Mailman 3 October 2005 - SciPy-Dev

newscipy
by Nils Wagner Oct. 26, 2005

Oct. 26, 2005

Hi all, How can I obtain information about the installed version of newscipy ? >>> scipy.base.__version__ '0.4.3.1354' yields the current version of newcore. Nils

2 2

Building newcore on the Itanium
by Andrew D Oct. 25, 2005

Oct. 25, 2005

Hi, I have been trying compiling the lastest scipy "newcore" on an intel itanium machine with Redhat Linux. On the latest svn code (updated today, 1pm) the command "python setup.py build" gives the output documented at http://agenda.ms11.net/code/itanium_build.log In particular it stopps trying to link with the command: error: Command "f77 -L/home/phillips/faculty/dandrew/usr/lib build/temp.linux-ia64-2.3/scipy/corelib/lapack_lite/lapack_litemodule.o -L/home/phillips/faculty/dandrew/usr/lib/ -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-ia64-2.3/scipy/lib/lapack_lite.so" failed with exit status 1 Also, when I do not have the path set for ATLAS to be found the build fails at: error: Command "f77 -L/home/phillips/faculty/dandrew/usr/lib build/temp.linux-ia64-2.3/scipy/corelib/blasdot/_dotblas.o -L/usr/lib -lblas -lg2c -o build/lib.linux-ia64-2.3/scipy/lib/_dotblas.so" failed with exit status 1 Upon manually linking with the command: "g77 -shared ..." newcore then builds and installs. [When using the intel compilers (ifort,icc) extra flags are required to link. However the building process ignores the flags put in the scipy/distutils/fcompiler/intel.py file. AND THE LINKING IS DONE WITH THE GCC COMPILER (see the logfile). To sucessfully build with the intel compiler, all libraries must be manually linked with the commands: "icc -i_dynamic -lirc -pthread -shared ..." "ifort -i_dynamic -lirc -pthread -shared ..." Build log: http://agenda.ms11.net/code/itanium_build_icc.log ] The tests run sucessfully: >>from scipy import * >>test(10,10) . . ---------------------------------------------------------------------- Ran 138 tests in 1.942s OK I have not tried to compile newscipy due to the linking problems. Too much manual linking.. Andrew Computer information: ~>cat /proc/cpuinfo processor : 0 vendor : GenuineIntel arch : IA-64 family : Itanium 2 model : 1 revision : 5 archrev : 0 features : branchlong cpu number : 0 cpu regs : 4 cpu MHz : 1300.000000 itc MHz : 1300.000000 BogoMIPS : 1946.15 [repeated 4 times, it's a 4-cpu box] ~>free total used free shared buffers cached Mem: 24779536 13069312 11710224 0 808784 10497376 -/+ buffers/cache: 1763152 23016384 Swap: 51477632 960 51476672 ~>cat /etc/issue Red Hat Enterprise Linux AS release 3 (Taroon Update 6) ~>gcc -v Reading specs from /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/specs Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --host=ia64-redhat-linux Thread model: posix gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-53) ->python Python 2.3 (#2, Oct 31 2003, 11:54:00) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-20)] on linux2 __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com

1 0

array dtypechar wrong or not
by Pearu Peterson Oct. 25, 2005

Oct. 25, 2005

Hi, Note that In [142]: array(array([1,2],dtype='I'),dtype='L').dtypechar Out[142]: 'I' In [143]: array(array([1,2],dtype='L'),dtype='I').dtypechar Out[143]: 'L' I have expected 'L' and 'I', respectively. It this a bug? Pearu

