Mailman 3 April 2006 - SciPy-User

ask help for scipy install
by imcs ee April 3, 2006

April 3, 2006

in ubuntu5.10 i install scipy with apt-get install scipy and run the unittest from scipy import * test(10) it shows the result as below. is here any guide to solve it? thanks in advance ====================================================================== FAIL: check_expon (scipy.stats.morestats.test_morestats.test_anderson) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/stats/tests/test_morestats.py", line 55, in check_expon assert_array_less(A, crit[-2:]) File "/usr/lib/python2.4/site-packages/scipy_test/testing.py", line 708, in assert_array_less assert cond,\ AssertionError: Arrays are not less-ordered (mismatch 50.0%): Array 1: 1.65613125073 Array 2: [ 1.587 1.9339999999999999] ---------------------------------------------------------------------- Ran 986 tests in 102.422s FAILED (failures=1) Out[3]: <unittest.TextTestRunner object at 0xb45a580c>

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Re: [SciPy-user] [mod_python] weird error in mod_python (3.1.4.r1) /scipy(0.4.8)/gentoo (~x86) web application
by Webb Sprague April 3, 2006

April 3, 2006

Thanks to Graham's help, I found the typo ("sys.path.append(os.getcwd)" should have been "sys.path.append(os.getcwd())"), and all is well. W On 4/2/06, Graham Dumpleton <grahamd(a)dscpl.com.au> wrote: > Webb Sprague wrote .. > > This may be un-reproducible, and it does NOT happen within ipython > > shell, but I am getting the backtrace below when trying to import > > scipy within my application. I would guess it has to do with the very > > outdated ebuild of mod_python, (see the gentoo bug: > > http://bugs.gentoo.org/show_bug.cgi?id=123852), but just in case > > anybody has any quick fixes, please let me know. > > > > I have restarted Apache numerous times to make sure there isn't some > > weird cache thing going on (the source of most of my phantom bug > > reports). Scipy 0.3.2 does not have this problem. > > Looking through pkg_resources.py, critical bit of code seems to be: > > class WorkingSet(object): > """A collection of active distributions on sys.path (or a similar list)""" > > def __init__(self, entries=None): > """Create working set from list of path entries (default=sys.path)""" > self.entries = [] > self.entry_keys = {} > self.by_key = {} > self.callbacks = [] > > if entries is None: > entries = sys.path > > for entry in entries: > self.add_entry(entry) > > Specifically, "entries" is set to 'sys.path' and then each entry in that is > processed. The final error suggests that one of the entries in 'sys.path' > is actually a function and not a string. > > Are you setting 'sys.path' using PythonPath directive in mod_python > and somehow stuffed it up, or are you setting 'sys.path' explicitly in > any other places? > > Graham > > > Backtrace follows. (6), with LcUtil.py, is where it tries to import > > and errors out. > > > > Mod_python error: "PythonHandler mod_python.publisher" > > > > Traceback (most recent call last): > > > > (1) File "/usr/lib/python2.4/site-packages/mod_python/apache.py", > > line 299, in HandlerDispatch > > result = object(req) > > > > (2) File "/usr/lib/python2.4/site-packages/mod_python/publisher.py", > > line 98, in handler > > path=[path]) > > > > (3) File "/usr/lib/python2.4/site-packages/mod_python/apache.py", > > line 457, in import_module > > module = imp.load_module(mname, f, p, d) > > > > (4) File "/var/www/localhost/htdocs/larry/lc.py", line 32, in ? > > import LcSinglePopObject > > > > (5) File "/var/www/localhost/htdocs/larry/LcSinglePopObject.py", line > > 40, in ? > > import LcUtil > > > > (6) File "/var/www/localhost/htdocs/larry/LcUtil.py", line 8, in ? > > import scipy as S > > > > File "/usr/lib/python2.4/site-packages/scipy/__init__.py", line 18, in > > ? > > import pkg_resources as _pr # activate namespace packages > > (manipulates __path__) > > > > File "/usr/lib/python2.4/site-packages/pkg_resources.py", line 2347, > > in ? > > working_set = WorkingSet() > > > > File "/usr/lib/python2.4/site-packages/pkg_resources.py", line 343, > > in __init__ > > self.add_entry(entry) > > > > File "/usr/lib/python2.4/site-packages/pkg_resources.py", line 358, > > in add_entry > > for dist in find_distributions(entry, True): > > > > File "/usr/lib/python2.4/site-packages/pkg_resources.py", line 1450, > > in find_distributions > > importer = get_importer(path_item) > > > > File "/usr/lib/python2.4/site-packages/pkg_resources.py", line 1407, > > in get_importer > > importer = hook(path_item) > > > > TypeError: zipimporter() argument 1 must be string, not > > builtin_function_or_method > > > > _______________________________________________ > > Mod_python mailing list > > Mod_python(a)modpython.org > > http://mailman.modpython.org/mailman/listinfo/mod_python >

