Use latest version 0.23.1 of pyvista instead of master #7318

GuillaumeFavelier · 2020-02-13T21:04:22Z

This PR updates the package requirements for the pyvista 3d backend.

GuillaumeFavelier · 2020-02-13T21:56:30Z

Azure strikes back.

GuillaumeFavelier · 2020-02-13T22:23:41Z

Anyway, because we use the interactor directly in:

https://github.com/mne-tools/mne-python/blob/master/mne/viz/_brain/_timeviewer.py#L213

It's not possible to use 0.23.1. I'll tag the next release.

codecov · 2020-02-14T09:32:10Z

Codecov Report

Merging #7318 into master will decrease coverage by 0.85%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #7318      +/-   ##
==========================================
- Coverage   89.49%   88.64%   -0.86%     
==========================================
  Files         449      450       +1     
  Lines       80179    81242    +1063     
  Branches    12906    12914       +8     
==========================================
+ Hits        71756    72013     +257     
- Misses       5547     6445     +898     
+ Partials     2876     2784      -92

GuillaumeFavelier · 2020-02-14T09:32:27Z

Following my concerns on pyvista/pyvista#603 (comment) I think it is top priority now.

GuillaumeFavelier · 2020-02-14T09:45:26Z

Of course, I plan to inform the users of _TimeViewer that pyvista 0.23.1 is now the recommended version. Overall, I think it's a better practice to avoid using master and ensure stability before anything else.

GuillaumeFavelier · 2020-02-14T12:47:49Z

@larsoner the issues on Circle are not related and the figures are duplicated as reported in #7228

Example: https://17989-1301584-gh.circle-artifacts.com/0/dev/auto_tutorials/source-modeling/plot_visualize_stc.html#sphx-glr-auto-tutorials-source-modeling-plot-visualize-stc-py

Details

Sphinx-gallery successfully executed 182 out of 185 files subselected by:

    gallery_conf["filename_pattern"] = '/plot'
    gallery_conf["ignore_pattern"]   = '__init__\\.py'

after excluding 0 files that had previously been run (based on MD5).


Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx/cmd/build.py", line 276, in build_main
    app.build(args.force_all, filenames)
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx/application.py", line 384, in build
    self.events.emit('build-finished', None)
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx/events.py", line 99, in emit
    results.append(callback(self.app, *args))
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_gallery.py", line 577, in summarize_failing_examples
    "\n" + "-" * 79)
ValueError: Here is a summary of the problems encountered when running the examples

Unexpected failing examples:
/home/circleci/project/tutorials/epochs/plot_10_epochs_overview.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 446, in _memory_usage
    multiprocess=True)
  File "/home/circleci/.local/lib/python3.7/site-packages/memory_profiler.py", line 343, in memory_usage
    returned = f(*args, **kw)
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 437, in __call__
    exec(self.code, self.globals)
  File "/home/circleci/project/tutorials/epochs/plot_10_epochs_overview.py", line 381, in <module>
    'EEG 056':'EEG 058'])
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1761, in __getitem__
    return self._getitem_tuple(key)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1271, in _getitem_tuple
    return self._getitem_lowerdim(tup)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1388, in _getitem_lowerdim
    section = self._getitem_axis(key, axis=i)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1953, in _getitem_axis
    return self._getitem_iterable(key, axis=axis)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1594, in _getitem_iterable
    keyarr, indexer = self._get_listlike_indexer(key, axis, raise_missing=False)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1546, in _get_listlike_indexer
    indexer = ax.get_indexer_for(key)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4502, in get_indexer_for
    return self.get_indexer(target, **kwargs)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexes/range.py", line 372, in get_indexer
    return super().get_indexer(target, method=method, tolerance=tolerance)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2729, in get_indexer
    target, method=method, limit=limit, tolerance=tolerance
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2753, in get_indexer
    indexer = self._engine.get_indexer(target._ndarray_values)
  File "pandas/_libs/index.pyx", line 287, in pandas._libs.index.IndexEngine.get_indexer
  File "pandas/_libs/hashtable_class_helper.pxi", line 1667, in pandas._libs.hashtable.PyObjectHashTable.lookup
TypeError: unhashable type: 'slice'


/home/circleci/project/tutorials/epochs/plot_epochs_to_data_frame.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 446, in _memory_usage
    multiprocess=True)
  File "/home/circleci/.local/lib/python3.7/site-packages/memory_profiler.py", line 343, in memory_usage
    returned = f(*args, **kw)
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 437, in __call__
    exec(self.code, self.globals)
  File "/home/circleci/project/tutorials/epochs/plot_epochs_to_data_frame.py", line 137, in <module>
    scaling_time=scaling_time, index=index)
TypeError: to_data_frame() got an unexpected keyword argument 'scaling_time'


