diehl | 23 Feb 19:26 2015

Getting Started with IPython Widgets

Hi Folks, 

I'd like to start experimenting with IPython widgets and use them in an
ongoing consulting project. Is the IPython 2.x implementation of widgets
stable now? Or is there some reason to start straightaway with 3.x? Any tips
on where I can find documentation? Seems a bit sparse. 



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Alexander Garcia Castro | 30 Jan 04:07 2015

ipython in scholarly communication

Dear all, Sepublica is particularly interested in getting submissions from ipython usrs/developers. we are very interested in seeing new ways of scholarly communication in action and we believe that ipython illustrates a path to be followed. 

SePublica 2015: Do show, do not tell!


Workshop website: http://sepublica.info/
Event hashtags: #SePublica #ESWC2015

in conjunction with

ESWC 2015
The 12th European Semantic Web Conference

At SePublica we are interested in addressing the question, how is Semantic Web technology being used as part of publication workflows.

Challenge us with a creative submission. Let us see and experience your take on publications for the Web of data; we want to see NEW ideas in action, INNOVATION that makes our lives easier. Is it about scholarly communication? Then what problem are you solving? How are you making the content interoperable? How is this different/better from traditional approaches?

Important Dates
* Submission deadline: 2015-03-06
* Notifications: 2015-04-03
* Camera ready version: 2015-04-17

Easychair: https://www.easychair.org/conferences/?conf=sepublica2015

Submissions will be peer reviewed. Accepted works have to be presented at the workshop (requires registering for the ESWC conference and the workshop). Every accepted submission will be published in the proceedings of the workshop.

Submission Types
### Call for Submissions
Deadline: 2015-03-06. Authors may submit their content in whatever way they consider is best for their purposes (e.g., HTML, RDFS/OWL, IPython, PDF, or any publicly executable script, etc). Please feel free to contact us to discuss your particular case if necessary. We will be happy to assist authors and support them as much as we can. Submissions are format free, GIT URLs are accepted just like OWL, XML etc. However, reviewers should not have to install software in order to review the submissions. Datasets are also accepted. In all cases everything must be publicly available. For those of you submitting a PDF please use the LNCS format, 12 pages is the limit –including references. Please, note that (X)HTML(+RDFa) submissions are also welcome as long as the layout complies with the LNCS style. For example, authors may use the template provided at https://github.com/csarven/linked-research

### Call for Polemics
Deadline: 2015-04-24. We would like to invite authors to send us a one page manuscript, 20 lines max, describing their position with respect to new technologies supporting the publication workflow: What are the most pressing issues to be addressed? What is their position with respect to the overall problem? What innovation is needed? etc. Polemics authors will have only 5 minutes to present; the format of this session is sequential, after each presentation the next follows with no questions in between. There will be a discussion and summary of all the issues at the end of all the polemics session.

Issues to be addressed
* Should papers be semantically annotated?
* How would you search or query for research objects?
* How can research objects be reused?
* What is an executable semantic paper?
* How can we create interactive research documents to better communicate and educate?
* Is there a format for semantic publishing or does it require a combination of formats?
* How can research documents be persistent and archived? Which formats are preferable and why?
* If we subscribe to science, free and open access to knowledge, what's the purpose of the arrangement between conferences and publishers? Or can big conferences manage the publication themselves?
* Is there visible change towards semantic authoring and publishing? If not, what are some of the underlying challenges to get there?
* Assume a 3-year plan to transition the SW research community to completely publish using SW technologies. Identify the milestones and explain how it would happen.
* Backend use of semantics by publishers in book, news, and scholarly publishing
* Publishing data-driven arguments for general news consumption or in scholarly papers
* Historical changes in publishing since the advent of online publishing: what is going right?

Organizing Committee
* Phillip Lord
* Alexander Garcia Castro
* Sarven Capadisli
* Jodi Schneider

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Denis Akhiyarov | 29 Jan 23:28 2015

survey/poll using ipython notebook on local network

Is it possible to create a survey/poll in ipython/jupyter notebook, e.g. using widgets? Why ipython - due to some built-in statistics.

