Re: [Numpy-discussion] Don't understand this error

Thanks, that was it. DG On Tue, Jul 27, 2010 at 3:02 PM, Robert Kern wrote: > On Tue, Jul 27, 2010 at 16:59, David Goldsmith > wrote: > > res = np.fromfunction(make_res, (nx, ny)) > >File "C:\Python26\lib\site-packages\numpy\core\numeric.py", line 1538, > in > > fromfunction > > args = ind

Re: [Numpy-discussion] First shot at svn->git conversion

On Mon, Jul 26, 2010 at 6:16 PM, David wrote: > On 07/26/2010 05:44 PM, Pauli Virtanen wrote: >> Mon, 26 Jul 2010 13:57:36 +0900, David Cournapeau wrote: >>> I have finally prepared and uploaded a test repository containing numpy >>> code: >>> >>> http://github.com/numpy/numpy_svn I put a new rep

Re: [Numpy-discussion] Don't understand this error

On Tue, Jul 27, 2010 at 16:59, David Goldsmith wrote: > res = np.fromfunction(make_res, (nx, ny)) >    File "C:\Python26\lib\site-packages\numpy\core\numeric.py", line 1538, in > fromfunction > args = indices(shape, dtype=dtype) >    File "C:\Python26\lib\site-packages\numpy\core\numeric.py", line

[Numpy-discussion] Don't understand this error

res = np.fromfunction(make_res, (nx, ny)) File "C:\Python26\lib\site-packages\numpy\core\numeric.py", line 1538, in fromfunction args = indices(shape, dtype=dtype) File "C:\Python26\lib\site-packages\numpy\core\numeric.py", line 1480, in indices tmp.shape = (1,)*i + (dim,)+(1,)*(N-i-1) ValueE

Re: [Numpy-discussion] subtract.reduce behavior

On 7/26/2010 9:41 AM, Johann Hibschman wrote: > if reduce were defined as a *right* fold, then it would make sense for > subtract (and divide) to use the right identity Instead of deviating from the Python definition of reduce, it would imo make more sense to introduce new functions, sayfoldl and

Re: [Numpy-discussion] 1.5 release schedule proposal

Pauli Virtanen wrote: >> These are a couple relevant tickets; >> >> http://projects.scipy.org/numpy/ticket/909 >> http://projects.scipy.org/numpy/ticket/883 > > The relevant thing for 1.5.x would probably be to check that fromfile/ > fromstring handle malformed data in a well-specified way, and be

Re: [Numpy-discussion] 1.5 release schedule proposal

Tue, 27 Jul 2010 10:50:51 -0700, Christopher Barker wrote: > Pauli Virtanen wrote: >> Tue, 27 Jul 2010 08:37:56 -0600, Jed Ludlow wrote: >>> On Tue, Jul 27, 2010 at 2:38 AM, Pauli Virtanen wrote: One low-hanging fruit to fix could be np.fromfile raising MemoryError when it encounters EO

Re: [Numpy-discussion] Help w/ indexing, please

On Tue, Jul 27, 2010 at 9:32 AM, John Salvatier wrote: > I am pretty sure you should be able to do > > R = C[L, :] and get the array you want. > > Try it with a small matrix where you know the result you want. You may > need to transpose some axes afterwards, but I don't think you should. > Tha

[Numpy-discussion] Datarray sprint July 28, 2010

Join us for a datarray sprint on July 28. Several of us will meet at UC Berkeley from 2pm (Pacific Time) until our fingers bleed from typing or until 6 or 7pm, whichever comes first. If you can't be there in person, grab an item from the issue tracker or create your own. I'm told some of us will h

Re: [Numpy-discussion] 1.5 release schedule proposal

Pauli Virtanen wrote: > Tue, 27 Jul 2010 08:37:56 -0600, Jed Ludlow wrote: >> On Tue, Jul 27, 2010 at 2:38 AM, Pauli Virtanen wrote: >>> One low-hanging fruit to fix could be np.fromfile raising MemoryError >>> when it encounters EOF, and other bugs in that part of the code. >> The EOF bug in np.f

[Numpy-discussion] atleast_3d() strips subclass info

I have filed ticket #1560: http://projects.scipy.org/numpy/ticket/1560 The .atleast_3d() function can not be used with arrays that are subclassed from ndarray(). Because the function uses .asarray() instead of .asanyarray(), subclass info such as masks for masked arrays are stripped from the resu

[Numpy-discussion] atleast_1d and atleast2d breaks masked arrays

I have filed ticket #1559: http://projects.scipy.org/numpy/ticket/1559 Calling a function like .atleast_2d() to change the number of dimensions an array has can break the original masked array object. See the following example using a 1d masked array: >>> import numpy >>> a = numpy.ma.masked_arra

