From nwagner at mecha.uni-stuttgart.de Tue Dec 2 04:54:29 2003 From: nwagner at mecha.uni-stuttgart.de (Nils Wagner) Date: Tue, 02 Dec 2003 10:54:29 +0100 Subject: [SciPy-dev] Solving linear matrix equations with scipy Message-ID: <3FCC6155.CDF44B8D@mecha.uni-stuttgart.de> Hi all, Are there any efforts to add solvers for linear matrix equations to scipy ? Nils References http://www.win.tue.nl/niconet/ http://www.math.tu-berlin.de/~benner/Publicat/pub/SimaBenner_ECC03.pdf From nwagner at mecha.uni-stuttgart.de Wed Dec 3 02:51:52 2003 From: nwagner at mecha.uni-stuttgart.de (Nils Wagner) Date: Wed, 03 Dec 2003 08:51:52 +0100 Subject: [SciPy-dev] [Fwd: [Math-atlas-devel] 3.5.13 drags itself from the rubble] Message-ID: <3FCD9618.D3A9666B@mecha.uni-stuttgart.de> -------------- next part -------------- An embedded message was scrubbed... From: rwhaley at cs.utk.edu (R Clint Whaley) Subject: [Math-atlas-devel] 3.5.13 drags itself from the rubble Date: Tue, 2 Dec 2003 17:45:19 -0500 (EST) Size: 6117 URL: From joe at enthought.com Wed Dec 3 17:36:45 2003 From: joe at enthought.com (Joe Cooper) Date: Wed, 03 Dec 2003 16:36:45 -0600 Subject: [SciPy-dev] Reboot and Zope Upgrade on SciPy.org Message-ID: <3FCE6593.8030804@enthought.com> Hi all, There will be a short (possibly longer than short, if all doesn't go well) service outage in a couple of hours on scipy.org (sometime between 6 and 7PM CST). All scipy.org/scipy.net services will be unavailable during this time. This includes mailing lists, the website, CVS, etc. I will be performing routine maintenence, a kernel upgrade, and a Zope upgrade. I expect the outage to last about five to ten minutes, though Zope has historically thwarted my attempts to achieve a quick and painless upgrade. Nothing should change significantly on the server, as the Zope upgrade is minor (2.6.1 to 2.6.2). There are plans afoot to bring SciPy.org into the modern age with a migration to Plone instead of the older CMF that we're currently using. The planners (mainly me) are adragging their afeet, however, so there's no telling when the switch will be pulled. If you have useful content (or merely content you are fond of) on the site that uses DTML, it would be in all of our interests for you to consider converting it to using ZPT or structured text. DTML is apparently deprecated in Plone, and there also seems to be some other content type issues that we'll be fighting with one day in the not too distant future. Let me know if you have anything there, and I'll see if I can assist with getting it ready for the migration to Plone. Holler if this service outage will cause significant pain for anyone. Thanks! From joe at enthought.com Wed Dec 3 19:53:38 2003 From: joe at enthought.com (Joe Cooper) Date: Wed, 03 Dec 2003 18:53:38 -0600 Subject: [SciPy-dev] SciPy.org is back up Message-ID: <3FCE85A8.6060409@enthought.com> Hi all, The upgrades seem to have gone smoothly, and the website, lists, mail, CVS, etc. should all be available again on scipy.org. If you run into any problems, let me know. Thanks! From nwagner at mecha.uni-stuttgart.de Mon Dec 8 09:06:44 2003 From: nwagner at mecha.uni-stuttgart.de (Nils Wagner) Date: Mon, 08 Dec 2003 15:06:44 +0100 Subject: [SciPy-dev] [Fwd: [Math-atlas-devel] 3.5.14, stable freeze] Message-ID: <3FD48574.606B4E12@mecha.uni-stuttgart.de> -------------- next part -------------- An embedded message was scrubbed... From: rwhaley at cs.utk.edu (R Clint Whaley) Subject: [Math-atlas-devel] 3.5.14, stable freeze Date: Sun, 7 Dec 2003 14:32:53 -0500 (EST) Size: 5816 URL: From nwagner at mecha.uni-stuttgart.de Mon Dec 8 09:07:10 2003 From: nwagner at mecha.uni-stuttgart.de (Nils Wagner) Date: Mon, 08 Dec 2003 15:07:10 +0100 Subject: [SciPy-dev] [Fwd: [Math-atlas-devel] testing for stable: please help] Message-ID: <3FD4858E.1F33A65D@mecha.uni-stuttgart.de> -------------- next part -------------- An embedded message was scrubbed... From: rwhaley at cs.utk.edu (R Clint Whaley) Subject: [Math-atlas-devel] testing for stable: please help Date: Sun, 7 Dec 2003 15:33:58 -0500 (EST) Size: 6626 URL: From list at jsaul.de Tue Dec 9 17:32:17 2003 From: list at jsaul.de (Joachim Saul) Date: Tue, 9 Dec 2003 23:32:17 +0100 Subject: [SciPy-dev] Apparently bug in filter_design.py Message-ID: <20031209223217.GC654@jsaul.de> Hi there, while using a IIR