2 5

test results
by Darren Dale Oct. 25, 2005

Oct. 25, 2005

I just updated from svn, and get the following message when I import: from scipy import * Importing io to scipy Importing special to scipy Importing fftpack to scipy Importing cluster to scipy Importing sparse to scipy Importing signal to scipy Failed to import signal cannot import name comb Importing utils to scipy Importing interpolate to scipy Importing integrate to scipy Importing optimize to scipy Importing linalg to scipy Here are my test results. My system is a P4, gentoo linux with fftw-2.1.5, blas/lapack/atlas version 3.6, and gcc-3.4.4. The last three errors are caused by signbit returning False for any number on my system, positive or negative. I have tested the libc signbit macro and it is working properly, though my example has to be compiled with ANSI C to gain access to the macro. Others here have not been able to reproduce this signbit error, and I am unsure how to proceed. Darren ====================================================================== ERROR: check_definition (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_diff) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 88, in check_definition assert_array_almost_equal(diff(sin(x)),direct_diff(sin(x))) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 48, in diff if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_expr (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_diff) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-pakages/scipy/fftpack/tests/test_pseudo_diffs.py", line 131, in check_expr d1 = diff(f) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 48, in diff if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_expr_large (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_diff) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 145, in check_expr_large assert_array_almost_equal(diff(f),df) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 48, in diff if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_int (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_diff) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 153, in check_int assert_array_almost_equal(diff(sin(x),-1),-cos(x)) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 48, in diff if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_period (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_diff) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 109, in check_period assert_array_almost_equal(diff(sin(2*pi*x),period=1), File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 48, in diff if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_random_even (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_diff) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 165, in check_random_even f = diff(diff(f,1),-1) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 48, in diff if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_random_odd (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_diff) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 177, in check_random_odd assert_array_almost_equal(diff(diff(f,k),-k),f) File "/usr/lib/python2.4/site-packages/scipy_test/testing.py", line 675, in assert_array_almost_equal reduced = ravel(equal(less_equal(around(abs(x-y),decimal),10.0**(-decimal)),1)) TypeError: unsupported operand type(s) for -: 'str' and 'float' ====================================================================== ERROR: check_sin (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_diff) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 117, in check_sin assert_array_almost_equal(diff(sin(x)),cos(x)) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 48, in diff if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_zero_nyquist (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_diff) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 187, in check_zero_nyquist f = diff(diff(f,1),-1) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 48, in diff if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_definition (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_hilbert) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 302, in check_definition y = hilbert(sin(x)) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 175, in hilbert if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_random_even (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_hilbert) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 333, in check_random_even f = diff(diff(f,1),-1) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 48, in diff if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_random_odd (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_hilbert) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 324, in check_random_odd assert_array_almost_equal(ihilbert(hilbert(f)),f) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 175, in hilbert if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_tilbert_relation (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_hilbert) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 312, in check_tilbert_relation y = hilbert(f) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 175, in hilbert if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_definition (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_ihilbert) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 371, in check_definition y = ihilbert(sin(x)) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 204, in ihilbert return -hilbert(x) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 175, in hilbert if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_itilbert_relation (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_ihilbert) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 381, in check_itilbert_relation y = ihilbert(f) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 204, in ihilbert return -hilbert(x) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 175, in hilbert if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_definition (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_itilbert) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 289, in check_definition y = itilbert(sin(x),h) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 136, in itilbert if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_definition (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_shift) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 393, in check_definition assert_array_almost_equal(shift(sin(x),a),direct_shift(sin(x),a)) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 404, in shift if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_definition (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_tilbert) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 228, in check_definition y = tilbert(sin(x),h) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 100, in tilbert if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_random_even (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_tilbert) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 