Re: [Numpy-discussion] loadtxt() behavior on single-line files

On Thu, Jun 24, 2010 at 1:53 PM, Benjamin Root wrote: > On Thu, Jun 24, 2010 at 1:00 PM, Warren Weckesser < > warren.weckes...@enthought.com> wrote: > >> Benjamin Root wrote: >> > Hi, >> > >> > I was having the hardest time trying to figure out an intermittent bug >> > in one of my programs. Ess

[Numpy-discussion] ANN: SciPy 0.8.0

I'm pleased to announce the release of SciPy 0.8.0. SciPy is a package of tools for science and engineering for Python. It includes modules for statistics, optimization, integration, linear algebra, Fourier transforms, signal and image processing, ODE solvers, and more. This release comes one and

Re: [Numpy-discussion] determinant of a scalar not handled

On Tue, Jul 27, 2010 at 11:36, Skipper Seabold wrote: > On Tue, Jul 27, 2010 at 12:00 PM, Robert Kern wrote: >> On Tue, Jul 27, 2010 at 07:51, Skipper Seabold wrote: >>> On Mon, Jul 26, 2010 at 10:05 PM, Alan G Isaac wrote: But I am still confused about the use case. What is the scala

Re: [Numpy-discussion] determinant of a scalar not handled

On Tue, Jul 27, 2010 at 12:00 PM, Robert Kern wrote: > On Tue, Jul 27, 2010 at 07:51, Skipper Seabold wrote: >> On Mon, Jul 26, 2010 at 10:05 PM, Alan G Isaac wrote: >>> But I am still confused about the use case. >>> What is the scalar- (or 1d-array-) returning procedure >>> invokedbefore takin

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

On Tue, Jul 27, 2010 at 9:29 AM, Robert Faryabi wrote: > I just looked at my system more carefully. > > There are two executable files > > /usr/local/bin/python > > and > > /usr/bin/python > this is a link to python2.6 > > I believe that the first one is source compiled version. So, how can I get

Re: [Numpy-discussion] Help w/ indexing, please

I am pretty sure you should be able to do R = C[L, :] and get the array you want. Try it with a small matrix where you know the result you want. You may need to transpose some axes afterwards, but I don't think you should. On Tue, Jul 27, 2010 at 9:10 AM, David Goldsmith wrote: > Hi! I have

Re: [Numpy-discussion] 1.5 release schedule proposal

On Tue, Jul 27, 2010 at 9:35 AM, Ralf Gommers wrote: > > > On Tue, Jul 27, 2010 at 10:17 PM, Benjamin Root wrote: > >> On Tue, Jul 27, 2010 at 3:38 AM, Pauli Virtanen wrote: >> >>> Mon, 26 Jul 2010 23:58:11 +0800, Ralf Gommers wrote: >>> > For numpy 1.5.0 no one has yet said they have urgent cha

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

I just looked at my system more carefully. There are two executable files /usr/local/bin/python and /usr/bin/python this is a link to python2.6 I believe that the first one is source compiled version. So, how can I get rid of it? On Tue, Jul 27, 2010 at 12:09 PM, Robert Faryabi wrote: > it r

Re: [Numpy-discussion] determinant of a scalar not handled

On Tue, Jul 27, 2010 at 10:01 AM, Alan G Isaac wrote: >> On Mon, Jul 26, 2010 at 10:05 PM, Alan G Isaac  wrote: >>> But I am still confused about the use case. >>> What is the scalar- (or 1d-array-) returning procedure >>> invoked before taking the determinant? > > > On 7/27/2010 8:51 AM, Skipper

[Numpy-discussion] Help w/ indexing, please

Hi! I have a large M x K, M, K ~ 1e3 array L of indices - non-negative integers in the range 0 to N-1 - and an N x 3 array C (a matplotlib colormap). I need to create an M x K x 3 array R such that R[m,k,j] = C[L[m,k], j], j = 0,1,2. I want to do so w/out having to loop through all the (m,k) ind

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

it returns /usr/local/bin/python On Tue, Jul 27, 2010 at 12:07 PM, Matthieu Brucher < matthieu.bruc...@gmail.com> wrote: > What does "which python" return? > > 2010/7/27 Robert Faryabi : > > I'm getting the same > > > sys.maxunicode > > 65535 > > > > I might have some "hand complied" python

