René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"matplotlib 3.5 breaks yt","articleBody":"### Bug report\r\n\r\n**Bug summary**\r\n\r\nI found a regression in yt (https://github.com/yt-project/yt) by running our CI against matplotlib's master branch.\r\n\r\n**Code for reproduction**\r\n\r\nHere's a \"minimal\" script using yt's api\r\n```python\r\nfrom yt.testing import fake_sph_grid_ds\r\nfrom yt.visualization.plot_window import ProjectionPlot\r\n\r\nds = fake_sph_grid_ds()\r\nplot = ProjectionPlot(ds, \"z\", (\"gas\", \"density\"))\r\nplot.save()\r\n```\r\nI apologise for not being able to provide a pure mpl minimal example at the moment. The data flow is unfortunately very hard to keep track of on the yt side, but I'm working on it.\r\nI think a better approach might be to go through the diff from the breaking commit and attempt a patch from there. I will attempt this and report here.\r\n\r\n**Actual outcome**\r\n\r\nHere's the traceback (using rich)\r\n```\r\nyt : [INFO     ] 2021-06-25 17:00:25,961 Parameters: current_time              = 0.0\r\nyt : [INFO     ] 2021-06-25 17:00:25,961 Parameters: domain_dimensions         = [1 1 1]\r\nyt : [INFO     ] 2021-06-25 17:00:25,961 Parameters: domain_left_edge          = [0. 0. 0.]\r\nyt : [INFO     ] 2021-06-25 17:00:25,961 Parameters: domain_right_edge         = [3. 3. 3.]\r\nyt : [INFO     ] 2021-06-25 17:00:25,962 Parameters: cosmological_simulation   = 0\r\nyt : [INFO     ] 2021-06-25 17:00:25,962 Allocating for 2.700e+01 particles\r\nyt : [INFO     ] 2021-06-25 17:00:28,828 xlim = 0.000000 3.000000\r\nyt : [INFO     ] 2021-06-25 17:00:28,828 ylim = 0.000000 3.000000\r\nyt : [INFO     ] 2021-06-25 17:00:28,828 xlim = 0.000000 3.000000\r\nyt : [INFO     ] 2021-06-25 17:00:28,828 ylim = 0.000000 3.000000\r\nyt : [INFO     ] 2021-06-25 17:00:28,836 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800\r\n\u003e /Users/robcleme/dev/yt-project/yt-py310/yt/visualization/plot_window.py(1072)_setup_plots()\r\n   1070             #balise 3\r\n   1071             # THE ISSUE IS HERE\r\n-\u003e 1072             self.plots = WindowPlotMPL(\r\n   1073                 ia,\r\n   1074                 self._field_transform.name,\r\n\r\n(Pdbr) c\r\n\u003e /Users/robcleme/dev/yt-project/yt-py310/yt/visualization/base_plot_types.py(238)_init_image()\r\n    236         # tuple colormaps are from palettable (or brewer2mpl)\r\n    237         breakpoint()\r\n--\u003e 238         if isinstance(cmap, tuple):\r\n    239             cmap = get_brewer_cmap(cmap)\r\n    240\r\n\r\n(Pdbr) c\r\n\u003e /Users/robcleme/dev/yt-project/yt-py310/yt/visualization/plot_window.py(1072)_setup_plots()\r\n   1070             #balise 3\r\n   1071             # THE ISSUE IS HERE\r\n-\u003e 1072             self.plots = WindowPlotMPL(\r\n   1073                 ia,\r\n   1074                 self._field_transform.name,\r\n\r\n(Pdbr) c\r\n\u003e /Users/robcleme/dev/yt-project/yt-py310/yt/visualization/base_plot_types.py(238)_init_image()\r\n    236         # tuple colormaps are from palettable (or brewer2mpl)\r\n    237         breakpoint()\r\n--\u003e 238         if isinstance(cmap, tuple):\r\n    239             cmap = get_brewer_cmap(cmap)\r\n    240\r\n\r\n(Pdbr) c\r\n╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮\r\n│ /Users/robcleme/dev/yt-project/yt-py310/repro_mpl_bug.py:49 in \u003cmodule\u003e                          │\r\n│                                                                                                  │\r\n│   46 │   return 0                                                                                │\r\n│   47                                                                                             │\r\n│   48 if __name__ == \"__main__\":                                                                  │\r\n│ ❱ 49 │   sys.exit(main())                                                                        │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/repro_mpl_bug.py:25 in main                              │\r\n│                                                                                                  │\r\n│   22 │                                                                                           │\r\n│   23 │   ds = fake_sph_grid_ds()                                                                 │\r\n│   24 │   plot = ProjectionPlot(ds, \"z\", (\"gas\", \"density\"))                                      │\r\n│ ❱ 25 │   plot.save()                                                                             │\r\n│   26 │   return 0                                                                                │\r\n│   27                                                                                             │\r\n│   28 def main2() -\u003e int:                                                                         │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/yt/visualization/plot_container.py:106 in newfunc        │\r\n│                                                                                                  │\r\n│    103 │   │   if not args[0]._plot_valid:                                                       │\r\n│    104 │   │   │   # it is the responsibility of _setup_plots to                                 │\r\n│    105 │   │   │   # call args[0].run_callbacks()                                                │\r\n│ ❱  106 │   │   │   args[0]._setup_plots()                                                        │\r\n│    107 │   │   rv = f(*args, **kwargs)                                                           │\r\n│    108 │   │   return rv                                                                         │\r\n│    109                                                                                           │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/yt/visualization/plot_window.py:1072 in _setup_plots     │\r\n│                                                                                                  │\r\n│   1069 │   │   │   breakpoint()                                                                  │\r\n│   1070 │   │   │   #balise 3                                                                     │\r\n│   1071 │   │   │   # THE ISSUE IS HERE                                                           │\r\n│ ❱ 1072 │   │   │   self.plots[f] = WindowPlotMPL(                                                │\r\n│   1073 │   │   │   │   ia,                                                                       │\r\n│   1074 │   │   │   │   self._field_transform[f].name,                                            │\r\n│   1075 │   │   │   │   self._field_transform[f].func,                                            │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/yt/visualization/plot_window.py:2268 in __init__         │\r\n│                                                                                                  │\r\n│   2265 │   │                                                                                     │\r\n│   2266 │   │   super().__init__(size, axrect, caxrect, zlim, figure, axes, cax)                  │\r\n│   2267 │   │                                                                                     │\r\n│ ❱ 2268 │   │   self._init_image(data, cbname, cblinthresh, cmap, extent, aspect)                 │\r\n│   2269 │   │                                                                                     │\r\n│   2270 │   │   # In matplotlib 2.1 and newer we'll be able to do this using                      │\r\n│   2271 │   │   # self.image.axes.ticklabel_format                                                │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/yt/visualization/base_plot_types.py:327 in _init_image   │\r\n│                                                                                                  │\r\n│   324 │   │   else:                                                                              │\r\n│   325 │   │   │   # this is where it breaks (but only on second pass)                            │\r\n│   326 │   │   │   #breakpoint()                                                                  │\r\n│ ❱ 327 │   │   │   self.cb = self.figure.colorbar(self.image, self.cax)                           │\r\n│   328 │   │   for which in [\"major\", \"minor\"]:                                                   │\r\n│   329 │   │   │   self.cax.tick_params(which=which, axis=\"y\", direction=\"in\")                    │\r\n│   330                                                                                            │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/matplotlib/lib/matplotlib/figure.py:1156 in colorbar     │\r\n│                                                                                                  │\r\n│   1153 │   │   │   │   │   │   │    'panchor']                                                   │\r\n│   1154 │   │   cb_kw = {k: v for k, v in kw.items() if k not in NON_COLORBAR_KEYS}               │\r\n│   1155 │   │                                                                                     │\r\n│ ❱ 1156 │   │   cb = cbar.Colorbar(cax, mappable, **cb_kw)                                        │\r\n│   1157 │   │                                                                                     │\r\n│   1158 │   │   if not kw['userax']:                                                              │\r\n│   1159 │   │   │   self.sca(current_ax)                                                          │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/matplotlib/lib/matplotlib/colorbar.py:1196 in __init__   │\r\n│                                                                                                  │\r\n│   1193 │   │   │   │   kwargs.setdefault('extend', mappable.cmap.colorbar_extend)                │\r\n│   1194 │   │   │   if isinstance(mappable, martist.Artist):                                      │\r\n│   1195 │   │   │   │   _add_disjoint_kwargs(kwargs, alpha=mappable.get_alpha())                  │\r\n│ ❱ 1196 │   │   │   super().__init__(ax, **kwargs)                                                │\r\n│   1197 │   │                                                                                     │\r\n│   1198 │   │   mappable.colorbar = self                                                          │\r\n│   1199 │   │   mappable.colorbar_cid = mappable.callbacksSM.connect(                             │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/matplotlib/lib/matplotlib/_api/deprecation.py:489 in     │\r\n│ wrapper                                                                                          │\r\n│                                                                                                  │\r\n│   486 │   │   │   │   \"positionally is deprecated since Matplotlib %(since)s; the \"              │\r\n│   487 │   │   │   │   \"parameter will become keyword-only %(removal)s.