[IPython-user] IPython1 0.3 prerelease : some failures

Johann Cohen-Tanugi cohen@slac.stanford....
Fri May 16 05:57:04 CDT 2008


hi Brian, thanks for the post. I will look at that page. Well, one of 
the things I am interested in these days relates to statistical 
resampling and applications of the bootstrap method. Imagine you have a 
statistics f, that can be as simple as computing the sample mean or as 
complex as a full fledged multi dimensional likelihood fit, what I 
systematically need to do is the following (in meta-code) :
def f(x):
    ... #compute quantities from the statistical sample x

x = openDataFile()
ndata=len(x)
Nsamples = 1000  #number of resamplings I want to do
for i in range(nsamples) :
    idx = np.randint(ndata)
    newdata = x(idx) # this is a resampling of x with possible 
repetition, the core idea of the bootstrap
    results=f(newdata)
    accumulate(results) # for instance in memory or in file

... and then I plot or compute variances etc... with the accumulated 
results. Clearly it is embarrassingly parallel, and I would expect 
ipython1 could help (I have a dual core so I guess I can speed up by ~2, 
but I also have access to a multi-processor farm).

best,
Johann

Brian Granger wrote:
> Sorry for the confusion....
>
> IPython1 will eventually be a full replacement for IPython0 (as we are
> calling it now).  But that part of IPython1 is not implemented yet.
> The stuff that *is* implemented (and actually fairly mature and
> stable) is for parallel computing:
>
> http://ipython.scipy.org/doc/ipython1/html/parallel_intro.html
>
> So, unless you need parallel computing capabilities, IPython1 won't be
> of much use for you yet.  But, if you need such things, IPython1 is
> quite useful.
>
> Brian
>
> On Wed, May 14, 2008 at 10:17 AM, Johann Cohen-Tanugi
> <cohen@slac.stanford.edu> wrote:
>   
>> ok good! And sorry for the multiple posts!
>> Now that I am at it, with ipython0 there is an executable ipython, very
>> basic wrapper to the 2 lines that call ipython app within python. I was
>> wondering why there is nothing like that with ipython1.
>> Otherwise stated, how do I start to play with ipython1 ? :) I am sure there
>> is a beginning of tutorial somewhere,  but could not find it out. I launched
>> ipnotebook but it stops at 2008/05/14 18:16 +0200 [-] Starting factory
>> <ipython1.external.twisted.web2.channel.http.HTTPFactory instance at
>> 0x9511d0c>
>> and does not do anything anymore after that, just hangs....
>>
>> anyway, keep up with the good work!
>> Johann
>>
>> Brian Granger wrote:
>>     
>>> Johann,
>>>
>>> Thanks for this.  These are knows errors/failures and they occur in a
>>> non-critical component that is still under heavy development.  So,
>>> everything looks great!
>>>
>>> Brian
>>>
>>> On Tue, May 13, 2008 at 3:03 PM, Johann Cohen-Tanugi
>>> <cohen@slac.stanford.edu> wrote:
>>>
>>>       
>>>> hello, here is my setup :
>>>> [root@jarrett ipython1-dev]# python setup.py install
>>>>
>>>> ============================================================================
>>>> BUILDING IPYTHON1
>>>>               python: 2.5.1 (r251:54863, Oct 30 2007, 13:54:11)  [GCC
>>>>                       4.1.2 20070925 (Red Hat 4.1.2-33)]
>>>>             platform: linux2
>>>>
>>>> REQUIRED DEPENDENCIES
>>>>              IPython: 0.8.3.svn.r3001
>>>>       Zope.Interface: yes
>>>>              Twisted: 2.5.0
>>>>
>>>> OPTIONAL DEPENDENCIES
>>>>              pexpect: yes
>>>>             httplib2: yes
>>>>           sqlalchemy: yes
>>>>           simplejson: yes
>>>>
>>>> everything goes ok when I trial ipython1, until :
>>>>
>>>>   testTaskIDs
>>>> ...                                                        [OK]
>>>>   testTaskResults
>>>> ...                                                    [OK]
>>>>                                               [ERROR]
>>>> ipython1.notebook.tests.test_notebook
>>>>  NotebookTestCase
>>>>   testTags
>>>> ...                                                           [OK]