243, in check_random_even assert_array_almost_equal(direct_tilbert(direct_itilbert(f,h),h),f) File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 61, in direct_itilbert w = 1j*tanh(w) AttributeError: 'float64_arrtype' object has no attribute 'tanh' ====================================================================== ERROR: check_random_odd (scipy.fftpack.pseudo_diffs.test_pseudo_diffs.test_tilbert) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_pseudo_diffs.py", line 252, in check_random_odd assert_array_almost_equal(itilbert(tilbert(f,h),h),f) File "/usr/lib/python2.4/site-packages/scipy/fftpack/pseudo_diffs.py", line 100, in tilbert if tmp.dtype in (scipy.Complex32, scipy.Complex64): NameError: global name 'scipy' is not defined ====================================================================== ERROR: check_djbfft (scipy.fftpack.basic.test_basic.test_irfft) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 361, in check_djbfft y1 = ifft2(x1) File "/usr/lib/python2.4/site-packages/Numeric/FFT/FFT.py", line 102, in inverse_fft a = Numeric.asarray(a).astype(Numeric.Complex) File "/usr/lib/python2.4/site-packages/Numeric/Numeric.py", line 134, in asarray return multiarray.array(a, typecode, copy=0, savespace=savespace) TypeError: only length-1 arrays can be converted to Python scalars ====================================================================== FAIL: check_definition (scipy.fftpack.basic.test_basic.test_fft) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 101, in check_definition assert_array_almost_equal(y,y1) File "/usr/lib/python2.4/site-packages/scipy/test/testing.py", line 727, in assert_array_almost_equal assert cond,\ AssertionError: Arrays are not almost equal (mismatch 100.0%): Array 1: [ 2.0000000e+01 +0.0000000e+00j 0.0000000e+00 +0.0000000e+00j -4.0000000e+00 +4.0000000e+00j 0.0000000e+00 +0.000... Array 2: [ 20. +3.j -0.7071068+0.7071068j -7. +4.j -0.7071068-0.7071068j -4. -3.j 0.707106... ====================================================================== FAIL: check_n_argument_complex (scipy.fftpack.basic.test_basic.test_fft) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 118, in check_n_argument_complex assert_array_almost_equal(y[0],direct_dft(x1)) File "/usr/lib/python2.4/site-packages/scipy/test/testing.py", line 727, in assert_array_almost_equal assert cond,\ AssertionError: Arrays are not almost equal (mismatch 100.0%): Array 1: [ 1.0000000e+01+0.j -2.0000000e+00+2.j -2.0000000e+00+0.j -2.0000000e+00-2.j] Array 2: [ 10.+1.j -3.+2.j -2.-1.j -1.-2.j] ====================================================================== FAIL: check_definition (scipy.fftpack.basic.test_basic.test_fftn) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 419, in check_definition assert_array_almost_equal(y,direct_dftn(x)) File "/usr/lib/python2.4/site-packages/scipy/test/testing.py", line 727, in assert_array_almost_equal assert cond,\ AssertionError: Arrays are not almost equal (mismatch 22.2222222222%): Array 1: [[ 4.5000000e+01+0.j -4.5000000e+00+2.5980762j -4.5000000e+00-2.5980762j] [ -1.3500000e+01+7.7942286j 0.0... Array 2: [[ 4.5000000e+01+0.j -4.5000000e+00+2.5980762j -4.5000000e+00-2.5980762j] [ -1.3500000e+01+0.j 0.0... ====================================================================== FAIL: check_definition (scipy.fftpack.basic.test_basic.test_ifft) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 184, in check_definition assert_array_almost_equal(y,y1) File "/usr/lib/python2.4/site-packages/scipy/test/testing.py", line 727, in assert_array_almost_equal assert cond,\ AssertionError: Arrays are not almost equal (mismatch 100.0%): Array 1: [ 2.5000000e+00 +0.0000000e+00j 0.0000000e+00 -0.0000000e+00j -5.0000000e-01 -5.0000000e-01j 0.0000000e+00 -0.000... Array 2: [ 2.5 +0.375j 0.0883883+0.0883883j -0.125 -0.5j 0.0883883-0.0883883j -0.5 -0.375j -0.0883883-0.0... ====================================================================== FAIL: check_random_real (scipy.fftpack.basic.test_basic.test_ifft) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 218, in check_random_real assert_array_almost_equal (ifft(fft(x)),x) File "/usr/lib/python2.4/site-packages/scipy/test/testing.py", line 727, in assert_array_almost_equal assert cond,\ AssertionError: Arrays are not almost equal (mismatch 98.0392156863%): Array 1: [ 2.7010335e-01 +0.0000000e+00j 1.5051924e-01 +1.9549653e-17j 3.9770871e-01 -4.2662293e-17j 5.5451658e-01 -5.476... Array 2: [ 0.2701033 0.0145507 0.5296276 0.2231588 0.6244757 0.1734576 0.4209751 0.6859024 0.888794 0.3217651 0.42293... ====================================================================== FAIL: check_definition (scipy.fftpack.basic.test_basic.test_ifftn) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 586, in check_definition assert_array_almost_equal(y,direct_idftn(x)) File "/usr/lib/python2.4/site-packages/scipy/test/testing.py", line 727, in assert_array_almost_equal assert cond,\ AssertionError: Arrays are not almost equal (mismatch 22.2222222222%): Array 1: [[ 5.0000000e+00+0.j -5.0000000e-01-0.2886751j -5.0000000e-01+0.2886751j] [ -1.5000000e+00-0.8660254j 0.0... Array 2: [[ 5.0000000e+00+0.j -5.0000000e-01-0.2886751j -5.0000000e-01+0.2886751j] [ -1.5000000e+00+0.j 0.0... ====================================================================== FAIL: check_definition (scipy.fftpack.basic.test_basic.test_irfft) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 338, in check_definition assert_array_almost_equal(y,ifft(x1)) File "/usr/lib/python2.4/site-packages/scipy/test/testing.py", line 727, in assert_array_almost_equal assert cond,\ AssertionError: Arrays are not almost equal (mismatch 50.0%): Array 1: [ 2.625 -1.6856602 -0.375 -1.1856602 0.625 0.4356602 -0.375 0.9356602] Array 2: [ 2.6250000e+00+0.j -3.7500000e-01-0.j -3.7500000e-01-0.j -3.7500000e-01-0.j 6.2500000e-01+0.j -3.7500000e-01+0.... ====================================================================== FAIL: check_generic (scipy.base.type_check.test_type_check.test_isneginf) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/base/tests/test_type_check.py", line 193, in check_generic assert(vals[0] == 1) AssertionError ====================================================================== FAIL: check_generic (scipy.base.type_check.test_type_check.test_isposinf) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/base/tests/test_type_check.py", line 186, in check_generic assert(vals[0] == 0) AssertionError ====================================================================== FAIL: check_generic (scipy.base.type_check.test_type_check.test_nan_to_num) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/base/tests/test_type_check.py", line 200, in check_generic assert_all(vals[0] < -1e10) and assert_all(isfinite(vals[0])) File "/usr/lib/python2.4/site-packages/scipy/base/tests/test_type_check.py", line 12, in assert_all assert(all(x)), x AssertionError: False ---------------------------------------------------------------------- Ran 550 tests in 1.718s FAILED (failures=10, errors=21)

