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Use latest version 0.23.1 of pyvista instead of master#7318

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larsoner merged 4 commits intomne-tools:masterfrom
GuillaumeFavelier:pyvista_v0.23.1
Feb 14, 2020
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Use latest version 0.23.1 of pyvista instead of master#7318
larsoner merged 4 commits intomne-tools:masterfrom
GuillaumeFavelier:pyvista_v0.23.1

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@GuillaumeFavelier GuillaumeFavelier commented Feb 13, 2020

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

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GuillaumeFavelier commented Feb 13, 2020

Azure strikes back.

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GuillaumeFavelier commented Feb 13, 2020

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.

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codecov bot commented Feb 14, 2020 •
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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

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GuillaumeFavelier commented Feb 14, 2020 •
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Following my concerns on pyvista/pyvista#603 (comment) I think it is top priority now.

@GuillaumeFavelier GuillaumeFavelier self-assigned this Feb 14, 2020
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GuillaumeFavelier commented Feb 14, 2020 •
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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.

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GuillaumeFavelier commented Feb 14, 2020 •
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@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
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larsoner commented Feb 14, 2020

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 larsoner merged commit b0bdabd into mne-tools:master Feb 14, 2020
This was referenced Feb 14, 2020
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larsoner commented Feb 15, 2020

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

larsoner added a commit to larsoner/mne-python that referenced this pull request Feb 15, 2020
@larsoner
MAINT: Revert mne-tools#7318
513eb3d
@larsoner larsoner mentioned this pull request Feb 15, 2020
Closed
AdoNunes pushed a commit to AdoNunes/mne-python that referenced this pull request Apr 6, 2020
@GuillaumeFavelier @AdoNunes
Use latest version 0.23.1 of pyvista instead of master (mne-tools#7318)
dbd6318 
* 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]
AdoNunes pushed a commit to AdoNunes/mne-python that referenced this pull request Apr 6, 2020
@GuillaumeFavelier @AdoNunes
Use latest version 0.23.1 of pyvista instead of master (mne-tools#7318)
4fac190 
* 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 GuillaumeFavelier deleted the pyvista_v0.23.1 branch June 11, 2020 09:49
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