On Mon, 21 Feb 2011 15:09:05 -0500, Skipper Seabold wrote:
[clip]
> Should I file a ticket?
Yes.
[clip]
> PS. Is there an incompatibility of numpy 1.5.1 and numpy 1.6.0 trunk for
> packages that depend on numpy?
It should be binary compatible.
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On Mon, 21 Feb 2011 16:03:43 -0500, Skipper Seabold wrote:
[clip]
> I had to reinstall scipy, matplotlib, etc. when I changed from 1.6.0
> back to 1.5.1.
Yes, it should be backward compatible (you should be able use binaries
compiled with 1.5.1 on 1.6.0), but not forward compatible (binaries
com
On Tue, 22 Feb 2011 16:44:56 -0500, Alan G Isaac wrote:
[clip]
> I don't believe the matrix multiplication results. Maybe I misunderstand
> them ...
>
> >>> t = timeit.Timer("np.dot(A,B)","import numpy as
> >>> np;N=1500;A=np.random.random((N,N));B=np.random.random((N,N))")
> >>> pr
On Tue, 22 Feb 2011 22:48:09 +0100, Gael Varoquaux wrote:
[clip]
> Probably because the numpy binary that the author was using was compiled
> without a blas implementation, and just using numpy's internal
> lapack_lite. This is a common problem in real life.
It doesn't use blas_lite at the moment.
y" in /home/idris/cos/scos190?
> Could you try cd-ing over to another directory and trying again?
Another possible reason is that Numpy was installed wrong (as the
numpy.__config__ module is apparently missing). Numpy needs to be
installed via &q
Thu, 24 Feb 2011 16:47:14 +, Pauli Virtanen wrote:
> Another possible reason is that Numpy was installed wrong (as the
> numpy.__config__ module is apparently missing). Numpy needs to be
> installed via "python setup.py install", manually copying the "numpy"
> d
go:
http://docs.scipy.org/doc/numpy/reference/maskedarray.html
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Mon, 28 Feb 2011 16:50:59 +0800, Ralf Gommers wrote:
> On Mon, Feb 28, 2011 at 4:00 PM, Ralf Gommers
> wrote:
>
>> The other thing that needs to be done is some (more) documentation of
>> new features. Einsum and the new iterator seem to be well documented,
>> but not described in the release not
On Fri, 04 Mar 2011 22:58:14 -0600, Benjamin Root wrote:
> I recently had to fix an example in matplotlib where there was a 1xN
> array being assigned to a 1-D slice of a numpy array. It used to work,
> but it now doesn't. I don't know if this was intended or not, though.
Probably not -- please
Mon, 07 Mar 2011 11:03:17 +0800, Ralf Gommers wrote:
[clip]
> If anyone has new deprecations they want to put in for 1.6, discussing
> them now would be good. I found one item in Trac, #1543. The proposal in
> the ticket is to deprecate assert_almost_equal because it is quite badly
> behaved. This
o have the
built-in ugliness of specifying precision via decimals= which is somewhat
clumsy for numerical work.
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uracy across the range of all floating
point values. For instance, this is quite useful for special functions,
whose range of values typically vary widely, but for which one still
wants to have accuracy which is as good as possible.
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on that this unnecessary check was removed in newer
Cython versions? If so, some of the existing code should not have this
problem.
However, the size of PyArray_Descr does not seem to have changed between
1.5.1 and the Git master. So I'm not
weird. Maybe the binaries you have were compiled
against Numpy < 1.5? If so, the same errors should come up with Numpy
1.5.x.
In any case, it seems to me that since there have been no changes in the
dtype struct contents since 1.5, the Git master should behave exactly the
same as 1.5 in t
> package).
Ok, seems this needs looking into. I don't immediately see how it can
happen, and agree that it shouldn't (AFAIK, there are no changes in 1.6
that require additions to the structs).
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Mon, 07 Mar 2011 10:01:21 -0500, Neal Becker wrote:
> reshape can view a 1d array as non-overlapping segments.
>
> Is there a convenient way to view a 1d array as a 2d array of
> overlapping segments?
>
> nonoverlapping:
> l: segment length
> k: overlap
> u is the 1d array
> v is a 2d array
>
>
, ('b', int)])
>>> y = np.array([(2, 3)], dtype=[('b', int), ('a', int)])
>>> x[:] = y
>>> x
array([(3, 2)],
dtype=[('a', '>> np.sin(np.zeros((5,5,5)).transpose(1,2,0)).st
Tue, 08 Mar 2011 00:12:35 -0800, Robert Bradshaw wrote:
[clip]
> Unfortunately, I don't think anyone's actively working on it right now.
