matplotlib-devel — matplotlib developers

[matplotlib-devel] Autogenerated docstrings, pyplot, and Windows code completion

[Paul H. <pmh...@gm...>]

Hey folks,

While I'm primarily a Vim/Sublime Text kind of guy, my employer provides me
with a Windows machine with Visual Studio and whatnot. So I've been giving
PTVS a shot (https://pytools.codeplex.com/). Seems perfectly nice so far.

But the point is that I just wanted the dev team to know that they've got
an open ticket about their Intellisense/code completion with the pyplot
module:
https://pytools.codeplex.com/workitem/1841

Basic summary is the autogenerated docstrings maybe the culprit.

I'm not suggesting any wholesale changes to MPL to accommodate this. It
just seemed like something y'all might want to know about in case any big
decisions in that area come up.

Note: that in my experience, you get good code completion and tooltips when
working directly with axes objects. So maybe that's all the more reason to
push users away from pyplot?

Cheers and as always, many thanks for the great tools!
-paul

[matplotlib-devel] "cached" member of Text class appearing in docs

[Benjamin R. <ben...@ou...>]

While looking up some information, I came across this hideousness:

http://matplotlib.org/api/artist_api.html?highlight=text#matplotlib.text.Text.cached

Why is this member made public? I would have thought it should be "private"?

Re: [matplotlib-devel] Error in import matplotlib.pyplot using Python/C API

[Eric F. <ef...@ha...>]

On 2013/09/11 8:49 AM, Filipe Saraiva wrote:
> Em Ter 10 Set 2013 19:21:01 BRT, Christoph Gohlke escreveu:
>> On 9/10/2013 1:54 PM, Eric Firing wrote:
>>> On 2013/09/10 5:43 AM, Michael Droettboom wrote:
>>>> Do any of those use ctypes?  Try creating a minimal ctypes example and
>>>> see if that works.
>>>
>>> Mike,
>>>
>>> I was a bit horrified to see that ctypes import and usage in mpl;
>>> fortunately it is a workaround for a PySide bug, and should only be
>>> temporary, if it should be there at all.
>>>
>>> Eric
>>>
>>
>> Don't be horrified. The Ctypes workaround went trough the mailing list,
>> a PR with discussions including most core developers, testing, several
>> beta/rc/final versions, and real word usage. It fixes a problem that is
>> still present today without it: the Qt4Agg backend is practically
>> unusable with any recent version of PySide on CPython 3.x. Anyway, the
>> Ctypes code could be put in a try/except statement for environments that
>> don't support Ctypes or Python's C API.
>
> If I understood correctly is there a problem with Qt4Agg in matplotlib
> 1.3?
>
> Another KDE developer typed:
>
> import matplotlib
> from matplotlib import pyplot as plt
>
> In my software (Cantor backend for python) and he got the error below:
>
> Traceback (most recent call last):
> File "", line 1, in
> File "/usr/lib/python2.7/site-packages/matplotlib/pyplot.py", line 98,
> in
> _backend_mod, new_figure_manager, draw_if_interactive, _show =
> pylab_setup()
> File
> "/usr/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line
> 25, in pylab_setup
> globals(),locals(),[backend_name])
> File
> "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py",
> line 13, in
> from backend_qt4 import QtCore, QtGui, FigureManagerQT, FigureCanvasQT,\
> File
> "/usr/lib/python2.7/site-packages/matplotlib/backends/backend_qt4.py",
> line 25, in
> from qt4_compat import QtCore, QtGui, _getSaveFileName, __version__
> File
> "/usr/lib/python2.7/site-packages/matplotlib/backends/qt4_compat.py",
> line 36, in
> import sip
> ImportError: /usr/lib/python2.7/site-packages/sip.so: undefined symbol:
> PyExc_SystemError

Again, this is a failure of a module to find a Python API symbol.  In 
this case, it is not a matplotlib module, it is sip, part of pyqt4.  It 
seems like some sort of linking problem.

>
> One more info, I removed matplotlib 1.3 and installed matplotlib 1.2
> using pip and it worked properly. I can use matplotlib in this version.

I'm glad you found something that works; but I don't know why it does.

Eric

>
> Thank you;
>
> --
> Filipe Saraiva
> http://filipesaraiva.info/
>
> ------------------------------------------------------------------------------
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Re: [matplotlib-devel] Error in import matplotlib.pyplot using Python/C API

[Filipe S. <ma...@fi...>]

Em Ter 10 Set 2013 19:21:01 BRT, Christoph Gohlke escreveu:
> On 9/10/2013 1:54 PM, Eric Firing wrote:
>> On 2013/09/10 5:43 AM, Michael Droettboom wrote:
>>> Do any of those use ctypes?  Try creating a minimal ctypes example and
>>> see if that works.
>>
>> Mike,
>>
>> I was a bit horrified to see that ctypes import and usage in mpl;
>> fortunately it is a workaround for a PySide bug, and should only be
>> temporary, if it should be there at all.
>>
>> Eric
>>
>
> Don't be horrified. The Ctypes workaround went trough the mailing list,
> a PR with discussions including most core developers, testing, several
> beta/rc/final versions, and real word usage. It fixes a problem that is
> still present today without it: the Qt4Agg backend is practically
> unusable with any recent version of PySide on CPython 3.x. Anyway, the
> Ctypes code could be put in a try/except statement for environments that
> don't support Ctypes or Python's C API.

If I understood correctly is there a problem with Qt4Agg in matplotlib 
1.3?

