Mailman 3 November 2008 - SciPy-Dev

Re: [SciPy-dev] docs.scipy.org -- new site for the documentation marathon
by jh＠physics.ucf.edu Nov. 14, 2008

Nov. 14, 2008

Pauli Virtanen wrote: > Mon, 27 Oct 2008 15:16:14 -0400, jh wrote: > [clip] > > For the top page layout, I propose (rationale below): > > > > (No left sidebar) > > ------------------------------------------------------------ > > DOCUMENTATION EDITOR > > Write, review, or proof the docs! > > > > MATURE DOCUMENTS > > > > Guide to Numpy > > PDF book by Travis Oliphant > > > > DOCUMENT-IN-PROGRESS SNAPSHOTS > > > > Numpy Reference Guide (as of yyyy-mm-dd) PDF zipped HTML > > refguide glossary shortcut > > > > Numpy User Guide (as of yyyy-mm-dd) > > PDF zipped HTML > > > > Scipy Reference Guide (as of yyyy-mm-dd) PDF zipped HTML > > > > SEE ALSO > > > > SciPy.org > > all things NumPy/SciPy (bug reports, downloads, conferences, etc.) > > > > SciPy.org/Documentation > > more documentation not (yet) in the right format for this site > > > > SciPy.org/Cookbook > > live, user-contributed examples and recipes for common tasks > > ------------------------------------------------------------ > I adapted this suggestion a bit -- it's now live on docs.scipy.org. The > "See also" part lives in the side bar, but otherwise it's almost as > above. The download links look definitely better on the front page. Looks great! The tag lines under the main links are all redundant except for the one on Travis's book. E.g.: Numpy Reference reference documentation for Numpy There's no new information in the extra line. Also, please add "Guide" to the title for this one. Would it be possible to take the latest stats graph and stick it next to the numpy reference manual on the front page? Just the graph for the last week and the key. Don't do this if it's real work, or if it slows loading much. We can add graphs for the others when they go under the wiki. Also, how difficult is it to put the current date of the works in progress? That would help those downloading it to see how recent it is and when to get an update. Again, don't do if it's a lot of work. > There's also an attempt to link the site visually to the parent scipy.org > site, but I'm no web designer, and it seems there are now too many snakes > on the page. Well, if it's not under that site, then maybe that's not a principal concern. If a web designer wants to step in, let 'em. Nicely done. --jh--

2 1

Two new test failures
by Christopher Hanley Nov. 14, 2008

Nov. 14, 2008

Hi, I am getting two new test failures from scipy. They appear to be from some test tests added yesterday in the stats package. ====================================================================== FAIL: test_discrete_chisquare.test_discrete_rvs_cdf('logser', (0.59999999999999998,)) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/chanley/dev/site-packages/lib/python/nose/case.py", line 182, in runTest self.test(*self.arg) File "/Users/chanley/dev/site-packages/lib/python/scipy/stats/tests/test_discrete_chisquare.py", line 77, in check_discrete_chisquare 'at arg = %s' % (distname,str(arg)) AssertionError: chisquare - test for logserat arg = (0.59999999999999998,) ====================================================================== FAIL: test_discrete_chisquare.test_discrete_rvs_cdf('nbinom', (5, 0.5)) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/chanley/dev/site-packages/lib/python/nose/case.py", line 182, in runTest self.test(*self.arg) File "/Users/chanley/dev/site-packages/lib/python/scipy/stats/tests/test_discrete_chisquare.py", line 77, in check_discrete_chisquare 'at arg = %s' % (distname,str(arg)) AssertionError: chisquare - test for nbinomat arg = (5, 0.5) ---------------------------------------------------------------------- Ran 3161 tests in 172.342s FAILED (SKIP=28, failures=2) <nose.result.TextTestResult run=3161 errors=0 failures=2> I am running OSX 10.5 on an Intel Mac. I have svn versions of both numpy and scipy: >>> scipy.__version__ '0.7.0.dev5090' >>> numpy.__version__ '1.3.0.dev6022' Chris -- Christopher Hanley Senior Systems Software Engineer Space Telescope Science Institute 3700 San Martin Drive Baltimore MD, 21218 (410) 338-4338

6 14

IPython TextMate Bundle
by Benjamin J. Racine Nov. 14, 2008

Nov. 14, 2008

I am sending this forward on behalf of Matt Foster... Be sure to look into pysmell (for completion) as well. >>>>>>>>>>>>>>>>>>>>>> Hi All, A similar mail has already been on the (ipython) users mailing list, so my apologies if you've seen most of this before. I've started working on a TextMate bundle for IPython, based on the info on the Wiki [1], the aim is to produce a BSD licensed bundle which helps to integrate TextMate with IPython. I have set up a project on Github [2] which currently contains: * Some help, which doubles as the README * commands for running the current file / line / section in IPython (via applescript, and Terminal.app) * a basic language grammar for ipythonrc config files. The GitHub page contains the README file which has instructions on how to get GetBundles, which will allow you to install the bundle (but not track changes). Alternatively, if you have git, you can get the bundle using the following commands: cd "~/Library/Application Support/TextMate/Bundles" git clone git://github.com/mattfoster/ipython-tmbundle.git IPython.tmbundle osascript -e 'tell app "TextMate" to reload bundles' GitHub users can fork the project and make their own changes. I'd really love to hear any ideas, suggestions or feature requests people have, and I've been told by Fernando that it's ok to use this list for discussions, provided we prefix mail subjects with [TextMate]. Thanks, Matt [1]: http://ipython.scipy.org/moin/Cookbook/UsingIPythonWithTextMate [2]: http://github.com/mattfoster/ipython-tmbundle/ -- Matt Foster | http://my-mili.eu/matt _______________________________________________ IPython-dev mailing list IPython-dev(a)scipy.org http://lists.ipython.scipy.org/mailman/listinfo/ipython-dev