filter designed using scipy.signal.iirfilter, an error occurs within lp2bp() and potentially in the other similar routines as well, where the line aprime[Dp-j] = val occurs. Since val can be complex, and aprime be e.g. of double type, an error may be (and im my situation is) issued: TypeError: can't convert complex to float; use abs(z) Which, in turn, doesn't quite make sense, at least *if* a real part of the values in aprime may be negative. A quick fix would be to modify lp2bp(): replace bprime = Num.zeros(Np+1,artype) aprime = Num.zeros(Dp+1,artype) by bprime = Num.zeros(Np+1, 'D') aprime = Num.zeros(Dp+1, 'D') and just before "return" add bprime = bprime.astype(artype) aprime = aprime.astype(artype) This would force aprime and bprime to be always double precision complex (which should never harm) and at the end cast to the originally wanted type. Since this is used in filter design only, the overhead though the conversion would be negligible. Any comments? Cheers, Joachim From nwagner at mecha.uni-stuttgart.de Wed Dec 10 04:14:46 2003 From: nwagner at mecha.uni-stuttgart.de (Nils Wagner) Date: Wed, 10 Dec 2003 10:14:46 +0100 Subject: [SciPy-dev] Scipy cannot handle singular eigenvalue problems Message-ID: <3FD6E406.8075307@mecha.uni-stuttgart.de> Hi all, Scipy cannot handle singular eigenvalue problems. Note, that both matrices are singular. from scipy import * A = array(([1.,-1.],[-1.,1.])) B = array(([1.0,0.0],[0.0,0.0])) w,vr = linalg.eig(A,B) print w print vr Traceback (most recent call last): File "sevp.py", line 4, in ? w,vr = linalg.eig(A,B) File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line 109, in eig return _geneig(a1,b,left,right,overwrite_a,overwrite_b) File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line 68, in _geneig vr = _make_complex_eigvecs(w, vr, t) File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line 29, in _make_complex_eigvecs vnew.real = scipy_base.take(vin,ind[::2],1) ValueError: matrices are not aligned for copy Any suggestion ? The output of MATLAB is enclosed as well (out.ps) Nils -------------- next part -------------- A non-text attachment was scrubbed... Name: out.ps Type: application/postscript Size: 4412 bytes Desc: not available URL: From pearu at scipy.org Wed Dec 10 05:27:36 2003 From: pearu at scipy.org (Pearu Peterson) Date: Wed, 10 Dec 2003 04:27:36 -0600 (CST) Subject: [SciPy-dev] Scipy cannot handle singular eigenvalue problems In-Reply-To: <3FD6E406.8075307@mecha.uni-stuttgart.de> Message-ID: On Wed, 10 Dec 2003, Nils Wagner wrote: > Hi all, > > Scipy cannot handle singular eigenvalue problems. Note, that both > matrices are singular. > > from scipy import * > A = array(([1.,-1.],[-1.,1.])) > B = array(([1.0,0.0],[0.0,0.0])) > w,vr = linalg.eig(A,B) > print w > print vr > > Traceback (most recent call last): > File "sevp.py", line 4, in ? > w,vr = linalg.eig(A,B) > File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line > 109, in eig > return _geneig(a1,b,left,right,overwrite_a,overwrite_b) > File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line > 68, in _geneig > vr = _make_complex_eigvecs(w, vr, t) > File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line > 29, in _make_complex_eigvecs > vnew.real = scipy_base.take(vin,ind[::2],1) > ValueError: matrices are not aligned for copy This error is caused by the fact that in Numeric (1+0j)/0.0 returns Inf+Nan*1j while Matlab returns Inf. It is a matter of taste which result to prefer. I (or Travis?) will see if scipy.eig can be made robust in this case. The code to be fixed is given in line w = (alphar+_I*alphai)/beta of linalg/decomp.py where for your example alphar = [0,1.41421356] alphai = [0,0] beta = [0.70710678,0] This results in w = [0+0j,inf+nanj] which should be w = [0+0j,inf+0j] in order to get Matlab's result. > Any suggestion ? Use small perturbation for now: In [1]: from scipy import * In [2]: w,vr=linalg.eig([[1,-1],[-1,1]],[[1,0],[0,1e-18j]]) In [3]: print w [ 0.00000000e+000 +0.00000000e+000j nan +infj] In [4]: print vr [[ 1.+0.j 0.+0.j] [ 1.+0.j 1.