gmane.comp.python.ipython.user

iPython Notebook profile under Windows

federico vaggi — 2012-05-25T20:21:42

Hi,

I usually use iPython and the notebook under Linux, but I ran into some
rather trivial problems under Windows.  After installing EPD (thank you
very much to Enthought) I noticed that the default save directory for
iPython notebooks is windows/system - which of course, the default user
does not have write access to.  This means that I can open existing iPython
notebooks, but I can't create new ones, because I am not able to change the
starting directory, and pressing new crashes Python with an error about
'lacking write access''

For reference, here is the log:

[NotebookApp] Using existing profile dir:
u'C:\\Users\\Fede\\.ipython\\profile_d
efault'
[NotebookApp] The IPython Notebook is running at: http://127.0.0.1:8888
[NotebookApp] Use Control-C to stop this server and shut down all kernels.
ERROR:root:Uncaught exception GET /new (127.0.0.1)
HTTPRequest(protocol='http', host='127.0.0.1:8888', method='GET',
uri='/new', ve
rsion='HTTP/1.1', remote_ip='127.0.0.1', body='', headers={'Connection':
'keep-a
live', 'Accept-Language': 'en-us,en;q=0.5', 'Accept-Encoding': 'gzip,
deflate',
'Referer': 'http://127.0.0.1:8888/', 'Host': '127.0.0.1:8888', 'Accept':
'text/h
tml,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8', 'User-Agent':
'Mozil
la/5.0 (Windows NT 6.0; rv:12.0) Gecko/20100101 Firefox/12.0'})
Traceback (most recent call last):
  File "C:\Python27\lib\site-packages\tornado\web.py", line 988, in _execute
    getattr(self, self.request.method.lower())(*args, **kwargs)
  File "C:\Python27\lib\site-packages\tornado\web.py", line 1739, in wrapper
    return method(self, *args, **kwargs)
  File
"C:\Python27\lib\site-packages\IPython\frontend\html\notebook\handlers.py
", line 245, in get
    notebook_id = nbm.new_notebook()
  File
"C:\Python27\lib\site-packages\IPython\frontend\html\notebook\notebookman
ager.py", line 253, in new_notebook
    with open(path,'w') as f:
IOError: [Errno 13] Permission denied:
u'C:\\Windows\\system32\\Untitled0.ipynb'


ERROR:root:500 GET /new (127.0.0.1) 498.00ms


What's the option in the config file:

C:\\Users\\Fede\\.ipython\\profile_default'

That I need to change to fix the start up directory?

Thank you very much,

Federico
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memory problem with passing numpy arrays in IPythonparallel

Charles Cadieu — 2012-05-25T15:32:09

Hi,

I'm writing a distributed stochastic gradient descent algo and need to pass
numpy arrays between a master node and the workers. These arrays are around
1000x1000 and I expect this algorithm to run for 100k iterations. I observe
that the communication is fast for the first few 1k iterations and then
begins to slow dramatically.

I've reduced the problem down to the following code. I'm experiencing what
looks like a memory leak with this code below. Am I using the correct
interface/paradigm for passing numpy arrays around? Or is there a deeper
problem with clearing references to these numpy arrays?

Thanks for any help!
Charles


from __future__ import print_function

import time
import numpy as np
from collections import defaultdict

from IPython import parallel

# create client & view
rc = parallel.Client()
dv = rc[:]
ids = rc.ids
# scatter 'id', so id=0,1,2 on engines 0,1,2
dv.scatter('id', rc.ids, flatten=True)
print("Engine IDs: ", dv['id'])

sz = (1000,500)

dv.execute('import numpy as np')
task = dv.execute('local_A = np.zeros((%d,%d))'%sz)
r = task.wait()
print(task.get())

def update_and_return(new_A,sz=sz):
    global local_A
    local_A[:] = new_A[:]
    return np.random.randn(sz[0],sz[1])

updates = 1000
num_engines = len(ids)
amr = [rc[i].apply_async(update_and_return,np.random.randn(*sz)) for i in
range(num_engines)]
for am in amr:
    am.wait()

