Created attachment 1339477 [details]
Test File for generating Error - Works Inline

Test file for generating the error - inline works, automatic graphic setting fails.

Apologies, should have stated - the graphics work for the inline setting. 

I examined bug https://bugzilla.redhat.com/show_bug.cgi?id=1494682 and this has not resolved.

I can reliably reproduce this on my end. If I set the backend to tk or gtk3, plot appears without problems.

If it's set to automatic, I get a similar error. I do not understand why yours needs qt4agg though.


 Traceback (most recent call last):

  File "<ipython-input-1-64557277dbff>", line 1, in <module>
    get_ipython().run_line_magic('matplotlib', 'qt5')

  File "/usr/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2095, in run_line_magic
    result = fn(*args,**kwargs)

  File "<decorator-gen-107>", line 2, in matplotlib

  File "/usr/lib/python3.6/site-packages/IPython/core/magic.py", line 187, in <lambda>
    call = lambda f, *a, **k: f(*a, **k)

  File "/usr/lib/python3.6/site-packages/IPython/core/magics/pylab.py", line 99, in matplotlib
    gui, backend = self.shell.enable_matplotlib(args.gui)

  File "/usr/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2978, in enable_matplotlib
    pt.activate_matplotlib(backend)

  File "/usr/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 307, in activate_matplotlib
    import matplotlib.pyplot

  File "/usr/lib64/python3.6/site-packages/matplotlib/pyplot.py", line 115, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()

  File "/usr/lib64/python3.6/site-packages/matplotlib/backends/__init__.py", line 32, in pylab_setup
    globals(),locals(),[backend_name],0)

ModuleNotFoundError: No module named 'matplotlib.backends.backend_qt5agg'



Can you file this upstream or do you want me to?

Hi Mukudan,

Can you file this upstream, as i am not sure how to progress that aspect. 

Thanks and regards,
Shadders.

Filed upstream report.

Shadders, can you try some stuff for me here?

Install python3-spyder, python3-matplotlib-qt5.

Line 38 in /etc/matplotlibrc should be 

"backend     : Qt5Agg"


Now, set the backend to automatic in spyder and try it.

You have mentioned that you tried editing /etc/matplotlibrc but I am not sure what is going on here.

I realized (only now, sorry!) that backend was set to TkAgg in /etc/matplotlibrc. After I change that, 'automatic' works for me.

Hi Mukundan,

after I crashed Spyder by selecting the automatic graphic backend once I don't get it to start no more.

Here is how the reproduce the crash: Take a fresh installation, start spyder3, crash it by selecting the wrong graphics backend. Try to restart spyder3 and take a look at the following error message:

$ spyder3
Traceback (most recent call last):
  File "/usr/bin/spyder3", line 3, in <module>
    start.main()
  File "/usr/lib/python3.6/site-packages/spyder/app/start.py", line 140, in main
    from spyder.app import mainwindow
  File "/usr/lib/python3.6/site-packages/spyder/app/mainwindow.py", line 92, in <module>
    from qtpy import QtWebEngineWidgets  # analysis:ignore
  File "/usr/lib/python3.6/site-packages/qtpy/QtWebEngineWidgets.py", line 43, in <module>
    from PyQt4.QtWebKit import QWebPage as QWebEnginePage
ModuleNotFoundError: No module named 'PyQt4.QtWebKit'



I tried to to delete the

~/.config/spyder-py3
~/.config/matplotlib

folders and restart Spyder but that does not make any difference. Is this related to the previous descriptions in this bug? I should mention that also in a python3 console you can't import QWebPage from PyQt4.WebKit

$python3
>>> from PyQt4.QtWebKit import QWebPage as QWebEnginePage
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'PyQt4.QtWebKit'

even though pyqt4-webkit is installed.

$ dnf list pyqt4*
Installed packages
PyQt4.x86_64                             4.12-4.fc26                    @updates
PyQt4-doc.noarch                         4.12-4.fc26                    @updates
PyQt4-webkit.x86_64                      4.12-4.fc26                    @updates


Regards

(In reply to Jakob Jakobson from comment #7)

> Hi Mukundan,
> 
> after I crashed Spyder by selecting the automatic graphic backend once I
> don't get it to start no more.
> Here is how the reproduce the crash: Take a fresh installation, start
> spyder3, crash it by selecting the wrong graphics backend. Try to restart
> spyder3 and take a look at the following error message:

That description is not exactly right. I can't reproduce the error (so I don't know if the automatic backend was the cause but it has to be related to the graphics backend) even though it happened.