+0.j]] Pearu From nwagner at mecha.uni-stuttgart.de Wed Dec 10 07:27:34 2003 From: nwagner at mecha.uni-stuttgart.de (Nils Wagner) Date: Wed, 10 Dec 2003 13:27:34 +0100 Subject: [SciPy-dev] Scipy cannot handle singular eigenvalue problems References: Message-ID: <3FD71136.2AE404B9@mecha.uni-stuttgart.de> Pearu Peterson schrieb: > > On Wed, 10 Dec 2003, Nils Wagner wrote: > > > Hi all, > > > > Scipy cannot handle singular eigenvalue problems. Note, that both > > matrices are singular. > > > > from scipy import * > > A = array(([1.,-1.],[-1.,1.])) > > B = array(([1.0,0.0],[0.0,0.0])) > > w,vr = linalg.eig(A,B) > > print w > > print vr > > > > Traceback (most recent call last): > > File "sevp.py", line 4, in ? > > w,vr = linalg.eig(A,B) > > File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line > > 109, in eig > > return _geneig(a1,b,left,right,overwrite_a,overwrite_b) > > File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line > > 68, in _geneig > > vr = _make_complex_eigvecs(w, vr, t) > > File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line > > 29, in _make_complex_eigvecs > > vnew.real = scipy_base.take(vin,ind[::2],1) > > ValueError: matrices are not aligned for copy > > This error is caused by the fact that in Numeric (1+0j)/0.0 > returns Inf+Nan*1j while Matlab returns Inf. It is a matter > of taste which result to prefer. I (or Travis?) will see if scipy.eig > can be made robust in this case. The code to be fixed is given in line > w = (alphar+_I*alphai)/beta > of linalg/decomp.py where for your example > alphar = [0,1.41421356] > alphai = [0,0] > beta = [0.70710678,0] > This results in > w = [0+0j,inf+nanj] > which should be > w = [0+0j,inf+0j] > in order to get Matlab's result. > > > Any suggestion ? > > Use small perturbation for now: > > In [1]: from scipy import * > > In [2]: w,vr=linalg.eig([[1,-1],[-1,1]],[[1,0],[0,1e-18j]]) > > In [3]: print w > [ 0.00000000e+000 +0.00000000e+000j nan +infj] > > In [4]: print vr > [[ 1.+0.j 0.+0.j] > [ 1.+0.j 1.+0.j]] > > Pearu > Pearu, The following reference might be of interest in this context http://www.cs.umu.se/research/nla/singular_pairs/guptri/ Nils > _______________________________________________ > Scipy-dev mailing list > Scipy-dev at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-dev From pearu at scipy.org Wed Dec 10 16:35:17 2003 From: pearu at scipy.org (Pearu Peterson) Date: Wed, 10 Dec 2003 15:35:17 -0600 (CST) Subject: [SciPy-dev] Scipy cannot handle singular eigenvalue problems In-Reply-To: <3FD6E406.8075307@mecha.uni-stuttgart.de> Message-ID: On Wed, 10 Dec 2003, Nils Wagner wrote: > Scipy cannot handle singular eigenvalue problems. Note, that both > matrices > are singular. > > from scipy import * > A = array(([1.,-1.],[-1.,1.])) > B = array(([1.0,0.0],[0.0,0.0])) > w,vr = linalg.eig(A,B) > print w > print vr > > Traceback (most recent call last): > ValueError: matrices are not aligned for copy This issue is now resolved in CVS. Thanks Travis! Pearu From wagner.nils at vdi.de Wed Dec 10 17:49:38 2003 From: wagner.nils at vdi.de (Nils Wagner) Date: Wed, 10 Dec 2003 23:49:38 +0100 Subject: [SciPy-dev] Scipy cannot handle singular eigenvalue problems In-Reply-To: Message-ID: <20031210225017.F30CE3EB3A@www.scipy.com> ------------------- On Wed, 10 Dec 2003, Nils Wagner wrote: > Scipy cannot handle singular eigenvalue problems. Note, that both > matrices > are singular. > > from scipy import * > A = array(([1.,-1.],[-1.,1.])) > B = array(([1.0,0.0],[0.0,0.0])) > w,vr = linalg.eig(A,B) > print w > print vr > > Traceback (most recent call last): > ValueError: matrices are not aligned for copy This issue is now resolved in CVS. Thanks Travis! Pearu It seems to be resolved. However, a second example doesn't work. >>> A array([[ 1., 0.], [ 0., 0.]]) >>> B array([[ 1., 0.], [ 0., 0.]]) >>> w,vr = linalg.eig(A,B) Traceback (most recent call last): File "", line 1, in ? File "/usr/local/lib/python2.3/site-packages/scipy/linalg/decomp.py", line 109, in eig return _geneig(a1,b,left,right,overwrite_a,overwrite_b) File "/usr/local/lib/python2.3/site-packages/scipy/linalg/decomp.py", line 68, in _geneig vr = _make_complex_eigvecs(w, vr, t) File "/usr/local/lib/python2.3/site-packages/scipy/linalg/decomp.py", line 29, in _make_complex_eigvecs vnew.real = scipy_base.take(vin,ind[::2],1) ValueError: matrices are not aligned for copy >>> Any comment ? Nils _______________________________________________ Scipy-dev mailing list Scipy-dev at scipy.net http://www.scipy.net/mailman/listinfo/scipy-dev From eric at enthought.com Sun Dec 14 01:01:12 2003 From: eric at enthought.com (eric