returned_A = np.zeros(sz)
def learn(max_updates):
    i = 0
    updates = 0
    not_done = True
    update_counter = defaultdict(int)
    time_history = []
    t0 = time.time()
    while not_done:
        if amr[i].ready():
            returned_A[:] = amr[i].get()
            time_last_update = time.time() - t0
            amr[i] =
rc[i].apply_async(update_and_return,np.random.randn(*sz))

            print("time last update", '%2.6f'%time_last_update)
            time_history.append(time_last_update)
            updates += 1
            update_counter[i] += 1
            t0 = time.time()

            if updates == max_updates:
                print("Done!")
                for engine in range(num_engines):
                    print("Engine %d Updates:
%d"%(engine,update_counter[engine]))
                not_done = False
        else:
            pass
            #print("engine %i not ready"%i)
        i = (i + 1)%num_engines
    return time_history

tic = time.time()
time_history = learn(updates)

p_time = time.time() - tic
print('Parallel IPython took %.3f'%p_time)
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0.12.1 install problem

Ryan Krauss — 2012-05-25T14:21:50

I am trying to do a fresh install of Python 2.7, numpy 1.6.2 (and
friends), and ipython 0.12.1 in windows.  When I run the ipython
0.12.1 exe (ipython-0.12.1.win32.exe), everything seems to go OK, but
I don't have an ipython folder in my All Programs menu.  Am I doing
something wrong or is this a bug?

Thanks,

Ryan

IPython notebook module dependencies

reckoner — 2012-05-23T22:07:35

hi

I am trying to distribute an IPython notebook and I want to make sure 
that people can actually run the computations, but I'm not sure how to 
communicate the long list of the dependent modules that a particular 
notebook requires. Is there some way I can automatically generate this? 
I would like to give them a list that they can simply do

% easy_install list_of_dependencies.txt

The tricky part here is that I have many more installed modules than are 
used in a specific IPython notebook so given anyone the list of items 
installed in my site-packages directory would be of no help. 
Furthermore, different notebooks would have different dependency lists.

Any help appreciated.

parallel data capture and write

Vasco Tenner — 2012-05-23T11:55:00

Hi,
I'm doing imaging experiments using a allied vision camera. Currently 
I'm using the 32bit pvapi driver and a python wrapper. I want to capture 
large datasets (around 10gb) as fast as possible. This does not fit into 
the memory I can access using a 32bit python installation. I was 
thinking about writing down the data while capturing. I do write 5mb files.

I'm trying to use IPython.parallel to achieve the simultanious data 
capture and write. I create 1 engine and send the data to this engine 
using apply_async. For some reason the engine does store all the data, 
also when it is already written on the disk. How do I clear the engine 
memmory?

Is there a better approach?

Kind regards,
Vasco Tenner
Vrije Universiteit in Amsterdam

Out problem

Adrian Klaver — 2012-05-21T20:34:43

I seem to be having a problem with Out not showing up in newer versions 
of ipython under certain conditions. It happens with  0.11+. Easiest to 
just show is as an example:

Python 2.7.3 (default, May  9 2012, 20:18:57)
IPython 0.12.1 -- 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]: l=[1,2,3]

In [2]: l[0]
Out[2]: 1

In [3]: for i in l:
     i
    ...:

In [4]: Out
Out[4]: {2: 1}


In previous versions iterating through a list would yield an Out:

Python 2.6.5 (r265:79063, Apr 16 2010, 13:09:56)
Type "copyright", "credits" or "license" for more information.

IPython 0.10 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object'. ?object also works, ?? prints more.

In [1]: l=[1,2,3]

In [2]: l[0]
Out[2]: 1

In [3]: for i in l:
    ...:     i
    ...:
    ...:
Out[3]: 1
Out[3]: 2
Out[3]: 3

In [4]: Out
Out[4]: {2: 1, 3: 3}


Any pointers would be appreciated.

ipython and python3

Alan — 2012-05-21T17:18:08

Hi there,

I am a Fink user on Mac OSX Lion and I have ipython 0.12, python 2.7 and
python 3.2 installed on my system.

