Mailman 3 November 2003 - SciPy-Dev

FAILED(failures=2)inscipy.test()with Python 2.3.2
by Nils Wagner Nov. 20, 2003

Nov. 20, 2003

Dear experts, In contrast to Python 2.2 scipy.test() with Python2.3.2 results in other failures, namely ====================================================================== FAIL: check_random_complex (scipy.linalg.decomp.test_decomp.test_cholesky) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.3/site-packages/scipy/linalg/tests/ test_decomp.py", line 276, in check_random_complex assert_array_almost_equal(cholesky(a),c) File "/usr/local/lib/python2.3/site-packages/scipy_test/testing.py", line 592, in assert_array_almost_equal assert alltrue(ravel(reduced)),\ AssertionError: Arrays are not almost equal: ====================================================================== FAIL: check_simple_complex (scipy.linalg.decomp.test_decomp.test_cholesky) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.3/site-packages/scipy/linalg/tests/ test_decomp.py", line 250, in check_simple_complex assert_array_almost_equal(cholesky(a),c) File "/usr/local/lib/python2.3/site-packages/scipy_test/testing.py", line 592, in assert_array_almost_equal assert alltrue(ravel(reduced)),\ AssertionError: Arrays are not almost equal: ---------------------------------------------------------------------- Ran 1028 tests in 2.334s FAILED (failures=2) <unittest.TextTestRunner object at 0x418e820c> >>> For what reason ? Nils

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FAILED(failures=3)inscipy.test()
by Nils Wagner Nov. 20, 2003

Nov. 20, 2003

Hi all, Thanks for the latest bugfixes. Now, scipy.test() results in 3 failures. Is it possible to fix these failures as well ? ====================================================================== FAIL: check_random_complex (scipy.linalg.decomp.test_decomp.test_cholesky) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/linalg/tests/ test_decomp.py", line 276, in check_random_complex assert_array_almost_equal(cholesky(a),c) File "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line 592, in assert_array_almost_equal assert alltrue(ravel(reduced)),\ AssertionError: Arrays are not almost equal: ====================================================================== FAIL: check_simple_complex (scipy.linalg.decomp.test_decomp.test_cholesky) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/linalg/tests/ test_decomp.py", line 250, in check_simple_complex assert_array_almost_equal(cholesky(a),c) File "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line 592, in assert_array_almost_equal assert alltrue(ravel(reduced)),\ AssertionError: Arrays are not almost equal: ====================================================================== FAIL: check_cdf (scipy.stats.distributions.test_distributions.test_arcsine) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 10, in check_cdf AssertionError: D = 0.299163544178; pval = 0.00353653914938; alpha = 0.01 args = ()

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ANN: MayaVi-1.3 released
by Prabhu Ramachandran Nov. 18, 2003

Nov. 18, 2003

Hi, This is to announce the availability of the MayaVi Data Visualizer version 1.3. MayaVi is a free, easy to use, scientific data visualizer. It is written in Python and uses the Visualization Toolkit (VTK) for the graphics. It provides a GUI written using Tkinter. MayaVi is free and distributed under a BSD license. It is also cross platform and should run on any platform where both Python and VTK are available. For more information, sources, binaries, screenshots, installation instructions, documentation etc. visit the MayaVi home page at: http://mayavi.sourceforge.net Also bundled with MayaVi is a VTK pipeline browser written in Python and a utility module that makes using VTK easier from the Python interpreter. New in this release: * New Modules: - Volume: Volume visualization using either texture or ray cast mappers. A useful GUI color transfer function editor is also built-in. - Glyph: Generic glyphs for scalars and vectors. - BandedSurfaceMap: Display banded contours of input data. - Labels: Automatic labeling of data used in other modules. - Text: Display 2D text strings. * New Filters: - ExtractGrid: Select part of a grid or subsample it. - StructuredPointsProbe: Probes any input data onto a structured points grid so the data can be used for Volume visualization. - Delaunay3D/Delaunay2D: Triangulate input point data. - UserDefined: Manage any user specified VTK filter. - CutPlane: Cut through any input dataset with a plane. * Support for VTK's new XML based files and for EnSight case files (EnSight6 and EnSightGold formats are supported). * Improved VectorCutPlane and VelocityVector so you can use a 3D arrow and any of the standard 2D glyphs. * The 'imv' module is now part of the mayavi.tools package. imv is a simple MayaVi based module that provides Matlab like one liners to view 2D surfaces and arrays from the Python interpreter. * Support to save rendered scene to vector EPS/PS/PDF or save the text to TeX output using GL2PS. Requires VTK to be built with GL2PS support (the MayaVi binaries support this). Also added support for exporting to a Wavefront OBJ file. * Support to save the stereo rendering options, the lookup table settings and the lighting as defaults. * Default lookup tables have better contrast. 28 user contributed lookup tables are also included in the sources. Any lookup table can be reversed. * Improved vtkPipeline modules: - ConfigVtkObj: Separated functionality of the ConfigVtkObj class into a separate ConfigVtkObjFrame and a driver class. More options to generate GUI's automatically. - VtkPickler: Can save/load state from a dictionary. * Fixes for Python-2.3 and Tk-8.4 related changes. * Fixes for the Mac OS X. * Many other fixes and improvements. Acknowledgements: Many thanks to the following folks. - Gerard Gorman: initial volume module with GUI CTF editor. - Axel Steuwer: initial Delaunay3D filter. - Richard Boardman: patch for OBJ export. - Fernando Perez and Arnd Baecker: user contributed lookup tables. - P. N. Badri Narayanan: Win32 VTK DLL's. - Thanks also to others who reported bugs and sent in bug fixes. Have fun! prabhu