/home/circleci/project/tutorials/stats-sensor-space/plot_stats_cluster_erp.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 446, in _memory_usage
    multiprocess=True)
  File "/home/circleci/.local/lib/python3.7/site-packages/memory_profiler.py", line 343, in memory_usage
    returned = f(*args, **kw)
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 437, in __call__
    exec(self.code, self.globals)
  File "/home/circleci/project/tutorials/stats-sensor-space/plot_stats_cluster_erp.py", line 58, in <module>
    A = long_df[elec].groupby("condition").mean()
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/series.py", line 1687, in groupby
    observed=observed,
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/groupby/groupby.py", line 409, in __init__
    mutated=self.mutated,
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/groupby/grouper.py", line 598, in get_grouper
    raise KeyError(gpr)
KeyError: 'condition'


-------------------------------------------------------------------------------

Exception occurred:
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_gallery.py", line 577, in summarize_failing_examples
    "\n" + "-" * 79)
ValueError: Here is a summary of the problems encountered when running the examples

Unexpected failing examples:
/home/circleci/project/tutorials/epochs/plot_10_epochs_overview.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 446, in _memory_usage
    multiprocess=True)
  File "/home/circleci/.local/lib/python3.7/site-packages/memory_profiler.py", line 343, in memory_usage
    returned = f(*args, **kw)
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 437, in __call__
    exec(self.code, self.globals)
  File "/home/circleci/project/tutorials/epochs/plot_10_epochs_overview.py", line 381, in <module>
    'EEG 056':'EEG 058'])
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1761, in __getitem__
    return self._getitem_tuple(key)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1271, in _getitem_tuple
    return self._getitem_lowerdim(tup)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1388, in _getitem_lowerdim
    section = self._getitem_axis(key, axis=i)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1953, in _getitem_axis
    return self._getitem_iterable(key, axis=axis)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1594, in _getitem_iterable
    keyarr, indexer = self._get_listlike_indexer(key, axis, raise_missing=False)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexing.py", line 1546, in _get_listlike_indexer
    indexer = ax.get_indexer_for(key)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4502, in get_indexer_for
    return self.get_indexer(target, **kwargs)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexes/range.py", line 372, in get_indexer
    return super().get_indexer(target, method=method, tolerance=tolerance)
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2729, in get_indexer
    target, method=method, limit=limit, tolerance=tolerance
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2753, in get_indexer
    indexer = self._engine.get_indexer(target._ndarray_values)
  File "pandas/_libs/index.pyx", line 287, in pandas._libs.index.IndexEngine.get_indexer
  File "pandas/_libs/hashtable_class_helper.pxi", line 1667, in pandas._libs.hashtable.PyObjectHashTable.lookup
TypeError: unhashable type: 'slice'


/home/circleci/project/tutorials/epochs/plot_epochs_to_data_frame.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 446, in _memory_usage
    multiprocess=True)
  File "/home/circleci/.local/lib/python3.7/site-packages/memory_profiler.py", line 343, in memory_usage
    returned = f(*args, **kw)
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 437, in __call__
    exec(self.code, self.globals)
  File "/home/circleci/project/tutorials/epochs/plot_epochs_to_data_frame.py", line 137, in <module>
    scaling_time=scaling_time, index=index)
TypeError: to_data_frame() got an unexpected keyword argument 'scaling_time'


/home/circleci/project/tutorials/stats-sensor-space/plot_stats_cluster_erp.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 446, in _memory_usage
    multiprocess=True)
  File "/home/circleci/.local/lib/python3.7/site-packages/memory_profiler.py", line 343, in memory_usage
    returned = f(*args, **kw)
  File "/home/circleci/.local/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 437, in __call__
    exec(self.code, self.globals)
  File "/home/circleci/project/tutorials/stats-sensor-space/plot_stats_cluster_erp.py", line 58, in <module>
    A = long_df[elec].groupby("condition").mean()
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/series.py", line 1687, in groupby
    observed=observed,
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/groupby/groupby.py", line 409, in __init__
    mutated=self.mutated,
  File "/home/circleci/.local/lib/python3.7/site-packages/pandas/core/groupby/grouper.py", line 598, in get_grouper
    raise KeyError(gpr)
KeyError: 'condition'


-------------------------------------------------------------------------------
The full traceback has been saved in /tmp/sphinx-err-6b5wngm0.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/joblib/externals/loky/backend/resource_tracker.py", line 246, in main
    cache[rtype].remove(name)
KeyError: '/loky-667-puk0vh2b'
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/joblib/externals/loky/backend/resource_tracker.py", line 246, in main
    cache[rtype].remove(name)
KeyError: '/loky-667-xrvrpzrn'
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/joblib/externals/loky/backend/resource_tracker.py", line 246, in main
    cache[rtype].remove(name)
KeyError: '/loky-667-csmr9xu4'
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/joblib/externals/loky/backend/resource_tracker.py", line 246, in main
    cache[rtype].remove(name)
KeyError: '/loky-667-iwkvscze'
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/joblib/externals/loky/backend/resource_tracker.py", line 246, in main
    cache[rtype].remove(name)
KeyError: '/loky-667-afeizwqi'
Traceback (most recent call last):
  File "/home/circleci/.local/lib/python3.7/site-packages/joblib/externals/loky/backend/resource_tracker.py", line 246, in main
    cache[rtype].remove(name)
KeyError: '/loky-667-u2irj_yj'
Makefile:44: recipe for target 'html_dev' failed
make: *** [html_dev] Error 2