jones) Date: Sun, 14 Dec 2003 00:01:12 -0600 Subject: [SciPy-dev] CVS build on windows -- ATLAS_INFO issues Message-ID: <3FDBFCA8.7080100@enthought.com> Hey guys, I just tried building from CVS on windows and got the following error (perhaps line numbers are slightly off due to my hacking around on it): c:\mingw\bin\gcc.exe -O2 -w -Wstrict-prototypes -DATLAS_INFO="None" -Ic:\python2 3\include -Ic:\python23\PC -c Lib\linalg\atlas_version.c -o build\temp.win32-2.3 \Release\lib\linalg\atlas_version.o Lib/linalg/atlas_version.c: In function `initatlas_version': Lib/linalg/atlas_version.c:14: `None' undeclared (first use in this function) Lib/linalg/atlas_version.c:14: (Each undeclared identifier is reported only once Lib/linalg/atlas_version.c:14: for each function it appears in.) error: command 'gcc' failed with exit status 1 It appears that ATLAS_INFO is getting set to None instead of a correct value and this isn't acceptable to the printf statement in the .c code. I haven't built in a while, so perhaps something else is wrong? I am on windows XP, python 2.3, an older atlas (don't remember version), and using gcc 3.2. thanks, eric From pearu at scipy.org Sun Dec 14 01:17:12 2003 From: pearu at scipy.org (Pearu Peterson) Date: Sun, 14 Dec 2003 00:17:12 -0600 (CST) Subject: [SciPy-dev] CVS build on windows -- ATLAS_INFO issues In-Reply-To: <3FDBFCA8.7080100@enthought.com> Message-ID: On Sun, 14 Dec 2003, eric jones wrote: > Hey guys, > > I just tried building from CVS on windows and got the following error > (perhaps line numbers are slightly off due to my hacking around on it): > > c:\mingw\bin\gcc.exe -O2 -w -Wstrict-prototypes -DATLAS_INFO="None" > -Ic:\python2 > 3\include -Ic:\python23\PC -c Lib\linalg\atlas_version.c -o > build\temp.win32-2.3 > \Release\lib\linalg\atlas_version.o > Lib/linalg/atlas_version.c: In function `initatlas_version': > Lib/linalg/atlas_version.c:14: `None' undeclared (first use in this > function) > Lib/linalg/atlas_version.c:14: (Each undeclared identifier is reported > only once > > Lib/linalg/atlas_version.c:14: for each function it appears in.) > error: command 'gcc' failed with exit status 1 > > It appears that ATLAS_INFO is getting set to None instead of a correct > value and this isn't acceptable to the printf statement in the .c code. > I haven't built in a while, so perhaps something else is wrong? > > I am on windows XP, python 2.3, an older atlas (don't remember version), > and using gcc 3.2. For older atlas versions -DATLAS_INFO="None" is correct definition. Maybe double-quotes in "None" are eaten by win32 shell? Could you try using -DATLAS_INFO=\"None\"? Pearu From wagner.nils at vdi.de Sun Dec 14 05:05:55 2003 From: wagner.nils at vdi.de (Nils Wagner) Date: Sun, 14 Dec 2003 11:05:55 +0100 Subject: [SciPy-dev] AttributeError:intel_itanium_fortran_compiler instance has no attribute 'version' Message-ID: <20031214100648.D247C3EB32@www.scipy.com> Traceback (most recent call last): File "setup.py", line 127, in ? setup_package(ignore_packages) File "setup.py", line 108, in setup_package url = "http://www.scipy.org", File "scipy_core/scipy_distutils/core.py", line 42, in setup return old_setup(**new_attr) File "/usr/local/lib/python2.3/distutils/core.py", line 149, in setup dist.run_commands() File "/usr/local/lib/python2.3/distutils/dist.py", line 907, in run_commands self.run_command(cmd) File "/usr/local/lib/python2.3/distutils/dist.py", line 927, in run_command cmd_obj.run() File "/usr/local/lib/python2.3/distutils/command/build.py", line 107, in run self.run_command(cmd_name) File "/usr/local/lib/python2.3/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/local/lib/python2.3/distutils/dist.py", line 926, in run_command cmd_obj.ensure_finalized() File "/usr/local/lib/python2.3/distutils/cmd.py", line 117, in ensure_finalized self.finalize_options() File "scipy_core/scipy_distutils/command/build_flib.py", line 177, in finalize_options verbose = self.verbose) File "scipy_core/scipy_distutils/command/build_flib.py", line 1671, in find_fortran_compiler compiler = compiler_class(fc,f90c,verbose = verbose) File "scipy_core/scipy_distutils/command/build_flib.py", line 1260, in __init__ if not self.get_version(): File "scipy_core/scipy_distutils/command/build_flib.py", line 617, in get_version if self.version is not None: AttributeError: intel_itanium_fortran_compiler instance has no attribute 'version' nwagner at linux:~/cvs/scipy> From pearu at scipy.org Sun Dec 14 05:39:40 2003 From: pearu at scipy.org (Pearu Peterson) Date: Sun, 14 Dec 2003 04:39:40 -0600 (CST) Subject: [SciPy-dev] AttributeError:intel_itanium_fortran_compiler instance has no attribute 'version' In-Reply-To: <20031214100648.D247C3EB32@www.scipy.com> Message-ID: On Sun, 14 Dec 2003, Nils Wagner wrote: > Traceback (most recent call last): > File "scipy_core/scipy_distutils/command/build_flib.py", line 617, > in get_version > if self.version is not None: > AttributeError: intel_itanium_fortran_compiler instance has no > attribute 'version' Fixed in CVS. Thanks, Pearu From nwagner at mecha.uni-stuttgart.de Tue Dec 16 09:40:52 2003 From: nwagner at mecha.uni-stuttgart.de (Nils Wagner) Date: Tue, 16 Dec 2003 15:40:52 +0100 Subject: [SciPy-dev] FAIL: check_normal (scipy.stats.morestats.test_morestats.test_anderson) Message-ID: <3FDF1974.7AA385BF@mecha.uni-stuttgart.de> ====================================================================== FAIL: check_normal (scipy.stats.morestats.test_morestats.test_anderson) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/stats/tests/test_morestats.py", line 49, in check_normal assert(scipy.all(A < crit[-2:])) AssertionError ---------------------------------------------------------------------- Ran 1028 tests in 3.709s FAILED (failures=1) >>> scipy.__version__ '0.2.1_251.4492' >>> From pearu at scipy.org Tue Dec 16 10:21:47 2003 From: pearu at scipy.org (Pearu Peterson) Date: Tue, 16 Dec 2003 09:21:47 -0600 (CST) Subject: [SciPy-dev] FAIL: check_normal (scipy.stats.morestats.test_morestats.test_anderson) In-Reply-To: <3FDF1974.7AA385BF@mecha.uni-stuttgart.de> Message-ID: On Tue, 16 Dec 2003, Nils Wagner wrote: > ====================================================================== > FAIL: check_normal (scipy.stats.morestats.test_morestats.test_anderson) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/usr/lib/python2.3/site-packages/scipy/stats/tests/test_morestats.py", > line 49, in check_normal > assert(scipy.all(A < crit[-2:])) > AssertionError When there are failures in scipy.stats testing then you should always rerun the tests to make sure that the failure is not due to "statistics". With the latest scipy from CVS such error messages like the above are now more informative. It might help using common sense when there are failures that can be ignored. Pearu From aza at uchicago.edu Wed Dec 24 16:25:48 2003 From: aza at uchicago.edu (Aza Raskin) Date: Wed, 24 Dec 2003 13:25:48 -0800 Subject: [SciPy-dev] An attempt to get Weave working on OSX Message-ID: I am attempting to get weave to work on OSX? and Linux too (RH 9)? however I am not able to get even the simplest weave.inline calls to work. On my OSX, box I have Python 2.3 and gcc 3.1 with a working version of wxPython 2.4.1.2. On my Linux box, I have Python 2.3.3 and gcc 3.2.2 with wxPython 2.4.2.4. Both give this error (although this particular message is from my OSX box): >>> import weave >>> weave.inline('1+1') In file included from /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/cxxsupport.cxx:6: /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1143: no class template named `random_access_iterator' in `std' /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1279: no class template named `random_access_iterator' in `std' /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1409: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1409: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1409: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1409: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1410: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1410: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1410: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1410: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1411: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1411: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1411: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1411: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1412: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1412: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1412: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1412: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1413: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1413: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1413: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1413: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1414: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1414: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1414: warning: ` typename Py::SeqBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1414: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1416: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1416: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1416: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1416: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1417: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1417: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1417: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1417: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1418: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1418: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1418: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1418: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1419: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1419: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1419: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1419: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1420: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1420: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1420: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1420: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1421: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1421: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1421: warning: ` typename Py::SeqBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1421: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2348: warning: ` typename Py::MapBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2348: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2348: warning: ` typename Py::MapBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2348: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2349: warning: ` typename Py::MapBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2349: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2349: warning: ` typename Py::MapBase::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2349: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2350: warning: ` typename Py::MapBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2350: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2350: warning: ` typename Py::MapBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2350: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2351: warning: ` typename Py::MapBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2351: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2351: warning: ` typename Py::MapBase::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2351: warning: implicit typename is deprecated, please see the documentation for details Traceback (most recent call last): File "", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/inline_tools.py", line 327, in inline auto_downcast = auto_downcast, File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/inline_tools.py", line 426, in compile_function verbose=verbose, **kw) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/ext_tools.py", line 349, in compile verbose = verbose, **kw) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/build_tools.py", line 194, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/ distutils/core.py", line 166, in setup raise SystemExit, "error: " + str(msg) weave.build_tools.CompileError: error: command 'gcc' failed with exit status 1 What am I doing wrong? -- Aza Raskin From rkern at ucsd.edu Fri Dec 26 17:16:35 2003 From: rkern at ucsd.edu (Robert Kern) Date: Fri, 26 Dec 2003 14:16:35 -0800 Subject: [SciPy-dev] An attempt to get Weave working on OSX In-Reply-To: References: Message-ID: <20031226221635.GA27191@taliesen.ucsd.edu> On Wed, Dec 24, 2003 at 01:25:48PM -0800, Aza Raskin wrote: > I am attempting to get weave to work on OSX? and Linux too (RH 9)? > however I am not able to get even the simplest weave.inline calls to > work. On my OSX, box I have Python 2.3 and gcc 3.1 with a working > version of wxPython 2.4.1.2. On my Linux box, I have Python 2.3.3 and > gcc 3.2.2 with wxPython 2.4.2.4. Both give this error (although this > particular message is from my OSX box): > > >>> import weave > >>> weave.inline('1+1') [snip] > What am I doing wrong? The string you are passing is not valid C. Please reread the documentation. >>> import scipy >>> scipy.weave.inline("return_val = PyInt_FromLong(1+1);") 2 works fine on my Powerbook. > -- Aza Raskin -- Robert Kern rkern at ucsd.