I'm not using surveymonkey, because this has to be on local network/intranet.

Otherwise I'll have to use an approach similar to this:

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Andrew Jaffe | 15 Jan 14:45 2015


Hi all,

I see that you can set the figure format(s) shown by the inline backend 
for matplotlib by assigning a set of appropriate strings to an IPython 
Config instance's InlineBackend.figure_formats. I don't quite understand 
what it means for there to be more than one member of the set. Which one 
(I think it's just one) is actually displayed? Are the others rendered 
but not displayed? How are they accessed? Or am I just missing the point?


Fernando Perez | 9 Jan 05:43 2015

Re: trapping error thrown by line magics?

Dear Catherine,

certain magics swallow their exceptions, %cd in particular.  We made that decision to make them more human-friendly, since magics were originally conceived really as a pure human-driven convenience while working interactively, not as a library/programming construct.

In general, the magic system does *not* swallow all exceptions, though, so you could add your own versions of the ones you need with different behavior.

Not an ideal answer, but at least the system doesn't intrinsically prevent what you're looking for (which I was afraid we might, so I actually went looking a bit).



On Tue, Jan 6, 2015 at 8:42 AM, Catherine Devlin <catherine.devlin <at> gmail.com> wrote:
I really enjoy being able to build informal IPython scripts that include line magics.  Maybe too much.

When I do so, is there a way to trap errors thrown by line magics?  This doesn't work as I had hoped:
try: %cd directory_that_does_not_existexcept Exception as err: print('error trapped!')
[Errno 2] No such file or directory: 'directory_that_does_not_exist' /home/catherine/werk/openFEC/data/tuning


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fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail
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Catherine Devlin | 6 Jan 17:42 2015

trapping error thrown by line magics?

I really enjoy being able to build informal IPython scripts that include line magics.  Maybe too much.

When I do so, is there a way to trap errors thrown by line magics?  This doesn't work as I had hoped:
try: %cd directory_that_does_not_existexcept Exception as err: print('error trapped!')
[Errno 2] No such file or directory: 'directory_that_does_not_exist' /home/catherine/werk/openFEC/data/tuning

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Aaron Reabow | 4 Jan 07:55 2015

ipython notebook kernel shows busy from start

I am having a problem whereby ipython notebook launches but the kernel shows as busy.  I haven't executed any commands at this point.  If i restart the kernel, the command line shows that this has happened but the message doesn't get through to the browser where the little red eye still stares at me.

It means that I can't run any code.  This is the first time I have installed using anaconda, and I wonder if that is related...

Anyway, any thoughts?  This is beginning to drive me crazy.  I can get it to function properly if I restart the computer on occasion, or after a period of time sometimes it goes away by itself...

warm regards,

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Darren Dale | 27 Dec 17:07 2014

embedding ipython, namespace question


I'm working on embedding an ipython qtconsole in my applilcation as a dock widget. The https://github.com/ipython/ipython/blob/master/examples/Embedding/inprocess_qtconsole.py example was a helpful first step. As variables are created or updated in the main application, I'd like to be able to inspect them in the qtconsole. Is it possible for the qtconsole's namespace to be shared or linked with that of the main application? It seems like this should be possible, based on the documentation for http://ipython.org/ipython-doc/1/api/generated/IPython.terminal.embed.html#IPython.terminal.embed.InteractiveShellEmbed . I'm creating my kernel and client at the beginning of my module, and then wiring up the widget when my application's main window is about to show. But if I run `dir()` in the embedded ipython qt console, the list is identical to what I get if I run `dir()` in the standalone `ipython qtconsole` program.

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Phillip Feldman | 24 Dec 06:45 2014

hiding code in ipython notebooks

There are situations where I would like to hide the code in a cell so that only the output
is visible. I've seen various posts (e.g., at http://blog.nextgenetics.net/?e=99) about hackish ways to accomplish this. Does anyone know if a better solution is in the works?