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

As Sebastian suggested, I might have some hand compiled python. Anyone could tell me how can I get rid of all my python and reinstall a fresh one? On Tue, Jul 27, 2010 at 10:33 AM, Matthieu Brucher < matthieu.bruc...@gmail.com> wrote: > It's a problem of compilation of Python and numpy with diff

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

What does "which python" return? 2010/7/27 Robert Faryabi : > I'm getting the same > sys.maxunicode > 65535 > > I might have some "hand complied" python. Once I compiled Biopython long > ago. > > The problem is I do not know how to clean up all the python version that I > have. I tried the re

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

I'm getting the same >>> sys.maxunicode 65535 I might have some "hand complied" python. Once I compiled Biopython long ago. The problem is I do not know how to clean up all the python version that I have. I tried the reinstall option. It does not work. I cannot remove the python. It will wipe ou

Re: [Numpy-discussion] determinant of a scalar not handled

On Tue, Jul 27, 2010 at 07:51, Skipper Seabold wrote: > On Mon, Jul 26, 2010 at 10:05 PM, Alan G Isaac wrote: >> But I am still confused about the use case. >> What is the scalar- (or 1d-array-) returning procedure >> invokedbefore taking the determinant? > > Recently I ran into this trying to ma

Re: [Numpy-discussion] numpydoc broken with sphinx 1.0

On Mon, Jul 26, 2010 at 1:56 PM, Gael Varoquaux wrote: > On Mon, Jul 26, 2010 at 01:52:06PM -0700, Matthew Brett wrote: >> http://old.nabble.com/numpydoc-broken-by-latest-sphinx-td28896476.html >> http://projects.scipy.org/numpy/ticket/1489 > > Darn, I should have googled :( Better an extra email

Re: [Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

On Tue, Jul 27, 2010 at 9:52 PM, Sandro Tosi wrote: > > I just built trunk (both for 2.5 and 2.6) on alpha, successfully :) > Now I'll extract only the needed patch (I think it's enough to apply > r8526, right?) and try to build the package using 1.4.1+patch, if it > builds successfully I'll uplo

Re: [Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

On Tue, Jul 27, 2010 at 14:52, Sandro Tosi wrote: > Hi, > > On Tue, Jul 27, 2010 at 12:28, David Cournapeau wrote: >> On Tue, Jul 20, 2010 at 3:44 AM, Sandro Tosi wrote: >> >>> ah if you say so, I trust you :) >> >> Could you try the last version of the trunk, I added the missing >> macros for a

Re: [Numpy-discussion] size_t or npy_intp?

On Tue, Jul 27, 2010 at 10:08 PM, Francesc Alted wrote: > Hi, > > I'm a bit confused on which datatype should I use when referring to NumPy > ndarray lengths.  In one hand I'd use `size_t` that is the canonical way to > refer to lengths of memory blocks.  In the other hand, `npy_intp` seems the >

Re: [Numpy-discussion] size_t or npy_intp?

On Tue, Jul 27, 2010 at 10:17 AM, Dag Sverre Seljebotn wrote: >  From PEP 353: > > >    Why not size_t56 > > An initial attempt to implement this feature tried to use size_t. It > quickly turned out that this cannot work: Python uses negative indices

Re: [Numpy-discussion] size_t or npy_intp?

A Tuesday 27 July 2010 17:17:55 Dag Sverre Seljebotn escrigué: > Kurt Smith wrote: > > Looking at the bufferinfo struct for the buffer protocol, it uses > > `Py_ssize_t`: > > > > struct bufferinfo { > > void *buf; > > Py_ssize_t len; > > int readonly; > > const char *format; > >

Re: [Numpy-discussion] size_t or npy_intp?

Kurt Smith wrote: > > Looking at the bufferinfo struct for the buffer protocol, it uses > `Py_ssize_t`: > > struct bufferinfo { > void *buf; > Py_ssize_t len; > int readonly; > const char *format; > int ndim; > Py_ssize_t *shape; > Py_ssize_t *strides; > Py_

Re: [Numpy-discussion] 1.5 release schedule proposal

Tue, 27 Jul 2010 08:37:56 -0600, Jed Ludlow wrote: > On Tue, Jul 27, 2010 at 2:38 AM, Pauli Virtanen wrote: >> >> One low-hanging fruit to fix could be np.fromfile raising MemoryError >> when it encounters EOF, and other bugs in that part of the code. > > The EOF bug in np.fromfile may already be

Re: [Numpy-discussion] size_t or npy_intp?

