[graph-tool] Building a Price Network Quickstart Error Message

[Jos J]

Hello,

I am going through the quickstart titled "An Example: Building a Price
Network" found here
https://graph-tool.skewed.de/static/doc/quickstart.html#an-example-building-a-price-network

After running the program, I receive the following output which is
different from what the quickstart suggests should be output. Here is what
I get:

--

vertex: 36063 in-degree: 0 out-degree: 1 age: 36063
vertex: 9075 in-degree: 4 out-degree: 1 age: 9075
vertex: 5967 in-degree: 3 out-degree: 1 age: 5967
vertex: 1113 in-degree: 7 out-degree: 1 age: 1113
vertex: 25 in-degree: 84 out-degree: 1 age: 25
vertex: 10 in-degree: 541 out-degree: 1 age: 10
vertex: 5 in-degree: 140 out-degree: 1 age: 5
vertex: 2 in-degree: 362 out-degree: 1 age: 2
vertex: 0 in-degree: 636 out-degree: 0 age: 0
Nowhere else to go... We found the main hub!

-

The output from "vertex: 36063 ..." down to "vertex: 5 ..." is as expected,
but at "vertex: 2 ..." onward is different, and I am receiving the
following error message, and the plot fails to be drawn

"ValueError: 'yerr' must not contain negative values"

The full error output is as follows

--

ValueErrorTraceback (most recent call last)
Cell In [2], line 92 89 err[err >= y] = y[err >= y] - 1e-2 91
figure(figsize=(6,4))---> 92 errorbar(in_hist[1][:-1], in_hist[0],
fmt="o", yerr=err, 93 label="in") 94
gca().set_yscale("log") 95 gca().set_xscale("log")

File 
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/matplotlib/pyplot.py:2480,
in errorbar(x, y, yerr, xerr, fmt, ecolor, elinewidth, capsize,
barsabove, lolims, uplims, xlolims, xuplims, errorevery, capthick,
data, **kwargs)   2474 @_copy_docstring_and_deprecators(Axes.errorbar)
  2475 def errorbar(   2476 x, y, yerr=None, xerr=None,
fmt='', ecolor=None,   2477 elinewidth=None, capsize=None,
barsabove=False, lolims=False,   2478 uplims=False,
xlolims=False, xuplims=False, errorevery=1,   2479
capthick=None, *, data=None, **kwargs):-> 2480 return
gca().errorbar(   2481 x, y, yerr=yerr, xerr=xerr, fmt=fmt,
ecolor=ecolor,   2482 elinewidth=elinewidth, capsize=capsize,
barsabove=barsabove,   2483 lolims=lolims, uplims=uplims,
xlolims=xlolims,   2484 xuplims=xuplims,
errorevery=errorevery, capthick=capthick,   2485 **({"data":
data} if data is not None else {}), **kwargs)

File 
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/matplotlib/__init__.py:1423,
in _preprocess_data..inner(ax, data, *args, **kwargs)   1420
@functools.wraps(func)   1421 def inner(ax, *args, data=None,
**kwargs):   1422 if data is None:-> 1423 return func(ax,
*map(sanitize_sequence, args), **kwargs)   1425 bound =
new_sig.bind(ax, *args, **kwargs)   1426 auto_label =
(bound.arguments.get(label_namer)   1427   or
bound.kwargs.get(label_namer))

File 
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/matplotlib/axes/_axes.py:3587,
in Axes.errorbar(self, x, y, yerr, xerr, fmt, ecolor, elinewidth,
capsize, barsabove, lolims, uplims, xlolims, xuplims, errorevery,
capthick, **kwargs)   3584 res = np.zeros(err.shape, dtype=bool)  #
Default in case of nan   3585 if np.any(np.less(err, -err, out=res,
where=(err == err))):   3586 # like err<0, but also works for
timedelta and nan.-> 3587 raise ValueError(   3588
f"'{dep_axis}err' must not contain negative values")   3589 # This is
like   3590 # elow, ehigh = np.broadcast_to(...)   3591 #
return dep - elow * ~lolims, dep + ehigh * ~uplims   3592 # except
that broadcast_to would strip units.   3593 low, high = dep +
np.row_stack([-(1 - lolims), 1 - uplims]) * err
ValueError: 'yerr' must not contain negative values

