Mailman 3 February 2008 - SciPy-Dev

status of splinalg
by Nathan Bell Feb. 6, 2008

Feb. 6, 2008

For those keeping score, here's the current status of scipy.splinalg. Completed tasks: (1) linalg.iterative -> splinalg.isolve http://projects.scipy.org/scipy/scipy/changeset/3861 For backwards compatibility scipy.linalg imports all the iterative solvers from splinalg.isolve . This is needed to avoid breaking things like 'from scipy.linalg import cg' These functions are wrapped with deprecation warnings. The new iterative solvers have an argument M for an optional preconditioner. The old A.psolve() method is still supported. (4) scipy.linsolve -> splinalg.dsolve http://projects.scipy.org/scipy/scipy/changeset/3862 Importing from scipy.linsolve generates a warning (6) create LinearOperator wrapper class and document it http://projects.scipy.org/scipy/scipy/changeset/3890 Iterative solvers now use aslinearoperator() to handle matrix-like input arguments. I will update the iterative solver docstrings to reflect the change. Remaining tasks with owners: (1) sandbox.lobpcg -> splinalg.eigen.lobpcg (2) sandbox.arpack -> splinalg.eigen.arpack (3) create splinalg.eigen.speigs (5) scipy.linsolve.umfpack -> scikit Remaining tasks: (7) document splinalg.dsolve (8) document splinalg.isolve (9) document splinalg.eigen -- Nathan Bell wnbell(a)gmail.com http://graphics.cs.uiuc.edu/~wnbell/

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help with svn (umfpack scikit)
by Robert Cimrman Feb. 6, 2008

Feb. 6, 2008

I would like to preserve the SVN history of umpfack.py and related files after I move them to the umfpack scikit. Is it possible somehow? regards, r.

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scipy.org is down
by Brian Granger Feb. 5, 2008

Feb. 5, 2008

Hi, It looks like scipy.org and friends are down right now. Brian

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openopt example mmp_1.py
by Nils Wagner Feb. 5, 2008

Feb. 5, 2008

Hi Dmitrey, the example mmp_1.py is broken. /usr/bin/python svn/openopt/scikits/openopt/examples/mmp_1.py starting solver nsmm (license: BSD) with problem unnamed incorrect func index type! Traceback (most recent call last): File "svn/openopt/scikits/openopt/examples/mmp_1.py", line 22, in ? r = p.solve('nsmm') File "/usr/lib/python2.4/site-packages/scikits/openopt/Kernel/BaseProblem.py", line 207, in solve return runProbSolver(self, solvers, *args, **kwargs) File "/usr/lib/python2.4/site-packages/scikits/openopt/Kernel/runProbSolver.py", line 156, in runProbSolver solver(p) File "/usr/lib/python2.4/site-packages/scikits/openopt/solvers/UkrOpt/nsmm.py", line 54, in __solver__ r2 = p2.solve('ralg') File "/usr/lib/python2.4/site-packages/scikits/openopt/Kernel/BaseProblem.py", line 207, in solve return runProbSolver(self, solvers, *args, **kwargs) File "/usr/lib/python2.4/site-packages/scikits/openopt/Kernel/runProbSolver.py", line 156, in runProbSolver solver(p) File "/usr/lib/python2.4/site-packages/scikits/openopt/solvers/UkrOpt/ralg.py", line 62, in __solver__ g, fname, ind = self.getRalgDirection(x, p) File "/usr/lib/python2.4/site-packages/scikits/openopt/solvers/UkrOpt/ralg.py", line 230, in getRalgDirection d = p.df(x) File "/usr/lib/python2.4/site-packages/scikits/openopt/Kernel/objFunRelated.py", line 138, in user_df df = user_df_func(*(x,) + p.args.f) File "/usr/lib/python2.4/site-packages/scikits/openopt/solvers/UkrOpt/nsmm.py", line 31, in df return p.df(x, ind) File "/usr/lib/python2.4/site-packages/scikits/openopt/Kernel/objFunRelated.py", line 105, in user_df if IND is not None: ind = p.getCorrectInd(IND) File "/usr/lib/python2.4/site-packages/scikits/openopt/Kernel/objFunRelated.py", line 358, in getCorrectInd p.err('incorrect func index type!') File "/usr/lib/python2.4/site-packages/scikits/openopt/Kernel/oologfcn.py", line 12, in ooerr raise OpenOptException(msg) oologfcn.OpenOptException: <oologfcn.OpenOptException instance at 0x42cc0bcc> Cheers Nils

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Re: [SciPy-dev] [SciPy-user] scipy.sparse.lil_matrix and fancy indexing
by Nathan Bell Feb. 3, 2008

Feb. 3, 2008

On Feb 3, 2008 4:29 PM, Anne Archibald <peridot.faceted(a)gmail.com> wrote: > Is this intended behaviour? Failure to raise an exception on bad > input? Just a bug? That's unlikely to be the intended behaviour. The lil_matrix. __setitem__ code is fairly ugly, is anyone actively maintaining it? http://projects.scipy.org/scipy/scipy/browser/trunk/scipy/sparse/lil.py#L273 -- Nathan Bell wnbell(a)gmail.com http://graphics.cs.uiuc.edu/~wnbell/

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Status of minres
by Nils Wagner Feb. 2, 2008

Feb. 2, 2008

Hi Nathan, I just tried to run minres. from scipy.splinalg.isolve import minres y = minres.minres(A,b) Traceback (most recent call last): File "test_minres.py", line 9, in ? y = minres.minres(A,b) File "/usr/lib/python2.4/site-packages/scipy/splinalg/isolve/minres.py", line 43, in minres b = asarray(b).ravel() NameError: global name 'asarray' is not defined Nils

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scipy.splinalg or bust
by Nathan Bell Feb. 1, 2008

Feb. 1, 2008

I've started migrating code to scipy.splinalg. Completed tasks: (1) linalg.iterative -> splinalg.isolve http://projects.scipy.org/scipy/scipy/changeset/3861 For backwards compatibility scipy.linalg imports all the iterative solvers from splinalg.isolve . This is needed to avoid breaking things like 'from scipy.linalg import cg' What's the best way to inform the user that these functions have moved? Is there a nice way to decorate these functions to issue a warning? Remaining tasks: (1) sandbox.lobpcg -> splinalg.eigen.lobpcg (2) sandbox.arpack -> splinalg.eigen.arpack (3) create splinalg.eigen.speigs (4) scipy.linsolve -> splinalg.dsolve (5) scipy.linsolve.umfpack -> scikit (6) create LinearOperator wrapper class and document it (7) document splinalg.dsolve (8) document splinalg.isolve (9) document splinalg.eigen I will start working on (4) now. Should I remove umfpack in the process? linalg Robert C, can you give us a timeline on (1) and (5)? Can (1) be done without symeig (perhaps using scipy.linalg.eig as a fallback)? Any volunteers for (2) and (3)? For reference: http://projects.scipy.org/scipy/scipy/wiki/ArpackWrapper Here are the remaining ARPACK tickets: http://projects.scipy.org/scipy/scipy/ticket/231 http://projects.scipy.org/scipy/scipy/ticket/366 http://projects.scipy.org/scipy/scipy/ticket/554 We discussed a plan for (6) in this thread: http://thread.gmane.org/gmane.comp.python.scientific.devel/7070/focus=7285 Any comments/suggestions are most welcome. -- Nathan Bell wnbell(a)gmail.com http://graphics.cs.uiuc.edu/~wnbell/

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