Remapping notebook is broken on RTD

[alioacar]

Summary

The remapping notebook currently renders a traceback on RTD, likely solver/env drift in HoloViews/Matplotlib stack. The failure happens at display time in the HoloViews matplotlib backend.

Details

holoviews.plotting.mpl.util.fix_aspect is computing NaN for aspect/height so matplotlib rejects the call to set_size_inches().

Potential Solution

Explicitly setting the fig_inches may be more robust here ?

Full traceback

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/core/dimension.py:1491, in Dimensioned._repr_mimebundle_(self, include, exclude)
   1484 def _repr_mimebundle_(self, include=None, exclude=None):
   1485     """Resolves the class hierarchy for the class rendering the
   1486     object using any display hooks registered on Store.display
   1487     hooks.  The output of all registered display_hooks is then
   1488     combined and returned.
   1489 
   1490     """
-> 1491     return Store.render(self)

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/core/options.py:1517, in Store.render(cls, obj)
   1515 data, metadata = {}, {}
   1516 for hook in hooks:
-> 1517     ret = hook(obj)
   1518     if ret is None:
   1519         continue

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/ipython/display_hooks.py:330, in pprint_display(obj)
    328 if not ip.display_formatter.formatters["text/plain"].pprint:
    329     return None
--> 330 return display(obj, raw_output=True)

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/ipython/display_hooks.py:301, in display(obj, raw_output, **kwargs)
    299 elif isinstance(obj, (Layout, NdLayout, AdjointLayout)):
    300     with option_state(obj):
--> 301         output = layout_display(obj)
    302 elif isinstance(obj, (HoloMap, DynamicMap)):
    303     with option_state(obj):

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/ipython/display_hooks.py:193, in display_hook.<locals>.wrapped(element)
    191 try:
    192     max_frames = OutputSettings.options["max_frames"]
--> 193     mimebundle = fn(element, max_frames=max_frames)
    194     if mimebundle is None:
    195         return {}, {}

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/ipython/display_hooks.py:261, in layout_display(layout, max_frames)
    258     max_frame_warning(max_frames)
    259     return None
--> 261 return render(layout)

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/ipython/display_hooks.py:62, in render(obj, **kwargs)
     59 if renderer.fig == "pdf":
     60     renderer = renderer.instance(fig="png")
---> 62 return renderer.components(obj, **kwargs)

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/plotting/renderer.py:430, in Renderer.components(self, obj, fmt, comm, **kwargs)
    428     plot = obj
    429 else:
--> 430     plot, fmt = self._validate(obj, fmt)
    432 if not isinstance(plot, Viewable):
    433     html = self._figure_data(plot, fmt, as_script=True, **kwargs)

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/plotting/renderer.py:361, in Renderer._validate(self, obj, fmt, **kwargs)
    359     plot = HoloViewsPane(obj, center=self.center, backend=self.backend, renderer=self)
    360 else:
--> 361     plot = self.get_plot(obj, renderer=self, **kwargs)
    363 all_formats = set(fig_formats + holomap_formats)
    364 if fmt not in all_formats:

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/plotting/renderer.py:291, in Renderer.get_plot(self_or_cls, obj, doc, renderer, comm, **kwargs)
    287     defaults = [kd.default for kd in plot.dimensions]
    288     init_key = tuple(
    289         v if d is None else d for v, d in zip(plot.keys[0], defaults, strict=None)
    290     )
--> 291     plot.update(init_key)
    292 else:
    293     plot = obj

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/plotting/mpl/plot.py:335, in MPLPlot.update(self, key)
    333 def update(self, key):
    334     if len(self) == 1 and key in (0, self.keys[0]) and not self.drawn:
--> 335         return self.initialize_plot()
    336     return self.__getitem__(key)

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/plotting/mpl/plot.py:64, in mpl_rc_context.<locals>.wrapper(self, *args, **kwargs)
     62 def wrapper(self, *args, **kwargs):
     63     with _rc_context(self.fig_rcparams):
---> 64         return f(self, *args, **kwargs)

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/plotting/mpl/plot.py:1283, in LayoutPlot.initialize_plot(self)
   1277 traverse_fn = lambda x: x.handles.get("bbox_extra_artists", None)
   1278 extra_artists = list(
   1279     chain.from_iterable(
   1280         artists for artists in self.traverse(traverse_fn) if artists is not None
   1281     )
   1282 )
-> 1283 fix_aspect(
   1284     fig,
   1285     self.rows,
   1286     self.cols,
   1287     title_obj,
   1288     extra_artists,
   1289     vspace=self.vspace * self.fig_scale,
   1290     hspace=self.hspace * self.fig_scale,
   1291 )
   1292 colorbars = self.traverse(specs=[lambda x: hasattr(x, "colorbar")])
   1293 for cbar_plot in colorbars:

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/holoviews/plotting/mpl/util.py:288, in fix_aspect(fig, nrows, ncols, title, extra_artists, vspace, hspace)
    286 if title and title.get_text():
    287     offset = title.get_window_extent().height / fig.dpi
--> 288 fig.set_size_inches(w, (w * aspect) + offset)
    290 # Redraw and adjust title position if defined
    291 fig.canvas.draw()

File ~/checkouts/readthedocs.org/user_builds/uxarray/conda/latest/lib/python3.14/site-packages/matplotlib/figure.py:3167, in Figure.set_size_inches(self, w, h, forward)
   3165 size = np.array([w, h])
   3166 if not np.isfinite(size).all() or (size < 0).any():
-> 3167     raise ValueError(f'figure size must be positive finite not {size}')
   3168 self.bbox_inches.p1 = size
   3169 if forward:

ValueError: figure size must be positive finite not [ 8. nan]

[Sevans711]

Some extra info as I tried to reproduce and debug: I don't see the crash when I try the code with hv.extension('bokeh'). Additionally, I can reproduce the crash on Python 3.14 and 3.13, but it makes plots just fine on Python 3.10. Maybe this will provide a hint about how to fix? I confirmed holoviews version is the same (holoviews 1.23.0) across my different Python environments.

[Sevans711]

A similar error is currently occurring in the MPAS atmosphere cookbook: https://projectpythia.org/unstructured-grid-viz-cookbook/notebooks/recipes/mpas-atmo/

Pasting that traceback below for future reference:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/core/dimension.py:1491, in Dimensioned._repr_mimebundle_(self, include, exclude)
   1484 def _repr_mimebundle_(self, include=None, exclude=None):
   1485     """Resolves the class hierarchy for the class rendering the
   1486     object using any display hooks registered on Store.display
   1487     hooks.  The output of all registered display_hooks is then
   1488     combined and returned.
   1489 
   1490     """
-> 1491     return Store.render(self)

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/core/options.py:1517, in Store.render(cls, obj)
   1515 data, metadata = {}, {}
   1516 for hook in hooks:
-> 1517     ret = hook(obj)
   1518     if ret is None:
   1519         continue

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/ipython/display_hooks.py:330, in pprint_display(obj)
    328 if not ip.display_formatter.formatters["text/plain"].pprint:
    329     return None
--> 330 return display(obj, raw_output=True)

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/ipython/display_hooks.py:301, in display(obj, raw_output, **kwargs)
    299 elif isinstance(obj, (Layout, NdLayout, AdjointLayout)):
    300     with option_state(obj):
--> 301         output = layout_display(obj)
    302 elif isinstance(obj, (HoloMap, DynamicMap)):
    303     with option_state(obj):

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/ipython/display_hooks.py:193, in display_hook.<locals>.wrapped(element)
    191 try:
    192     max_frames = OutputSettings.options["max_frames"]
--> 193     mimebundle = fn(element, max_frames=max_frames)
    194     if mimebundle is None:
    195         return {}, {}

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/ipython/display_hooks.py:261, in layout_display(layout, max_frames)
    258     max_frame_warning(max_frames)
    259     return None
--> 261 return render(layout)

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/ipython/display_hooks.py:62, in render(obj, **kwargs)
     59 if renderer.fig == "pdf":
     60     renderer = renderer.instance(fig="png")
---> 62 return renderer.components(obj, **kwargs)

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/plotting/renderer.py:430, in Renderer.components(self, obj, fmt, comm, **kwargs)
    428     plot = obj
    429 else:
--> 430     plot, fmt = self._validate(obj, fmt)
    432 if not isinstance(plot, Viewable):
    433     html = self._figure_data(plot, fmt, as_script=True, **kwargs)

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/plotting/renderer.py:361, in Renderer._validate(self, obj, fmt, **kwargs)
    359     plot = HoloViewsPane(obj, center=self.center, backend=self.backend, renderer=self)
    360 else:
--> 361     plot = self.get_plot(obj, renderer=self, **kwargs)
    363 all_formats = set(fig_formats + holomap_formats)
    364 if fmt not in all_formats:

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/plotting/renderer.py:291, in Renderer.get_plot(self_or_cls, obj, doc, renderer, comm, **kwargs)
    287     defaults = [kd.default for kd in plot.dimensions]
    288     init_key = tuple(
    289         v if d is None else d for v, d in zip(plot.keys[0], defaults, strict=None)
    290     )
--> 291     plot.update(init_key)
    292 else:
    293     plot = obj

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/plotting/mpl/plot.py:335, in MPLPlot.update(self, key)
    333 def update(self, key):
    334     if len(self) == 1 and key in (0, self.keys[0]) and not self.drawn:
--> 335         return self.initialize_plot()
    336     return self.__getitem__(key)

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/plotting/mpl/plot.py:64, in mpl_rc_context.<locals>.wrapper(self, *args, **kwargs)
     62 def wrapper(self, *args, **kwargs):
     63     with _rc_context(self.fig_rcparams):
---> 64         return f(self, *args, **kwargs)

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/plotting/mpl/plot.py:1283, in LayoutPlot.initialize_plot(self)
   1277 traverse_fn = lambda x: x.handles.get("bbox_extra_artists", None)
   1278 extra_artists = list(
   1279     chain.from_iterable(
   1280         artists for artists in self.traverse(traverse_fn) if artists is not None
   1281     )
   1282 )
-> 1283 fix_aspect(
   1284     fig,
   1285     self.rows,
   1286     self.cols,
   1287     title_obj,
   1288     extra_artists,
   1289     vspace=self.vspace * self.fig_scale,
   1290     hspace=self.hspace * self.fig_scale,
   1291 )
   1292 colorbars = self.traverse(specs=[lambda x: hasattr(x, "colorbar")])
   1293 for cbar_plot in colorbars:

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/holoviews/plotting/mpl/util.py:288, in fix_aspect(fig, nrows, ncols, title, extra_artists, vspace, hspace)
    286 if title and title.get_text():
    287     offset = title.get_window_extent().height / fig.dpi
--> 288 fig.set_size_inches(w, (w * aspect) + offset)
    290 # Redraw and adjust title position if defined
    291 fig.canvas.draw()

File ~/micromamba/envs/unstructured-grid-viz-cookbook-dev/lib/python3.14/site-packages/matplotlib/figure.py:3167, in Figure.set_size_inches(self, w, h, forward)
   3165 size = np.array([w, h])
   3166 if not np.isfinite(size).all() or (size < 0).any():
-> 3167     raise ValueError(f'figure size must be positive finite not {size}')
   3168 self.bbox_inches.p1 = size
   3169 if forward:

ValueError: figure size must be positive finite not [ 8. nan]

[Sevans711]

A probably-similar bug is affecting the "Reading Structured Grids" page: https://uxarray.readthedocs.io/en/latest/user-guide/structured.html

There's no crash message, but the plot looks similar to what I was seeing when trying to reproduce the issue from the remapping page using a single plot instead of a Layout with 2 plots in a column. The plot is hidden except for a sliver on the right, and also the colorbar is visible.

[Sevans711]

There is also a similar crash in the "Constructing a Grid from Points" page: https://uxarray.readthedocs.io/en/latest/user-guide/from-points.html

The traceback is similar to what I copy-pasted in prior message, but ends with ValueError: figure size must be positive finite not [12. nan] instead. (This one is supposed to be a layout with 3 plots; I am noticing the error message follows the pattern [4 * number of plots, nan])

I think this last one concludes the list of uxarray documentation pages / cookbooks which are being affected by this bug; I just finished looking through most (all?) docs and cookbooks. Next step is to debug, then check if the solution actually fixes all of these examples.

[Sevans711]

Progress update: I believe I've narrowed it down to the latest matplotlib update, 3.11.0. When I downgrade to the latest pre-3.11 version, matplotlib 3.10.9, I don't get the crash, I instead get nice plots.

If we need a very quick fix, we could change dependencies to require matplotlib<3.11 for now. In the meantime, I'll see if I can find a fix when still using matplotlib 3.11.

Summary:

Python version	matplotlib 3.10.9	matplotlib 3.11.0
3.10.20	plots look good	(not available for Python 3.10)
3.13.14	plots look good	bug occurs
3.14.6	plots look good	bug occurs

[Sevans711]

This looks like an upstream issue; I was able to reproduce it without using UXarray at all. See holoviz/geoviews#850 for more details!