python-matplotlib: should it propagate numpy?

python-matplotlib: should it propagate numpy?

[Ricardo Wurmus]

Hi Guix,

with a profile containing python-2.7.10 and python2-matplotlib I did
this:

~~~~~~~~~~~~~~~~~~~~~~~~
[rwurmus@guix-builder:~] $ export GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0"
[rwurmus@guix-builder:~] $ export PYTHONPATH=$HOME/.guix-profile/lib/python2.7/site-packages
[rwurmus@guix-builder:~] $ python
Python 2.7.10 (default, Oct  9 2015, 22:48:33) 
[GCC 4.9.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib.pyplot as plt
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/__init__.py", line 180, in <module>
    from matplotlib.cbook import is_string_like
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/cbook.py", line 33, in <module>
    import numpy as np
ImportError: No module named numpy
>>> 
~~~~~~~~~~~~~~~~~~~~~~~~


So I installed python2-numpy into the same profile and tried again.
This time the import statement did pass, but I cannot actually plot
anything.


~~~~~~~~~~~~~~~~~~~~~~~~
>>> import matplotlib.pyplot as plt
>>> import numpy as np
>>> t = np.r_[0:5]
>>> plt.plot(t, t)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 3092, in plot
    ax = gca()
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 828, in gca
    ax =  gcf().gca(**kwargs)
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 462, in gcf
    return figure()
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 435, in figure
    **kwargs)
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gtk3agg.py", line 110, in new_figure_manager
    return new_figure_manager_given_figure(num, thisFig)
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gtk3agg.py", line 117, in new_figure_manager_given_figure
    canvas = FigureCanvasGTK3Agg(figure)
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gtk3agg.py", line 25, in __init__
    backend_gtk3.FigureCanvasGTK3.__init__(self, figure)
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gtk3.py", line 210, in __init__
    self._idle_event_id = GLib.idle_add(self.idle_event)
  File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/gi/types.py", line 44, in function
    return info.invoke(*args)
TypeError: Error invoking GLib.idle_add: Unexpected value for argument 'function'
>>> 
~~~~~~~~~~~~~~~~~~~~~~~~


Does anyone know how to make this work?  Is this related to bug #20888?

~~ Ricardo

python-matplotlib: should it propagate numpy?

[Federico Beffa]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

> Hi Guix,
>
> with a profile containing python-2.7.10 and python2-matplotlib I did
> this:
>
> ~~~~~~~~~~~~~~~~~~~~~~~~
> [rwurmus@guix-builder:~] $ export
> GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0"
> [rwurmus@guix-builder:~] $ export
> PYTHONPATH=$HOME/.guix-profile/lib/python2.7/site-packages
> [rwurmus@guix-builder:~] $ python
> Python 2.7.10 (default, Oct  9 2015, 22:48:33)
> [GCC 4.9.3] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import matplotlib.pyplot as plt
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/__init__.py", line 180, in <module>
>     from matplotlib.cbook import is_string_like
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/cbook.py", line 33, in <module>
>     import numpy as np
> ImportError: No module named numpy
>>>>
> ~~~~~~~~~~~~~~~~~~~~~~~~

Yeah, we should propagate numpy really.

>
>
> So I installed python2-numpy into the same profile and tried again.
> This time the import statement did pass, but I cannot actually plot
> anything.
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~
>>>> import matplotlib.pyplot as plt
>>>> import numpy as np
>>>> t = np.r_[0:5]
>>>> plt.plot(t, t)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 3092, in plot
>     ax = gca()
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 828, in gca
>     ax =  gcf().gca(**kwargs)
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 462, in gcf
>     return figure()
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 435, in figure
>     **kwargs)
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gtk3agg.py", line 110, in new_figure_manager
>     return new_figure_manager_given_figure(num, thisFig)
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gtk3agg.py", line 117, in new_figure_manager_given_figure
>     canvas = FigureCanvasGTK3Agg(figure)
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gtk3agg.py", line 25, in __init__
>     backend_gtk3.FigureCanvasGTK3.__init__(self, figure)
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gtk3.py", line 210, in __init__
>     self._idle_event_id = GLib.idle_add(self.idle_event)
>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/gi/types.py", line 44, in function
>     return info.invoke(*args)
> TypeError: Error invoking GLib.idle_add: Unexpected value for argument 'function'
>>>>
> ~~~~~~~~~~~~~~~~~~~~~~~~
>
>
> Does anyone know how to make this work?  Is this related to bug #20888?

Yes, it looks like it is related to bug #20888. You may wont to try the
'magic' command '%matplotlib' before importing it.

Matplotlib supports several back-ends, some of them like 'Agg' can only
be used to generate files, while others like 'GTK3Agg' do support
interactive operation. Of all the interactive ones, 'GTK3Agg' was the
only one where we had all the pieces to make it work. Unfortunately an
upgrade of GTK+ did break interoperability with matplotlib.