> It's probably a superficial fix for someone who knows NumPy and Cython
> decently well, but I have no idea myself (not having looked that deeply
> into it.) Doe
Thu, 10 Mar 2011 15:23:59 +0800, Ralf Gommers wrote:
[clip]
>> x = np.array([1.5])
>> x.view(int)
>> array([4609434218613702656])
Yes, `view` is meant to do exactly that. Use `astype` if you want a type
cast.
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On Fri, 11 Mar 2011 11:47:58 -0700, Charles R Harris wrote:
[clip]
> What about views? Wouldn't it be easier to write another object wrapping
> an ndarray?
I think the buffer interfaces and all other various ways Numpy provides
exports for arrays make keeping tabs on modification impossible to do
Tue, 15 Mar 2011 10:06:09 -0700, Matthew Brett wrote:
> Sorry to ask, and I ask partly because I'm in the middle of a py3k port,
> but is this the right fix to this problem? I was confused by the
> presence of the old PyString_AsString function.
It's not a correct fix. The original code seems als
Tue, 15 Mar 2011 10:23:35 -0700, Matthew Brett wrote:
[clip]
> OK - I realize I'm being very lazy here but, do you mean:
>
> PyErr_Format(PyExc_ValueError,
>>> "field named %s not found.",
>>> PyString_AsString(PyObject_Repr(index)));
>
>> The PyS
some code out there that touches the `names` attribute,
so it's not clear if this can be fixed in the 1.x series.
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On Wed, 23 Mar 2011 14:17:20 -0500, Bruce Southey wrote:
> I can not figure out what is different between git and this version :-(
>
> All the paths appear to be the same.
> Further it continues onwards when I do: $python3.1 -m pdb setup.py build
>
> I added these lines to the start of "numpy/com
omstring is lacking an adequate error
> handling for that case.
>
> Is it a bug ?
It was fixed in r5438 and the fix is also in Numpy 1.1.1.
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esult or returning zeros or garbage.
This is of course an API change...
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em back in only after we actually have some guarantees
about inf/nan handling.
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g evil, like this:
import os
if os.environ.get('NUMPY_VIA_API', '0') != '0':
from numpy.lib.fromnumeric import *
...
But I'm not sure how many milliseconds must be gained to justify this...
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for this, and marked failing ones as skipped.
However, it turned out that different tests fail on different platforms,
which means that the inf/nan handling of our complex-valued functions is
effectively undefined. Eventually, most of the tests had to be marked as
skipped, an
we have already agreed on can be used
without problems. What we have now can be found here:
https://code.launchpad.net/~pauli-virtanen/scipy/numpy-refguide
https://code.launchpad.net/~stefanv/scipy/numpy-refguide
Splitting the docstrings so that there's one docstring pe
Mon, 25 Aug 2008 11:18:52 +, Pauli Virtanen wrote:
[clip]
> https://code.launchpad.net/~pauli-virtanen/scipy/numpy-refguide
>
> https://code.launchpad.net/~stefanv/scipy/numpy-refguide
For coordination: I'm starting to add and Sphinxify relevant C-API
reference
Tue, 26 Aug 2008 11:24:24 +, Pauli Virtanen wrote:
[clip]
> For coordination: I'm starting to add and Sphinxify relevant C-API
> reference documentation parts from Travis's book [1]
> (numpy/doc/numpybook/ capi.lyx) to the above "reference manual".
Ok, one Sph
> =
() are not list delimiters in Python; [] are, see [1,2]:
>>> a = (1)
>>> type(a)
>>> a = [1]
>>> type(a)
.. [1] http://docs.python.org/tut/node5.html#SECTION00514
.. [2] http:/
t(1)
> >>> a
> array([[1, 4],
>[1, 3]])
> >>> a.sort(0)
> >>> a
> array([[1, 3],
>[1, 4]])
These examples were fixed a couple of weeks ago in the editor.
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)
http://www.iki.fi/pav/tmp/numpy-refguide/index.xhtml
http://www.iki.fi/pav/tmp/numpy-refguide/NumPy.pdf
Source is here: (Stéfan, if it looks ok to you, could you pull and check
if it builds for you when you have time?)
https://code.launchpad.net/~pauli-virtanen/scipy/numpy
Hi,
The buildbot slave Windows_XP_x86_64_MSVC seems to have some bogus files
left over in its installation directory (in numpy\doc\) which cause the
tests to fail.