Another KDE developer typed:

import matplotlib
from matplotlib import pyplot as plt

In my software (Cantor backend for python) and he got the error below:

Traceback (most recent call last):
File "", line 1, in
File "/usr/lib/python2.7/site-packages/matplotlib/pyplot.py", line 98, 
in
_backend_mod, new_figure_manager, draw_if_interactive, _show = 
pylab_setup()
File 
"/usr/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line
25, in pylab_setup
globals(),locals(),[backend_name])
File 
"/usr/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py",
line 13, in
from backend_qt4 import QtCore, QtGui, FigureManagerQT, FigureCanvasQT,\
File 
"/usr/lib/python2.7/site-packages/matplotlib/backends/backend_qt4.py",
line 25, in
from qt4_compat import QtCore, QtGui, _getSaveFileName, __version__
File 
"/usr/lib/python2.7/site-packages/matplotlib/backends/qt4_compat.py",
line 36, in
import sip
ImportError: /usr/lib/python2.7/site-packages/sip.so: undefined symbol:
PyExc_SystemError

One more info, I removed matplotlib 1.3 and installed matplotlib 1.2 
using pip and it worked properly. I can use matplotlib in this version.

Thank you;

--
Filipe Saraiva
http://filipesaraiva.info/

Re: [matplotlib-devel] Error in import matplotlib.pyplot using Python/C API

[Christoph G. <cg...@uc...>]

On 9/10/2013 1:54 PM, Eric Firing wrote:
> On 2013/09/10 5:43 AM, Michael Droettboom wrote:
>> Do any of those use ctypes?  Try creating a minimal ctypes example and
>> see if that works.
>
> Mike,
>
> I was a bit horrified to see that ctypes import and usage in mpl;
> fortunately it is a workaround for a PySide bug, and should only be
> temporary, if it should be there at all.
>
> Eric
>

Don't be horrified. The Ctypes workaround went trough the mailing list, 
a PR with discussions including most core developers, testing, several 
beta/rc/final versions, and real word usage. It fixes a problem that is 
still present today without it: the Qt4Agg backend is practically 
unusable with any recent version of PySide on CPython 3.x. Anyway, the 
Ctypes code could be put in a try/except statement for environments that 
don't support Ctypes or Python's C API.

Christoph

Re: [matplotlib-devel] Error in import matplotlib.pyplot using Python/C API

[Eric F. <ef...@ha...>]

On 2013/09/10 5:43 AM, Michael Droettboom wrote:
> Do any of those use ctypes?  Try creating a minimal ctypes example and
> see if that works.

Mike,

I was a bit horrified to see that ctypes import and usage in mpl; 
fortunately it is a workaround for a PySide bug, and should only be 
temporary, if it should be there at all.

Eric

Re: [matplotlib-devel] Error in import matplotlib.pyplot using Python/C API

[Michael D. <md...@st...>]

On 09/10/2013 10:05 AM, Filipe Saraiva wrote:
> Em Ter 10 Set 2013 09:33:37 BRT, Michael Droettboom escreveu:
>> On 09/10/2013 08:23 AM, Filipe Saraiva wrote:
>>> Em Ter 03 Set 2013 17:02:28 BRT, Benjamin Root escreveu:
>>>> On Mon, Sep 2, 2013 at 12:27 AM, Filipe Saraiva
>>>> <ma...@fi... <mailto:ma...@fi...>> wrote:
>>>>
>>>>       Hello,
>>>>
>>>>       First, thanks for this great library.
>>>>
>>>>       My name is Filipe Saraiva, I am developing a python backend for
>>>>       Cantor, the KDE mathematical software. More infos can be read in
>>>> http://blog.filipesaraiva.info/?tag=gsoc2013-python-backend (in
>>>>       portuguese and english).
>>>>
>>>>       Currently I have a problem when I try import pyplot in Cantor. I
>>>>       am using Python 2.7.5 and matplotlib 1.3.0. The error is below:
>>>>
>>>>       import matplotlib.pyplot as plt
>>>>       Traceback (most recent call last):
>>>>         File "<string>", line 1, in <module>
>>>>         File 
>>>> "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py",
>>>>       line 98, in <module>
>>>>           _backend_mod, new_figure_manager, draw_if_interactive, 
>>>> _show =
>>>>       pylab_setup()
>>>>         File
>>>> "/usr/lib64/python2.7/site-packages/matplotlib/backends/__init__.py",
>>>>       line 25, in pylab_setup
>>>>           globals(),locals(),[backend_name])
>>>>         File
>>>> "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py",
>>>>       line 19, in <module>
>>>>           _decref = ctypes.pythonapi.Py_DecRef
>>>>         File "/usr/lib64/python2.7/ctypes/__init__.py", line 378, in
>>>>       __getattr__
>>>>           func = self.__getitem__(name)
>>>>         File "/usr/lib64/python2.7/ctypes/__init__.py", line 383, in
>>>>       __getitem__
>>>>           func = self._FuncPtr((name_or_ordinal, self))
>>>>       AttributeError: kde/bin/cantor: undefined symbol: Py_DecRef
>>>>
>>>>       Well, anyone have any idea about how can I fix it?
>>>>
>>>>       Thank you,
>>>>
>>>>
>>>> My only guess is that there is some sort of linking/build error.
>>>> Perhaps the python-qt4 library was built and linked against a
>>>> different python on your system?
>>>>
>>>> Cheers!
>>>> Ben Root
>>> Really I don't know. I will question it to matplotlib maintainer.
>>>
>>> The pyplot import in python iteractive mode (python terminal) is
>>> working properly. I can run a matplotlib example using pyplot in this
>>> mode. I get the error just in Python/C API.
>>>
>>
>> It looks like it's failing inside of ctypes.  How are you including
>> Python in your application.  Perhaps the ctypes module (which is a C
>> extension module that comes in the Python standard library) is not being
>> included or found.  I'm at a bit of a loss, but this seems like more of
>> a general "embedding python in a C application" question, which you
>> might try asking on the Python mailing list.
>>
>> Mike
>>
>
> I am using my code with several python modules and I can not get any 
> error. I tried scipy, numpy, Spade, matplotlib... interesting, I don't 
> get error when I import matplotlib.animation.

