Matplotlib version [Urgent, maybe] #236
Comments
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This looks to me like a bilby problem, not a corner issue. Please see if you can reproduce the issue directly with corner. Thanks! |
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I checked the relevant Bilby code, I can affirm that issue is not from there. The |
But this seems inconsistent, if the issue only appears deep in wrapped code! I'm going to close this issue since it can't be reproduced, but please feel free to reopen with a simple example that doesn't rely on bilby or another downstream package. Thanks! |
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Just to note that I see this same problem too (using Matplotlib v3.8.0 and corner v2.2.2), but also going through gravitational-wave code, in this case accessing corner through pesummary. It doesn't seem to be a problem when using Matplotlib v3.7.2 and corner v2.2.1. |
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Thanks! I'd love to see this reproduced without a wrapper because I haven't been able to reproduce locally. Happy to investigate if we can! |
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I can't reproduce it with just corner either - I've tried with the same input kwargs that are being passed in my code that goes through pesummary. In fact, if I just use the pesummary |
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But @mattpitkin Also, |
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Ok, so I have more of a hint towards the problem. The following does not cause an error: import numpy as np
from corner import corner
data = np.random.randn(500, 4)
fig = corner(data)However, if I import in something from GWPy, e.g., from gwpy.plot.colors import GW_OBSERVATORY_COLORS
fig = corner(data)
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[13], line 1
----> 1 fig = corner(data)
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/corner/corner.py:248, in corner(data, bins, range, axes_scale, weights, color, hist_bin_factor, smooth, smooth1d, labels, label_kwargs, titles, show_titles, title_quantiles, title_fmt, title_kwargs, truths, truth_color, scale_hist, quantiles, verbose, fig, max_n_ticks, top_ticks, use_math_text, reverse, labelpad, hist_kwargs, group, var_names, filter_vars, coords, divergences, divergences_kwargs, labeller, **hist2d_kwargs)
236 if (
237 var_names is not None
238 or filter_vars is not None
(...)
242 or labeller is not None
243 ):
244 logging.warning(
245 "Please install arviz to use the advanced features of corner"
246 )
--> 248 return corner_impl(
249 data,
250 bins=bins,
251 range=range,
252 axes_scale=axes_scale,
253 weights=weights,
254 color=color,
255 hist_bin_factor=hist_bin_factor,
256 smooth=smooth,
257 smooth1d=smooth1d,
258 labels=labels,
259 label_kwargs=label_kwargs,
260 titles=titles,
261 show_titles=show_titles,
262 title_quantiles=title_quantiles,
263 title_fmt=title_fmt,
264 title_kwargs=title_kwargs,
265 truths=truths,
266 truth_color=truth_color,
267 scale_hist=scale_hist,
268 quantiles=quantiles,
269 verbose=verbose,
270 fig=fig,
271 max_n_ticks=max_n_ticks,
272 top_ticks=top_ticks,
273 use_math_text=use_math_text,
274 reverse=reverse,
275 labelpad=labelpad,
276 hist_kwargs=hist_kwargs,
277 **hist2d_kwargs,
278 )
280 return arviz_corner(
281 data,
282 bins=bins,
(...)
316 **hist2d_kwargs,
317 )
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/corner/core.py:370, in corner_impl(xs, bins, range, axes_scale, weights, color, hist_bin_factor, smooth, smooth1d, labels, label_kwargs, titles, show_titles, title_fmt, title_kwargs, truths, truth_color, scale_hist, quantiles, title_quantiles, verbose, fig, max_n_ticks, top_ticks, use_math_text, reverse, labelpad, hist_kwargs, **hist2d_kwargs)
367 if hasattr(y, "compressed"):
368 y = y.compressed()
--> 370 hist2d(
371 y,
372 x,
373 ax=ax,
374 range=[range[j], range[i]],
375 axes_scale=[axes_scale[j], axes_scale[i]],
376 weights=weights,
377 color=color,
378 smooth=smooth,
379 bins=[bins[j], bins[i]],
380 new_fig=new_fig,
381 force_range=force_range,
382 **hist2d_kwargs,
383 )
385 if max_n_ticks == 0:
386 ax.xaxis.set_major_locator(NullLocator())
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/corner/core.py:755, in hist2d(x, y, bins, range, axes_scale, weights, levels, smooth, ax, color, quiet, plot_datapoints, plot_density, plot_contours, no_fill_contours, fill_contours, contour_kwargs, contourf_kwargs, data_kwargs, pcolor_kwargs, new_fig, force_range, **kwargs)
753 data_kwargs["mec"] = data_kwargs.get("mec", "none")
754 data_kwargs["alpha"] = data_kwargs.get("alpha", 0.1)
--> 755 ax.plot(x, y, "o", zorder=-1, rasterized=True, **data_kwargs)
757 # Plot the base fill to hide the densest data points.
