Mailman 3 November 2008 - SciPy-Dev

subversion commit policy for rename files question
by josef.pktd＠gmail.com Nov. 22, 2008

Nov. 22, 2008

I want to do the renaming and importing in __all__ discussed here: http://projects.scipy.org/pipermail/scipy-dev/2008-November/010241.html For this I had to resolve some circular imports and add some missing functions to __all__. Is there a policy whether renames should be committed separately or can it be together with changes in the file, or it doesn't matter? BTW: Is there an opinion about percentileofscore? Josef

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Scipy Trac broken?
by Pauli Virtanen Nov. 21, 2008

Nov. 21, 2008

Hi, When logging in or trying to view Scipy roadmap in Scipy's Trac, I get the error: Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/trac/web/main.py", line 387, in dispatch_request dispatcher.dispatch(req) File "/usr/lib/python2.4/site-packages/trac/web/main.py", line 244, in dispatch req.session.save() File "/usr/lib/python2.4/site-packages/trac/web/session.py", line 206, in save (mintime,)) File "/usr/lib/python2.4/site-packages/trac/db/util.py", line 50, in execute return self.cursor.execute(sql_escape_percent(sql), args) File "/usr/src/build/539311-i386/install//usr/lib/python2.4/site- packages/sqlite/main.py", line 255, in execute DatabaseError: database disk image is malformed -- Pauli Virtanen

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make html in scipy/doc
by Nils Wagner Nov. 21, 2008

Nov. 21, 2008

Hi all, make html doesn't work for me with latest svn: stats.uniform generated/scipy.stats.var generated/scipy.stats.variation generated/scipy.stats.wald generated/scipy.stats.weibull_max generated/scipy.stats.weibull_min generated/scipy.stats.wilcoxon generated/scipy.stats.wrapcauchy generated/scipy.stats.z generated/scipy.stats.zipf generated/scipy.stats.zmap generated/scipy.stats.zs index integrate interpolate io linalg maxentropy misc ndimage odr optimize signal sparse sparse.linalg spatial spatial.distance Math extension error: latex exited with error: [stderr] [stdout] This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4) entering extended mode (/tmp/tmpJTO7je/math.tex LaTeX2e <2003/12/01> Babel <v3.8d> and hyphenation patterns for american, french, german, ngerman, b ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch, esperanto, e stonian, finnish, greek, icelandic, irish, italian, latin, magyar, norsk, polis h, portuges, romanian, russian, serbian, slovak, slovene, spanish, swedish, tur kish, ukrainian, nohyphenation, loaded. (/usr/share/texmf/tex/latex/base/article.cls Document Class: article 2004/02/16 v1.4f Standard LaTeX document class (/usr/share/texmf/tex/latex/base/size12.clo)) (/usr/share/texmf/tex/latex/base/inputenc.sty (/usr/share/texmf/tex/latex/base/utf8.def (/usr/share/texmf/tex/latex/base/t1enc.dfu) (/usr/share/texmf/tex/latex/base/ot1enc.dfu) (/usr/share/texmf/tex/latex/base/omsenc.dfu))) (/usr/share/texmf/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texmf/tex/latex/amsmath/amstext.sty (/usr/share/texmf/tex/latex/amsmath/amsgen.sty)) (/usr/share/texmf/tex/latex/amsmath/amsbsy.sty) (/usr/share/texmf/tex/latex/amsmath/amsopn.sty)) (/usr/share/texmf/tex/latex/amscls/amsthm.sty) (/usr/share/texmf/tex/latex/amsfonts/amssymb.sty (/usr/share/texmf/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texmf/tex/latex/tools/bm.sty) (/usr/share/texmf/tex/latex/preview/preview.sty No auxiliary output files. ) No file math.aux. Preview: Fontsize 12pt (/usr/share/texmf/tex/latex/amsfonts/umsa.fd) (/usr/share/texmf/tex/latex/amsfonts/umsb.fd) ! Missing } inserted. <inserted text> } l.16 \end{gather} ! Missing { inserted. <inserted text> { l.16 \end{gather} ! Missing } inserted. <inserted text> } l.16 \end{gather} ! Missing { inserted. <inserted text> { l.16 \end{gather} [1] ) (see the transcript file for additional information) Output written on /tmp/tmpJTO7je/math.dvi (1 page, 560 bytes). Transcript written on /tmp/tmpJTO7je/math.log. make: *** [html] Error 1