Do any of those use ctypes?  Try creating a minimal ctypes example and 
see if that works.

Mike

-- 
                    _
|\/|o _|_  _. _ | | \.__  __|__|_|_  _  _ ._ _
|  ||(_| |(_|(/_| |_/|(_)(/_|_ |_|_)(_)(_)| | |

http://www.droettboom.com

Re: [matplotlib-devel] Error in import matplotlib.pyplot using Python/C API

[Filipe S. <ma...@fi...>]

Em Ter 10 Set 2013 09:33:37 BRT, Michael Droettboom escreveu:
> On 09/10/2013 08:23 AM, Filipe Saraiva wrote:
>> Em Ter 03 Set 2013 17:02:28 BRT, Benjamin Root escreveu:
>>> On Mon, Sep 2, 2013 at 12:27 AM, Filipe Saraiva
>>> <ma...@fi... <mailto:ma...@fi...>> wrote:
>>>
>>>       Hello,
>>>
>>>       First, thanks for this great library.
>>>
>>>       My name is Filipe Saraiva, I am developing a python backend for
>>>       Cantor, the KDE mathematical software. More infos can be read in
>>>       http://blog.filipesaraiva.info/?tag=gsoc2013-python-backend (in
>>>       portuguese and english).
>>>
>>>       Currently I have a problem when I try import pyplot in Cantor. I
>>>       am using Python 2.7.5 and matplotlib 1.3.0. The error is below:
>>>
>>>       import matplotlib.pyplot as plt
>>>       Traceback (most recent call last):
>>>         File "<string>", line 1, in <module>
>>>         File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py",
>>>       line 98, in <module>
>>>           _backend_mod, new_figure_manager, draw_if_interactive, _show =
>>>       pylab_setup()
>>>         File
>>>       "/usr/lib64/python2.7/site-packages/matplotlib/backends/__init__.py",
>>>       line 25, in pylab_setup
>>>           globals(),locals(),[backend_name])
>>>         File
>>>       "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py",
>>>       line 19, in <module>
>>>           _decref = ctypes.pythonapi.Py_DecRef
>>>         File "/usr/lib64/python2.7/ctypes/__init__.py", line 378, in
>>>       __getattr__
>>>           func = self.__getitem__(name)
>>>         File "/usr/lib64/python2.7/ctypes/__init__.py", line 383, in
>>>       __getitem__
>>>           func = self._FuncPtr((name_or_ordinal, self))
>>>       AttributeError: kde/bin/cantor: undefined symbol: Py_DecRef
>>>
>>>       Well, anyone have any idea about how can I fix it?
>>>
>>>       Thank you,
>>>
>>>
>>> My only guess is that there is some sort of linking/build error.
>>> Perhaps the python-qt4 library was built and linked against a
>>> different python on your system?
>>>
>>> Cheers!
>>> Ben Root
>> Really I don't know. I will question it to matplotlib maintainer.
>>
>> The pyplot import in python iteractive mode (python terminal) is
>> working properly. I can run a matplotlib example using pyplot in this
>> mode. I get the error just in Python/C API.
>>
>
> It looks like it's failing inside of ctypes.  How are you including
> Python in your application.  Perhaps the ctypes module (which is a C
> extension module that comes in the Python standard library) is not being
> included or found.  I'm at a bit of a loss, but this seems like more of
> a general "embedding python in a C application" question, which you
> might try asking on the Python mailing list.
>
> Mike
>

I am using my code with several python modules and I can not get any 
error. I tried scipy, numpy, Spade, matplotlib... interesting, I don't 
get error when I import matplotlib.animation.

You can see reports of several uses of python commands and modules in 
my software accessing my blog in 
http://blog.filipesaraiva.info/?tag=gsoc2013-python-backend

Interesting, I used with success pyplot in the first version of this 
backend, last year. The blogpost have a picture of this 
http://blog.filipesaraiva.info/?p=779.

Well, I ask to another KDE developers for test my code and verify if 
the pyplot error that I am getting is reproducible.

Thank you,

--
Filipe Saraiva
http://filipesaraiva.info/

Re: [matplotlib-devel] Error in import matplotlib.pyplot using Python/C API

[Michael D. <md...@st...>]