2 1

Sparse matrix module
by Ed Schofield Oct. 25, 2005

Oct. 25, 2005

Robert Cimrman wrote: > Ed Schofield wrote: >> I wrote in the SVN change log: >> >> This is the beginning of a merge of Roman Geus's PySparse into scipy. >> The goals are to make it more 'Pythonic', integrate sparse matrix types >> into scipy so they act similarly to dense arrays, and to support more >> a few more sparse data types, particularly CSC, in a nice OO hierarchy. > > > Does this basically mean to make Roman's spmatrix extension type also > a subclass of the original Travis' spmatrix? Or would you prefer to > keep scipy-ized PySparse separately and ultimately (merge &) replace > the original? > ... > > Here is a little summary of the situation as I see it now: > > existing module (TravisSparse): > - Python spmatrix class + a number of Python subclasses with a > possible fortran/C underlying implementation > - pros: trivial addition of new methods / attributes, speeding up > could be done "later"; handles (or will handle :-) all numeric scipy > types (ints, floats, doubles, ...) automagically > - cons: speed in some situations? > > experimental module (RomanSparse) (random remarks, since I know nuts > about it): > - C extension class > - pros: constructor speed? and speed in general? > - cons: not so easy to change the low-level implementation, 'cause > it's on that level already?; the solvers (umfpack etc.) are > hand-wrapped - I would certainly prefer a generated interface (swig?) > which would be AFAIK much more flexible. > > I am personally in favor of the TravisSparse approach as the base with > RomanSparse subclass of spmatrix with a key feature "*speed* *speed* > *speed*". Also the _solvers_ should be split as much as practical from > the sparse matrix _type_. Of course, having some 'recommended format > hinting' (e.g. CSR for umfpack), that would tell the user "use this if > you want speed and to avoid implicit matrix conversion" would be > necessary. > Yes, I agree that a Python implementation would be simpler and more flexible than one in C. Perhaps our goal should be to build on the existing TravisSparse module but replace the sparsetools Fortran code with code from PySparse, which is probably better tested and debugged. I've had a look at how objects with both C and Python member functions are possible in the Python standard library. An example is the random module: there's a randommodule.c file that is imported in the Python random.py file and used as a base class for Python objects: import _random class Random(_random.Random): Then the functions exported by the C module are wrapped like this: def seed(self, a=None): super(Random, self).seed(a) Why don't we adopt a similar structure? Then we'd use Travis's spmatrix as the base class, and derive csr_matrix from both spmatrix and an object we import from C. Or is it possible for a C module to derive directly from a Python class?! -- Ed

