Mailman 3 November 2008 - SciPy-Dev

scipy.signal.signaltools: filtfilt calls missing function
by Eric Firing Nov. 26, 2008

Nov. 26, 2008

The filtfilt() function calls lfilter_zi, which is absent from scipy. A version of it is in the Cookbook: http://www.scipy.org/Cookbook/FiltFilt. It looks to me like a bit of reworking would be in order before adding it to scipy; it is using matrices. I hope this can be fixed before the 0.7 release. Is it essential that I create a ticket, or is this email sufficient? Eric

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New scipy.test() failures
by Nils Wagner Nov. 26, 2008

Nov. 26, 2008

Hi all, I found some new test failures. Can someone reproduce these failures ? ====================================================================== FAIL: test_simple (test_fblas.TestCgemv) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/scipy/lib/blas/tests/test_fblas.py", line 325, in test_simple assert_array_almost_equal(desired_y,y) File "/usr/local/lib64/python2.5/site-packages/numpy/testing/utils.py", line 310, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/local/lib64/python2.5/site-packages/numpy/testing/utils.py", line 295, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal (mismatch 33.3333333333%) x: array([ -5.82329798 +5.82329798j, 8.58068085 -6.58068085j, -12.74014378+16.74014282j], dtype=complex64) y: array([ -5.82329798 +5.82329798j, 8.58068085 -6.58068085j, -12.74014378+16.74014473j], dtype=complex64) ====================================================================== FAIL: test_imresize (test_pilutil.TestPILUtil) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/numpy/testing/decorators.py", line 82, in skipper return f(*args, **kwargs) File "/usr/local/lib64/python2.5/site-packages/scipy/misc/tests/test_pilutil.py", line 24, in test_imresize assert_equal(im1.shape,(11,22)) File "/usr/local/lib64/python2.5/site-packages/numpy/testing/utils.py", line 174, in assert_equal assert_equal(len(actual),len(desired),err_msg,verbose) File "/usr/local/lib64/python2.5/site-packages/numpy/testing/utils.py", line 183, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: ACTUAL: 0 DESIRED: 2 ====================================================================== FAIL: test_kdtree.test_distance_matrix ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/nose-0.10.4-py2.5.egg/nose/case.py", line 182, in runTest self.test(*self.arg) File "/usr/local/lib64/python2.5/site-packages/scipy/spatial/tests/test_kdtree.py", line 416, in test_distance_matrix assert_equal(distance(xs[i],ys[j]),ds[i,j]) File "/usr/local/lib64/python2.5/site-packages/numpy/testing/utils.py", line 183, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: ACTUAL: 2.775628274295713 DESIRED: 2.7756282742957135 ---------------------------------------------------------------------- Ran 2858 tests in 43.229s FAILED (KNOWNFAIL=2, SKIP=16, failures=3) <nose.result.TextTestResult run=2858 errors=0 failures=3> >>> scipy.__version__ '0.7.0.dev5193'

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friedmanchisquare fixed, test based on R help ?
by josef.pktd＠gmail.com Nov. 24, 2008

Nov. 24, 2008

I applied the patch from ticket:117 for stats.friedmanchisquare, after verifying with matlab and R, the solution is identical to both. I added tests based on examples in the patch. One copyright question: I also added an example from the R help file to the tests, which is based on a paper published in 1973. Are there any copyright problems for doing this? Josef

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close tickets, add doc for odes
by Benny Malengier Nov. 24, 2008

Nov. 24, 2008

Hi, can somebody close: http://projects.scipy.org/scipy/scipy/ticket/615 http://www.scipy.org/scipy/scipy/ticket/730 They are part of new odes scikit. I have put documentation now on my site (http://cage.ugent.be/~bm/progs.html) but would like to update http://scipy.org/scipy/scikits/ I have no edit button on that wiki page though although the text says I should have. I suppose the page is protected. Can somebody add an entry for odes or give me permission? I will then add more on a separate wiki page. My login on the wiki is user 'bmcage' >From my point of view, the PR around scikits could indeed use some improvement/streamlining. Benny

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Numpy documentation editable @ docs.scipy.org
by Pauli Virtanen Nov. 24, 2008