I am wondering how can I use ipython with python3. Besides, what is
"ipython --profile=python3" since I still see:

Python 2.7.3 (default, Apr 19 2012, 10:52:47)
Type "copyright", "credits" or "license" for more information.

IPython 0.12.1 -- An enhanced Interactive Python.

?

Thanks,

Alan

fail to update edited script when using %run withinipython?

Chao YUE — 2012-05-20T20:59:41

Dear all,

I have a problem is that, I use %run script.py to run the script within
ipython (with %pdb on),
then I add one line of print something before the line where exception is
raised.
Then I use ctrl+d to exit debugger and use %run to run the script again, I
found the script in
traceback is updated but the print part is not executed. Then I have to log
out of current ipython session
and start ipython again and use %run command, the print part has been
executed.

Does anyone else see this problem and I guess there is some flag to update
the script?

thanks,

Chao

call function with set break point?

Chao YUE — 2012-05-20T18:38:17

Dear all,

Just a one line question:
I have %run -d b20 script.py to set the break point at line20 when run the
script. Is there a way I can do the similar when I call a function?

thanks,

Chao

MacOSX import error pyside and pyqt

Rajeev Jain — 2012-05-19T18:37:42

This is on Mac OSX, I'm trying to do ipython qtconsole:-

/Users/rajeevjain
==> brew install PySide
Error: pyside-1.1.0 already installed

/Users/rajeevjain
==> brew install PyQt
Error: pyqt-4.9.1 already installed

/Users/rajeevjain
==> ipython
Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
Type "copyright", "credits" or "license" for more information.

IPython 0.12.1 -- 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]: from IPython.external.qt import QtCore, QtGui
ImportError Traceback (most recent call last)
/Users/rajeevjain/ in ()
----> 1 from IPython.external.qt import QtCore, QtGui

/Library/Python/2.7/site-packages/IPython/external/qt.py in ()
40 QT_API = QT_API_PYQT
41 except ImportError:
---> 42 raise ImportError('Cannot import PySide >= 1.0.3 or PyQt4 >= 4.7')
43
44 elif QT_API == QT_API_PYQT:

ImportError: Cannot import PySide >= 1.0.3 or PyQt4 >= 4.7


Rajeev

create all variables that are inside function inipython

Chao YUE — 2012-05-19T15:12:02

Dear all,

I am frustrated by debugging code now... Is there a way that when I call a
function, all the variables within the function will be created in current
ipython interactive session namespace
and then I can run the script in a way of %run -i myjob.py, if there is any
bug, I can print the most recent variable in the loop and check what's
going one, rather than modifying the code again
and again with try-except blocks or adding pdb.set_trace() here and there.
This might no be good practice but I think for not large amount of data,
it's a good way to debug.

thanks et cheers,

Chao

Using the IPython notebook architecture

K Krish — 2012-05-18T20:08:17

Hello IPython group,

I have some Python-based algorithms which I want to share with other
researchers via a webpage.
The users will able to run the algorithms on their uploaded data files, and
they can view the results in plots (displayed on the webpage) etc.
Since the IPython notebook interface already provides something that can do
this (and much more!), I was thinking of basically copying and modifying
the implementation for my webpage. I won't need an interactive shell as
most of the users won't be programmers and won't know Python -- the UI in
the webpage will using their settings and parameters to run the Python
scripts in the background.

Here's my question/request to the group ---
Note: My experience in web development is very very basic.

1) This seems like straightforward task, since most of the things I need
are already implemented in the notebook interface: the web server, calling
the IPython kernel from the webpage, plotting graphs in the webpage etc. Do
you recommend starting with the existing notebook interface and modifying
it into a new package?

2) What would be a good starting point to start hacking the notebook
interface? Can you suggest some simple tasks I could try to start modifying
the webpage layout and calling the kernel from the webpage?


