[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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