>>>>   testappendNode ...
>>>> [ERROR]
>>>>   testdropNode ...
>>>> [ERROR]
>>>>   testeditNode ...
>>>> [ERROR]
>>>>   testinsertNode ...
>>>> [ERROR]
>>>>   testmergeUsers ...
>>>> [ERROR]
>>>>   testmoveNode ...
>>>> [ERROR]
>>>>   testmultiUser ...
>>>> [ERROR]
>>>>   testnidAgreement ...
>>>> [ERROR]
>>>>   testprependNode ...
>>>> [ERROR]
>>>>   testxmlBackup ...
>>>> [ERROR]
>>>> doctest
>>>>  DocTestCase
>>>>   fullPath
>>>> ...                                                           [OK]
>>>>  DocFileCase
>>>>   tst_tools_utils_doctest_txt
>>>> ...                                        [OK]
>>>>   tst_tools_utils_doctest2_txt
>>>> ...                                       [OK]
>>>>  DocTestCase
>>>>   extractVars
>>>> ...                                                        [OK]
>>>>   list_strings
>>>> ...                                                       [OK]
>>>>   marquee
>>>> ...                                                            [OK]
>>>>   shexp
>>>> ...                                                              [OK]
>>>>
>>>>
>>>> ===============================================================================
>>>> [ERROR]: ipython1.kernel.tests.test_multienginexmlrpc
>>>>
>>>> Traceback (most recent call last):
>>>>  File "/usr/lib/python2.5/site-packages/twisted/trial/runner.py", line
>>>> 555, in loadPackage
>>>>   module = modinfo.load()
>>>>  File "/usr/lib/python2.5/site-packages/twisted/python/modules.py",
>>>> line 386, in load
>>>>   return self.pathEntry.pythonPath.moduleLoader(self.name)
>>>>  File "/usr/lib/python2.5/site-packages/twisted/python/modules.py",
>>>> line 621, in moduleLoader
>>>>   return self._moduleLoader(modname)
>>>>  File "/usr/lib/python2.5/site-packages/twisted/python/reflect.py",
>>>> line 357, in namedAny
>>>>   topLevelPackage = __import__(trialname)
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/kernel/tests/test_multienginexmlrpc.py",
>>>> line 16, in <module>
>>>>   from ipython1.kernel.multienginexmlrpc import IXMLRPCMultiEngineFactory
>>>>  File
>>>> "/usr/lib/python2.5/site-packages/ipython1/kernel/multienginexmlrpc.py",
>>>> line 30, in <module>
>>>>   from twisted.web import xmlrpc as webxmlrpc
>>>> exceptions.ImportError: No module named web
>>>>
>>>> ===============================================================================
>>>> [ERROR]: ipython1.kernel.tests.test_taskxmlrpc
>>>>
>>>> Traceback (most recent call last):
>>>>  File "/usr/lib/python2.5/site-packages/twisted/trial/runner.py", line
>>>> 555, in loadPackage
>>>>   module = modinfo.load()
>>>>  File "/usr/lib/python2.5/site-packages/twisted/python/modules.py",
>>>> line 386, in load
>>>>   return self.pathEntry.pythonPath.moduleLoader(self.name)
>>>>  File "/usr/lib/python2.5/site-packages/twisted/python/modules.py",
>>>> line 621, in moduleLoader
>>>>   return self._moduleLoader(modname)
>>>>  File "/usr/lib/python2.5/site-packages/twisted/python/reflect.py",
>>>> line 357, in namedAny
>>>>   topLevelPackage = __import__(trialname)
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/kernel/tests/test_taskxmlrpc.py",
>>>> line 17, in <module>
>>>>   from ipython1.kernel import taskxmlrpc
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/kernel/taskxmlrpc.py",
>>>> line 29, in <module>
>>>>   from twisted.web import xmlrpc as webxmlrpc
>>>> exceptions.ImportError: No module named web
>>>>
>>>> ===============================================================================
>>>> [ERROR]:
>>>> ipython1.notebook.tests.test_notebook.NotebookTestCase.testappendNode
>>>>
>>>> Traceback (most recent call last):
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 65, in testappendNode
>>>>   self.u.addNode(self.nb.root.nodeID, c)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 451, in addNode
>>>>   return self.nbc.addNode(self.user.userID, parentID, node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 196, in addNode
