Mailman 3 February 2010 - SciPy-Dev

0.8 release date?
by Warren Weckesser Feb. 23, 2010

Feb. 23, 2010

Is there currently a target date (even a tentative one) for the release of 0.8? Warren

9 12

Reg: google summer of code 2010
by Mohit Goyal Feb. 22, 2010

Feb. 22, 2010

I am a masters student doing research in data engineering. I know python and have done projects on data mining and web mining past 3 years. I want to contribute to scipy via gsoc 2010. I am interested in working on data related projects in scipy like improving data sources and integrate it into all the numpy/scipy , adding data sets and examples to scipy, data analysis etc. Somebody suggest how to proceed or info about the concerned persons. Thank You. -- The Game is Not Over Because i haven't Won Yet. -Mohit Goyal

2 1

Scipy meets pychecker
by Arkapravo Bhaumik Feb. 22, 2010

Feb. 22, 2010

Dear Friends *Has anyone tried to 'test' scipy using pychecker ?* What results have you got ? Please reply, preferably with examples etc. Much appreciated Regards Arkapravo

1 0

Segfault on OS X 10.6.2/Py-2.6.4 with SciPy FFT tests
by Tom Loredo Feb. 22, 2010

Feb. 22, 2010

Hi folks- I'm trying to install NumPy & SciPy on 10.6.2 (Snow Leopard) with 64-bit Python 2.6.4 (a new framework build, not Apple's 2.6.1). I've built FFTW and AMD/UMFPACK and they pass their respective tests. NumPy-1.4.0 builds fine and passes all tests (except for 3 Knowns and 1 Skip). I've verified it's finding FFTW & AMD/UMF. SciPy-0.7.1 builds fine and imports without issue, but quickly into the tests has several failures & then a segfault crash. I tried installing a recent SVN SciPy (0.8.0.dev6220) but it crashes with a similar segfault. In both cases it's during the FFT tests. I removed both packages from site-packages and re-installed, this time having removed FFTW (verifying no fftw lib was found), and again there is a crash in the FFT tests, presumably pointing to a problem with numpy/scipy rather than FFTW. I've copied below the tail end of the output from scipy.test(verbose=10) from both SciPy versions (without FFTW). There's an indication that an object is being modified after its memory is freed. I haven't done malloc-level debugging so I'm not sure how to help at this point. If anyone can have a look or provide more explicit pointers, I'd be grateful! Thanks, Tom ~~~~~~~~~~~~ scipy-0.7.1: test_definition (test_basic.TestFft) ... ok test_djbfft (test_basic.TestFft) ... ok test_n_argument_real (test_basic.TestFft) ... ok test_axes_argument (test_basic.TestFftn) ... ok test_definition (test_basic.TestFftn) ... ok test_shape_argument (test_basic.TestFftn) ... ok test_shape_argument_more (test_basic.TestFftn) ... ok test_shape_axes_argument (test_basic.TestFftn) ... ok test_shape_axes_argument2 (test_basic.TestFftn) ... ok test_definition (test_basic.TestIfft) ... FAIL test_djbfft (test_basic.TestIfft) ... FAIL test_random_complex (test_basic.TestIfft) ... FAIL test_random_real (test_basic.TestIfft) ... Python(15804,0x7fff7065dbe0) malloc: *** error for object 0x105376448: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap ~~~~~~~~~~~~ scipy-0.8.0.dev6220 test_definition (test_basic.TestDoubleFFT) ... ok test_djbfft (test_basic.TestDoubleFFT) ... ok test_n_argument_real (test_basic.TestDoubleFFT) ... ok test_definition (test_basic.TestDoubleIFFT) ... Python(29515,0x7fff7065dbe0) malloc: *** error for object 0x1012fbf28: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

1 0

Latex and docstrings
by David Cournapeau Feb. 19, 2010

Feb. 19, 2010

Hi, I noticed that some of the docstrings I have written for DCT have been changed to latex format. While I have no issue with having latex in the documentation, I thought the consensus was to use them sparingly in docstrings ? For example, the dct I formula used to be (fixed width font assumed): for 0 <= k < N, N-1 y[k] = x[0] + (-1)**k x[N-1] + 2 * sum x[n]*cos(pi*k*n/(N-1)) n=0 But now, it is: y_k = x_0 + (-1)^k x_{N-1} + 2\\sum_{n=1}^{N-2} x_n \\cos\\left({\\pi nk\\over N-1}\\right), \\qquad 0 \\le k < N. I much prefer the former (the latter is unreadable in a terminal IMO). I have of course no issue in putting the latex formula in the scipy docs, thanks, David