I tried several times to fix the 'GTK3Agg' back-end without success. So,
after a while I started asking to include the library 'tkinter' in our
python (see bug #20889). This would allows us to use another interactive
back-end. We are almost there, but not quite yet.

In the mean time I discovered and packaged 'emacs-ob-ipython' which
allows one to use ipython, including plotting with maptlotlib, inside of
an org-mode buffer.

Regards,
Fede

Re: python-matplotlib: should it propagate numpy?

[Ludovic Courtès]

Federico Beffa <beffa@ieee.org> skribis:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>
>> Hi Guix,
>>
>> with a profile containing python-2.7.10 and python2-matplotlib I did
>> this:
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~
>> [rwurmus@guix-builder:~] $ export
>> GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0"
>> [rwurmus@guix-builder:~] $ export
>> PYTHONPATH=$HOME/.guix-profile/lib/python2.7/site-packages
>> [rwurmus@guix-builder:~] $ python
>> Python 2.7.10 (default, Oct  9 2015, 22:48:33)
>> [GCC 4.9.3] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> import matplotlib.pyplot as plt
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/__init__.py", line 180, in <module>
>>     from matplotlib.cbook import is_string_like
>>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/cbook.py", line 33, in <module>
>>     import numpy as np
>> ImportError: No module named numpy
>>>>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~
>
> Yeah, we should propagate numpy really.

So, what’s the status of this discussion?  To propagate or not to
propagate?  :-)

Ludo’.

Re: python-matplotlib: should it propagate numpy?

[Federico Beffa]

On Sun, Dec 6, 2015 at 11:22 PM, Ludovic Courtès <ludo@gnu.org> wrote:
> Federico Beffa <beffa@ieee.org> skribis:
>
>> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>>
>>> Hi Guix,
>>>
>>> with a profile containing python-2.7.10 and python2-matplotlib I did
>>> this:
>>>
>>> ~~~~~~~~~~~~~~~~~~~~~~~~
>>> [rwurmus@guix-builder:~] $ export
>>> GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0"
>>> [rwurmus@guix-builder:~] $ export
>>> PYTHONPATH=$HOME/.guix-profile/lib/python2.7/site-packages
>>> [rwurmus@guix-builder:~] $ python
>>> Python 2.7.10 (default, Oct  9 2015, 22:48:33)
>>> [GCC 4.9.3] on linux2
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>> import matplotlib.pyplot as plt
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/__init__.py", line 180, in <module>
>>>     from matplotlib.cbook import is_string_like
>>>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/cbook.py", line 33, in <module>
>>>     import numpy as np
>>> ImportError: No module named numpy
>>>>>>
>>> ~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> Yeah, we should propagate numpy really.
>
> So, what’s the status of this discussion?  To propagate or not to
> propagate?  :-)

I just tried out using matplotlib without numpy and it actually works:

--------------------------------------------------
$ ipython
Python 3.4.3 (default, Jan  1 1970, 00:00:01)
Type "copyright", "credits" or "license" for more information.

IPython 3.2.1 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: import matplotlib.pyplot as plt

In [2]: t = range(5)

In [3]: plt.plot(t, t)
Out[3]: [<matplotlib.lines.Line2D at 0x7f17b930ccf8>]

In [4]: plt.show()

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

Therefore, despite numpy being the standard data crunching base
format, I don't think we need to propagate it.

Regards,
Fede

Re: python-matplotlib: should it propagate numpy?

[Ludovic Courtès]

Federico Beffa <beffa@ieee.org> skribis:

> On Sun, Dec 6, 2015 at 11:22 PM, Ludovic Courtès <ludo@gnu.org> wrote:
>> Federico Beffa <beffa@ieee.org> skribis:
>>
>>> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>>>
>>>> Hi Guix,
>>>>
>>>> with a profile containing python-2.7.10 and python2-matplotlib I did
>>>> this:
>>>>
>>>> ~~~~~~~~~~~~~~~~~~~~~~~~
>>>> [rwurmus@guix-builder:~] $ export
>>>> GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0"
>>>> [rwurmus@guix-builder:~] $ export
>>>> PYTHONPATH=$HOME/.guix-profile/lib/python2.7/site-packages
>>>> [rwurmus@guix-builder:~] $ python
>>>> Python 2.7.10 (default, Oct  9 2015, 22:48:33)
>>>> [GCC 4.9.3] on linux2
>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>>> import matplotlib.pyplot as plt
>>>> Traceback (most recent call last):
>>>>   File "<stdin>", line 1, in <module>
>>>>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/__init__.py", line 180, in <module>
>>>>     from matplotlib.cbook import is_string_like
>>>>   File "/home/rwurmus/.guix-profile/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/cbook.py", line 33, in <module>
>>>>     import numpy as np
>>>> ImportError: No module named numpy
>>>>>>>
>>>> ~~~~~~~~~~~~~~~~~~~~~~~~
>>>
>>> Yeah, we should propagate numpy really.
>>
>> So, what’s the status of this discussion?  To propagate or not to
>> propagate?  :-)
>
> I just tried out using matplotlib without numpy and it actually works:
>
> --------------------------------------------------
> $ ipython
> Python 3.4.3 (default, Jan  1 1970, 00:00:01)
> Type "copyright", "credits" or "license" for more information.
>
> IPython 3.2.1 -- An enhanced Interactive Python.
> ?         -> Introduction and overview of IPython's features.
> %quickref -> Quick reference.
> help      -> Python's own help system.
> object?   -> Details about 'object', use 'object??' for extra details.
>
> In [1]: import matplotlib.pyplot as plt
>
> In [2]: t = range(5)
>
> In [3]: plt.plot(t, t)
> Out[3]: [<matplotlib.lines.Line2D at 0x7f17b930ccf8>]
>
> In [4]: plt.show()
>
> --------------------------------------------------
>
> Therefore, despite numpy being the standard data crunching base
> format, I don't think we need to propagate it.