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scipy.test()FAILED(failures=8, errors=2)
by Nils Wagner Nov. 18, 2003

Nov. 18, 2003

Hi all, This is the result of scipy.test() when using Python 2.3+ (#1, Sep 23 2003, 23:07:16) [GCC 3.3.1 (SuSE Linux)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> scipy.__version__ '0.2.1_249.4433' >>> Numeric.__version__ '23.1' ====================================================================== ERROR: check_data (scipy.stats.morestats.test_morestats.test_binom_test) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/stats/tests/ test_morestats.py", line 101, in check_data pval = stats.binom_test(100,250) File "/usr/lib/python2.3/site-packages/scipy/stats/morestats.py", line 683, in binom_test d = distributions.binom.pdf(x,n,p) AttributeError: binom_gen instance has no attribute 'pdf' ====================================================================== ERROR: check_pdf (scipy.stats.distributions.test_distributions.test_randint) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/stats/tests/ test_distributions.py", line 91, in check_pdf vals = stats.randint.pdf(k,5,30) AttributeError: randint_gen instance has no attribute 'pdf' ====================================================================== FAIL: check_simple (scipy.linalg.fblas.test_fblas.test_sgemv) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/linalg/tests/test_fblas.py", line 315, in check_simple assert(allclose(desired_y,y)) AssertionError ====================================================================== FAIL: check_random_complex (scipy.linalg.decomp.test_decomp.test_cholesky) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/linalg/tests/ test_decomp.py", line 276, in check_random_complex assert_array_almost_equal(cholesky(a),c) File "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line 592, in assert_array_almost_equal assert alltrue(ravel(reduced)),\ AssertionError: Arrays are not almost equal: ====================================================================== FAIL: check_simple_complex (scipy.linalg.decomp.test_decomp.test_cholesky) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/linalg/tests/ test_decomp.py", line 250, in check_simple_complex assert_array_almost_equal(cholesky(a),c) File "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line 592, in assert_array_almost_equal assert alltrue(ravel(reduced)),\ AssertionError: Arrays are not almost equal: ====================================================================== FAIL: check_sph_in (scipy.special.basic.test_basic.test_sph_in) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/special/tests/ test_basic.py", line 1939, in check_sph_in assert_array_almost_equal(i1n[0],array([1.00668001,0.06693370]),8) File "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line 592, in assert_array_almost_equal assert alltrue(ravel(reduced)),\ AssertionError: Arrays are not almost equal: ====================================================================== FAIL: check_sph_jn (scipy.special.basic.test_basic.test_sph_jn) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/special/tests/ test_basic.py", line 1955, in check_sph_jn assert_almost_equal(s1,0.0059615249,8) File "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line 536, in assert_almost_equal assert round(abs(desired - actual),decimal) == 0, msg AssertionError: Items are not equal: DESIRED: 0.0059615249 ACTUAL: 0.0 ====================================================================== FAIL: check_sph_kn (scipy.special.basic.test_basic.test_sph_kn) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/special/tests/ test_basic.py", line 1972, in check_sph_kn assert_array_almost_equal(kn[0],array([ 6.43029630, 38.5817778]),8) File "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line 592, in assert_array_almost_equal assert alltrue(ravel(reduced)),\ AssertionError: Arrays are not almost equal: ====================================================================== FAIL: check_cdf (scipy.stats.distributions.test_distributions.test_foldnorm) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 10, in check_cdf AssertionError: D = 0.312293158009; pval = 0.00212607354437; alpha = 0.01 args = (1.3275833471460694,) ====================================================================== FAIL: check_cdf (scipy.stats.distributions.test_distributions.test_nct) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 10, in check_cdf AssertionError: D = 0.434285651463; pval = 5.80078147339e-06; alpha = 0.01 args = (1.7513774539410023, 1.3175489373516882) ---------------------------------------------------------------------- Ran 1028 tests in 2.690s FAILED (failures=8, errors=2) <unittest.TextTestRunner object at 0x429c6acc>