On 09/10/2013 08:23 AM, Filipe Saraiva wrote:
> Em Ter 03 Set 2013 17:02:28 BRT, Benjamin Root escreveu:
>> On Mon, Sep 2, 2013 at 12:27 AM, Filipe Saraiva
>> <ma...@fi... <mailto:ma...@fi...>> wrote:
>>
>>      Hello,
>>
>>      First, thanks for this great library.
>>
>>      My name is Filipe Saraiva, I am developing a python backend for
>>      Cantor, the KDE mathematical software. More infos can be read in
>>      http://blog.filipesaraiva.info/?tag=gsoc2013-python-backend (in
>>      portuguese and english).
>>
>>      Currently I have a problem when I try import pyplot in Cantor. I
>>      am using Python 2.7.5 and matplotlib 1.3.0. The error is below:
>>
>>      import matplotlib.pyplot as plt
>>      Traceback (most recent call last):
>>        File "<string>", line 1, in <module>
>>        File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py",
>>      line 98, in <module>
>>          _backend_mod, new_figure_manager, draw_if_interactive, _show =
>>      pylab_setup()
>>        File
>>      "/usr/lib64/python2.7/site-packages/matplotlib/backends/__init__.py",
>>      line 25, in pylab_setup
>>          globals(),locals(),[backend_name])
>>        File
>>      "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py",
>>      line 19, in <module>
>>          _decref = ctypes.pythonapi.Py_DecRef
>>        File "/usr/lib64/python2.7/ctypes/__init__.py", line 378, in
>>      __getattr__
>>          func = self.__getitem__(name)
>>        File "/usr/lib64/python2.7/ctypes/__init__.py", line 383, in
>>      __getitem__
>>          func = self._FuncPtr((name_or_ordinal, self))
>>      AttributeError: kde/bin/cantor: undefined symbol: Py_DecRef
>>
>>      Well, anyone have any idea about how can I fix it?
>>
>>      Thank you,
>>
>>
>> My only guess is that there is some sort of linking/build error.
>> Perhaps the python-qt4 library was built and linked against a
>> different python on your system?
>>
>> Cheers!
>> Ben Root
> Really I don't know. I will question it to matplotlib maintainer.
>
> The pyplot import in python iteractive mode (python terminal) is
> working properly. I can run a matplotlib example using pyplot in this
> mode. I get the error just in Python/C API.
>

It looks like it's failing inside of ctypes.  How are you including 
Python in your application.  Perhaps the ctypes module (which is a C 
extension module that comes in the Python standard library) is not being 
included or found.  I'm at a bit of a loss, but this seems like more of 
a general "embedding python in a C application" question, which you 
might try asking on the Python mailing list.

Mike

-- 
                    _
|\/|o _|_  _. _ | | \.__  __|__|_|_  _  _ ._ _
|  ||(_| |(_|(/_| |_/|(_)(/_|_ |_|_)(_)(_)| | |

http://www.droettboom.com

Re: [matplotlib-devel] Error in import matplotlib.pyplot using Python/C API

[Filipe S. <ma...@fi...>]

Em Ter 03 Set 2013 17:02:28 BRT, Benjamin Root escreveu:
>
> On Mon, Sep 2, 2013 at 12:27 AM, Filipe Saraiva
> <ma...@fi... <mailto:ma...@fi...>> wrote:
>
>     Hello,
>
>     First, thanks for this great library.
>
>     My name is Filipe Saraiva, I am developing a python backend for
>     Cantor, the KDE mathematical software. More infos can be read in
>     http://blog.filipesaraiva.info/?tag=gsoc2013-python-backend (in
>     portuguese and english).
>
>     Currently I have a problem when I try import pyplot in Cantor. I
>     am using Python 2.7.5 and matplotlib 1.3.0. The error is below:
>
>     import matplotlib.pyplot as plt
>     Traceback (most recent call last):
>       File "<string>", line 1, in <module>
>       File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py",
>     line 98, in <module>
>         _backend_mod, new_figure_manager, draw_if_interactive, _show =
>     pylab_setup()
>       File
>     "/usr/lib64/python2.7/site-packages/matplotlib/backends/__init__.py",
>     line 25, in pylab_setup
>         globals(),locals(),[backend_name])
>       File
>     "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py",
>     line 19, in <module>
>         _decref = ctypes.pythonapi.Py_DecRef
>       File "/usr/lib64/python2.7/ctypes/__init__.py", line 378, in
>     __getattr__
>         func = self.__getitem__(name)
>       File "/usr/lib64/python2.7/ctypes/__init__.py", line 383, in
>     __getitem__
>         func = self._FuncPtr((name_or_ordinal, self))
>     AttributeError: kde/bin/cantor: undefined symbol: Py_DecRef
>
>     Well, anyone have any idea about how can I fix it?
>
>     Thank you,
>
>
> My only guess is that there is some sort of linking/build error.
> Perhaps the python-qt4 library was built and linked against a
> different python on your system?
>
> Cheers!
> Ben Root

Really I don't know. I will question it to matplotlib maintainer.

The pyplot import in python iteractive mode (python terminal) is 
working properly. I can run a matplotlib example using pyplot in this 
mode. I get the error just in Python/C API.

--
Filipe Saraiva
http://filipesaraiva.info/

[matplotlib-devel] Error in building Matplotlib

[alifar76 <Ali...@uc...>]

Hi everyone!

I'm trying to build matplotlib 1.1.0 using Python-2.7.3 on CentOS 6.4. I
constantly keep getting the following error:

/usr/bin/ld: /usr/local/lib/libpython2.7.a(parsetok.o): relocation
R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared
object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error: command 'g++' failed with exit status 1

Can anyone please advice on what is going on and how I can resolve the
issue? Thanks a lot.

Regards,
Ali



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/Error-in-building-Matplotlib-tp41968.html
Sent from the matplotlib - devel mailing list archive at Nabble.com.

Re: [matplotlib-devel] Error in import matplotlib.pyplot using Python/C API

[Benjamin R. <ben...@ou...>]

On Mon, Sep 2, 2013 at 12:27 AM, Filipe Saraiva <ma...@fi...>wrote:

>  Hello,
>
> First, thanks for this great library.
>
> My name is Filipe Saraiva, I am developing a python backend for Cantor,
> the KDE mathematical software. More infos can be read in
> http://blog.filipesaraiva.info/?tag=gsoc2013-python-backend (in
> portuguese and english).
>
> Currently I have a problem when I try import pyplot in Cantor. I am using
> Python 2.7.5 and matplotlib 1.3.0. The error is below:
>
> import matplotlib.pyplot as plt
> Traceback (most recent call last):
>   File "<string>", line 1, in <module>
>   File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py", line 98,
> in <module>
>     _backend_mod, new_figure_manager, draw_if_interactive, _show =
> pylab_setup()
>   File
> "/usr/lib64/python2.7/site-packages/matplotlib/backends/__init__.py", line
> 25, in pylab_setup
>     globals(),locals(),[backend_name])
>   File
> "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py",
> line 19, in <module>
>     _decref = ctypes.pythonapi.Py_DecRef
>   File "/usr/lib64/python2.7/ctypes/__init__.py", line 378, in __getattr__
>     func = self.__getitem__(name)
>   File "/usr/lib64/python2.7/ctypes/__init__.py", line 383, in __getitem__
>     func = self._FuncPtr((name_or_ordinal, self))
> AttributeError: kde/bin/cantor: undefined symbol: Py_DecRef
>
> Well, anyone have any idea about how can I fix it?
>
> Thank you,
>
>
My only guess is that there is some sort of linking/build error. Perhaps
the python-qt4 library was built and linked against a different python on
your system?

Cheers!
Ben Root

Re: [matplotlib-devel] [IPython-dev] Basemap Segfault in IPython; Works in Python

[Patrick M. <pat...@gm...>]

Sorry if this is a double post; used the wrong email in the first reply and
got at least one failure notice...

This is terminal IPython and IPython Notebook. (I noticed it first in the
IPython Notebook). The backends are the same in both Python and IPython
(and IPython Notebook). I have not changed any of the default IPython
settings.

I'm wondering if this is a path issue of some sorts…namely IPython is
picking up an old version of geos that I cannot seem to find. At least this
is the angle I'm currently trying to work on. I should add that I've remove
all my manually installed modules and "started over". I built Numpy,
Matplotlib, Basemap, and then IPython (in that order), and still have the
same segfault issue.


Patrick



On Tue, Sep 3, 2013 at 1:15 PM, MinRK <ben...@gm...> wrote:

> This is terminal IPython?
>
> Is there a chance that the matplotlib backend is different in each case?
> Have you enabled matplotlib eventloop integration in IPython (otherwise, it
> will block when you draw a plot).
>
>
> On Tue, Sep 3, 2013 at 9:36 AM, Patrick Marsh <pat...@gm...>wrote:
>
>> Hi, All,
>>
>> I'm not sure what is going on, but the following fails in IPython
>> (terminal and notebook) but works just fine in regular Python.
>>
>> I'm using OS X 10.8.4; git master for git master for Matplotlib
>> (a091f6d), IPython (9f92804), and Basemap (1d7664c); and geos version 3.4.2
>> (built by Homebrew).
>>
>> The following script will work from a Python prompt but fails (segfaults)
>> from the IPython prompt. After doing some digging it appears that the
>> segfault occurs when accessing some of the methods associated with the
>> generated geos module (_geoslib.so). I've rolled back to previous versions
>> of everything and I still have the same issues.
>>
>> What I cannot figure out is why this would work with a pure Python
>> interpreter, but fail in the IPython console.
>>
>>
>> =====
>> import matplotlib.pyplot as plt
>> from mpl_toolkits.basemap import Basemap
>>
>> m = Basemap()    # This is where the segfault occurs
>>
>> m.drawcoastlines()
>> plt.show()
>> =====
>>
>>
>> I originally posted this on the IPython Users list and got no response,
>> so I thought I would try here before posting a bug on both IPython and
>> Basemap's Github issue trackers.
>>
>>
>> Thanks for any help or ideas on fixing this issue, or at least on how to
>> track down this issue...
>>
>>
>> Patrick
>>
>> _______________________________________________
>> IPython-dev mailing list
>> IPy...@sc...
>> http://mail.scipy.org/mailman/listinfo/ipython-dev
>>
>>
>
> _______________________________________________
> IPython-dev mailing list
> IPy...@sc...
> http://mail.scipy.org/mailman/listinfo/ipython-dev
>
>

Re: [matplotlib-devel] [IPython-dev] Basemap Segfault in IPython; Works in Python

[MinRK <ben...@gm...>]

This is terminal IPython?

Is there a chance that the matplotlib backend is different in each case?
Have you enabled matplotlib eventloop integration in IPython (otherwise, it
will block when you draw a plot).


On Tue, Sep 3, 2013 at 9:36 AM, Patrick Marsh <pat...@gm...>wrote:

> Hi, All,
>
> I'm not sure what is going on, but the following fails in IPython
> (terminal and notebook) but works just fine in regular Python.
>
> I'm using OS X 10.8.4; git master for git master for Matplotlib (a091f6d),
> IPython (9f92804), and Basemap (1d7664c); and geos version 3.4.2 (built by
> Homebrew).
>
> The following script will work from a Python prompt but fails (segfaults)
> from the IPython prompt. After doing some digging it appears that the
> segfault occurs when accessing some of the methods associated with the
> generated geos module (_geoslib.so). I've rolled back to previous versions
> of everything and I still have the same issues.
>
> What I cannot figure out is why this would work with a pure Python
> interpreter, but fail in the IPython console.
>
>
> =====
> import matplotlib.pyplot as plt
> from mpl_toolkits.basemap import Basemap
>
> m = Basemap()    # This is where the segfault occurs
>
> m.drawcoastlines()
> plt.show()
> =====
>
>
> I originally posted this on the IPython Users list and got no response, so
> I thought I would try here before posting a bug on both IPython and
> Basemap's Github issue trackers.
>
>
> Thanks for any help or ideas on fixing this issue, or at least on how to
> track down this issue...
>
>
> Patrick
>
> _______________________________________________
> IPython-dev mailing list
> IPy...@sc...
> http://mail.scipy.org/mailman/listinfo/ipython-dev
>
>

[matplotlib-devel] Basemap Segfault in IPython; Works in Python

[Patrick M. <pat...@gm...>]

Hi, All,

I'm not sure what is going on, but the following fails in IPython (terminal
and notebook) but works just fine in regular Python.