OK, sounds reasonable.  Thanks for checking!

Ludo’.

Re: python-matplotlib: should it propagate numpy?

[Ricardo Wurmus]

Federico Beffa <beffa@ieee.org> writes:

> I just tried out using matplotlib without numpy and it actually works:

[...]

> Therefore, despite numpy being the standard data crunching base
> format, I don't think we need to propagate it.

I cannot confirm this.  I used

   guix environment --container --ad-hoc python-2.7.10 python2-matplotlib -- python2
   ...
   Python 2.7.10 (default, Jan  1 1970, 00:00:01) 
   [GCC 4.9.3] on linux2
   Type "help", "copyright", "credits" or "license" for more information.
   >>> import matplotlib.pyplot as plt
   Traceback (most recent call last):
     File "<stdin>", line 1, in <module>
     File "/gnu/store/8k926blraf9mg3l4qjlxpnabrgx09jr8-python2-matplotlib-1.4.2/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/__init__.py", line 180, in <module>
       from matplotlib.cbook import is_string_like
     File "/gnu/store/8k926blraf9mg3l4qjlxpnabrgx09jr8-python2-matplotlib-1.4.2/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/cbook.py", line 33, in <module>
       import numpy as np
   ImportError: No module named numpy
   >>>

So, numpy still needs to be propagated in my opinion.  I haven’t tried
‘python-matplotlib’ and ‘python’ yet, just ‘python2-matplotlib’ as
above.  Does this make a difference?

~~ Ricardo

Re: python-matplotlib: should it propagate numpy?

[Federico Beffa]

On Wed, Dec 9, 2015 at 11:03 PM, Ricardo Wurmus
<ricardo.wurmus@mdc-berlin.de> wrote:
>
> Federico Beffa <beffa@ieee.org> writes:
>
>> I just tried out using matplotlib without numpy and it actually works:
>
> [...]
>
>> Therefore, despite numpy being the standard data crunching base
>> format, I don't think we need to propagate it.
>
> I cannot confirm this.  I used
>
>    guix environment --container --ad-hoc python-2.7.10 python2-matplotlib -- python2
>    ...
>    Python 2.7.10 (default, Jan  1 1970, 00:00:01)
>    [GCC 4.9.3] on linux2
>    Type "help", "copyright", "credits" or "license" for more information.
>    >>> import matplotlib.pyplot as plt
>    Traceback (most recent call last):
>      File "<stdin>", line 1, in <module>
>      File "/gnu/store/8k926blraf9mg3l4qjlxpnabrgx09jr8-python2-matplotlib-1.4.2/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/__init__.py", line 180, in <module>
>        from matplotlib.cbook import is_string_like
>      File "/gnu/store/8k926blraf9mg3l4qjlxpnabrgx09jr8-python2-matplotlib-1.4.2/lib/python2.7/site-packages/matplotlib-1.4.2-py2.7-linux-x86_64.egg/matplotlib/cbook.py", line 33, in <module>
>        import numpy as np
>    ImportError: No module named numpy
>    >>>
>
> So, numpy still needs to be propagated in my opinion.  I haven’t tried
> ‘python-matplotlib’ and ‘python’ yet, just ‘python2-matplotlib’ as
> above.  Does this make a difference?

I forgot the flag '--pure' and my test was picking up the numpy in my
profile. With the flag it doesn't work for me either.

Regards,
Fede

Re: python-matplotlib: should it propagate numpy?

[Federico Beffa]

On Wed, Dec 9, 2015 at 11:03 PM, Ricardo Wurmus
<ricardo.wurmus@mdc-berlin.de> wrote:
> So, numpy still needs to be propagated in my opinion.  I haven’t tried
> ‘python-matplotlib’ and ‘python’ yet, just ‘python2-matplotlib’ as
> above.  Does this make a difference?

I was about to move it to the propagated inputs, when I recalled
myself that matplotlib uses a special version of numpy. This special
version does not build the documentation as for that it needs
matplotlib. So, the special version is a 'bootstrap' version which
should not be installed in a profile and should only be used for its
purpose (it's not even exported).

So, I think it's not possible to propagate the regular version of numpy.

Regards,
Fede