-


Any idea as to what the issue might be? I am running Python 3.8,
Matplotlib 3.6.0, and graph-tool 2.45


Apologies for the previous message for the wrong library to this list,
I am testing out a few libraries and hastily sent that message to the
wrong project.
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[graph-tool] Re: Installing igraph tutorial from website: AttributeError: 'AxesSubplot' object has no attribute 'arc'

[Jos J]

My sincerest apologies

On Wed, Sep 21, 2022 at 3:52 AM Tiago de Paula Peixoto 
wrote:

> Hi,
>
> I can't believe I have to explain this, but this is the mailing list for
> graph-tool, not for igraph.
>
> Please refer to the igraph mailing list for help.
>
> Best,
> Tiago
>
> Am 21.09.22 um 12:21 schrieb Jos J:
> > I have python 3.8.13, igraph 0.10.1, with matplotlib 3.6.0, and when
> > running the sample scripts from the install page on the website, I am
> > receiving an error. The scripts can be found here:
> > https://igraph.org/python/tutorial/latest/install.html
> > 
> >
> > I am referring to the following
> >
> >  >>> import matplotlib.pyplot as plt
> >  >>> import igraph as ig
> >  >>> fig, ax = plt.subplots()
> >  >>> g = ig.Graph.Famous("petersen")
> >  >>> ig.plot(g, target=ax)
> >  >>> plt.show()
> >
> > I receive the following errors at the ig.plot(g, target=ax) line:
> >
> >
> ---
> > AttributeErrorTraceback (most recent call
> last)
> > Cell In [120], line 6
> >4 fig, ax = plt.subplots()
> >5 g = ig.Graph.Famous("petersen")
> > > 6 ig.plot(g, target=ax)
> >8 plt.show()
> >
> > File
> >
> ~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/__init__.py:245,
> in plot(obj, target, bbox, *args, **kwds)
> >  243 return
> >  244 else:
> > --> 245 plotter(
> >  246 backend,
> >  247 target,
> >  248 palette=palette,
> >  249 *args,
> >  250 **kwds,
> >  251 )
> >  252 return target
> >  254 # Cairo backend
> >
> > File
> >
> ~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/graph.py:558,
> in __plot__(self, backend, context, *args, **kwds)
> >  552 from igraph.drawing import DrawerDirectory
> >  554 drawer = kwds.pop(
> >  555 "drawer_factory",
> >  556 DrawerDirectory.resolve(self, backend)(context),
> >  557 )
> > --> 558 drawer.draw(self, *args, **kwds)
> >
> > File
> >
> ~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/matplotlib/graph.py:233,
> in MatplotlibGraphDrawer.draw(self, graph, *args, **kwds)
> >  231 drawer_method = vertex_drawer.draw
> >  232 for vertex, visual_vertex, coords in vertex_coord_iter:
> > --> 233 drawer_method(visual_vertex, vertex, coords)
> >  235 # Construct the iterator that we will use to draw the vertex
> labels
> >  236 vs = graph.vs
> >
> > File
> >
> ~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/matplotlib/vertex.py:60,
> in MatplotlibVertexDrawer.draw(self, visual_vertex, vertex, coords)
> >   49 width = (
> >   50 visual_vertex.width
> >   51 if visual_vertex.width is not None
> >   52 else visual_vertex.size
> >   53 )
> >   54 height = (
> >   55 visual_vertex.height
> >   56 if visual_vertex.height is not None
> >   57 else visual_vertex.size
> >   58 )
> > ---> 60 stroke = visual_vertex.shape.draw_path(
> >   61 ax,
> >   62 coords[0],
> >   63 coords[1],
> >   64 width,
> >   65 height,
> >   66 facecolor=visual_vertex.color,
> >   67 edgecolor=visual_vertex.frame_color,
> >   68 linewidth=visual_vertex.frame_width,
> >   69 zorder=visual_vertex.zorder,
> >   70 )
> >   71 ax.add_patch(stroke)
> >
> > File
> >
> ~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/shapes.py:168,
> in CircleDrawer.draw_path(ctx, center_x, center_y, width, height, **kwargs)
> >  166 return mpl.patches.Circle((center_x, center_y), width / 2,
> > **kwargs)
> >  167 else:
> > --> 168 ctx.arc(center_x, center_y, width / 2, 0, 2 * pi)
> >
> > AttributeError: 'AxesSubplot' object has no attribute 'arc'
> >
> >
> > -
> >
> > Not sure if its my python or package versions, or if its a configuration
> > issue, or possibly an issue with igraph or matplotlib. Any advice would
> > be most welcome
> >
> > ___
> > graph-tool mailing list -- graph-tool@skewed.de
> > To unsubscribe send an email to graph-tool-le...@skewed.de
>
> --
> Tiago de Paula Peixoto 
>
> ___
> graph-tool mailing list -- graph-tool@skewed.de
> To unsubscribe send an email to graph-tool-le...@skewed.de
>
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[graph-tool] Re: Installing igraph tutorial from website: AttributeError: 'AxesSubplot' object has no attribute 'arc'