Nov. 24, 2008

Dear all, All of the Sphinx-generated documentation of Numpy (not only the docstrings!) can be now edited in the wiki at http://docs.scipy.org/numpy/ for example, http://docs.scipy.org/numpy/docs/numpy-docs/reference/arrays.ndarray.rst/ Contributing should now be quite a lot easier, and does not require you to install Sphinx and check out the docs from SVN any more. There's still a small amount of work left to make the same be true also for Scipy, but this is not far off. -- Pauli Virtanen

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beta 1 tagged in a few hours
by Jarrod Millman Nov. 24, 2008

Nov. 24, 2008

I will be tagging the first beta for 0.7 in a few hours. Please let me know if there is any reason that this needs to be delayed. Thanks for everyone who has helped get the trunk ready for a beta release. Once the release is tagged, David and I will create binaries and make the actual release. -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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percentileofscore in svn
by josef.pktd＠gmail.com Nov. 24, 2008

Nov. 24, 2008

To ariel.rokem (I don't know your email address) You beat me in correcting percentileofscore, however, your version still has a bias for multiple ties. >>> percentileofscorein([1,1,1,1],1) # yours 62.5 >>> percentileofscore([1,1,1,1],1) # wikipedia 50.0 >>> percentileofscore([1,1,1,1,1,2,2,2,2,2],1) # wikipedia 25.0 >>> percentileofscorein([1,1,1,1,1,2,2,2,2,2],1) # yours 30.0 >>> percentileofscorein([1,1,1],1) # yours 66.666666666666657 >>> percentileofscore([1,1,1],1) # wikipedia 50.0 >>> percentileofscorein([1,1,1,1,1,2,2,2,2,2],2) # yours 80.0 >>> percentileofscore([1,1,1,1,1,2,2,2,2,2],2) # wikipedia 75.0 Since we were discussing definitions, do you have a definition of your method? I'm not too convinced of the wikipedia version, but it looks like a consistent definition I renamed my version temporarily to percentileofscore2 Josef

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cephes broken (revision 5176)
by Xavier Gnata Nov. 24, 2008

Nov. 24, 2008

Hi, There are some missing declaration in the cephes module (rev 5197) scipy/special/_cephesmodule.c: In function ‘Cephes_InitOperators’: scipy/special/_cephesmodule.c:340: error: ‘PyUFunc_f_f_As_d_d’ undeclared (first use in this function) scipy/special/_cephesmodule.c:340: error: (Each undeclared identifier is reported only once scipy/special/_cephesmodule.c:340: error: for each function it appears in.) scipy/special/_cephesmodule.c:341: error: ‘PyUFunc_d_d’ undeclared (first use in this function) scipy/special/_cephesmodule.c:364: error: ‘PyUFunc_ff_f_As_dd_d’ undeclared (first use in this function) scipy/special/_cephesmodule.c:365: error: ‘PyUFunc_dd_d’ undeclared (first use in this function) scipy/special/_cephesmodule.c: In function ‘Cephes_InitOperators’: scipy/special/_cephesmodule.c:340: error: ‘PyUFunc_f_f_As_d_d’ undeclared (first use in this function) scipy/special/_cephesmodule.c:340: error: (Each undeclared identifier is reported only once scipy/special/_cephesmodule.c:340: error: for each function it appears in.) scipy/special/_cephesmodule.c:341: error: ‘PyUFunc_d_d’ undeclared (first use in this function) scipy/special/_cephesmodule.c:364: error: ‘PyUFunc_ff_f_As_dd_d’ undeclared (first use in this function) scipy/special/_cephesmodule.c:365: error: ‘PyUFunc_dd_d’ undeclared (first use in this function) Xavier

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Reverting eigh code ?
by David Cournapeau Nov. 23, 2008

Nov. 23, 2008

Hi, A few days ago, new code for eigh decomposition has been added, and it fails running correctly. Since we are days - even hours away from beta, and I am a bit tired looking at fortran problems, unless someone else solves it, I would like to set the changes asides from 0.7. If nobody complains within the beta time, I will remove it myself, David

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nearest neighbour interpolation
by Robin Nov. 22, 2008

Nov. 22, 2008

Hi, I just got bitten by this bug: http://www.scipy.org/scipy/scipy/ticket/773 It is quite nasty I think (I lost a lot of time...) and could be fixed easily just by changing the documentation. (At least so people don't loose so much time). My wiki username for the documentation is robince, so if I am enabled for write access I could make this change. Is there any way to get nearest neighbour interpolation in scipy? This bug looks related: http://www.scipy.org/scipy/scipy/ticket/305 Perhaps this could be reopened? Thanks, Robin

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