Tiago
I have that too but am still getting the same error :(
On 18 Nov 2014, at 15:39, Tiago de Paula Peixoto tiago@skewed.de wrote:
On 18.11.2014 16:35, Charlie Harrison wrote:
I’ve just installed libsvg and libsvg-cairo but neither one removes the error.
You need to install librsvg (not libsvg).
Best, Tiago
-- Tiago de Paula Peixoto tiago@skewed.de
graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
On 18.11.2014 16:46, Charlie Harrison wrote:
I have that too but am still getting the same error :(
Well, strange. This is probably a homebrew bug. Looking at
https://github.com/Homebrew/homebrew/blob/master/Library/Formula/librsvg.rb
it looks like the version there is pretty old, and for some reason introspection is not enabled.
I should report this problem to them.
Best, Tiago
Ok, I’ll do that.
Thanks again for your efforts.
Cheers,
Charlie
On 18 Nov 2014, at 15:54, Tiago de Paula Peixoto tiago@skewed.de wrote:
On 18.11.2014 16:46, Charlie Harrison wrote:
I have that too but am still getting the same error :(
Well, strange. This is probably a homebrew bug. Looking at
https://github.com/Homebrew/homebrew/blob/master/Library/Formula/librsvg.rb
it looks like the version there is pretty old, and for some reason introspection is not enabled.
I should report this problem to them.
Best, Tiago
-- Tiago de Paula Peixoto tiago@skewed.de
graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
Hi again Tiago!
I tried editing the Homebrew formula for librsvg to obtain the latest version and enable introspection, and sure enough I can now produce an interactive graph! Hooray! I've posted the issue on the Homebrew github page that you referred.
BUT: now I have a different problem. In my beautiful interactive graphs, the second node I select infallibly triggers a fatal error that kills the kernel. Here it is:
/usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.py:493: Warning: g_object_ref: assertion 'G_IS_OBJECT (object)' failed icon = self.render_icon(Gtk.STOCK_EXECUTE, Gtk.IconSize.BUTTON) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.pyc in draw(self, da, cr) 492 if self.surface_callback is not None: 493 icon = self.render_icon(Gtk.STOCK_EXECUTE, Gtk.IconSize.BUTTON) --> 494 Gdk.cairo_set_source_pixbuf(cr, icon, 10, 10) 495 cr.paint() 496
TypeError: Argument 1 does not allow None as a value
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) /usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.pyc in draw(self, da, cr) 492 if self.surface_callback is not None: 493 icon = self.render_icon(Gtk.STOCK_EXECUTE, Gtk.IconSize.BUTTON) --> 494 Gdk.cairo_set_source_pixbuf(cr, icon, 10, 10) 495 cr.paint() 496
TypeError: Argument 1 does not allow None as a value
Any ideas? Thanks!
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On 18.11.2014 19:12, charlie wrote:
Hi again Tiago!
I tried editing the Homebrew formula for librsvg to obtain the latest version and enable introspection, and sure enough I can now produce an interactive graph! Hooray! I've posted the issue on the Homebrew github page that you referred.
BUT: now I have a different problem. In my beautiful interactive graphs, the second node I select infallibly triggers a fatal error that kills the kernel. Here it is:
/usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.py:493: Warning: g_object_ref: assertion 'G_IS_OBJECT (object)' failed icon = self.render_icon(Gtk.STOCK_EXECUTE, Gtk.IconSize.BUTTON)
TypeError Traceback (most recent call last) /usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.pyc in draw(self, da, cr) 492 if self.surface_callback is not None: 493 icon = self.render_icon(Gtk.STOCK_EXECUTE, Gtk.IconSize.BUTTON) --> 494 Gdk.cairo_set_source_pixbuf(cr, icon, 10, 10) 495 cr.paint() 496
TypeError: Argument 1 does not allow None as a value
TypeError Traceback (most recent call last) /usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.pyc in draw(self, da, cr) 492 if self.surface_callback is not None: 493 icon = self.render_icon(Gtk.STOCK_EXECUTE, Gtk.IconSize.BUTTON) --> 494 Gdk.cairo_set_source_pixbuf(cr, icon, 10, 10) 495 cr.paint() 496
TypeError: Argument 1 does not allow None as a value
Any ideas? Thanks!
Well, this is obviously a Gtk bug, since it is failing to render a stock icon. You should also report this to the homebrew people.
(Alternatively, you may try Macports, where it is reported to work)
Best, Tiago
Thanks Tiago. Using the Macports install was the very first thing I tried, I’m rather committed to Homebrew through other packages. The two of them don’t play nicely together, and I ended up breaking a lot of other things. I might look into trying to get them to cooperate if I can’t get a fix for GTK.
Cheers,
Charlie
On 18 Nov 2014, at 18:42, Tiago de Paula Peixoto tiago@skewed.de wrote:
On 18.11.2014 19:12, charlie wrote:
Hi again Tiago!
I tried editing the Homebrew formula for librsvg to obtain the latest version and enable introspection, and sure enough I can now produce an interactive graph! Hooray! I've posted the issue on the Homebrew github page that you referred.
BUT: now I have a different problem. In my beautiful interactive graphs, the second node I select infallibly triggers a fatal error that kills the kernel. Here it is:
/usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.py:493: Warning: g_object_ref: assertion 'G_IS_OBJECT (object)' failed icon = self.render_icon(Gtk.STOCK_EXECUTE, Gtk.IconSize.BUTTON)
TypeError Traceback (most recent call last) /usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.pyc in draw(self, da, cr) 492 if self.surface_callback is not None: 493 icon = self.render_icon(Gtk.STOCK_EXECUTE, Gtk.IconSize.BUTTON) --> 494 Gdk.cairo_set_source_pixbuf(cr, icon, 10, 10) 495 cr.paint() 496
TypeError: Argument 1 does not allow None as a value
TypeError Traceback (most recent call last) /usr/local/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.pyc in draw(self, da, cr) 492 if self.surface_callback is not None: 493 icon = self.render_icon(Gtk.STOCK_EXECUTE, Gtk.IconSize.BUTTON) --> 494 Gdk.cairo_set_source_pixbuf(cr, icon, 10, 10) 495 cr.paint() 496
TypeError: Argument 1 does not allow None as a value
Any ideas? Thanks!
Well, this is obviously a Gtk bug, since it is failing to render a stock icon. You should also report this to the homebrew people.
(Alternatively, you may try Macports, where it is reported to work)
Best, Tiago
-- Tiago de Paula Peixoto <tiago@skewed.de mailto:tiago@skewed.de>
graph-tool mailing list graph-tool@skewed.de mailto:graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool http://lists.skewed.de/mailman/listinfo/graph-tool
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charlie -
Charlie Harrison
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Tiago de Paula Peixoto