Any help is much appreciated!
-NT
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ipython notebook doesn't launch browser "could not open file(notebook) for safe execution

robertking — 2012-05-18T09:28:58

Launching notepad gives the error below, and opens ipython as usual, but not
the browser.

Microsoft Windows [Version 6.0.6002]
Copyright (c) 2006 Microsoft Corporation.  All rights reserved.

*C:\Windows\system32>ipython notebook
Could not open file <notebook> for safe execution.*
Python 2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit (Intel)]
Type "copyright", "credits" or "license" for more information.

IPython 0.10.2 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object'. ?object also works, ?? prints more.

In [1]: import tornado, zmq

In [2]: tornado.version
Out[2]: '2.2.1'

In [3]: zmq.__version__
Out[3]: '2.2.0'

In [4]: import simplejson


--
View this message in context: http://python.6.n6.nabble.com/ipython-notebook-doesn-t-launch-browser-could-not-open-file-notebook-for-safe-execution-tp4975037.html
Sent from the IPython - User mailing list archive at Nabble.com.

Print colours

2012-05-17T14:46:26

Hi.

I am playing around with the client-server stuff via  the blocking kernel manager (based on MinRK's reply at http://stackoverflow.com/questions/9977446/connecting-to-a-remote-ipython-instance).
If I get an error back the traceback contains ascii colour information like so:

[u'\x1b[1;31m---------------------------------------------------------------------------\x1b[0m\n\x1b[1;31mNameError\x1b[0m   etc.

Is there a quick way of rendering this correctly with colours via an IPython shell?

Thanks,

Matt

simple math error noted under weird circumstance

Kevin — 2012-05-17T03:08:23

Hello all.

Not sure if this is the appropriate spot to discuss this.
The following takes place when using Notebook.

I noticed an error dependent upon the presence of an extra linefeed on
the last line.
The following gives two different answers dependent upon the presence
of a linefeed:

pV = V*iV
p1 = v1*i1
p2 = v2*i2
p_sum = pV + p1 + p2
print "The sum of the powers (in Watts) entering all of the elements
is: %f" % p_sum

Without linefeed:

The sum of the powers (in Watts) entering all of the elements is: -5.306667

With linefeed:

The sum of the powers (in Watts) entering all of the elements is: 0.000000

The last output is the correct output.
I've seen simple math errors before using Notebook and now I'll have
to go back and check if it is linefeed related.

Any idea why this might be occurring?

Kevin

How to get the "??" to show the code of a decoratedfunction on IPython

Filipe Pires Alvarenga Fernandes — 2012-05-15T15:47:00

Hi, I have a decorator that goes more or less like this:

class match_args_return(object):
    def __init__(self, func):
        self.func = func
        self.__doc__ = func.__doc__
        self.__name__ = func.__name__

So far I can use IPython "?" to see the docstring, bit the "??" only
shows the decorator code instead of the decorated function.  Does
anyone know a work-around to this issue?

Thanks, Filipe.

Error Using IPython Notebook on Windows 7

Trevor Sweetnam — 2012-05-15T13:45:48

Hi All, 
I have recently discovered the IPython notebook feature. It's revolutionised my data analysis work.
Anyway I have encountered the following error when using notebooks in Chrome on Windows 7. Everything loads and appears to function ok until I try to execute a cell.- In the notebook itself nothing happens and in the command prompt I get the output below.- I don't know where this flag '-f' is coming from...I think if I could find and remove it that should fix my error. 
Any thoughts?
Cheers,
Trevor

