[Bug]: ax.bar raises for all-nan data on matplotlib 3.6.1 #24127

mwaskom · 2022-10-08T12:04:30Z

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

The text was updated successfully, but these errors were encountered:

oscargus · 2022-10-08T12:35:36Z

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

See matplotlib/matplotlib#24127 for details

mwaskom · 2022-10-08T13:18:20Z

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 · 2022-10-08T13:42:21Z

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 · 2022-10-08T13:50:48Z

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 · 2022-10-08T14:05:41Z

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 · 2022-10-08T14:11:52Z

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.)

See matplotlib/matplotlib#24127 for details

Summary: Matplotlib 3.6.1 has a bug with NaN handling (matplotlib/matplotlib#24127), leading to errors when running the tutorial. This implements a workaround, replacing `yerr` with NaNs with `None`. Differential Revision: D40232488 fbshipit-source-id: 5ee8343cc8ea67a302355fe0e93897a08383f862

Summary: Pull Request resolved: pytorch#1446 Matplotlib 3.6.1 has a bug with NaN handling (matplotlib/matplotlib#24127), leading to errors when running the tutorial. This implements a workaround, replacing `yerr` with NaNs with `None`. Differential Revision: D40232488 fbshipit-source-id: ccb8dab6d3d8b3798bfbc7aaf5e3f1f1390bfd9d

Summary: Pull Request resolved: pytorch#1446 Matplotlib 3.6.1 has a bug with NaN handling (matplotlib/matplotlib#24127), leading to errors when running the tutorial. This implements a workaround, replacing `yerr` with NaNs with `None`. Differential Revision: D40232488 fbshipit-source-id: a80a31c42ea4426638dcf864731c72e554729c00

Summary: Pull Request resolved: #1446 Matplotlib 3.6.1 has a bug with NaN handling (matplotlib/matplotlib#24127), leading to errors when running the tutorial. This implements a workaround, replacing `yerr` with NaNs with `None`. Reviewed By: ItsMrLin Differential Revision: D40232488 fbshipit-source-id: a2322d46454c96a869a93fe37aa3800db6c6ad8d

…58) * add df_to_arrays() in pymatviz/utils.py and change func signatures in pymatviz/parity.py to accept dfs and column names as well as arrays * add test_df_to_arrays() in test_utils.py and include coverage for df signature in test_parity.py * pin matplotlib below 3.6.1 until matplotlib/matplotlib#24127 resolves

tacaswell · 2022-10-12T20:00:37Z

✔ 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.

closes matplotlib#24127

…b#24127 and matplotlib/matplotlib#24316

sophiamaedler · 2024-04-12T14:41:20Z

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)

…58) * add df_to_arrays() in pymatviz/utils.py and change func signatures in pymatviz/parity.py to accept dfs and column names as well as arrays * add test_df_to_arrays() in test_utils.py and include coverage for df signature in test_parity.py * pin matplotlib below 3.6.1 until matplotlib/matplotlib#24127 resolves

mwaskom changed the title ~~[Bug]: Matplotlib 3.6.1 breaks~~ [Bug]: ax.bar raises for all-nan data on matplotlib 3.6.1 Oct 8, 2022

oscargus added this to the v3.6.2 milestone Oct 8, 2022

mwaskom added a commit to mwaskom/seaborn that referenced this issue Oct 8, 2022

Mark as non-compatibile with matplotlib 3.6.1

438248b

See matplotlib/matplotlib#24127 for details

mwaskom mentioned this issue Oct 8, 2022

Mark as non-compatible with matplotlib 3.6.1 mwaskom/seaborn#3060

Merged

mwaskom added a commit to mwaskom/seaborn that referenced this issue Oct 8, 2022

Mark as non-compatibile with matplotlib 3.6.1 (#3060)

f033f5d

See matplotlib/matplotlib#24127 for details

jarrodmillman mentioned this issue Oct 9, 2022

Remove matplotlib pin scipy-lectures/scientific-python-lectures#543

Merged

michalk8 mentioned this issue Oct 10, 2022

fix ligrec from pandas update scverse/squidpy#609

Merged

saitcakmak mentioned this issue Oct 10, 2022

Fix matplotlib error in BOPE tutorial pytorch/botorch#1446

Closed

This was referenced Oct 10, 2022

Bug: StopIteration error in histplot mwaskom/seaborn#3072

Closed

pairplot fails with matplotlib 3.6.1 mwaskom/seaborn#3073

Closed

ivirshup mentioned this issue Oct 11, 2022

Pin matplotlib for doc builds scverse/scanpy#2349

Merged

janosh added a commit to janosh/pymatviz that referenced this issue Oct 11, 2022

pin matplotlib below 3.6.1 until matplotlib/matplotlib#24127 resolves

ec84b61

hagenw mentioned this issue Oct 12, 2022

audplot.distribution() fails for new matplotlib/seaborn version audeering/audplot#41