I'm using OS X 10.8.4; git master for git master for Matplotlib (a091f6d),
IPython (9f92804), and Basemap (1d7664c); and geos version 3.4.2 (built by
Homebrew).

The following script will work from a Python prompt but fails (segfaults)
from the IPython prompt. After doing some digging it appears that the
segfault occurs when accessing some of the methods associated with the
generated geos module (_geoslib.so). I've rolled back to previous versions
of everything and I still have the same issues.

What I cannot figure out is why this would work with a pure Python
interpreter, but fail in the IPython console.


=====
import matplotlib.pyplot as plt
from mpl_toolkits.basemap import Basemap

m = Basemap()    # This is where the segfault occurs

m.drawcoastlines()
plt.show()
=====


I originally posted this on the IPython Users list and got no response, so
I thought I would try here before posting a bug on both IPython and
Basemap's Github issue trackers.


Thanks for any help or ideas on fixing this issue, or at least on how to
track down this issue...


Patrick

Re: [matplotlib-devel] Faceted plotting

[Chris B. <bea...@ha...>]

Hi Damon,

Thanks for your thoughts on how this should fit in with MPLs API. My $0.02:

What would feel more natural is if I could do the following:
> f = Facet(...)
> ax.facet(f, 'scatter')
>

Three things about this style bother me:

1. It seems too verbose ("facet" gets typed a lot -- 4 times if you call
the variable facet instead of f).

2. I don't love having to invoke methods like 'scatter' by naming them as a
string. It feels kludgy for some reason.

3. I think the axes plotting methods belong to a different category than a
facet. The former are "artist factories" that add artists like
lines/patches/etc to axes. A facet, on the other hand, is a higher-level
"axes factory" that creates multiple subplot axes objects. Making facet an
axes method seems out of place, since I think it's more natural to have a
separate axes for each subplot. What do you think?

Admittedly, functions like plot() are a total disaster, they take a
> plethora of different argument orders and types and try to conform to many
> calling signatures at once.  Specifically, the way the data is passed to
> the plotting method varies wildly.
>

Good point. My implementation relies on a pretty general (but not universal
or formally documented) property of most plot functions: the first
arguments for each method are usually data arrays. This means that, in most
situations, Facet can extract the appropriate subset of the original data,
pass them as the first arguments to an axes method, and this will "do the
right thing". This works most of the time, but might be considered a hack.
The iterator interface is meant to address the cases where this doesn't
work (for example, calling Facet.imshow or Facet.streamplot doesn't work).

I think your Faceted plotting API supports exactly what I'm hoping to see
> matplotlib will move towards:
>
> class Facet(matplotlib.Plottable)
>     def __init__(self, ...)
>         ...
>
> f = Facet(...)
> ax.scatter(f)
>

This interface addresses my first two concerns above, but not the third --
I don't think that all facets should live in a single axes. I'm not sure
what you envision the Plottable interface looks like, but I imagine it
provides methods to extract data, so that you can plot things besides
arrays. In this case, I think a facet could *use* Plottables when building
subplots, but I'm not sure a facet *is* a plottable.

Tangential to the notion of Plottable objects: if there were a standard
protocol for passing data and style arguments to all plotting methods, it
would be easier to build robust, higher level axes factories. Facets are
one such factory, but there are others. For example (and not the prettiest,
I admit), see the map at
http://www.tableausoftware.com/public/gallery/new-jersey-test-score-analysis-visualization.
It's basically a faceted group of pie charts, that are positioned and sized
according to more data. The generalized description is something like:

atomic_plot + faceted_by(variable) + positioned_by(x, y) + sized_by(z)

Where atomic_plot is an axes plot method (e.g., ax.pie, but why not ax.bar
or any other single-variable plot?). You could imagine building a layered
API like this, and it would be easier if the interface for all atomic_plot
objects were compatible. Matplotlib was first built to win converts over
from matplotlib -- with a layered API, you can start converting the
ggplot/d3/bokeh/vega community :)

Cheers,
Chris

[matplotlib-devel] Error in import matplotlib.pyplot using Python/C API

[Filipe S. <ma...@fi...>]

Hello,

First, thanks for this great library.

My name is Filipe Saraiva, I am developing a python backend for Cantor, 
the KDE mathematical software. More infos can be read in 
http://blog.filipesaraiva.info/?tag=gsoc2013-python-backend (in 
portuguese and english).

Currently I have a problem when I try import pyplot in Cantor. I am 
using Python 2.7.5 and matplotlib 1.3.0. The error is below:

import matplotlib.pyplot as plt
Traceback (most recent call last):
   File "<string>", line 1, in <module>
   File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py", line 
98, in <module>
     _backend_mod, new_figure_manager, draw_if_interactive, _show = 
pylab_setup()
   File 
"/usr/lib64/python2.7/site-packages/matplotlib/backends/__init__.py", 
line 25, in pylab_setup
     globals(),locals(),[backend_name])
   File 
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", 
line 19, in <module>
     _decref = ctypes.pythonapi.Py_DecRef
   File "/usr/lib64/python2.7/ctypes/__init__.py", line 378, in __getattr__
     func = self.__getitem__(name)
   File "/usr/lib64/python2.7/ctypes/__init__.py", line 383, in __getitem__
     func = self._FuncPtr((name_or_ordinal, self))
AttributeError: kde/bin/cantor: undefined symbol: Py_DecRef

Well, anyone have any idea about how can I fix it?

