[SciPy-User] bugs in scipy.stats

Oleksandr Huziy guziy.sasha@gmail....
Tue Jun 11 23:37:33 CDT 2013


Thank you Josef,

for the detailed description. Though I have one more question concerning
the workflow.

After I've cloned the project locally can I develop and run tests from
inside the directory without reinstalling it? (I suppose build is necessary
when fortran code changes), but I would like to be able to edit and run the
code from the same place.. (this would permit for example to use it as a
project in my favourite IDE). But when I try to run test_morestats.py from
inside the project I get the following exception:

Traceback (most recent call last):
  File
"/home/san/.IntelliJIdea11/config/plugins/python/helpers/pycharm/utrunner.py",
line 113, in <module>
    modules = [loadSource(a[0])]
  File
"/home/san/.IntelliJIdea11/config/plugins/python/helpers/pycharm/utrunner.py",
line 44, in loadSource
    module = imp.load_source(moduleName, fileName)
  File
"/home/san/Python/scipy_project/scipy/stats/tests/test_morestats.py", line
14, in <module>
    import scipy.stats as stats
  File "/home/san/Python/scipy_project/scipy/__init__.py", line 120, in
<module>
    raise ImportError(msg)
ImportError: Error importing scipy: you cannot import scipy while
        being in scipy source directory; please exit the scipy source
        tree first, and relaunch your python intepreter.

How do you work on it? I understand that installing it (using virtualenv,
which I am currently using for scipy testing) and then running tests in a
different place would work, but is it the only way, it does not seem
efficient.

Cheers
--
Sasha




2013/6/11 <josef.pktd@gmail.com>

> On Tue, Jun 11, 2013 at 1:58 PM,  <josef.pktd@gmail.com> wrote:
> > On Tue, Jun 11, 2013 at 1:24 PM, Oleksandr Huziy <guziy.sasha@gmail.com>
> wrote:
> >> Hi Josef,
> >>
> >> could you, please, list the functions which need to be tested?
> >> And the link to the testing approach that you'd prefer me to use
> unittest,
> >> nose, doctest? I am not experienced tester but really want to help.
> >
> > Hi Sasha,
> >
> > I didn't run the test coverage on scipy.stats in a long time
> > This was my old list (2009) which is very outdated
> > https://github.com/scipy/scipy/issues/1554
> >
> > All tests are run with nose, scipy doesn't have doctests. The testing
> > guidelines are at
> > https://github.com/numpy/numpy/blob/master/doc/TESTS.rst.txt
> >
> > The pattern for the tests can be seen in the test suite
> > https://github.com/scipy/scipy/tree/master/scipy/stats/tests
> > especially test_stats.py and test_morestats.py, and those for mstats
> >
> > One check that would also be very helpful is to try out different
> > kinds of arguments.
> > For example, I think there might still be problems with 2d arrays in
> > some functions. Some will raise ValueErrors if they cannot handle 2d
> > arrays, but some might just return incorrect numbers.
> >
> > Example: I never looked closely at `mood` which has unit tests, so a
> quick try:
> >>>> stats.mood(np.random.randn(10,2), np.random.randn(15,2))
> > (26.664783935766987, 1.2060935978310698e-156)
> >>>> stats.mood(np.random.randn(10), np.random.randn(15))
> > (-0.46553454010068451, 0.64154870791874163)
> >
> > the first result looks pretty weird
> >
> > In these cases we should add a `raise ValueError` or try to enhance it
> to 2d.
>
> If you check a function and it works as advertised, then this would
> also be good to know
> We still have an old milestone for the stats review, where we can also
> note that everything is fine
> https://github.com/scipy/scipy/issues?milestone=4&state=open
>
> or open a new issue and note the functions that you checked there, so
> we have a record.
>
> Other hypothesis test that I never looked at in detail and tried out
> only with "nice" numbers are
> fligner, ansari, bartlett, ...
>
> >>> x, y = np.random.randn(10,2), np.random.randn(15,2)
> >>> stats.bartlett(x, y)
> (4.7695839486013287e-05, 0.99448967952524281)
> >>> stats.bartlett(x.ravel(), y.ravel())
> (0.00010231554134127248, 0.99192944393408666)
>
> looks also wrong
>
> (ttests are vectorized, ks tests raise an exception somewhere in the
> code with 2d)
>
> Josef
>
>
> >
> > Thank you,
> >
> > Josef
> >
> >>
> >> Cheers
> >> --
> >> Oleksandr (Sasha) Huziy
> >>
> >> _______________________________________________
> >> SciPy-User mailing list
> >> SciPy-User@scipy.org
> >> http://mail.scipy.org/mailman/listinfo/scipy-user
> >>
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