Phillip M. Feldman
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Julien Schueller | PHIMECA | 16 Dec 12:28 2014

graph displayed twice while overloading _repr_svg_ for notebook


I'm having trouble overloading _repr_svg_ for graph inlining in the notebook; my object is displayed
twice if I call plt.plot just before.
I assumed a figure was left open or something, but even if I call plt.close('all') between the matplotlib
calls, the result remains the same.

I did some imports first:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
from scipy.stats import norm
import sys
import io
print('matplotlib version %s' % matplotlib.__version__)
import IPython
print('IPython version %s' % IPython.__version__)

Here'my object:
class NormGraph(object):
    def __init__(self):
        super(NormGraph, self).__init__()
    def _repr_svg_(self):
        if sys.version_info[0] >= 3:
            output = io.StringIO()
            output = io.BytesIO()
        self._fig = plt.figure()
        axes_kwargs = {}
        plot_kwargs = {}
        self._ax = [self._fig.add_subplot(111, **axes_kwargs)]
        x = np.arange(-10, 10, 0.001)
        y = norm.pdf(x,0,2)
        self._ax[0].plot(x, y, **plot_kwargs)
        self._fig.savefig(output, format='svg')

        return output.getvalue()

Then a basic call to pyplot:
%matplotlib inline
plt.plot(0, 1)

Then if I try to inline my object it's displayed twice:

I atached the complete notebook.


Julien Schueller
Phimeca Engineering
Attachment (Untitled0.ipynb): application/octet-stream, 53 KiB
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John ZuHone | 11 Dec 05:18 2014

Trouble with configuration file in notebook


I used 

ipython profile create 

to create the default configuration file, and then I uncommented a few lines in
.ipython/profile_default/ipython_notebook_config.py to set different configuration options, e.g.:

c.NotebookApp.open_browser = False
c.NotebookApp.log_level = 20

However, none of them seem to be actually changing:

ipython notebook —debug

2014-12-10 23:15:50.654 [NotebookApp] Config changed:
2014-12-10 23:15:50.654 [NotebookApp] {'Application': {'log_level': 10}}
2014-12-10 23:15:50.655 [NotebookApp] IPYTHONDIR set to: /Users/jzuhone/.ipython
2014-12-10 23:15:50.659 [NotebookApp] Using existing profile dir: u'/Users/jzuhone/.ipython/profile_default'
2014-12-10 23:15:50.660 [NotebookApp] Searching path [u'/Users/jzuhone',
u'/Users/jzuhone/.ipython/profile_default'] for config files
2014-12-10 23:15:50.660 [NotebookApp] Attempting to load config file: ipython_config.py
2014-12-10 23:15:50.661 [NotebookApp] Loaded config file: /Users/jzuhone/.ipython/profile_default/ipython_config.py
2014-12-10 23:15:50.661 [NotebookApp] Attempting to load config file: ipython_notebook_config.py
2014-12-10 23:15:50.662 [NotebookApp] Loaded config file: /Users/jzuhone/.ipython/profile_default/ipython_notebook_config.py
2014-12-10 23:15:50.669 [NotebookApp] Using MathJax from CDN: https://cdn.mathjax.org/mathjax/latest/MathJax.js
2014-12-10 23:15:50.684 [NotebookApp] The port 8888 is already in use, trying another random port.
2014-12-10 23:15:50.685 [NotebookApp] Serving notebooks from local directory: /Users/jzuhone
2014-12-10 23:15:50.685 [NotebookApp] 0 active kernels 
2014-12-10 23:15:50.685 [NotebookApp] The IPython Notebook is running at: http://localhost:8889/
2014-12-10 23:15:50.685 [NotebookApp] Use Control-C to stop this server and shut down all kernels (twice
to skip confirmation).

The “config changed” message does not show up after loading the notebook config, and the change in the
config option does not even take place. Can anyone clarify what is going on here? 


John ZuHone

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