11 24

New scipy.test() errors in trunk
by Nils Wagner Feb. 19, 2010

Feb. 19, 2010

====================================================================== ERROR: Regression test for #880: empty array for zi crashes. ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/tests/test_signaltools.py", line 458, in test_empty_zi y, zf = lfilter(b, a, x, zi=zi) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/signaltools.py", line 603, in lfilter return sigtools._linear_filter(b, a, x, axis, zi) NotImplementedError: input type 'object' not supported ====================================================================== ERROR: test_rank1 (test_signaltools.TestLinearFilterDecimal) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/tests/test_signaltools.py", line 360, in test_rank1 assert_array_almost_equal(lfilter(b, a, x), y_r) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/signaltools.py", line 601, in lfilter return sigtools._linear_filter(b, a, x, axis) NotImplementedError: input type 'object' not supported ====================================================================== ERROR: test_rank2 (test_signaltools.TestLinearFilterDecimal) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/tests/test_signaltools.py", line 401, in test_rank2 y = lfilter(b, a, x, axis = 0) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/signaltools.py", line 601, in lfilter return sigtools._linear_filter(b, a, x, axis) NotImplementedError: input type 'object' not supported ====================================================================== ERROR: test_rank2_init_cond_a0 (test_signaltools.TestLinearFilterDecimal) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/tests/test_signaltools.py", line 435, in test_rank2_init_cond_a0 y, zf = lfilter(b, a, x, axis = 0, zi = np.ones((1, 3))) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/signaltools.py", line 603, in lfilter return sigtools._linear_filter(b, a, x, axis, zi) NotImplementedError: input type 'object' not supported ====================================================================== ERROR: test_rank2_init_cond_a1 (test_signaltools.TestLinearFilterDecimal) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/tests/test_signaltools.py", line 419, in test_rank2_init_cond_a1 y, zf = lfilter(b, a, x, axis = 1, zi = np.ones((4, 1))) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/signaltools.py", line 603, in lfilter return sigtools._linear_filter(b, a, x, axis, zi) NotImplementedError: input type 'object' not supported ====================================================================== ERROR: test_rank3 (test_signaltools.TestLinearFilterDecimal) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/tests/test_signaltools.py", line 447, in test_rank3 y = lfilter(b, a, x) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/signal/signaltools.py", line 601, in lfilter return sigtools._linear_filter(b, a, x, axis) NotImplementedError: input type 'object' not supported ====================================================================== ERROR: test_mpmath.test_hyp2f1_real_some ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/special/tests/test_mpmath.py", line 117, in test_hyp2f1_real_some except (TypeError, mpmath.libhyper.NoConvergence): AttributeError: 'module' object has no attribute 'libhyper' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.bernoulli_gen object at 0x2636ad0>, (0.29999999999999999,), array([0, 0, 0, ..., 1, 0, 0]), 0.01, 'bernoulli chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.binom_gen object at 0x26368d0>, (5, 0.40000000000000002), array([2, 2, 2, ..., 4, 1, 3]), 0.01, 'binom chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.boltzmann_gen object at 0x26ec590>, (1.3999999999999999, 19), array([0, 0, 0, ..., 2, 0, 0]), 0.01, 'boltzmann chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.dlaplace_gen object at 0x26eca50>, (0.80000000000000004,), array([ 0, 0, 0, ..., 4, -1, 0]), 0.01, 'dlaplace chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.geom_gen object