[Tiago de Paula Peixoto]

Hi,

I can't believe I have to explain this, but this is the mailing list for 
graph-tool, not for igraph.


Please refer to the igraph mailing list for help.

Best,
Tiago

Am 21.09.22 um 12:21 schrieb Jos J:
I have python 3.8.13, igraph 0.10.1, with matplotlib 3.6.0, and when 
running the sample scripts from the install page on the website, I am 
receiving an error. The scripts can be found here: 
https://igraph.org/python/tutorial/latest/install.html 



I am referring to the following

 >>> import matplotlib.pyplot as plt
 >>> import igraph as ig
 >>> fig, ax = plt.subplots()
 >>> g = ig.Graph.Famous("petersen")
 >>> ig.plot(g, target=ax)
 >>> plt.show()

I receive the following errors at the ig.plot(g, target=ax) line:

---
AttributeError                            Traceback (most recent call last)
Cell In [120], line 6
       4 fig, ax = plt.subplots()
       5 g = ig.Graph.Famous("petersen")
> 6 ig.plot(g, target=ax)
       8 plt.show()

File 
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/__init__.py:245, in plot(obj, target, bbox, *args, **kwds)

     243         return
     244     else:
--> 245         plotter(
     246             backend,
     247             target,
     248             palette=palette,
     249             *args,
     250             **kwds,
     251         )
     252         return target
     254 # Cairo backend

File 
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/graph.py:558, in __plot__(self, backend, context, *args, **kwds)

     552 from igraph.drawing import DrawerDirectory
     554 drawer = kwds.pop(
     555     "drawer_factory",
     556     DrawerDirectory.resolve(self, backend)(context),
     557 )
--> 558 drawer.draw(self, *args, **kwds)

File 
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/matplotlib/graph.py:233, in MatplotlibGraphDrawer.draw(self, graph, *args, **kwds)

     231 drawer_method = vertex_drawer.draw
     232 for vertex, visual_vertex, coords in vertex_coord_iter:
--> 233     drawer_method(visual_vertex, vertex, coords)
     235 # Construct the iterator that we will use to draw the vertex labels
     236 vs = graph.vs

File 
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/matplotlib/vertex.py:60, in MatplotlibVertexDrawer.draw(self, visual_vertex, vertex, coords)

      49 width = (
      50     visual_vertex.width
      51     if visual_vertex.width is not None
      52     else visual_vertex.size
      53 )
      54 height = (
      55     visual_vertex.height
      56     if visual_vertex.height is not None
      57     else visual_vertex.size
      58 )
---> 60 stroke = visual_vertex.shape.draw_path(
      61     ax,
      62     coords[0],
      63     coords[1],
      64     width,
      65     height,
      66     facecolor=visual_vertex.color,
      67     edgecolor=visual_vertex.frame_color,
      68     linewidth=visual_vertex.frame_width,
      69     zorder=visual_vertex.zorder,
      70 )
      71 ax.add_patch(stroke)