Can you try launching spyder using after doing this?

spyder3 --reset

This will reset ALL your configuration files.

I will investigate other issues (perhaps move it to a new bug if needed).

(In reply to Jakob Jakobson from comment #7)
> $python3
> >>> from PyQt4.QtWebKit import QWebPage as QWebEnginePage
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> ModuleNotFoundError: No module named 'PyQt4.QtWebKit'
> 
> even though pyqt4-webkit is installed.
> 
> $ dnf list pyqt4*
> Installed packages
> PyQt4.x86_64                             4.12-4.fc26                   
> @updates
> PyQt4-doc.noarch                         4.12-4.fc26                   
> @updates
> PyQt4-webkit.x86_64                      4.12-4.fc26                   
> @updates
> 
> 
> Regards

Well, this is working correctly. If you are using python3, you need to install python3-PyQt4-Webkit.

Hi,

I implemented the reset command, changed to "automatic", restarted spyder3, ran the file and the same error. 

python3-PyQt4-Webkit is already installed. 

Regards,
Shadders.

Would you be willing to add some info here?

This is starting to move beyond my troubleshooting skills ... 

https://github.com/spyder-ide/spyder/issues/5541




As for webkit import, I cannot reproduce that either inside spyder or in a separate python3 shell.

Hi Mukundan,

--------------------------------
The latest from github :

 ccordoba12 commented 2 hours ago

    The matplotlibrc file is located in the /etc directory

So, this is a problem with Fedora setting a default backend in its Matplotlib package. There's nothing we can do about it, except catching the errors above to prevent these crashes.
--------------------------------
I checked my paths

~/.config/spyder-py3
~/.config/matplotlib

And there is nothing in the matplotlib directory.

For further investigation, if someone could state which file gets changed when selecting "automatic" i can then check if it is completing the change.

Thanks and regards,
Shadders.

> --------------------------------
> The latest from github :
> 
>  ccordoba12 commented 2 hours ago
> 
>     The matplotlibrc file is located in the /etc directory
> 
> So, this is a problem with Fedora setting a default backend in its Matplotlib > package. There's nothing we can do about it, except catching the errors above > to prevent these crashes.
> --------------------------------

I don't find a matplotlibrc file in the matplotlib github repository (as an "official" reference), 
If you compare the matplotlibrc file shipped by Fedora with the matplotlibrc from its GitHup repository
The only interesting difference in these files that I can find is

< backend      : $TEMPLATE_BACKEND (Matplotlib's matplotlibrc.template file)
---
> backend      : TkAgg (Fedora's /etc/matplotlibrc file)

and Fedora, Debian and Ubuntu choose the TkAgg backend. So the TkAgg choice doesn't seem to be a Fedora specific one.



>
> For further investigation, if someone could state which file gets changed
> when selecting "automatic" i can then check if it is completing the change.
> 

The user's configuration of Spyder3 seems to be saved in 

~/.config/spyder-py3/spyder.ini

and the interesting lines seem to be 

[ipython_console]
... (skipping lines)
pylab/backend = 0

pylab/backend = 0 equals internal
pylab/backend = 1 equals automatic
up to
pylab/backend = 8 equals tkinter

Hi Jakob,

Thanks - i have checked and the setting is equal to 1, so "automatic" has been set. Permissions are ok too. 

Regards,
Shadders.

Not to mention, pt plot window is the only one that shows up weird (without showing the plot) ...

Hi,
I have solved the issue - i needed to install :

python3-matplotlib-qt4 

Once this has been installed and spyder3 restarted (automatic) then the following error is received :

[lots of text not show]
  File "/usr/lib64/python3.6/site-packages/matplotlib/backends/qt_compat.py", line 127, in <module>
    from PyQt5 import QtCore, QtGui, QtWidgets

RuntimeError: the PyQt5.QtCore and PyQt4.QtCore modules both wrap the QObject class

If yourself and Jakob can reproduce - after adding the python3-matplotlib-qt4, then i asume we can close - and i will investigate the issue with regards to the error above. 