[NotebookApp] Using existing profile dir: u'C:\\Users\**USERNAME**\\.ipython\\profile_default'[NotebookApp] The IPython Notebook is running at: http://127.0.0.1:8888[NotebookApp] Use Control-C to stop this server and shut down all kernels.[NotebookApp] Using local MathJax[NotebookApp] Kernel started: 5945074f-2d83-4ed5-9f24-c104b0729f07IPython: an enhanced interactive Python shell.
Options-------
IPython command-line arguments are passed as '--<flag>', or '--<name>=<value>'.
Arguments that take values are actually convenience aliases to fullConfigurables, whose aliases are listed on the help line. For more informationon full configurables, see '--help-all'.
--no-autoindent    Turn off autoindenting.--deep-reload    Enable deep (recursive) reloading by default. IPython can use the    deep_reload module which reloads changes in modules recursively (it    replaces the reload() function, so you don't need to change anything to    use it). deep_reload() forces a full reload of modules whose code may    have changed, which the default reload() function does not.  When    deep_reload is off, IPython will use the normal reload(), but...
    **SNIP - THIS IS THE STANDARD OPTIONS SPIEL**
    ...Default: ''    Start logging to the given file in append mode.--log-level=<Enum> (Application.log_level)    Default: 30    Choices: (0, 10, 20, 30, 40, 50, 'DEBUG', 'INFO', 'WARN', 'ERROR', 'CRITICAL')    Set the log level by value or name.--ext=<Unicode> (InteractiveShellApp.extra_extension)    Default: ''    dotted module name of an IPython extension to load.
To see all available configurables, use `--help-all`
[IPKernelApp] Unrecognized flag: '-f'



























































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ipython 0.12.1 crashing when embedded in Django onwindows 7

Leo Shklovskii — 2012-05-13T22:28:40

I've been using ipython 0.10 forever and wanted to upgrade to the latest version 
ipython.

When I install ipython 0.12, the Django manage.py shell command intermittently 
crashes in various ways that indicate memory corruption.

Looking at the code, this is all that Django is doing:

 > from IPython import embed
 > embed()

I'm running a 64bit version of Windows 7 (latest SP) but I'm running a 32bit 
python build since a number of the binaries of certain packages out there don't 
exist in 64bit versions.

The crash happens intermittently (~50% of the time) and there are several 
different actual crashes that happen:

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

c:\test>manage.py shell
Traceback (most recent call last):
   File "C:\test\manage.py", line 25, in <module>
     execute_manager(settings)
   File "C:\Python27\lib\site-packages\django\core\management\__init__.py", line 
459, in execute_manager
     utility.execute()
   File "C:\Python27\lib\site-packages\django\core\management\__init__.py", line 
382, in execute
     self.fetch_command(subcommand).run_from_argv(self.argv)
   File "C:\Python27\lib\site-packages\django\core\management\base.py", line 
196, in run_from_argv
     self.execute(*args, **options.__dict__)
   File "C:\Python27\lib\site-packages\django\core\management\base.py", line 
232, in execute
     output = self.handle(*args, **options)
   File "C:\Python27\lib\site-packages\django\core\management\base.py", line 
371, in handle
     return self.handle_noargs(**options)
   File 
"C:\Python27\lib\site-packages\django\core\management\commands\shell.py", line 
54, in handle_noargs
     self.run_shell()
   File 
"C:\Python27\lib\site-packages\django\core\management\commands\shell.py", line 
37, in run_shell
     return getattr(self, shell)()
   File 
"C:\Python27\lib\site-packages\django\core\management\commands\shell.py", line 
17, in ipython
     embed()
   File "C:\Python27\lib\site-packages\IPython\frontend\terminal\embed.py", line 
270, in embed
     _embedded_shell = InteractiveShellEmbed(**kwargs)
   File "C:\Python27\lib\site-packages\IPython\frontend\terminal\embed.py", line 
88, in __init__
     display_banner=display_banner
   File 
"C:\Python27\lib\site-packages\IPython\frontend\terminal\interactiveshell.py", 
line 183, in __init__
     user_module=user_module, custom_exceptions=custom_exceptions
   File "C:\Python27\lib\site-packages\IPython\core\interactiveshell.py", line 
431, in __init__
     self.init_history()
   File "C:\Python27\lib\site-packages\IPython\core\interactiveshell.py", line 
1439, in init_history
     self.history_manager = HistoryManager(shell=self, config=self.config)
   File "C:\Python27\lib\site-packages\IPython\core\history.py", line 409, in 
__init__
     self.new_session()
   File "<string>", line 2, in new_session
   File "C:\Python27\lib\site-packages\IPython\core\history.py", line 63, in 
needs_sqlite
     return f(*a,**kw)
   File "C:\Python27\lib\site-packages\IPython\core\history.py", line 427, in 
new_session
     NULL, "") """, (datetime.datetime.now(),))
MemoryError