Closed

tacaswell added a commit to tacaswell/matplotlib that referenced this issue Oct 12, 2022

FIX: handle input to ax.bar that is all nan

5d1f31e

closes matplotlib#24127

tacaswell mentioned this issue Oct 12, 2022

FIX: handle input to ax.bar that is all nan #24149

Merged

2 tasks

tacaswell added a commit to tacaswell/matplotlib that referenced this issue Oct 12, 2022

FIX: handle input to ax.bar that is all nan

7c5b99f

closes matplotlib#24127

timhoffm closed this as completed in #24149 Oct 13, 2022

hagenw mentioned this issue Oct 14, 2022

Require flake<5.0.0 + matplotlib!=3.6.1 audeering/audplot#42

Merged

vvsotnikov mentioned this issue Oct 16, 2022

StopIteration ultralytics/yolov5#9786

Closed

1 task

chahak13 pushed a commit to chahak13/matplotlib that referenced this issue Oct 18, 2022

FIX: handle input to ax.bar that is all nan

a8f73ba

closes matplotlib#24127

mattpitkin mentioned this issue Oct 21, 2022

bilby feedstock has been patched so pip check should now work conda-forge/cwinpy-feedstock#29

Merged

5 tasks

pratimugale pushed a commit to pratimugale/matplotlib that referenced this issue Oct 24, 2022

FIX: handle input to ax.bar that is all nan

bd481e8

closes matplotlib#24127

dilpath mentioned this issue Nov 18, 2022

Unfix matplotlib version ICB-DCM/pyPESTO#977

Merged

melissawm pushed a commit to melissawm/matplotlib that referenced this issue Dec 19, 2022

FIX: handle input to ax.bar that is all nan

e7a2bcc

closes matplotlib#24127

ahcm mentioned this issue Feb 14, 2023

[Bug]: TypeError: '>' not supported between instances of 'NoneType' and 'NoneType' #24316

Closed

ahcm added a commit to ahcm/longread_plots that referenced this issue Feb 14, 2023

Avoid matplotlib 3.6.1 which breaks seaborn. See matplotlib/matplotli…

a5da510

…b#24127 and matplotlib/matplotlib#24316

Nanta-Sp mentioned this issue Mar 25, 2023

[Bug]: plt.errorbar error for all-nan xerr and yerr #25549

Closed

sophiamaedler mentioned this issue Apr 12, 2024

[Bug]: #28066

Closed

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[Bug]: ax.bar raises for all-nan data on matplotlib 3.6.1 #24127

[Bug]: ax.bar raises for all-nan data on matplotlib 3.6.1 #24127

mwaskom commented Oct 8, 2022

oscargus commented Oct 8, 2022

mwaskom commented Oct 8, 2022

tacaswell commented Oct 8, 2022

mwaskom commented Oct 8, 2022

jklymak commented Oct 8, 2022

oscargus commented Oct 8, 2022

tacaswell commented Oct 12, 2022

sophiamaedler commented Apr 12, 2024

[Bug]: ax.bar raises for all-nan data on matplotlib 3.6.1 #24127

[Bug]: ax.bar raises for all-nan data on matplotlib 3.6.1 #24127

Comments

mwaskom commented Oct 8, 2022

Bug summary

Code for reproduction

Actual outcome

Expected outcome

Additional information

Operating system

Matplotlib Version

Matplotlib Backend

Python version

Jupyter version

Installation

oscargus commented Oct 8, 2022

mwaskom commented Oct 8, 2022

tacaswell commented Oct 8, 2022

mwaskom commented Oct 8, 2022

jklymak commented Oct 8, 2022

oscargus commented Oct 8, 2022

tacaswell commented Oct 12, 2022

sophiamaedler commented Apr 12, 2024