Regards,
Shadders.

Hi Shadders,

Well, replacing one error by another doesn't really seem as a solution.
But I can reproduce the error message produced by the automatic backend posted by you. To be complete below is the complete error message:

In [1]: import matplotlib.pyplot as plt
Traceback (most recent call last):

  File "<ipython-input-1-eff513f636fd>", line 1, in <module>
    import matplotlib.pyplot as plt

  File "/usr/lib64/python3.6/site-packages/matplotlib/pyplot.py", line 115, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()

  File "/usr/lib64/python3.6/site-packages/matplotlib/backends/__init__.py", line 32, in pylab_setup
    globals(),locals(),[backend_name],0)

  File "/usr/lib64/python3.6/site-packages/matplotlib/backends/backend_qt4agg.py", line 18, in <module>
    from .backend_qt5agg import FigureCanvasQTAggBase as _FigureCanvasQTAggBase

  File "/usr/lib64/python3.6/site-packages/matplotlib/backends/backend_qt5agg.py", line 16, in <module>
    from .backend_qt5 import QtCore

  File "/usr/lib64/python3.6/site-packages/matplotlib/backends/backend_qt5.py", line 26, in <module>
    import matplotlib.backends.qt_editor.figureoptions as figureoptions

  File "/usr/lib64/python3.6/site-packages/matplotlib/backends/qt_editor/figureoptions.py", line 20, in <module>
    import matplotlib.backends.qt_editor.formlayout as formlayout

  File "/usr/lib64/python3.6/site-packages/matplotlib/backends/qt_editor/formlayout.py", line 56, in <module>
    from matplotlib.backends.qt_compat import QtGui, QtWidgets, QtCore

  File "/usr/lib64/python3.6/site-packages/matplotlib/backends/qt_compat.py", line 127, in <module>
    from PyQt5 import QtCore, QtGui, QtWidgets

RuntimeError: the PyQt5.QtCore and PyQt4.QtCore modules both wrap the QObject class



And for the completeness a list the installed packages.

PyQt4.x86_64                             4.12-4.fc26              @updates
PyQt4-webkit.x86_64                      4.12-4.fc26              @updates
python3-PyQt4.x86_64                     4.12-4.fc26              @updates
python3-PyQt4-webkit.x86_64              4.12-4.fc26              @updates

python3-qt5.x86_64                         5.8.1-4.fc26           @updates
python3-qt5-base.x86_64                    5.8.1-4.fc26           @updates
python3-qt5-webkit.x86_64                  5.8.1-4.fc26           @updates
python3-qtconsole.noarch                   4.2.1-7.fc26           @fedora 

python3-QtPy.noarch                 1.3.1-1.fc26                  @updates

python3-matplotlib.x86_64                2.0.0-2.fc26.2            @fedora
python3-matplotlib-gtk3.x86_64           2.0.0-2.fc26.2            @fedora
python3-matplotlib-qt4.x86_64            2.0.0-2.fc26.2            @fedora
python3-matplotlib-qt5.x86_64            2.0.0-2.fc26.2            @fedora
python3-matplotlib-tk.x86_64             2.0.0-2.fc26.2            @fedora


But to me this bug seems to get out of hand as now also PyQt packages seem to be considered.


Regards

*** Bug 1506244 has been marked as a duplicate of this bug. ***

The problem is that installing python3-matplotlib-qt4 also bring -qt5 version of the package.