c:\test>manage.py shell
Python 2.7.3 (default, Apr 10 2012, 23:31:26) [MSC v.1500 32 bit (Intel)]
Type "copyright", "credits" or "license" for more information.

IPython 0.12.1 -- 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]:
------------------

Sometimes, the crash doesn't dump anything to the console, or dumps a partial 
traceback and then gives a standard windows application error. From the logs, 
there's several variations to this:


Log Name:      Application
Source:        Application Error
Date:          5/13/2012 3:15:01 PM
Event ID:      1000
Task Category: (100)
Level:         Error
Keywords:      Classic
User:          N/A
Computer:      *****
Description:
Faulting application name: python.exe, version: 0.0.0.0, time stamp: 0x4f84a6c8
Faulting module name: ntdll.dll, version: 6.1.7601.17725, time stamp: 0x4ec49b8f
Exception code: 0xc0000005
Fault offset: 0x000343d6
Faulting process id: 0x11c4
Faulting application start time: 0x01cd3155d565fa76
Faulting application path: C:\Python27\python.exe
Faulting module path: C:\Windows\SysWOW64\ntdll.dll
Report Id: 14d1b0ab-9d49-11e1-ac32-00a0c6000000
Event Xml:
<Event xmlns="http://schemas.microsoft.com/win/2004/08/events/event">
   <System>
     <Provider Name="Application Error" />
     <EventID Qualifiers="0">1000</EventID>
     <Level>2</Level>
     <Task>100</Task>
     <Keywords>0x80000000000000</Keywords>
     <TimeCreated SystemTime="2012-05-13T22:15:01.000000000Z" />
     <EventRecordID>24664</EventRecordID>
     <Channel>Application</Channel>
     <Computer>*****</Computer>
     <Security />
   </System>
   <EventData>
     <Data>python.exe</Data>
     <Data>0.0.0.0</Data>
     <Data>4f84a6c8</Data>
     <Data>ntdll.dll</Data>
     <Data>6.1.7601.17725</Data>
     <Data>4ec49b8f</Data>
     <Data>c0000005</Data>
     <Data>000343d6</Data>
     <Data>11c4</Data>
     <Data>01cd3155d565fa76</Data>
     <Data>C:\Python27\python.exe</Data>
     <Data>C:\Windows\SysWOW64\ntdll.dll</Data>
     <Data>14d1b0ab-9d49-11e1-ac32-00a0c6000000</Data>
   </EventData>
</Event>

Log Name:      Application
Source:        Application Error
Date:          5/13/2012 8:07:13 AM
Event ID:      1000
Task Category: (100)
Level:         Error
Keywords:      Classic
User:          N/A
Computer:      *****
Description:
Faulting application name: python.exe, version: 0.0.0.0, time stamp: 0x4df4ba7c
Faulting module name: unknown, version: 0.0.0.0, time stamp: 0x00000000
Exception code: 0xc0000005
Fault offset: 0x00000000
Faulting process id: 0x460
Faulting application start time: 0x01cd311a134db828
Faulting application path: C:\Python27\python.exe
Faulting module path: unknown
Report Id: 517fff66-9d0d-11e1-ac32-00a0c6000000
Event Xml:
<Event xmlns="http://schemas.microsoft.com/win/2004/08/events/event">
   <System>
     <Provider Name="Application Error" />
     <EventID Qualifiers="0">1000</EventID>
     <Level>2</Level>
     <Task>100</Task>
     <Keywords>0x80000000000000</Keywords>
     <TimeCreated SystemTime="2012-05-13T15:07:13.000000000Z" />
     <EventRecordID>24607</EventRecordID>
     <Channel>Application</Channel>
     <Computer>*****</Computer>
     <Security />
   </System>
   <EventData>
     <Data>python.exe</Data>
     <Data>0.0.0.0</Data>
     <Data>4df4ba7c</Data>
     <Data>unknown</Data>
     <Data>0.0.0.0</Data>
     <Data>00000000</Data>
     <Data>c0000005</Data>
     <Data>00000000</Data>
     <Data>460</Data>
     <Data>01cd311a134db828</Data>
     <Data>C:\Python27\python.exe</Data>
     <Data>unknown</Data>
     <Data>517fff66-9d0d-11e1-ac32-00a0c6000000</Data>
   </EventData>
</Event>

