[Bug]: ax.bar raises for all-nan data on matplotlib 3.6.1

[mwaskom]

Bug summary

ax.bar raises an exception in 3.6.1 when passed only nan data. This irrevocably breaks seaborn's histogram function (which draws and then removes a "phantom" bar to trip the color cycle).

Code for reproduction

import numpy as np
import matplotlib.pyplot as plt
f, ax = plt.subplots()
ax.bar([np.nan], [np.nan])

Actual outcome

---------------------------------------------------------------------------
StopIteration                             Traceback (most recent call last)
Cell In [1], line 4
      2 import matplotlib.pyplot as plt
      3 f, ax = plt.subplots()
----> 4 ax.bar([np.nan], [np.nan])[0].get_x()

File ~/miniconda/envs/py310/lib/python3.10/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 ~/miniconda/envs/py310/lib/python3.10/site-packages/matplotlib/axes/_axes.py:2373, in Axes.bar(self, x, height, width, bottom, align, **kwargs)
   2371 x0 = x
   2372 x = np.asarray(self.convert_xunits(x))
-> 2373 width = self._convert_dx(width, x0, x, self.convert_xunits)
   2374 if xerr is not None:
   2375     xerr = self._convert_dx(xerr, x0, x, self.convert_xunits)

File ~/miniconda/envs/py310/lib/python3.10/site-packages/matplotlib/axes/_axes.py:2182, in Axes._convert_dx(dx, x0, xconv, convert)
   2170 try:
   2171     # attempt to add the width to x0; this works for
   2172     # datetime+timedelta, for instance
   (...)
   2179     # removes the units from unit packages like `pint` that
   2180     # wrap numpy arrays.
   2181     try:
-> 2182         x0 = cbook._safe_first_finite(x0)
   2183     except (TypeError, IndexError, KeyError):
   2184         pass

File ~/miniconda/envs/py310/lib/python3.10/site-packages/matplotlib/cbook/__init__.py:1749, in _safe_first_finite(obj, skip_nonfinite)
   1746     raise RuntimeError("matplotlib does not "
   1747                        "support generators as input")
   1748 else:
-> 1749     return next(val for val in obj if safe_isfinite(val))

StopIteration: 

Expected outcome

On 3.6.0 this returns a BarCollection with one Rectangle, having nan for x and height.

Additional information

I assume it's related to this bullet in the release notes:

• Fix barplot being empty when first element is NaN

But I don't know the context for it to investigate further (could these link to PRs?)

Further debugging:

ax.bar([np.nan], [0])  # Raises
ax.bar([0], [np.nan])  # Works

So it's about the x position specifically.

Operating system

Macos

Matplotlib Version

3.6.1

Matplotlib Backend

No response

Python version

No response

Jupyter version

No response

Installation

pip

[oscargus]

This is the PR in question: #23751 (although I have not checked is that is causing it).

[mwaskom]

Thanks @oscargus that indeed looks like the culprit: it asks for the "next" finite value and does not handle the StopIteration exception that you get if there isn't one.

[tacaswell]

which draws and then removes a "phantom" bar to trip the color cycle

We should definitely fix this regression, but is there a better way for seaborn to be managing the colors that does not require adding and removing artists? I assume you use np.nan to avoid triggering any of the autoscaling?

[mwaskom]

We should definitely fix this regression, but is there a better way for seaborn to be managing the colors that does not require adding and removing artists?

Definitely open to that but none that I am aware of! I don't think there's a public API for advancing the property cycle? AFAIK one would need to do something like ax._get_patches_for_fill.get_next_color().

I assume you use np.nan to avoid triggering any of the autoscaling?

Yep, exactly. Actually in most cases I just pass empty data, but ax.bar([], []) doesn't return an artist (just an empty BarContainer so it doesn't work with that pattern. See here for more details: https://github.com/mwaskom/seaborn/blob/5386adc5a482ef3d0aef958ebf37d39ce0b06b88/seaborn/utils.py#L138

[jklymak]

Just as a meta comment I guess this should not have been milestones so aggressively? The pr fixed a bug, but an old one so maybe could have waited for 3.7?