at 0x2636dd0>, (0.5,), array([1, 1, 2, ..., 6, 1, 2]), 0.01, 'geom chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.hypergeom_gen object at 0x2636f50>, (30, 12, 6), array([1, 1, 4, ..., 3, 2, 2]), 0.01, 'hypergeom chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.hypergeom_gen object at 0x2636f50>, (21, 3, 12), array([2, 3, 2, ..., 2, 2, 1]), 0.01, 'hypergeom chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.hypergeom_gen object at 0x2636f50>, (21, 18, 11), array([ 9, 8, 9, ..., 10, 10, 10]), 0.01, 'hypergeom chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.logser_gen object at 0x26ec110>, (0.59999999999999998,), array([1, 1, 1, ..., 1, 1, 4]), 0.01, 'logser chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.nbinom_gen object at 0x2636c50>, (5, 0.5), array([0, 2, 6, ..., 3, 3, 3]), 0.01, 'nbinom chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.nbinom_gen object at 0x2636c50>, (0.40000000000000002, 0.40000000000000002), array([0, 0, 0, ..., 0, 0, 0]), 0.01, 'nbinom chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.planck_gen object at 0x26ec410>, (0.51000000000000001,), array([1, 1, 1, ..., 7, 0, 2]), 0.01, 'planck chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.poisson_gen object at 0x26ec290>, (0.59999999999999998,), array([0, 0, 0, ..., 1, 0, 0]), 0.01, 'poisson chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.randint_gen object at 0x26ec710>, (7, 31), array([27, 10, 15, ..., 16, 9, 17]), 0.01, 'randint chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.skellam_gen object at 0x26ecbd0>, (15, 8), array([ 4, 6, 10, ..., 5, 14, 15]), 0.01, 'skellam chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== ERROR: test_discrete_basic.test_discrete_basic(<scipy.stats.distributions.zipf_gen object at 0x26ec8d0>, (4,), array([1, 1, 1, ..., 1, 1, 1]), 0.01, 'zipf chisquare') ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/stats/tests/test_discrete_basic.py", line 252, in check_discrete_chisquare freq,hsupp = np.histogram(rvs,histsupp,new=True) TypeError: histogram() got an unexpected keyword argument 'new' ====================================================================== FAIL: test_lambertw.test_values ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/special/tests/test_lambertw.py", line 80, in test_values FuncData(w, data, (0,1), 2, rtol=1e-10, atol=1e-13).check() File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/special/tests/testutils.py", line 187, in check assert False, "\n".join(msg) AssertionError: Max |adiff|: 1.77636e-15 Max |rdiff|: 2.06237e-16 Bad results for the following points (in output 0): (-0.40000000000000002+0.40000000000000002j) 0j => (nan+nan*j) != (-0.10396515323290657+0.61899273315171632j) (rdiff 0.0) (-0.44800000000000001+0.40000000000000002j) 0j => (nan+nan*j) != (-0.11855133765652383+0.66570534313583418j) (rdiff 0.0) (-0.44800000000000001-0.40000000000000002j) 0j => (nan+nan*j) != (-0.11855133765652383-0.66570534313583418j) (rdiff 0.0) ====================================================================== FAIL: test_mpmath.test_hyp2f1_some_points_2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/numpy/testing/decorators.py", line 146, in skipper_func return f(*args, **kwargs) File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/special/tests/test_mpmath.py", line 106, in test_hyp2f1_some_points_2 FuncData(sc.hyp2f1, dataset, (0,1,2,3), 4, rtol=1e-10).check() File "/home/nwagner/local/lib64/python2.6/site-packages/scipy/special/tests/testutils.py", line 187, in check assert False, "\n".join(msg) AssertionError: Max |adiff|: 1.48367e-22 Max |rdiff|: 0.989172 Bad results for the following points (in output 0): 112.0 5.0999999999999996 -0.90000000000000002 -0.99999000000000005 => -1.6241361047970947e-24 != -1.499910195656332e-22 (rdiff 0.98917177768708742) ---------------------------------------------------------------------- Ran 4332 tests in 76.236s FAILED (KNOWNFAIL=11, SKIP=17, errors=24, failures=2) <nose.result.TextTestResult run=4332 errors=24 failures=2>