1 0

docs.scipy.org: Add edit permissions for hans_meine
by Hans Meine Nov. 13, 2008

Nov. 13, 2008

Hi, please give me (hans_meine) edit permissions for the docstrings. Thanks, Hans

2 1

Commit rights for josef.pktd@gmail.com?
by Charles R Harris Nov. 13, 2008

Nov. 13, 2008

Hi All, Josef has been doing a lot of work on the stats package and I think it would be helpful if he could have commit permissions so he could apply his fixes. Can we do that? Chuck

2 1

patchfiles in 745
by josef.pktd＠gmail.com Nov. 13, 2008

Nov. 13, 2008

3 3

scipy 0.6 with python 2.6 leads to strange keyword argument errors
by Pierre Gueth Nov. 13, 2008

Nov. 13, 2008

Hi, I compiled scipy 0.6 with python 2.6 and this patch to solve the superlu compilation problem: https://bugs.gentoo.org/attachment.cgi?id=171446 I can import scipy and scipy.linalg but when i try to call some function like pinv or inv, i get a "RuntimeError: more argument specifiers than keyword list entries" error: [...] >>> import scipy as s >>> import scipy.linalg as l >>> l.pinv(s.array([[1,0],[0,1]])) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line 468, in pinv return lstsq(a, b, cond=cond)[0] File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line 441, in lstsq lwork = calc_lwork.gelss(gelss.prefix,m,n,nrhs)[1] RuntimeError: more argument specifiers than keyword list entries (remaining format:'|:calc_lwork.gelss') [...] Does anyone knows how to solve this problem?? Regards pierre

1 0

Missed gfortran library when linking umfpack
by Nathan Bell Nov. 12, 2008

Nov. 12, 2008

Has anyone encountered this problem before or know of a solution? I know we're dropping UMFPACK support after 0.7, but this is likely to pop up again in the UMFPACK scikit. Also, this is the last outstanding ticket in scipy.sparse or scipy.sparse.linalg, so I'd like to resolve it :) http://scipy.org/scipy/scipy/ticket/790 Description: I had a problem when using umfpack (both scipy and scikits) due to a missing -lgfortran. I had to re-compile by hand after the regular build. I dont know if it is some problem with my umfpack/atlas build (gcc and gfortran) or some issue in the configuration. -- Nathan Bell wnbell(a)gmail.com http://graphics.cs.uiuc.edu/~wnbell/

2 1

scipy.cluster
by Nils Wagner Nov. 12, 2008

Nov. 12, 2008

>>> from scipy import cluster >>> cluster.test() ====================================================================== FAIL: Tests fcluster(Z, criterion='maxclust', t=2) on a random 3-cluster data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 457, in test_fcluster_maxclusts_2 self.failUnless(is_isomorphic(T, expectedT)) AssertionError ====================================================================== FAIL: Tests fcluster(Z, criterion='maxclust', t=3) on a random 3-cluster data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 466, in test_fcluster_maxclusts_3 self.failUnless(is_isomorphic(T, expectedT)) AssertionError ====================================================================== FAIL: Tests fcluster(Z, criterion='maxclust', t=4) on a random 3-cluster data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 475, in test_fcluster_maxclusts_4 self.failUnless(is_isomorphic(T, expectedT)) AssertionError ====================================================================== FAIL: Tests fclusterdata(X, criterion='maxclust', t=2) on a random 3-cluster data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 434, in test_fclusterdata_maxclusts_2 self.failUnless(is_isomorphic(T, expectedT)) AssertionError ====================================================================== FAIL: Tests fclusterdata(X, criterion='maxclust', t=3) on a random 3-cluster data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 441, in test_fclusterdata_maxclusts_3 self.failUnless(is_isomorphic(T, expectedT)) AssertionError ====================================================================== FAIL: Tests fclusterdata(X, criterion='maxclust', t=4) on a random 3-cluster data set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 448, in test_fclusterdata_maxclusts_4 self.failUnless(is_isomorphic(T, expectedT)) AssertionError ---------------------------------------------------------------------- Ran 166 tests in 20.086s FAILED (errors=1, failures=6) <nose.result.TextTestResult run=166 errors=1 failures=6> >>> from scipy import cluster >>> scipy.__version__ '0.7.0.dev5035' ====================================================================== ERROR: Tests leaders using a flat clustering generated by single linkage. ---------------------------------------------------------------------- Traceback (most recent call last): File "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/cluster/tests/test_hierarchy.py", line 487, in test_leaders_single self.failUnless((L[0] == Lright[0]).all() and (L[1] == Lright[1]).all()) AttributeError: 'bool' object has no attribute 'all'

2 5

[Fwd: Re: [Fwd: Re: Do we care about the LAPACK C interface?]]
by Travis E. Oliphant Nov. 12, 2008

Nov. 12, 2008

1 0