File 
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/shapes.py:168, in CircleDrawer.draw_path(ctx, center_x, center_y, width, height, **kwargs)
     166     return mpl.patches.Circle((center_x, center_y), width / 2, 
**kwargs)

     167 else:
--> 168     ctx.arc(center_x, center_y, width / 2, 0, 2 * pi)

AttributeError: 'AxesSubplot' object has no attribute 'arc'


-

Not sure if its my python or package versions, or if its a configuration 
issue, or possibly an issue with igraph or matplotlib. Any advice would 
be most welcome


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--
Tiago de Paula Peixoto 



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[graph-tool] Installing igraph tutorial from website: AttributeError: 'AxesSubplot' object has no attribute 'arc'

[Jos J]

I have python 3.8.13, igraph 0.10.1, with matplotlib 3.6.0, and when
running the sample scripts from the install page on the website, I am
receiving an error. The scripts can be found here:
https://igraph.org/python/tutorial/latest/install.html

I am referring to the following

>>> import matplotlib.pyplot as plt
>>> import igraph as ig
>>> fig, ax = plt.subplots()
>>> g = ig.Graph.Famous("petersen")
>>> ig.plot(g, target=ax)
>>> plt.show()

I receive the following errors at the ig.plot(g, target=ax) line:

---
AttributeErrorTraceback (most recent call last)
Cell In [120], line 6
  4 fig, ax = plt.subplots()
  5 g = ig.Graph.Famous("petersen")
> 6 ig.plot(g, target=ax)
  8 plt.show()

File
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/__init__.py:245,
in plot(obj, target, bbox, *args, **kwds)
243 return
244 else:
--> 245 plotter(
246 backend,
247 target,
248 palette=palette,
249 *args,
250 **kwds,
251 )
252 return target
254 # Cairo backend

File
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/graph.py:558,
in __plot__(self, backend, context, *args, **kwds)
552 from igraph.drawing import DrawerDirectory
554 drawer = kwds.pop(
555 "drawer_factory",
556 DrawerDirectory.resolve(self, backend)(context),
557 )
--> 558 drawer.draw(self, *args, **kwds)

File
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/matplotlib/graph.py:233,
in MatplotlibGraphDrawer.draw(self, graph, *args, **kwds)
231 drawer_method = vertex_drawer.draw
232 for vertex, visual_vertex, coords in vertex_coord_iter:
--> 233 drawer_method(visual_vertex, vertex, coords)
235 # Construct the iterator that we will use to draw the vertex labels
236 vs = graph.vs

File
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/matplotlib/vertex.py:60,
in MatplotlibVertexDrawer.draw(self, visual_vertex, vertex, coords)
 49 width = (
 50 visual_vertex.width
 51 if visual_vertex.width is not None
 52 else visual_vertex.size
 53 )
 54 height = (
 55 visual_vertex.height
 56 if visual_vertex.height is not None
 57 else visual_vertex.size
 58 )
---> 60 stroke = visual_vertex.shape.draw_path(
 61 ax,
 62 coords[0],
 63 coords[1],
 64 width,
 65 height,
 66 facecolor=visual_vertex.color,
 67 edgecolor=visual_vertex.frame_color,
 68 linewidth=visual_vertex.frame_width,
 69 zorder=visual_vertex.zorder,
 70 )
 71 ax.add_patch(stroke)

File
~/anaconda3/envs/rapids-2208/lib/python3.8/site-packages/igraph/drawing/shapes.py:168,
in CircleDrawer.draw_path(ctx, center_x, center_y, width, height, **kwargs)
166 return mpl.patches.Circle((center_x, center_y), width / 2,
**kwargs)
167 else:
--> 168 ctx.arc(center_x, center_y, width / 2, 0, 2 * pi)

AttributeError: 'AxesSubplot' object has no attribute 'arc'


-

Not sure if its my python or package versions, or if its a configuration
issue, or possibly an issue with igraph or matplotlib. Any advice would be
most welcome
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