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Sparse module update
by Ed Schofield Oct. 25, 2005

Oct. 25, 2005

I've been working on the sparse matrix module. Now all but three tests pass on my machine (x86 Linux). Could someone please look at the distutils setup for the sparse module, especially the sparsetools Fortran code? I'm not sure I'm doing the right thing. I needed to change a line in the test module from: from sparse import csc_matrix, csr_matrix, dok_matrix to from scipy.sparse import csc_matrix, csr_matrix, dok_matrix -- Ed

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random module not working on opteron
by Arnd Baecker Oct. 24, 2005

Oct. 24, 2005

Hi, I recently reported that from scipy.basic.random import normal a = normal(0.,1.,(3,3)) leads to a hang on the opteron. It turns out that the whole random module does not work as it should: In [2]: import scipy.basic.random In [3]: scipy.basic.random.uniform() Out[3]: 3804495653.9744735 In [4]: scipy.basic.random.uniform() Out[4]: 2804588197.3068576 In [5]: scipy.basic.random.uniform() Out[5]: 998177869.76781905 # this one also hangs In [6]: scipy.basic.random.randn(5) I have no idea what is causing this, in particular because there are no warnings during the compile of mtrand.c. Can anyone with a 64 Bit machine confirm this behaviour? What could one do to hunt this one down? (For the hangs one could add print statements to the .pyx source. Unfortunately I don't have the right pyxrc as I get a different output than the one from svn.). Best, Arnd

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NameError: global name 'hasattry' is not defined
by Nils Wagner Oct. 24, 2005

Oct. 24, 2005

w,vr = linalg.eig(Kd,Gd) File "/usr/local/lib/python2.4/site-packages/scipy/linalg/decomp.py", line 120, in eig return _geneig(a1,b,left,right,overwrite_a,overwrite_b) File "/usr/local/lib/python2.4/site-packages/scipy/linalg/decomp.py", line 52, in _geneig overwrite_b = overwrite_b or (b1 is not b and not hasattry(b,'__array__')) NameError: global name 'hasattry' is not defined

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xplt in newscipy
by Nils Wagner Oct. 24, 2005

Oct. 24, 2005

Hi all, Is it still possible to use xplt in newscipy ? It is faster than matplotlib. Nils

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TypeError: __array_data__ must return a string providing the pointer to data
by Nils Wagner Oct. 22, 2005

Oct. 22, 2005

Python 2.4 (#2, May 12 2005, 14:45:33) [GCC 3.3.3 (SuSE Linux)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from MLab import * >>> A = rand(3,3) >>> A array([[ 0.9462472 , 0.30814099, 0.65772529], [ 0.29040523, 0.58193587, 0.25232399], [ 0.8339496 , 0.36152322, 0.58090246]]) >>> triu(A) array([[ 0.9462472 , 0.30814099, 0.65772529], [ 0. , 0.58193587, 0.25232399], [ 0. , 0. , 0.58090246]]) >>> tril(A) array([[ 0.9462472 , 0. , 0. ], [ 0.29040523, 0.58193587, 0. ], [ 0.8339496 , 0.36152322, 0.58090246]]) >>> from scipy import * Importing io to scipy Importing special to scipy Importing sparse to scipy Importing utils to scipy Importing interpolate to scipy Importing optimize to scipy Importing linalg to scipy >>> triu(A) Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/local/lib/python2.4/site-packages/scipy/base/twodim_base.py", line 103, in triu m = asarray(m) File "/usr/local/lib/python2.4/site-packages/scipy/base/numeric.py", line 36, in asarray return array(a, dtype, copy=0, fortran=fortran) TypeError: __array_data__ must return a string providing the pointer to data.

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