# inpkg python3-matplotlib-qt4
Last metadata expiration check: 0:23:02 ago on Thu 26 Oct 2017 05:55:04 PM EDT.
Dependencies resolved.
================================================================================
 Package                      Arch       Version               Repository  Size
================================================================================
Installing:
 python3-matplotlib-qt4       x86_64     2.0.0-3.fc27          fedora      29 k
Installing dependencies:
 kde-filesystem               x86_64     4-57.fc27             fedora      50 k
 phonon                       x86_64     4.9.1-5.fc27          fedora     213 k
 phonon-backend-gstreamer     x86_64     2:4.9.0-4.fc27        fedora     152 k
 python3-PyQt4                x86_64     4.12.1-4.fc27         fedora     2.9 M
 python3-matplotlib-qt5       x86_64     2.0.0-3.fc27          fedora      47 k

Transaction Summary
================================================================================
Install  6 Packages

Total download size: 3.4 M
Installed size: 16 M
Is this ok [y/N]: 

I think this is now beyond spyder, honestly. I suggest opening a bug report, possibly against matplotlib or PyQt{4,5}. Perhaps, that would be more useful. Sorry.

Created attachment 1344229 [details]
Specifying Qt4Agg explicitly in matplotlib

Created attachment 1344230 [details]
Specifying Qt5Agg directly in matplotlib

To make things worse I got one more question: If the backend is broken, should it also throw an error message if I run my files directly by
$python3 matplotlib_script.py ? If it should throw an error continue reading, if it shouldn't throw an error dismiss the rest of the post.

So coming back to your comment:

> I think this is now beyond spyder, honestly. I suggest opening a bug report,
> possibly against matplotlib or PyQt{4,5}. Perhaps, that would be more
> useful. Sorry.

Is my previous assumption about the backend right or wrong? My test files (Qt4Agg.py and Qt5Agg.py) are doing fine if I call them directly with python3.
So my less educated guess would be that the backends per se work as they should but Spyder3 has some bug/missing dependency/something else in its import routine.


Regards

Hi Jakob,

I have tried this yesterday - fails to work on my installation. 

Still get the error :

 File "/usr/lib64/python3.6/site-packages/matplotlib/backends/qt_compat.py", line 127, in <module>
    from PyQt5 import QtCore, QtGui, QtWidgets

RuntimeError: the PyQt5.QtCore and PyQt4.QtCore modules both wrap the QObject class

Regards,
Shadders.

Hi Jakob,

Thanks - i ran the script from the command line, and the plot is presented, so it is a Spyder installation issue ?

Thanks and regards,
Shadders.

(In reply to Jakob Jakobson from comment #23)
> 
> Is my previous assumption about the backend right or wrong? My test files
> (Qt4Agg.py and Qt5Agg.py) are doing fine if I call them directly with
> python3.
> So my less educated guess would be that the backends per se work as they
> should but Spyder3 has some bug/missing dependency/something else in its
> import routine.
> 

Yup. I can run this too. $python3 qt4agg.py and $python3 qt5agg.py both work.

Furthermore, if I deactivate graphics support (Tools --> Preferences --> Ipython console --> Graphics tab --> uncheck graphics support)for ipython in spyder, it works.

Let me see if I can find what is being imported.

Hi Mukundan,

Thanks for progressing - yes, this works for me also. 

Regards,
Shadders.

Hi All,

As an update, if you run Jakob's Qt5Agg.py example, it works. If you then close the graphic and run again, the console in Spyder3 hangs and no graphic is displayed. 

Pressing CTRL+C causes the kernel to die and then restart. 

Regards,
Shadders.

(In reply to Mukundan Ragavan from comment #12)
> Would you be willing to add some info here?
> 
> This is starting to move beyond my troubleshooting skills ... 
> 
> https://github.com/spyder-ide/spyder/issues/5541
> 
> 
> 
> 
> As for webkit import, I cannot reproduce that either inside spyder or in a
> separate python3 shell.

As this bug opens a lot of other questions that don't seem to be very simple to answer, there is a (well not very elegant, but useful) workaround:
Activate the an external system terminal via

Preferences -> Run -> Console: "Execute in an external system terminal"

This opens each time an external python3 console you plot something but at least it works.

Can you take at look at this pull request in the spyder repository:

https://github.com/spyder-ide/spyder/pull/5758

It is supposed to help fixing our problems here.

Thanks! I will build this later today as a test package and post the link here.

hmmm ..the patch is a little more complicated than I thought. I will try to do this over the next few days.

I am following that github issue. I will wait for some more testing and feedback from you.

Thanks!

I trust this was fixed with 3.2.5.

Can you check?

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