Thank you,


-- Filipe Saraiva http://filipesaraiva.info/

Re: [matplotlib-devel] Faceted plotting

[Damon M. <dam...@gm...>]

On Sat, Aug 31, 2013 at 10:21 AM, Chris Beaumont <bea...@ha...>wrote:

> Pandas has some nice tools to make faceted plots -- small multiples of
> plots where data is grouped by category (
> http://pandas.pydata.org/pandas-docs/stable/rplot.html). However, I think
> there would be value in having this functionality built into matplotlib.
> Mainly:
>
> 1. Not every dataset lives in a dataframe
> 2. The pandas library mimics the ggplot interface, and some people would
> prefer an interface closer to matplotlib
> 3. Properly implemented, I think a matplotlib facet system would enable a
> wider variety of faceted plots than the pandas tools.
>
> I've taken a stab at this, and came up with an interface that I think has
> potential. This currently exists as a separate repository at
> https://github.com/ChrisBeaumont/mplfacet, and an example notebook at
> http://bit.ly/17u1JzP
>
> There two basic ways to use a facet object:
>
> Facet(key, data).method()
>
> will group one or more data arrays by key, and build a subplot for each
> group by calling method (which is any axes plot method). Alternatively,
>
> for item in Facet(key, data):
>     x, y = item.data
>     item.axes.scatter(x, y)
>
> sets up the subplots and groups the data for you, but gives you more
> freedom to populate each subplot however you like.
>
> Is there interest in building this into matplotlib? If so, I would like to
> polish it up and submit a PR.
>
> Cheers,
> Chris
>

Chris,

This is lovely work.  Thanks for taking the time to put this together, I
think it has a lot of potential.

I'd like to get a discussion going regarding the current implementation of
the API you've rolled together for faceted plots.  Overall, I like the
flexibility you have provided.  However, I have some reservations and I'd
like to outline those now.

The current workflow is:  Organise your data and create a Facet object.
 Then call one of the Facet's plotting methods.

You have designed the Facet object to respond to calls to matplotlib's
plotting methods.  That's pretty cool.  My reservation here is that I'm not
sure it aligns with the design of matplotlib.  At present, the Axes object
implements the plotting methods, and each method will have its own way of
plotting the various types of matplotlib objects.  These are Collections,
PolyCollections, LineCollections, Line2D, etc...  What would feel more
natural is if I could do the following:

f = Facet(...)
ax.facet(f, 'scatter')

Granted, this isn't as flexible, but it aligns with the current design
philosophy.  That is, the user plots objects to the axes, not the other way
around.

In short, this is the matplotlib workflow:  Organise your data, and pass it
to one of the axes object's plotting methods.

The way you have implemented Facet reminds of a discussion Mike, Phil, Ben
and myself were having over beers at the SciPy conference in Austin.  We
were talking about how matplotlib's plotting API should move forward.
 Admittedly, functions like plot() are a total disaster, they take a
plethora of different argument orders and types and try to conform to many
calling signatures at once.  Specifically, the way the data is passed to
the plotting method varies wildly.

ax.plot(x1, y1, x2, y3, ...)
ax.plot((x1, x2, x3), (y1, y2, y3), ...)

This goes for the ax.tri* methods too.  In addition to this, I tried to
extend this in a pull request<
https://github.com/matplotlib/matplotlib/pull/1143> by allowing the user to
pass in a callable object, to ax.fplot(), and have matplotlib decide how to
plot it.  Fernando then asked the killer question, "So are you going to
write an fcontour, fcontourf, ftriplot, ftricontour, etc?"  Obviously, no.
 You have to draw the line somewhere.  This led to the following line of
thinking:  What if matplotlib's plotting methods just acted on an object of
type Plottable?  That is, it doesn't matter whether your data is an array,
a function, or in your case, a Facet object.  The Plottable class will
carve out an interface that each of matplotlib's plotting methods can
utilise that interface to do the drawing.

This is the new workflow:  The user organises their data into a Plottable
object.  Pass that Plottable object to any one of matplotlib's plotting
methods.

I think your Faceted plotting API supports exactly what I'm hoping to see
matplotlib will move towards:

class Facet(matplotlib.Plottable)
    def __init__(self, ...)
        ...

f = Facet(...)
ax.scatter(f)

Thoughts?

Thanks for the hard work.
Best wishes,
Damon

-- 
Damon McDougall
http://www.damon-is-a-geek.com
Institute for Computational Engineering Sciences
201 E. 24th St.
Stop C0200
The University of Texas at Austin
Austin, TX 78712-1229

[matplotlib-devel] Faceted plotting

[Chris B. <bea...@ha...>]

Pandas has some nice tools to make faceted plots -- small multiples of
plots where data is grouped by category (
http://pandas.pydata.org/pandas-docs/stable/rplot.html). However, I think
there would be value in having this functionality built into matplotlib.
Mainly:

1. Not every dataset lives in a dataframe
2. The pandas library mimics the ggplot interface, and some people would
prefer an interface closer to matplotlib
3. Properly implemented, I think a matplotlib facet system would enable a
wider variety of faceted plots than the pandas tools.

I've taken a stab at this, and came up with an interface that I think has
potential. This currently exists as a separate repository at
https://github.com/ChrisBeaumont/mplfacet, and an example notebook at
http://bit.ly/17u1JzP

There two basic ways to use a facet object:

Facet(key, data).method()

will group one or more data arrays by key, and build a subplot for each
group by calling method (which is any axes plot method). Alternatively,

for item in Facet(key, data):
    x, y = item.data
    item.axes.scatter(x, y)

sets up the subplots and groups the data for you, but gives you more
freedom to populate each subplot however you like.

Is there interest in building this into matplotlib? If so, I would like to
polish it up and submit a PR.

