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graph-tool@skewed.de

September 2022

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Building a Price Network Quickstart Error Message
by Jos J 22 Sep '22

22 Sep '22

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… 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 -------------- ValueError Traceback (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.<locals>.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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Installing igraph tutorial from website: AttributeError: 'AxesSubplot' object has no attribute 'arc'
by Jos J 21 Sep '22

21 Sep '22

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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