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

Can anyone offer any suggestions for either how to fix, or if there's anything I 
can do to help troubleshoot this issue?

--
--Leo

execfile doesn't work from command line

Joe Miller — 2012-05-11T15:18:20

Hi,

I've starting using ipython 0.12 and I'm having a problem running execfile from the command line

% cat tmp.py
print ("HERE")

% ipython -c "execfile (tmp.py)"
<ipython usage information...>
[TerminalIPythonApp] Bad config encountered during initialization:
[TerminalIPythonApp] The 'code_to_run' trait of a TerminalIPythonApp instance must be a unicode string, but a value of None <type 'NoneType'> was specified.
% ipython -V
0.12


This used to work in ipython 0.10
% ipython -c "execfile ('tmp.py')"
HERE
% ipython -V
0.10

I understand that I can just run the file on the command line with ipython (e.g. ipython tmp.py). But if I want to run other commands along with executing the file it no longer works 

% ipython -c "print ('THERE')" tmp.py
THERE

Any suggestion would be greatly appreciated. Thanks

-joe
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Closed pandas.HDFStore causes ipython/whos error...

Marc Shivers — 2012-05-11T22:53:47

Hi,

I'm not sure whether this is more appropriately an issue for pandas or
ipython, so I'm sending to both.  I get the error below whenever I open a
pandas.HDFStore object, then close() it, and call the ipython whos command,
which seems to croak when it tries to populate the "Data/Info" field for a
closed HDFStore...

Any idea whether there's an easy fix?

THanks,
Marc

In [27]: whos
Variable      Type          Data/Info
-------------------------------------
data_dir      str           /disk/local/pycache/
features      HDFStore      <class 'pandas.io.pytable<...>me\nXOPp60
DataFrame
lr_coeffs     DataFrame     <class 'pandas.core.frame<...>XOP\ndtypes:
float64(133)
lr_model      HDFStore
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
/genauto/global/dept_syseqms_stc_x/python_files/eea/<ipython-input-27-3e8664a026ba>
in <module>()
----> 1 get_ipython().magic(u'whos ')

/usr/local/python/2.7.2/lib/python2.7/site-packages/IPython/core/interactiveshell.py
in magic(self, arg_s, next_input)
   1996                 self._magic_locals = sys._getframe(1).f_locals
   1997             with self.builtin_trap:
-> 1998                 result = fn(magic_args)
   1999             # Ensure we're not keeping object references around:

   2000             self._magic_locals = {}

/usr/local/python/2.7.2/lib/python2.7/site-packages/IPython/core/magic.py
in magic_whos(self, parameter_s)
    948             else:
    949                 try:
--> 950                     vstr = str(var)
    951                 except UnicodeEncodeError:
    952                     vstr =
unicode(var).encode(sys.getdefaultencoding(),

/usr/local/python/2.7.2/lib/python2.7/site-packages/pandas/io/pytables.py
in __repr__(self)
    174         output = '%s\nFile path: %s\n' % (type(self), self.path)
    175
--> 176         if len(self) > 0:
    177             keys = []
    178             values = []

/usr/local/python/2.7.2/lib/python2.7/site-packages/pandas/io/pytables.py
in __len__(self)
    169
    170     def __len__(self):
--> 171         return len(self.handle.root._v_children)
    172
    173     def __repr__(self):

AttributeError: 'File' object has no attribute 'root'
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History DB repeatedly crashes

Douglas Applegate — 2012-05-11T17:49:45

Hi-

I'm running IPython 0.12 on a RHEL Client release 5.8 (Tikanga)
2.6.18-308.1.1.el5 (4x2613MHz X2200 M2) machine.