Exited with code exit status 2

larsoner · 2020-02-14T13:07:43Z

Agreed we should not use master if possible. PyVista releases fairly frequently so hopefully we don't have to wait too long to merge your future PRs that use new features.

larsoner · 2020-02-15T23:52:34Z

I noticed during some testing that it took a long time (e.g., at least 10 sec) for a PyVista window to appear at one point. And now I'm noticing some very long test times for the PyVista runs:

https://travis-ci.org/mne-tools/mne-python/jobs/650898534?utm_medium=notification&utm_source=github_status

I think that this is because 0.23.1 has depth peeling enabled by default, which means that 1) rendering is slower, and 2) even opening a window calls check_depth_peeling which is slow. On my laptop when I ctrl-C'ed during the slow startup it was checking depth peeling I think.

So I think we might want to revert this until they release their next version that has pyvista/pyvista#618 incorporated.

I'll try opening a PR to revert this change, and if it runs significantly faster I'll merge. I think this is part of what is breaking things like https://travis-ci.org/mne-tools/mne-python/jobs/650898535?utm_medium=notification&utm_source=github_status hitting a timeout

* Use version 0.23.1 of pyvista * TST: Trigger CIs [circle full] * Use the plotter as interactor (this is not valid after pyvista 0.23.1) * TST: Trigger CIs [circle full]

GuillaumeFavelier added 2 commits February 13, 2020 21:59

Use version 0.23.1 of pyvista

b07d93b

TST: Trigger CIs [circle full]

b1a699f

agramfort approved these changes Feb 13, 2020

View reviewed changes

GuillaumeFavelier closed this Feb 13, 2020

GuillaumeFavelier reopened this Feb 14, 2020

Use the plotter as interactor (this is not valid after pyvista 0.23.1)

16366ed

GuillaumeFavelier self-assigned this Feb 14, 2020

GuillaumeFavelier added the VIZ label Feb 14, 2020

TST: Trigger CIs [circle full]

1cf29af

larsoner merged commit b0bdabd into mne-tools:master Feb 14, 2020

This was referenced Feb 14, 2020

ENH: New interface for Brain #7162

Closed

MRG: Enable point picking in _TimeViewer #7247

Merged

larsoner added a commit to larsoner/mne-python that referenced this pull request Feb 15, 2020

MAINT: Revert mne-tools#7318

513eb3d

larsoner mentioned this pull request Feb 15, 2020

MAINT: Revert #7318 #7330

Closed

GuillaumeFavelier deleted the pyvista_v0.23.1 branch June 11, 2020 09:49

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Use latest version 0.23.1 of pyvista instead of master #7318

Use latest version 0.23.1 of pyvista instead of master #7318

Uh oh!

GuillaumeFavelier commented Feb 13, 2020

Uh oh!

GuillaumeFavelier commented Feb 13, 2020

Uh oh!

GuillaumeFavelier commented Feb 13, 2020

Uh oh!

codecov bot commented Feb 14, 2020 •

edited

Loading

Uh oh!

GuillaumeFavelier commented Feb 14, 2020 •

edited

Loading

Uh oh!

GuillaumeFavelier commented Feb 14, 2020 •

edited

Loading

Uh oh!

GuillaumeFavelier commented Feb 14, 2020 •

edited

Loading

Uh oh!

larsoner commented Feb 14, 2020

Uh oh!

larsoner commented Feb 15, 2020

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Uh oh!

Use latest version 0.23.1 of pyvista instead of master #7318

Use latest version 0.23.1 of pyvista instead of master #7318

Uh oh!

Conversation

GuillaumeFavelier commented Feb 13, 2020

Uh oh!

GuillaumeFavelier commented Feb 13, 2020

Uh oh!

GuillaumeFavelier commented Feb 13, 2020

Uh oh!

codecov bot commented Feb 14, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

GuillaumeFavelier commented Feb 14, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

GuillaumeFavelier commented Feb 14, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

GuillaumeFavelier commented Feb 14, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

larsoner commented Feb 14, 2020

Uh oh!

larsoner commented Feb 15, 2020

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

codecov bot commented Feb 14, 2020 •

edited

Loading

GuillaumeFavelier commented Feb 14, 2020 •

edited

Loading

GuillaumeFavelier commented Feb 14, 2020 •

edited

Loading

GuillaumeFavelier commented Feb 14, 2020 •

edited

Loading