\",                         │\r\n│   488 │   │   │   │   name=name, obj_type=f\"parameter of {func.__name__}()\")                     │\r\n│ ❱ 489 │   │   return func(*args, **kwargs)                                                       │\r\n│   490 │                                                                                          │\r\n│   491 │   return wrapper                                                                         │\r\n│   492                                                                                            │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/matplotlib/lib/matplotlib/colorbar.py:421 in __init__    │\r\n│                                                                                                  │\r\n│    418 │   │   │   ['uniform', 'proportional'], spacing=spacing)                                 │\r\n│    419 │   │                                                                                     │\r\n│    420 │   │   # wrap the axes so that it can be positioned as an inset axes:                    │\r\n│ ❱  421 │   │   ax = ColorbarAxes(ax, userax=userax)                                              │\r\n│    422 │   │   self.ax = ax                                                                      │\r\n│    423 │   │   ax.set(navigate=False)                                                            │\r\n│    424                                                                                           │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/matplotlib/lib/matplotlib/colorbar.py:260 in __init__    │\r\n│                                                                                                  │\r\n│    257 │   │   │   │   parent._axes.add_child_axes(outer_ax)                                     │\r\n│    258 │   │   │   │   outer_ax._axes.child_axes.remove(parent)                                  │\r\n│    259 │   │   │   else:                                                                         │\r\n│ ❱  260 │   │   │   │   parent.remove()                                                           │\r\n│    261 │   │   else:                                                                             │\r\n│    262 │   │   │   outer_ax = parent                                                             │\r\n│    263                                                                                           │\r\n│                                                                                                  │\r\n│ /Users/robcleme/dev/yt-project/yt-py310/matplotlib/lib/matplotlib/artist.py:163 in remove        │\r\n│                                                                                                  │\r\n│    160 │   │   # protected attribute if Python supported that sort of thing.  The                │\r\n│    161 │   │   # callback has one parameter, which is the child to be removed.                   │\r\n│    162 │   │   if self._remove_method is not None:                                               │\r\n│ ❱  163 │   │   │   self._remove_method(self)                                                     │\r\n│    164 │   │   │   # clear stale callback                                                        │\r\n│    165 │   │   │   self.stale_callback = None                                                    │\r\n│    166 │   │   │   _ax_flag = False                                                              │\r\n╰──────────────────────────────────────────────────────────────────────────────────────────────────╯\r\nValueError: list.remove(x): x not in list\r\n```\r\n\r\nA CI log with multiple such failures can be found here https://github.com/yt-project/yt/runs/2899209479?check_suite_focus=true\r\n\r\n\r\n**Expected outcome**\r\n\r\nThe script is supposed to output a file named \"ParticleData_Projection_z_density.png\".\r\nIt works fine with matplotlib 3.4.0, and I was able to identify (git bisect) the breaking commit in matplotilb: 146856b03e85aa4b1becdd89fe1628f98fed2a05\r\n\r\n**Matplotlib version**\r\n  * Operating system: OsX\r\n  * Matplotlib version (`import matplotlib; print(matplotlib.__version__)`): 3.4.2.post863+g146856b03\r\n  * Matplotlib backend (`print(matplotlib.get_backend())`): \r\n  * Python version: I used 3.10.0b2 but I don't believe it is relevant\r\n  * Jupyter version (if applicable): \r\n  * Other libraries: yt (installed from source, main branch, commit c3054df545b51871ae22ef900a4d0e56cf0f2428) https://github.com/yt-project/yt\r\n\r\nI installed matplotlib with\r\n```\r\npip install git+https://github.com/matplotlib/matplotlib.git\r\n```\r\nand reinstalled on every iteration of my `git bisect` run.","author":{"url":"https://github.com/neutrinoceros","@type":"Person","name":"neutrinoceros"},"datePublished":"2021-06-25T15:17:05.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":9},"url":"https://github.com/20520/matplotlib/issues/20520"}