Every 2-3 days, IPython will refuse to launch, or will crash randomly in
the middle of a session, reporting that the SQLite history database has
become corrupted. IPython refuses to re-launch until I manually delete the
database file at ~/.ipython/profile_default/history.sqlite.

Here is the detailed crash backtrace:

ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (293, 0))
Error in sys.excepthook:
Traceback (most recent call last):
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/core/application.py",
line 175, in excepthook
    return self.crash_handler(etype, evalue, tb)
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/core/crashhandler.py",
line 158, in __call__
    traceback = TBhandler.text(etype,evalue,etb,context=31)
  File "/u/ki/dapple/lib/python2.7/site-packages/IPython/core/ultratb.py",
line 402, in text
    tb_offset, context)
  File "/u/ki/dapple/lib/python2.7/site-packages/IPython/core/ultratb.py",
line 964, in structured_traceback
    ipinst = ipapi.get()
  File "/u/ki/dapple/lib/python2.7/site-packages/IPython/core/ipapi.py",
line 28, in get
    return InteractiveShell.instance()
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/config/configurable.py",
line 318, in instance
    inst = cls(*args, **kwargs)
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/core/interactiveshell.py",
line 431, in __init__
    self.init_history()
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/core/interactiveshell.py",
line 1439, in init_history
    self.history_manager = HistoryManager(shell=self, config=self.config)
  File "/u/ki/dapple/lib/python2.7/site-packages/IPython/core/history.py",
line 407, in __init__
    self.new_session()
  File "<string>", line 2, in new_session
  File "/u/ki/dapple/lib/python2.7/site-packages/IPython/core/history.py",
line 61, in needs_sqlite
    return f(*a,**kw)
  File "/u/ki/dapple/lib/python2.7/site-packages/IPython/core/history.py",
line 426, in new_session
    self.session_number = cur.lastrowid
sqlite3.OperationalError: database is locked

Original exception was:
Traceback (most recent call last):
  File "/u/ki/dapple/bin/ipython", line 7, in <module>
    launch_new_instance()
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/frontend/terminal/ipapp.py",
line 402, in launch_new_instance
    app.initialize()
  File "<string>", line 2, in initialize
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/config/application.py",
line 84, in catch_config_error
    return method(app, *args, **kwargs)
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/frontend/terminal/ipapp.py",
line 312, in initialize
    self.init_shell()
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/frontend/terminal/ipapp.py",
line 332, in init_shell
    ipython_dir=self.ipython_dir)
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/config/configurable.py",
line 318, in instance
    inst = cls(*args, **kwargs)
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/frontend/terminal/interactiveshell.py",
line 183, in __init__
    user_module=user_module, custom_exceptions=custom_exceptions
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/core/interactiveshell.py",
line 456, in __init__
    self.init_readline()
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/core/interactiveshell.py",
line 1785, in init_readline
    self.refill_readline_hist()
  File
"/u/ki/dapple/lib/python2.7/site-packages/IPython/core/interactiveshell.py",
line 1797, in refill_readline_hist
    include_latest=True):
  File "/u/ki/dapple/lib/python2.7/site-packages/IPython/core/history.py",
line 251, in get_tail
    (n,), raw=raw, output=output)
  File "/u/ki/dapple/lib/python2.7/site-packages/IPython/core/history.py",
line 197, in _run_sql
    (toget, sqlfrom) + sql, params)
sqlite3.DatabaseError: database disk image is malformed

How can I stop this from happening?

Cheers,
Douglas Applegate
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