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[SciPy-dev] scipy.test() FAILED (failures=6, errors=8) in latest cvs
by Nils Wagner Nov. 18, 2003

Nov. 18, 2003

Just a short report of scipy.test() with latest cvs Nils >>> scipy.__version__ '0.2.1_249.4430' >>> Numeric.__version__ '23.1' Python 2.1.2 (#1, Feb 25 2002, 18:04:21) [GCC 2.95.3 20010315 (SuSE)] on linux2 Type "copyright", "credits" or "license" for more information. ====================================================================== ERROR: check_cdf (scipy.stats.distributions.test_distributions.test_fatiguelife) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 5, in check_cdf File "/usr/local/lib/python2.1/site-packages/scipy/stats/stats.py", line 1521, in kstest vals = sb.sort(rvs(*args,**kwds)) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 432, in rvs vals = reshape(self._rvs(*args),size) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 1195, in _rvs z = norm(size=self._size) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 761, in __call__ raise ValueError ValueError ====================================================================== ERROR: check_cdf (scipy.stats.distributions.test_distributions.test_foldnorm) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 5, in check_cdf File "/usr/local/lib/python2.1/site-packages/scipy/stats/stats.py", line 1521, in kstest vals = sb.sort(rvs(*args,**kwds)) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 432, in rvs vals = reshape(self._rvs(*args),size) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 1274, in _rvs return abs(norm(mu=c,size=self._size)) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 761, in __call__ raise ValueError ValueError ====================================================================== ERROR: check_cdf (scipy.stats.distributions.test_distributions.test_gilbrat) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 5, in check_cdf File "/usr/local/lib/python2.1/site-packages/scipy/stats/stats.py", line 1521, in kstest vals = sb.sort(rvs(*args,**kwds)) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 432, in rvs vals = reshape(self._rvs(*args),size) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 1738, in _rvs return lognorm_gen._rvs(self, 1.0) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 1718, in _rvs return exp(s * norm(size=self._size)) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 761, in __call__ raise ValueError ValueError ====================================================================== ERROR: check_cdf (scipy.stats.distributions.test_distributions.test_halfnorm) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 5, in check_cdf File "/usr/local/lib/python2.1/site-packages/scipy/stats/stats.py", line 1521, in kstest vals = sb.sort(rvs(*args,**kwds)) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 432, in rvs vals = reshape(self._rvs(*args),size) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 1540, in _rvs return abs(norm(size=self._size)) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 761, in __call__ raise ValueError ValueError ====================================================================== ERROR: check_cdf (scipy.stats.distributions.test_distributions.test_lognorm) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 5, in check_cdf File "/usr/local/lib/python2.1/site-packages/scipy/stats/stats.py", line 1521, in kstest vals = sb.sort(rvs(*args,**kwds)) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 432, in rvs vals = reshape(self._rvs(*args),size) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 1718, in _rvs return exp(s * norm(size=self._size)) File "/usr/local/lib/python2.1/site-packages/scipy/stats/distributions.py", line 761, in __call__ raise ValueError ValueError ====================================================================== ERROR: check_linear_constant (scipy.interpolate.fitpack.test_fitpack.test_LSQBivariateSpline) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.1/site-packages/scipy/interpolate/tests/test_fitpack.py", line 52, in check_linear_constant lut = LSQBivariateSpline(x,y,z,tx,ty,kx=1,ky=1) File "/usr/local/lib/python2.1/site-packages/scipy/interpolate/fitpack2.py", line 399, in __init__ kx,ky,eps,lwrk2=1) error: (len(y)==m) failed for 3rd argument z ====================================================================== ERROR: check_linear_1d (scipy.interpolate.fitpack.test_fitpack.test_SmoothBivariateSpline) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.1/site-packages/scipy/interpolate/tests/test_fitpack.py", line 72, in check_linear_1d lut = SmoothBivariateSpline(x,y,z,kx=1,ky=1) File "/usr/local/lib/python2.1/site-packages/scipy/interpolate/fitpack2.py", line 356, in __init__ kx,ky,s=s,eps=eps,lwrk2=1) error: (len(y)==m) failed for 3rd argument z ====================================================================== ERROR: check_linear_constant (scipy.interpolate.fitpack.test_fitpack.test_SmoothBivariateSpline) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.1/site-packages/scipy/interpolate/tests/test_fitpack.py", line 62, in check_linear_constant lut = SmoothBivariateSpline(x,y,z,kx=1,ky=1) File "/usr/local/lib/python2.1/site-packages/scipy/interpolate/fitpack2.py", line 356, in __init__ kx,ky,s=s,eps=eps,lwrk2=1) error: (len(y)==m) failed for 3rd argument z ====================================================================== FAIL: check_cdf (scipy.stats.distributions.test_distributions.test_nct) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 10, in check_cdf AssertionError: D = 0.62956452799; pval = 2.42827979946e-12; alpha = 0.01 args = (1.0156077768803375, 1.3891921950688992) ====================================================================== FAIL: check_pro_ang1_cv (scipy.special.cephes.test_cephes.test_cephes) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.1/site-packages/scipy/special/tests/test_cephes.py", line 355, in check_pro_ang1_cv assert_equal(cephes.pro_ang1_cv(1,1,1,1,0),(1.0,0.0)) File "/usr/local/lib/python2.1/site-packages/scipy_test/testing.py", line 519, in assert_equal assert desired == actual, msg AssertionError: Items are not equal: DESIRED: (1.0, 0.0) ACTUAL: (0.99999999999999989, 0.0) ====================================================================== FAIL: check_pro_ang1_cv (scipy.special.basic.test_basic.test_cephes) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.1/site-packages/scipy/special/tests/test_basic.py", line 384, in check_pro_ang1_cv assert_equal(cephes.pro_ang1_cv(1,1,1,1,0),(1.0,0.0)) File "/usr/local/lib/python2.1/site-packages/scipy_test/testing.py", line 519, in assert_equal assert desired == actual, msg AssertionError: Items are not equal: DESIRED: (1.0, 0.0) ACTUAL: (0.99999999999999989, 0.0) ====================================================================== FAIL: check_sph_in (scipy.special.basic.test_basic.test_sph_in) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.1/site-packages/scipy/special/tests/test_basic.py", line 1939, in check_sph_in assert_array_almost_equal(i1n[0],array([1.00668001,0.06693370]),8) File "/usr/local/lib/python2.1/site-packages/scipy_test/testing.py", line 592, in assert_array_almost_equal assert alltrue(ravel(reduced)),\ AssertionError: Arrays are not almost equal: ====================================================================== FAIL: check_sph_jn (scipy.special.basic.test_basic.test_sph_jn) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.1/site-packages/scipy/special/tests/test_basic.py", line 1955, in check_sph_jn assert_almost_equal(s1,0.0059615249,8) File "/usr/local/lib/python2.1/site-packages/scipy_test/testing.py", line 536, in assert_almost_equal assert round(abs(desired - actual),decimal) == 0, msg AssertionError: Items are not equal: DESIRED: 0.0059615249 ACTUAL: 0.0 ====================================================================== FAIL: check_sph_kn (scipy.special.basic.test_basic.test_sph_kn) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.1/site-packages/scipy/special/tests/test_basic.py", line 1972, in check_sph_kn assert_array_almost_equal(kn[0],array([ 6.43029630, 38.5817778]),8) File "/usr/local/lib/python2.1/site-packages/scipy_test/testing.py", line 592, in assert_array_almost_equal assert alltrue(ravel(reduced)),\ AssertionError: Arrays are not almost equal: ---------------------------------------------------------------------- Ran 959 tests in 3.447s FAILED (failures=6, errors=8) <unittest.TextTestRunner instance at 0x8b80ed4>