On Tue, Jul 27, 2010 at 9:45 AM, Francesc Alted wrote: > A Tuesday 27 July 2010 15:20:47 Charles R Harris escrigué: >> On Tue, Jul 27, 2010 at 7:08 AM, Francesc Alted wrote: >> > Hi, >> > >> > I'm a bit confused on which datatype should I use when referring to NumPy >> > ndarray lengths.  In one

Re: [Numpy-discussion] size_t or npy_intp?

Francesc Alted wrote: > A Tuesday 27 July 2010 15:20:47 Charles R Harris escrigué: > >> On Tue, Jul 27, 2010 at 7:08 AM, Francesc Alted wrote: >> >>> Hi, >>> >>> I'm a bit confused on which datatype should I use when referring to NumPy >>> ndarray lengths. In one hand I'd use `size_t` tha

Re: [Numpy-discussion] size_t or npy_intp?

A Tuesday 27 July 2010 15:20:47 Charles R Harris escrigué: > On Tue, Jul 27, 2010 at 7:08 AM, Francesc Alted wrote: > > Hi, > > > > I'm a bit confused on which datatype should I use when referring to NumPy > > ndarray lengths. In one hand I'd use `size_t` that is the canonical way > > to refer to

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

The origin of this problem is the fact that Python supports (at least) 2 types of Unicode: 2 bytes and/or 4 bytes per character. Additionally, for some incomprehensible reason the Python source code (as downloaded from python.org) defaults to 2ByteUnicode whereas all (major) Linux distributions de

Re: [Numpy-discussion] 1.5 release schedule proposal

On Tue, Jul 27, 2010 at 2:38 AM, Pauli Virtanen wrote: > > One low-hanging fruit to fix could be np.fromfile raising MemoryError > when it encounters EOF, and other bugs in that part of the code. The EOF bug in np.fromfile may already be fixed: http://projects.scipy.org/numpy/ticket/1152 unless

Re: [Numpy-discussion] 1.5 release schedule proposal

On Tue, Jul 27, 2010 at 10:17 PM, Benjamin Root wrote: > On Tue, Jul 27, 2010 at 3:38 AM, Pauli Virtanen wrote: > >> Mon, 26 Jul 2010 23:58:11 +0800, Ralf Gommers wrote: >> > For numpy 1.5.0 no one has yet said they have urgent changes that need >> > to go in. If you do, please reply with the wh

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

It's a problem of compilation of Python and numpy with different parameters. But I've tried the same yesterday, and the Ubuntu repository are OK in that respect, so there is something not quite right with your configuration. Matthieu 2010/7/27 Robert Faryabi : > I can see the numpy now, but I hav

Re: [Numpy-discussion] 1.5 release schedule proposal

On Tue, Jul 27, 2010 at 9:40 PM, Bruce Southey wrote: > On Tue, Jul 27, 2010 at 3:38 AM, Pauli Virtanen wrote: > > Mon, 26 Jul 2010 23:58:11 +0800, Ralf Gommers wrote: > >> For numpy 1.5.0 no one has yet said they have urgent changes that need > >> to go in. If you do, please reply with the what

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

I can see the numpy now, but I have the problem with a shared library. Here is the error >>> import numpy Traceback (most recent call last): File "", line 1, in File "/usr/lib/python2.6/dist-packages/numpy/__init__.py", line 130, in import add_newdocs File "/usr/lib/python2.6/dist-pack

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

Yes, It seems there is a problem with some sort of header. I have no Idea. Look at this http://article.gmane.org/gmane.comp.python.numeric.general/3508/match=numpy+core+multiarray+so+_pyunicodeucs4_iswhitespace On Tue, Jul 27, 2010 at 10:03 AM, Matthieu Brucher < matthieu.bruc...@gmail.com> wr

Re: [Numpy-discussion] 1.5 release schedule proposal

On Tue, Jul 27, 2010 at 3:38 AM, Pauli Virtanen wrote: > Mon, 26 Jul 2010 23:58:11 +0800, Ralf Gommers wrote: > > For numpy 1.5.0 no one has yet said they have urgent changes that need > > to go in. If you do, please reply with the what and why. If nothing big > > has to go in, I propose the foll

Re: [Numpy-discussion] dtype.type for structured arrays

Thomas Robitaille wrote: > > I seem to remember that this used not to be the case, and that even for > vector columns, one could access array.dtype[0].type to get the numerical > type. Is this a bug, or deliberate? > I submitted a bug report: http://projects.scipy.org/numpy/ticket/1557 Cheer

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

On Tue, Jul 27, 2010 at 7:46 AM, Robert Faryabi wrote: > I am new to numpy. Hopefully this is a correct forum to post my question. > > I have Ubuntu Luci system. I installed Python 2.6.5 and Python 3.0 as well > as python-numpy using Ubuntu repository. > When I import the numpy into python, I get