>>>>   n = parent.addChild(node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/models.py",
>>>> line 473, in addChild
>>>>   n.insertAfter(child)
>>>> exceptions.AttributeError: 'NoneType' object has no attribute
>>>> 'insertAfter'
>>>>
>>>> ===============================================================================
>>>> [ERROR]:
>>>> ipython1.notebook.tests.test_notebook.NotebookTestCase.testdropNode
>>>>
>>>> Traceback (most recent call last):
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 84, in testdropNode
>>>>   self.u.addNode(self.nb.root.nodeID, c)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 451, in addNode
>>>>   return self.nbc.addNode(self.user.userID, parentID, node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 196, in addNode
>>>>   n = parent.addChild(node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/models.py",
>>>> line 473, in addChild
>>>>   n.insertAfter(child)
>>>> exceptions.AttributeError: 'NoneType' object has no attribute
>>>> 'insertAfter'
>>>>
>>>> ===============================================================================
>>>> [ERROR]:
>>>> ipython1.notebook.tests.test_notebook.NotebookTestCase.testeditNode
>>>>
>>>> Traceback (most recent call last):
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 92, in testeditNode
>>>>   self.u.addNode(self.nb.root.nodeID, c)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 451, in addNode
>>>>   return self.nbc.addNode(self.user.userID, parentID, node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 196, in addNode
>>>>   n = parent.addChild(node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/models.py",
>>>> line 473, in addChild
>>>>   n.insertAfter(child)
>>>> exceptions.AttributeError: 'NoneType' object has no attribute
>>>> 'insertAfter'
>>>>
>>>> ===============================================================================
>>>> [ERROR]:
>>>> ipython1.notebook.tests.test_notebook.NotebookTestCase.testinsertNode
>>>>
>>>> Traceback (most recent call last):
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 78, in testinsertNode
>>>>   self.u.addNode(self.nb.root.nodeID, c, 1)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 451, in addNode
>>>>   return self.nbc.addNode(self.user.userID, parentID, node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 196, in addNode
>>>>   n = parent.addChild(node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/models.py",
>>>> line 473, in addChild
>>>>   n.insertAfter(child)
>>>> exceptions.AttributeError: 'NoneType' object has no attribute
>>>> 'insertAfter'
>>>>
>>>> ===============================================================================
>>>> [ERROR]:
>>>> ipython1.notebook.tests.test_notebook.NotebookTestCase.testmergeUsers
>>>>
>>>> Traceback (most recent call last):
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 115, in testmergeUsers
>>>>   self.loadNodes(4)
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 59, in loadNodes
>>>>   l.append(self.u.addNode(parent.nodeID, c, index))
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 451, in addNode
>>>>   return self.nbc.addNode(self.user.userID, parentID, node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 194, in addNode
>>>>   assert user in parent.notebook.writers or user is
>>>> parent.notebook.user,\
>>>> exceptions.AttributeError: 'NoneType' object has no attribute 'writers'
>>>>
>>>> ===============================================================================
>>>> [ERROR]:
>>>> ipython1.notebook.tests.test_notebook.NotebookTestCase.testmoveNode
>>>>
>>>> Traceback (most recent call last):
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 127, in testmoveNode
>>>>   self.u.addNode(self.nb.root.nodeID, c)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 451, in addNode
>>>>   return self.nbc.addNode(self.user.userID, parentID, node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 196, in addNode
>>>>   n = parent.addChild(node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/models.py",