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Possibly bug in savetxt
by Nils Wagner Nov. 21, 2008

Nov. 21, 2008

Hi all, The colon is missing in the output file when I use savetxt('dsvnode_nw.dat',A,fmt='%6i %6i', delimiter=':') to store A. >>> shape(A) (5760, 2) >>> type(A) <type 'numpy.ndarray'> Am I missing something ? Nils

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arpack wrapper status
by Jarrod Millman Nov. 21, 2008

Nov. 21, 2008

I think this ticket should be closed: http://projects.scipy.org/scipy/scipy/ticket/231 I know that there is still work planned on this, but it might be more appropriate to create a new ticket to enhance the arpack wrapper. It would also be great if Aric (or someone else) could go ahead and an entry to the release notes: http://projects.scipy.org/scipy/scipy/milestone/0.7.0 Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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are masked array statistical function hidden intentionally?
by josef.pktd＠gmail.com Nov. 21, 2008

Nov. 21, 2008

scipy\stats\mstats.py and scipy\stats\mmorestats.py are masked array version of many of the statistical function. They are not imported in any __init__.py and I did not find them in the new documentation for scipy at http://docs.scipy.org/doc/scipy/reference/stats.html. Is this on purpose or not? Josef

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LAPACK 3.2
by Nils Wagner Nov. 20, 2008

Nov. 20, 2008

FWIW Nils -------- Original Message -------- Date: Wed, 19 Nov 2008 06:03:40 -0800 From: James Demmel <demmel(a)cs.berkeley.edu> To: Kreinovich, Vladik <vladik(a)utep.edu>, reliable computing <owner-reliable_computing(a)interval.louisiana.edu> CC: James Demmel <demmel(a)cs.berkeley.edu> Subject: Announcement for Reliable Computing I would appreciate it if you could post this on your mailing list. Thanks, Jim Demmel Subject: New LAPACK release with "guaranteed" error bounds We have just released LAPACK 3.2, which among other improvements includes iterative refinement for solving linear systems with "guaranteed" error bounds, measured both normwise and componentwise. Portable high precision arithmetic (using another package we just released called XBLAS) is used to compute residuals. What we mean by "guarantee" is that either the error bound is correctly O(machine_epsilon), or a warning is returned that the condition number is ~1/machine_epsilon or larger. In extensive testing, we have never found it to fail, either by returning a too-small error bound, or failing to solve a problem whose condition number is at least a little below 1/machine_epsilon. But if there is a community that can find a failure, it is this one, and we would be very interested if you can find one. Since we are not doing interval arithmetic, we expect to keep "guaranteed" in quotation marks. For more information, please see http://www.netlib.org/lapack/ and http://www.netlib.org/xblas/ http://www.netlib.org/lapack/lapack-3.2.html Regards, Jim Demmel, and the rest of the LAPACK team

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scipy.test() error
by Nils Wagner Nov. 20, 2008

Nov. 20, 2008

test_decomp.test_eigh('general ', 6, 'd', False, True, False, (2, 4)) ... ok test_decomp.test_eigh('ordinary', 6, 'd', False, False, False, (2, 4)) ... ok test_decomp.test_eigh('general ', 6, 'd', False, False, False, (2, 4)) ... ok test_decomp.test_eigh('ordinary', 6, 'F', True, True, True, None) ... ** On entry to CSTEGR parameter number 17 had an illegal value nwagner@noname:~> >>> scipy.__version__ '0.7.0.dev5151'

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test coverage for each individual functions ?
by josef.pktd＠gmail.com Nov. 19, 2008

Nov. 19, 2008

I would like to make a list of functions in scipy.stats that have no or low test coverage? Figleaf and coverage seem to work only on the module level. Does anyone know if this is easily possible or does anyone have a script for this? Thanks, Josef

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vonmises_cython exposes all of numpy to np.lookfor
by josef.pktd＠gmail.com Nov. 19, 2008

Nov. 19, 2008

vonmises_cython exposes all of numpy to np.lookfor It looks like there is no __all__ in vonmises_cython, instead it exports np, scipy and __builtins__ which seems to confuse np.lookfor >>> dir(stats.vonmises_cython) ['__builtins__', '__doc__', '__file__', '__name__', 'i0', 'np', 'numpy', 'scipy' , 'von_mises_cdf', 'von_mises_cdf_normalapprox'] Josef

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