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

Python 2.6.5 from Ubuntu? I tried the same yesterday evening, and it worked like a charm. Matthieu 2010/7/27 Robert Faryabi : > I am using 2.5.6 > > Python 2.6.5 (r265:79063, Jun 28 2010, 20:31:28) > [GCC 4.4.3] on linux2 > > > > On Tue, Jul 27, 2010 at 9:51 AM, Matthieu Brucher > wrote: >> >> W

Re: [Numpy-discussion] determinant of a scalar not handled

> On Mon, Jul 26, 2010 at 10:05 PM, Alan G Isaac wrote: >> But I am still confused about the use case. >> What is the scalar- (or 1d-array-) returning procedure >> invoked before taking the determinant? On 7/27/2010 8:51 AM, Skipper Seabold wrote: > Recently I ran into this trying to make the lo

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

I am using 2.5.6 Python 2.6.5 (r265:79063, Jun 28 2010, 20:31:28) [GCC 4.4.3] on linux2 On Tue, Jul 27, 2010 at 9:51 AM, Matthieu Brucher < matthieu.bruc...@gmail.com> wrote: > Which version of Python are you actually using in this example? > > Matthieu > > 2010/7/27 Robert Faryabi : > > I am

Re: [Numpy-discussion] Problem with importing numpy in Ubuntu

Which version of Python are you actually using in this example? Matthieu 2010/7/27 Robert Faryabi : > I am new to numpy. Hopefully this is a correct forum to post my question. > > I have Ubuntu Luci system. I installed Python 2.6.5 and Python 3.0 as well > as python-numpy using Ubuntu repository.

[Numpy-discussion] Problem with importing numpy in Ubuntu

I am new to numpy. Hopefully this is a correct forum to post my question. I have Ubuntu Luci system. I installed Python 2.6.5 and Python 3.0 as well as python-numpy using Ubuntu repository. When I import the numpy into python, I get the following error. >> import numpy Traceback (most recent call

Re: [Numpy-discussion] 1.5 release schedule proposal

On Tue, Jul 27, 2010 at 3:38 AM, Pauli Virtanen wrote: > Mon, 26 Jul 2010 23:58:11 +0800, Ralf Gommers wrote: >> For numpy 1.5.0 no one has yet said they have urgent changes that need >> to go in. If you do, please reply with the what and why. If nothing big >> has to go in, I propose the followin

Re: [Numpy-discussion] size_t or npy_intp?

On Tue, Jul 27, 2010 at 7:08 AM, Francesc Alted wrote: > Hi, > > I'm a bit confused on which datatype should I use when referring to NumPy > ndarray lengths. In one hand I'd use `size_t` that is the canonical way to > refer to lengths of memory blocks. In the other hand, `npy_intp` seems the >

[Numpy-discussion] size_t or npy_intp?

Hi, I'm a bit confused on which datatype should I use when referring to NumPy ndarray lengths. In one hand I'd use `size_t` that is the canonical way to refer to lengths of memory blocks. In the other hand, `npy_intp` seems the standard data type used in NumPy for this. Which one would you r

Re: [Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

Hi, On Tue, Jul 27, 2010 at 12:28, David Cournapeau wrote: > On Tue, Jul 20, 2010 at 3:44 AM, Sandro Tosi wrote: > >> ah if you say so, I trust you :) > > Could you try the last version of the trunk, I added the missing > macros for alpha ? I just built trunk (both for 2.5 and 2.6) on alpha, su

Re: [Numpy-discussion] determinant of a scalar not handled

On Mon, Jul 26, 2010 at 10:05 PM, Alan G Isaac wrote: > But I am still confused about the use case. > What is the scalar- (or 1d-array-) returning procedure > invokedbefore taking the determinant? > Recently I ran into this trying to make the log-likelihood of a multivariate and univariate autore

Re: [Numpy-discussion] Numpy 1.4.1 fails to build on (Debian) alpha and powepc

On Tue, Jul 20, 2010 at 3:44 AM, Sandro Tosi wrote: > ah if you say so, I trust you :) Could you try the last version of the trunk, I added the missing macros for alpha ? cheers, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http

Re: [Numpy-discussion] 1.5 release schedule proposal

Mon, 26 Jul 2010 23:58:11 +0800, Ralf Gommers wrote: > For numpy 1.5.0 no one has yet said they have urgent changes that need > to go in. If you do, please reply with the what and why. If nothing big > has to go in, I propose the following release schedule: > > Aug 1 : beta 1 > Aug 15: rc 1 > Aug