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter From rkern at ucsd.edu Fri Dec 26 17:38:24 2003 From: rkern at ucsd.edu (Robert Kern) Date: Fri, 26 Dec 2003 14:38:24 -0800 Subject: [SciPy-dev] More OSX fun Message-ID: <20031226223824.GA27236@taliesen.ucsd.edu> I have managed to compile scipy on Mac OS X using unstable Fink's Python, ATLAS, and FFTW. I fixed the problem that prevented Chris Fonnesbeck from compiling, but as there are no unittests, I'm not sure it totally works. The fix is a bit of a hack, but it compiles. Turns out some of the enum names in supermatrix.h are #defined constants in some header. My grep-fu hasn't yet revealed where they are from, yet, but I can conditionally #undef them. I also fixed a problem in fastumath by porting in some changes from Numeric 23.1's umath's logical_* functions to address the same problem. Unfortunately, porting in similar changes from the equal, less, greater, etc. functions breaks things. I'll look into that some more when I can steal some more time. Below are the last two failures from the tests. They are errors in numerical accuracy only. ====================================================================== FAIL: check_bei_zeros (scipy.special.basic.test_basic.test_bei_zeros) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.3/site-packages/scipy/special/tests/test_basic.py", line 580, in check_bei_zeros -7.940178689168587]),11) File "/sw/lib/python2.3/site-packages/scipy_test/testing.py", line 635, in assert_array_almost_equal assert cond,\ AssertionError: Arrays are not almost equal (mismatch 20.0%): Array 1: [-2.294439682614 -4.073155089072 -5.512395729664 -6.78129444599 -7.940178689185] Array 2: [-2.294439682614 -4.073155089072 -5.512395729664 -6.78129444599 -7.940178689169] ====================================================================== FAIL: check_nrdtrimn (scipy.special.basic.test_basic.test_cephes) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.3/site-packages/scipy/special/tests/test_basic.py", line 344, in check_nrdtrimn assert_equal(cephes.nrdtrimn(0.5,1,1),1.0) File "/sw/lib/python2.3/site-packages/scipy_test/testing.py", line 546, in assert_equal assert desired == actual, msg AssertionError: Items are not equal: DESIRED: 1.0 ACTUAL: 0.99999999999999989 ---------------------------------------------------------------------- Ran 1028 tests in 9.264s FAILED (failures=2) -- Robert Kern rkern at ucsd.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter From claes.hagstrom at swipnet.se Sun Dec 28 11:15:39 2003 From: claes.hagstrom at swipnet.se (=?utf-8?Q?Claes_Hagstr=C3=B6m?=) Date: Sun, 28 Dec 2003 17:15:39 +0100 Subject: [SciPy-dev] Linear filter Message-ID: Hi! About a year ago I noted that the linear filter (signal.lfilter) had a bug when filtering 3D matrices: http://www.scipy.net/pipermail/scipy-user/2002-March/000201.html Working in Unix I made a fix in the sigtoolsmodule.c RawFilter code: while (num_loops--) { filt(ptrb, ptra, ptrX, ptrY, ptrVf, filt_size, len, stride_X, stride_Y); incr = increment(loop_index, ndims, max_index); /* Returns number of N-D indices incremented. */ k = ndims - incr; if (num_loops > 0) { /* Adjust index array and move pointers to right place for next iteration */ if ( k==0 && ndims==2 ) { ptrX -= loop_strides_X[1]*(max_index[1]-1); /* Stride information */ ptrY -= loop_strides_Y[1]*(max_index[1]-1); /* 20020304 */ } ptrX += loop_strides_X[k]; /* Stride information */ ptrY += loop_strides_Y[k]; which I think fixes the problem for the 3D case I now increasingly work in windows, so I wonder if you would consider fixing the problem I haven't been able to compile the fix and make it work in windows yet. Claes Hagstr?m -- Using M2, Opera's revolutionary e-mail client: http://www.opera.com/m2/