758 if (plot_contours or plot_density) and not no_fill_contours:
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/matplotlib/axes/_axes.py:1721, in Axes.plot(self, scalex, scaley, data, *args, **kwargs)
1478 """
1479 Plot y versus x as lines and/or markers.
1480
(...)
1718 (``'green'``) or hex strings (``'#008000'``).
1719 """
1720 kwargs = cbook.normalize_kwargs(kwargs, mlines.Line2D)
-> 1721 lines = [*self._get_lines(self, *args, data=data, **kwargs)]
1722 for line in lines:
1723 self.add_line(line)
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/matplotlib/axes/_base.py:303, in _process_plot_var_args.__call__(self, axes, data, *args, **kwargs)
301 this += args[0],
302 args = args[1:]
--> 303 yield from self._plot_args(
304 axes, this, kwargs, ambiguous_fmt_datakey=ambiguous_fmt_datakey)
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/matplotlib/axes/_base.py:539, in _process_plot_var_args._plot_args(self, axes, tup, kwargs, return_kwargs, ambiguous_fmt_datakey)
537 return list(result)
538 else:
--> 539 return [l[0] for l in result]
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/matplotlib/axes/_base.py:539, in <listcomp>(.0)
537 return list(result)
538 else:
--> 539 return [l[0] for l in result]
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/matplotlib/axes/_base.py:532, in <genexpr>(.0)
529 else:
530 labels = [label] * n_datasets
--> 532 result = (make_artist(axes, x[:, j % ncx], y[:, j % ncy], kw,
533 {**kwargs, 'label': label})
534 for j, label in enumerate(labels))
536 if return_kwargs:
537 return list(result)
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/matplotlib/axes/_base.py:398, in _process_plot_var_args._makefill(self, axes, x, y, kw, kwargs)
392 self._setdefaults(default_dict, kwargs)
394 seg = mpatches.Polygon(np.column_stack((x, y)),
395 facecolor=facecolor,
396 fill=kwargs.get('fill', True),
397 closed=kw['closed'])
--> 398 seg.set(**kwargs)
399 return seg, kwargs
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/matplotlib/artist.py:147, in Artist.__init_subclass__.<locals>.<lambda>(self, **kwargs)
139 if not hasattr(cls.set, '_autogenerated_signature'):
140 # Don't overwrite cls.set if the subclass or one of its parents
141 # has defined a set method set itself.
142 # If there was no explicit definition, cls.set is inherited from
143 # the hierarchy of auto-generated set methods, which hold the
144 # flag _autogenerated_signature.
145 return
--> 147 cls.set = lambda self, **kwargs: Artist.set(self, **kwargs)
148 cls.set.__name__ = "set"
149 cls.set.__qualname__ = f"{cls.__qualname__}.set"
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/matplotlib/artist.py:1227, in Artist.set(self, **kwargs)
1223 def set(self, **kwargs):
1224 # docstring and signature are auto-generated via
1225 # Artist._update_set_signature_and_docstring() at the end of the
1226 # module.
-> 1227 return self._internal_update(cbook.normalize_kwargs(kwargs, self))
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/matplotlib/artist.py:1219, in Artist._internal_update(self, kwargs)
1212 def _internal_update(self, kwargs):
1213 """
1214 Update artist properties without prenormalizing them, but generating
1215 errors as if calling `set`.
1216
1217 The lack of prenormalization is to maintain backcompatibility.
1218 """
-> 1219 return self._update_props(
1220 kwargs, "{cls.__name__}.set() got an unexpected keyword argument "
1221 "{prop_name!r}")
File ~/.conda/envs/cwinpy/lib/python3.9/site-packages/matplotlib/artist.py:1193, in Artist._update_props(self, props, errfmt)
1191 func = getattr(self, f"set_{k}", None)
1192 if not callable(func):
-> 1193 raise AttributeError(
1194 errfmt.format(cls=type(self), prop_name=k))
1195 ret.append(func(v))
1196 if ret:
AttributeError: Polygon.set() got an unexpected keyword argument 'markersize'These use:
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Good debugging! It looks like (by default) importing gwpy updates the matplotlib rcParams, which must somehow be causing both |
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But in the rc.py, there's no
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I think the markersize issue is a red herring. We have another error in Bilby that I think is more informative. Something is going wrong with the type that is being returned leading to having |
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@ColmTalbot I can confirm that, if I install GWPy from source so that it includes gwpy/gwpy#1661, then the problem goes away. So, we'll just have to wait for the next GWPy release. |
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Thanks all for tracking this down! |
With
Matplotlib >= 3.8andPython >=3.9,corner.pyraises theAttributeError: Polygon.set() got an unexpected keyword argument 'markersize'. To avoid this eithercorner.pyneeds to updated or Matplotlib should be restricted to< 3.8.Here is an extended version of the error:
Error (Click to expand)
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