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From NASTRAN to MATLAB to Scipy [Fwd: loadop4/saveop4]
by Nils Wagner Nov. 17, 2003

Nov. 17, 2003

Dear experts, I was looking for a NASTRAN/MATLAB interface. The result of my inquiry is enclosed. Maybe Scipy can use this interface as well. Any comments or suggestions ? Nils

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Strange import-related bug caused by scipy
by Fernando Perez Nov. 15, 2003

Nov. 15, 2003

Here's how to reproduce it. Start with two very simple files: planck[import]> cat one.py from weave import inline,converters planck[import]> cat two.py import scipy import one Here's what happens if you execfile() these: planck[import]> python Python 2.2.2 (#1, Feb 24 2003, 19:13:11) [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-4)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> execfile("one.py") >>> execfile("two.py") Traceback (most recent call last): File "<stdin>", line 1, in ? File "two.py", line 3, in ? import one File "one.py", line 1, in ? from weave import inline,converters ImportError: cannot import name converters Now, the funny thing is that if you reverse the order of the imports in two.py and put 'import scipy' _last_, then there's no problem. Somehow, the games scipy plays with the import mechanism are breaking something. For the time being, I've resorted to putting my 'import scipy' statements last in my code. Best, f.

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Bug in F-distribution
by Robert Kern Nov. 3, 2003

Nov. 3, 2003

In answering a SciPy question on c.l.py, I noticed that there's a bug in the PPF of the F-distribution. from scipy.stats.distributions import f x1 = 4.26 Fx1 = f.cdf(x1, 2, 9) x2 = f.ppf(Fx1, 2, 9) x3 = f.ppf(1.0-Fx1, 2, 9) # x1 is not even close to x2 # but x3 is -- Robert Kern kern(a)ugcs.caltech.edu "In the fields of Hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter

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