2 3

Best interface for computing the logarithm of the determinant?
by Nathaniel Smith Feb. 19, 2010

Feb. 19, 2010

So when you have a matrix whose determinant you want, it's often wise to compute the logarithm of the determinant instead of the determinant itself, because determinants involve lots and lots of multiplications and the result might otherwise underflow/overflow. Therefore, in scikits.sparse, I'd like to provide an API for doing this (and this is well-supported by the underlying libraries). But the problem is that for a general matrix, the determinant may be zero or negative. Obviously we can deal with this, but what's the best API? I'd like to use one consistently across the different factorizations in scikits.sparse, and perhaps eventually in numpy as well. Some options: 1) Split off the sign into a separate return value ('sign' may be 1, -1, 0): sign, value = logdet(A) actual_determinant = sign * exp(value) 2) Allow complex/infinite return values, even when A is a real matrix: logdet(eye(3)) == pi*1j logdet(zeros((3, 3))) == -Inf 3) "Scientific notation" (This is what UMFPACK's API does): return a mantissa and base-10 exponent: mantissa, exponent = logdet(A) actual_determinant = mantissa * 10 ** exponent 4) Have separate functions for computing the sign, and the log of the absolute value (This is what GSL does, though it seems pointlessly inefficient): sign = sgndet(A) value = logdet(A) actual_determinant = sign * exp(value) These are all kind of ugly looking, unfortunately, but that seems unavoidable, unless someone has a clever idea. Any preferences? -- Nathaniel

5 9

Mail Delivery (failure scipy-dev@scipy.org)
by oliphant＠ee.byu.edu Feb. 19, 2010

Feb. 19, 2010

1 0

Build error for scipy
by Far McKon Feb. 18, 2010

Feb. 18, 2010

Hey, I'm working on a MacBookPro, and trying to get scipy an numpy happy. I am working from instructions at : http://www.scipy.org/Installing_SciPy/Mac_OS_X I just 'setup.py' built and installed numpy, no problems. When try to build scipy via 'sudo setup.py build" I get the error stream below. I checked, and indeed, the file 'npymath.ini' does not exist on my machine. Help? What went wrong? Do I have to do some werid comfig change and rebuild numpy? thanks in advance for any help, - Far McKon == Error Stream ===== Warning: No configuration returned, assuming unavailable. blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers'] lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3'] umfpack_info: libraries umfpack not found in /System/Library/Frameworks/Python.framework/Versions/2.5/lib libraries umfpack not found in /usr/local/lib libraries umfpack not found in /usr/lib libraries umfpack not found in /opt/local/lib libraries umfpack not found in /sw/lib /Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/system_info.py:452: UserWarning: UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/) not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [umfpack]) or by setting the UMFPACK environment variable. warnings.warn(self.notfounderror.__doc__) NOT AVAILABLE Traceback (most recent call last): File "setup.py", line 160, in <module> setup_package() File "setup.py", line 152, in setup_package configuration=configuration ) File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 118, in configuration config.add_subpackage('scipy') File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/misc_util.py", line 957, in add_subpackage caller_level = 2) File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/misc_util.py", line 926, in get_subpackage caller_level = caller_level + 1) File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/misc_util.py", line 863, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 20, in configuration config.add_subpackage('special') File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/misc_util.py", line 957, in add_subpackage caller_level = 2) File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/misc_util.py", line 926, in get_subpackage caller_level = caller_level + 1) File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/misc_util.py", line 863, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/special/setup.py", line 45, in configuration extra_info=get_info("npymath") File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/misc_util.py", line 2068, in get_info pkg_info = get_pkg_info(pkgname, dirs) File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/misc_util.py", line 2020, in get_pkg_info return read_config(pkgname, dirs) File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/npy_pkg_config.py", line 343, in read_config v = _read_config_imp(pkg_to_filename(pkgname), dirs) File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/npy_pkg_config.py", line 317, in _read_config_imp meta, vars, sections, reqs = _read_config(filenames) File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/npy_pkg_config.py", line 301, in _read_config meta, vars, sections, reqs = parse_config(f, dirs) File "/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/distutils/npy_pkg_config.py", line 273, in parse_config raise PkgNotFound("Could not find file(s) %s" % str(filenames)) numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/Library/Python/2.5/site-packages/numpy-1.4.0-py2.5-macosx-10.5-i386.egg/numpy/core/lib/npy-pkg-config/npymath.ini']

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maxentropy docs / parent class methods
by Skipper Seabold Feb. 18, 2010

Feb. 18, 2010

The docs on the methods for the maxentropy model class that are inherited from basemodel are not picked up by sphinx. It seems that most of the .rst files explicitly list the methods, but since basemodel is not intended to be public (and some subclasses overwrite the parent class methods), is there a better way than to start listing the basemodel methods? I started to make the changes, but I don't think this is the right way forward. Other thoughts? http://docs.scipy.org/scipy/docs/scipy-docs/maxentropy.rst/ Cheers, Skipper

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