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weird error in mod_python (3.1.4.r1) /scipy (0.4.8)/gentoo (~x86) web application
by Webb Sprague April 3, 2006

April 3, 2006

This may be un-reproducible, and it does NOT happen within ipython shell, but I am getting the backtrace below when trying to import scipy within my application. I would guess it has to do with the very outdated ebuild of mod_python, (see the gentoo bug: http://bugs.gentoo.org/show_bug.cgi?id=123852), but just in case anybody has any quick fixes, please let me know. I have restarted Apache numerous times to make sure there isn't some weird cache thing going on (the source of most of my phantom bug reports). Scipy 0.3.2 does not have this problem. Backtrace follows. (6), with LcUtil.py, is where it tries to import and errors out. Mod_python error: "PythonHandler mod_python.publisher" Traceback (most recent call last): (1) File "/usr/lib/python2.4/site-packages/mod_python/apache.py", line 299, in HandlerDispatch result = object(req) (2) File "/usr/lib/python2.4/site-packages/mod_python/publisher.py", line 98, in handler path=[path]) (3) File "/usr/lib/python2.4/site-packages/mod_python/apache.py", line 457, in import_module module = imp.load_module(mname, f, p, d) (4) File "/var/www/localhost/htdocs/larry/lc.py", line 32, in ? import LcSinglePopObject (5) File "/var/www/localhost/htdocs/larry/LcSinglePopObject.py", line 40, in ? import LcUtil (6) File "/var/www/localhost/htdocs/larry/LcUtil.py", line 8, in ? import scipy as S File "/usr/lib/python2.4/site-packages/scipy/__init__.py", line 18, in ? import pkg_resources as _pr # activate namespace packages (manipulates __path__) File "/usr/lib/python2.4/site-packages/pkg_resources.py", line 2347, in ? working_set = WorkingSet() File "/usr/lib/python2.4/site-packages/pkg_resources.py", line 343, in __init__ self.add_entry(entry) File "/usr/lib/python2.4/site-packages/pkg_resources.py", line 358, in add_entry for dist in find_distributions(entry, True): File "/usr/lib/python2.4/site-packages/pkg_resources.py", line 1450, in find_distributions importer = get_importer(path_item) File "/usr/lib/python2.4/site-packages/pkg_resources.py", line 1407, in get_importer importer = hook(path_item) TypeError: zipimporter() argument 1 must be string, not builtin_function_or_method

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Re: [SciPy-user] maxentropy
by Matthew Cooper April 3, 2006

April 3, 2006

Hi Ed, Thanks very much for your reply. I think it helped a lot, but I may be a bit confused about conditional versus unconditional modeling. What I'm doing is similar to text categorization. I observe some text (vector X) and want to determine if a binary label (scalar y) should be applied (y=1) or not (y=0). So, I look at this as using maxent to estimate P(y|X). In this case, is my sample space simply {0,1} or is it the space from which X is sampled? I had thought this was conditional modelling, but I don't want to explicitly train models for every different X, rather I want to select and weight features from the whole corpus that in turn imply, for each X', some P(y|X'). I assumed it was conditional because I'm not modelling P(y',X'). I have been trying to build models using a sample space with tuples as elements like (X_n,y_n). I then am greedily building a set of feature functions using information gain to select features. It's not quite working, and I'm worried I'm not defining the sample space properly. I will try to figure out how to define the sample space as {0,1} and then redefine the features, but I'd appreciate any advice. Also, if I get this working, I'd be happy to try and help with adding some feature selection examples to your documentation. At the moment, I'm still, as you can tell, figuring out what I'm doing. Thanks, Matt

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docstring improvement
by Gary Ruben April 3, 2006

April 3, 2006

Just looking at Robert Kern's checklist from a user's p.o.v., it would be nice to add some simple (one-liner) function call examples to each docstring. This is something I think is lacking from most functions in scipy. Gary R. Robert Kern wrote: > In the interest of improving the quality of the scipy.stats package, > I hereby declare April and May of 2006 to be Statistics Review > Months. I propose that we set ourselves a goal to review each > function in stats.py and morestats.py (and a few others) for > correctness and completeness of implementation by the end of May. By > my count, that's about 2.5 functions every day. Surely this is a > reasonable amount of effort for a rather large payoff: a robust, > well-tested and thorough statistics library. > > I have added a Wiki page describing the details: > http://projects.scipy.org/scipy/scipy/wiki/StatisticsReview

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