[oscargus]

If I understand correctly, it did work in 3.6.0 for the all-nan case, but not for a leading nan (and other non-nan values). So although a bug was fixed in 3.6.1, this was introduced there as well.

(If my understanding is wrong then it could for sure have waited.)

[tacaswell]

✔ 15:28:08 $ git diff
diff --git a/lib/matplotlib/axes/_axes.py b/lib/matplotlib/axes/_axes.py
index fdac0f3560..de4a99f71d 100644
--- a/lib/matplotlib/axes/_axes.py
+++ b/lib/matplotlib/axes/_axes.py
@@ -2182,11 +2182,19 @@ class Axes(_AxesBase):
                 x0 = cbook._safe_first_finite(x0)
             except (TypeError, IndexError, KeyError):
                 pass
+            except StopIteration:
+                # this means we found no finite element, fall back to first
+                # element unconditionally
+                x0 = cbook.safe_first_element(x0)

             try:
                 x = cbook._safe_first_finite(xconv)
             except (TypeError, IndexError, KeyError):
                 x = xconv
+            except StopIteration:
+                # this means we found no finite element, fall back to first
+                # element unconditionally
+                x = cbook.safe_first_element(xconv)

             delist = False
             if not np.iterable(dx):

I think this is the fix, need to commit it and add a test.

---

My memory of this was that this was a 3.6 regression from 3.5 but looking at the linked issue that was clearly wrong.

[sophiamaedler]

So interestingly I am still encountering this error with a recent version of matplotlib on MacOS. On a linux based system it is working as expected.

Test code:

import matplotlib
print('matplotlib: {}'.format(matplotlib.__version__))

import numpy as np
import matplotlib.pyplot as plt
f, ax = plt.subplots()
ax.bar([np.nan], [np.nan])

Output Linux:

Output MacOS:

matplotlib: 3.8.4
---------------------------------------------------------------------------
StopIteration                             Traceback (most recent call last)
Cell In[7], line 7
      5 import matplotlib.pyplot as plt
      6 f, ax = plt.subplots()
----> 7 ax.bar([np.nan], [np.nan])

File ~/mambaforge/envs/stitching/lib/python3.10/site-packages/matplotlib/__init__.py:1465, in _preprocess_data.<locals>.inner(ax, data, *args, **kwargs)
   1462 @functools.wraps(func)
   1463 def inner(ax, *args, data=None, **kwargs):
   1464     if data is None:
-> 1465         return func(ax, *map(sanitize_sequence, args), **kwargs)
   1467     bound = new_sig.bind(ax, *args, **kwargs)
   1468     auto_label = (bound.arguments.get(label_namer)
   1469                   or bound.kwargs.get(label_namer))

File ~/mambaforge/envs/stitching/lib/python3.10/site-packages/matplotlib/axes/_axes.py:2451, in Axes.bar(self, x, height, width, bottom, align, **kwargs)
   2449 x0 = x
   2450 x = np.asarray(self.convert_xunits(x))
-> 2451 width = self._convert_dx(width, x0, x, self.convert_xunits)
   2452 if xerr is not None:
   2453     xerr = self._convert_dx(xerr, x0, x, self.convert_xunits)

File ~/mambaforge/envs/stitching/lib/python3.10/site-packages/matplotlib/axes/_axes.py:2244, in Axes._convert_dx(dx, x0, xconv, convert)
   2232 try:
...
   1713                        "support generators as input")
   1714 else:
-> 1715     return next(val for val in obj if safe_isfinite(val))

StopIteration:

Here the info to the installed python versions

Linux

Python version
3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:45:18) [GCC 12.3.0]
Version info.
sys.version_info(major=3, minor=10, micro=14, releaselevel='final', serial=0)

MacOS:

Python version
3.10.11 | packaged by conda-forge | (main, May 10 2023, 19:01:19) [Clang 14.0.6 ]
Version info.
sys.version_info(major=3, minor=10, micro=11, releaselevel='final', serial=0)