>>>> line 473, in addChild
>>>>   n.insertAfter(child)
>>>> exceptions.AttributeError: 'NoneType' object has no attribute
>>>> 'insertAfter'
>>>>
>>>> ===============================================================================
>>>> [ERROR]:
>>>> ipython1.notebook.tests.test_notebook.NotebookTestCase.testmultiUser
>>>>
>>>> Traceback (most recent call last):
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 109, in testmultiUser
>>>>   ub.addNode(nb.root.nodeID, c)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 451, in addNode
>>>>   return self.nbc.addNode(self.user.userID, parentID, node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 196, in addNode
>>>>   n = parent.addChild(node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/models.py",
>>>> line 473, in addChild
>>>>   n.insertAfter(child)
>>>> exceptions.AttributeError: 'NoneType' object has no attribute
>>>> 'insertAfter'
>>>>
>>>> ===============================================================================
>>>> [ERROR]:
>>>> ipython1.notebook.tests.test_notebook.NotebookTestCase.testnidAgreement
>>>>
>>>> Traceback (most recent call last):
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 210, in testnidAgreement
>>>>   self.loadNodes(16)
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 59, in loadNodes
>>>>   l.append(self.u.addNode(parent.nodeID, c, index))
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 451, in addNode
>>>>   return self.nbc.addNode(self.user.userID, parentID, node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 194, in addNode
>>>>   assert user in parent.notebook.writers or user is
>>>> parent.notebook.user,\
>>>> exceptions.AttributeError: 'NoneType' object has no attribute 'writers'
>>>>
>>>> ===============================================================================
>>>> [ERROR]:
>>>> ipython1.notebook.tests.test_notebook.NotebookTestCase.testprependNode
>>>>
>>>> Traceback (most recent call last):
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 71, in testprependNode
>>>>   self.u.addNode(self.nb.root.nodeID, c, 0)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 451, in addNode
>>>>   return self.nbc.addNode(self.user.userID, parentID, node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 196, in addNode
>>>>   n = parent.addChild(node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/models.py",
>>>> line 476, in addChild
>>>>   self[index].insertBefore(child)
>>>> exceptions.AttributeError: 'NoneType' object has no attribute
>>>> 'insertBefore'
>>>>
>>>> ===============================================================================
>>>> [ERROR]:
>>>> ipython1.notebook.tests.test_notebook.NotebookTestCase.testxmlBackup
>>>>
>>>> Traceback (most recent call last):
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 160, in testxmlBackup
>>>>   self.loadNodes(8)
>>>>  File
>>>>
>>>> "/usr/lib/python2.5/site-packages/ipython1/notebook/tests/test_notebook.py",
>>>> line 59, in loadNodes
>>>>   l.append(self.u.addNode(parent.nodeID, c, index))
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 451, in addNode
>>>>   return self.nbc.addNode(self.user.userID, parentID, node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/notebook.py",
>>>> line 196, in addNode
>>>>   n = parent.addChild(node, index)
>>>>  File "/usr/lib/python2.5/site-packages/ipython1/notebook/models.py",
>>>> line 476, in addChild
>>>>   self[index].insertBefore(child)
>>>> exceptions.AttributeError: 'NoneType' object has no attribute
>>>> 'insertBefore'
>>>>
>>>> -------------------------------------------------------------------------------
>>>> Ran 278 tests in 22.519s
>>>>
>>>> FAILED (errors=12, successes=268)
>>>>
>>>> best,
>>>> Johann
>>>> _______________________________________________
>>>> IPython-user mailing list
>>>> IPython-user@scipy.org
>>>> http://lists.ipython.scipy.org/mailman/listinfo/ipython-user
>>>>
>>>>
>>>>         


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