Cheers,
Chris

[matplotlib-devel] Failed test images

[Michael D. <md...@st...>]

When a test fails on Travis, it will now upload the failed result images 
to Amazon S3.  Just scroll down to the bottom on the Travis console 
output, and there will be a URL there to a .tar.bz2 data containing the 
test results.  Handy.

Details:

Note, that we don't pay anything to upload to S3, only to download. And 
if it's only us developers really using these files, our download fees 
should be quite low.  In order to save storage costs, these result files 
are automatically deleted after 30 days.

Cheers,
Mike

Re: [matplotlib-devel] python2 vs. python3 matplotlib different results

[Michael D. <md...@st...>]

You provide a single standalone example to reproduce this. Most of our 
files have |from __future__ import division|, so I'm not entirely sure 
what could be going on...

Mike

On 08/28/2013 11:56 AM, Benjamin Root wrote:

>
>
> On Wed, Aug 28, 2013 at 10:45 AM, Neal Becker <ndb...@gm... 
> <mailto:ndb...@gm...>> wrote:
>
>     Autoscaling is producing a different result on p2 vs p3.  Maybe a
>     missed
>     N/M -> N//M ??
>
>     [nbecker@nbecker7 dvbs2x_iter]$ rpm -q python-matplotlib
>     python-matplotlib-1.2.0-14.fc19.x86_64
>     [nbecker@nbecker7 dvbs2x_iter]$ rpm -q python3-matplotlib
>     python3-matplotlib-1.2.0-14.fc19.x86_64
>
>
> Cheers!
> Ben Root
>
>
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk
>
>
> _______________________________________________
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> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel

Re: [matplotlib-devel] python2 vs. python3 matplotlib different results

[Benjamin R. <ben...@ou...>]

On Wed, Aug 28, 2013 at 10:45 AM, Neal Becker <ndb...@gm...> wrote:

> Autoscaling is producing a different result on p2 vs p3.  Maybe a missed
> N/M -> N//M ??
>
> [nbecker@nbecker7 dvbs2x_iter]$ rpm -q python-matplotlib
> python-matplotlib-1.2.0-14.fc19.x86_64
> [nbecker@nbecker7 dvbs2x_iter]$ rpm -q python3-matplotlib
> python3-matplotlib-1.2.0-14.fc19.x86_64
>
>
Cheers!
Ben Root

Re: [matplotlib-devel] cartopy: test suite questions

[Phil E. <pel...@gm...>]

Thanks Andreas,

> I couldn't find any test runner script / method.

There is currently no "python setup.py tests" type runner (which would be
welcomed), but the obvious test runner is to use "nose" - something like
"nosetests cartopy" should do the trick. It'd also be very easy to put a
function in the cartopy.tests module so that one may run the tests with
"import cartopy.tests; cartopy.tests.run_all()" - if that'd encourage you
to run the tests, I'd be supportive of adding it :-)

> the test_img_nest.py script fails on my machine

Hmmm, yes, it makes use of the hardcoded path based on __file__ of cartopy.
It'd be pretty quick to change this to use the cartopy.config['data_dir']
location, which should be writeable. Would you mind opening an issue or if
you're keen a PR?

> Thanks for making cartopy, this is awesome :)

Cool. Glad you like it - there are still some issues to address, but in
principle it is looking very promising IMHO.

Cheers,

Phil



On 27 August 2013 17:22, andreas-h <li...@hi...> wrote:

> Hi,
>
> I'm in the progress of packaging cartopy for Ubuntu. Some questions about
> the test suite:
>
> - I couldn't find any test runner script / method. It would be handy to
> have
> a script "run_tests.py" which performs all unit tests, or a method
> cartopy.run_tests(), or both. Otherwise, running the tests is a lot of
> manual work (which means it's less likely to happen).
>
> - the test_img_nest.py script fails on my machine (after installing the
> package), because it tries to write to the directory in which cartopy is
> installed. It would be better if filesystem write access would happen in
> some tempdir (which could be automatically cleaned up after the test).
>
> Thanks for making cartopy, this is awesome :)
>
> Cheers, Andreas.
>
>
>
> --
> View this message in context:
> http://matplotlib.1069221.n5.nabble.com/cartopy-test-suite-questions-tp41914.html
> Sent from the matplotlib - devel mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-devel mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
>

[matplotlib-devel] python2 vs. python3 matplotlib different results

[Neal B. <ndb...@gm...>]

Autoscaling is producing a different result on p2 vs p3.  Maybe a missed
N/M -> N//M ??

[nbecker@nbecker7 dvbs2x_iter]$ rpm -q python-matplotlib
python-matplotlib-1.2.0-14.fc19.x86_64
[nbecker@nbecker7 dvbs2x_iter]$ rpm -q python3-matplotlib
python3-matplotlib-1.2.0-14.fc19.x86_64

[matplotlib-devel] cartopy: test suite questions

[andreas-h <li...@hi...>]

Hi,

I'm in the progress of packaging cartopy for Ubuntu. Some questions about
the test suite:

- I couldn't find any test runner script / method. It would be handy to have
a script "run_tests.py" which performs all unit tests, or a method
cartopy.run_tests(), or both. Otherwise, running the tests is a lot of
manual work (which means it's less likely to happen).

- the test_img_nest.py script fails on my machine (after installing the
package), because it tries to write to the directory in which cartopy is
installed. It would be better if filesystem write access would happen in
some tempdir (which could be automatically cleaned up after the test).

Thanks for making cartopy, this is awesome :)

Cheers, Andreas.



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/cartopy-test-suite-questions-tp41914.html
Sent from the matplotlib - devel mailing list archive at Nabble.com.