Removing the installation directory probably helps.
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eyword arguments, the signature formatting needs to
be changed again so that 'outN' look like keyword arguments.
Currently the 'sig' and 'extobj' arguments are not shown in the
signature. I'm not sure whether it makes sense to add them, since they
appear to be
ntation and not being able to test or render plots easily.
-1
4) Steal or adapt the plot:: ReST directive from matplotlib, and use that,
as Stéfan suggested at some point. Haven't got yet around to
implementing this.
Tentatively +1; depends a bit of how the implem
Thu, 04 Sep 2008 19:07:24 +, Pauli Virtanen wrote:
[clip]
> I'd say that the settings are "unintended" in the sense that they run
> all examples in all docstrings. There are quite a few of these, and some
> indeed plot some graphs.
>
> Ideally, all examples shoul
Fri, 05 Sep 2008 15:27:56 +0900, David Cournapeau wrote:
> Those two symbols are mentioned in the numpy C-API book, but with my
> work on cleaning the math configuration, those are not needed by numpy
> anymore (I grep into numpy and scipy sources, and they are only used in
> umathmodule.c.src,
Sat, 06 Sep 2008 12:15:59 +0900, David Cournapeau wrote:
> On Fri, Sep 5, 2008 at 4:50 PM, Pauli Virtanen <[EMAIL PROTECTED]> wrote:
>>
>> If you remove them, please put a reminder somewhere (eg ticket) to
>> update the documentation accordingly.
>
> Is th
n you have installed. Eg. what does "f2py -v" output?
And "python -c 'import numpy; print numpy.__version__'"
- The exact commands you typed that didn't work as expected.
- Full output produced by the commands.
- A minimal example, with s
ts under different locales and calling
setlocale(LC_ALL, "") may reveal some additional points to address.
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ipy.org/F2PY_Windows
http://cens.ioc.ee/projects/f2py2e/usersguide/index.html
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on linux2 Type "help", "copyright", "credits" or "license"
> for more information.
>>>> from numpy.f2py import main
>>>>
>>>>
> Nils
Do you have different versions of
be polished a bit and
contributed to sphinx.ext as an extra math back-end. The pngmath and
jsmath backends share some code that do part of the work, so the current
code would need to be tweaked a bit.
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Hi,
Tue, 23 Sep 2008 15:48:22 -0700, joep wrote:
> A possible solution would be in
>
> http://bazaar.launchpad.net/~pauli-virtanen/scipy/pydocweb/revision/386
>
> It seems to be possible to be used in the same way when iter_modules is
> not available.
> The usage in ``_l
Wed, 24 Sep 2008 11:18:43 +, Pauli Virtanen wrote:
> Tue, 23 Sep 2008 15:48:22 -0700, joep wrote:
>> A possible solution would be in
>>
>> http://bazaar.launchpad.net/~pauli-virtanen/scipy/pydocweb/revision/386
>>
>> It seems to be possible to be used in the
y harmless, but may lead to problems if your
code relies on the choice of branch at the branch cut.
Could you check if this is really the case? If log seems to work OK, then
it's a problem with the test and not the functions.
The current implementation of complex log seemed to work on
gt; The result is what you expected.
Do you mean that the problem is with the test, or with the branch cut of
log?
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Mon, 29 Sep 2008 12:33:32 +0200, Matthieu Brucher wrote:
> 2008/9/29 Pauli Virtanen <[EMAIL PROTECTED]>:
>> Mon, 29 Sep 2008 12:07:53 +0200, Matthieu Brucher wrote:
>>
>>>>>>> np.log(-1 + 0j)
>>>> 3.1415926535897931j
>>>>>>&g
endorses using assert (and uses it in its own tests).
Should we go ahead and change all "assert FOO" in Numpy's tests to
something like 'self.failUnless'?
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e author would have input on this? At least Nose seems to
be the place where any warnings saying that tests won't work with -OO
should go.
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ey are not; though I'm not sure if this could account for what you see.
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efcount(na)
refcounts correctly.
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welcome!
Currently, the sources for the Sphinx stuff can be found here:
https://code.launchpad.net/~pauli-virtanen/scipy/numpy-refguide
http://www.iki.fi/pav/tmp/scipy-refguide.tar.gz
http://www.iki.fi/pav/tmp/docsscipy-frontpage.tar.gz
(The latter two are tarballs
Thu, 30 Oct 2008 22:19:01 +, Jan-Willem van de Meent wrote:
> On Thursday 30 October 2008 18:41:51 Charles R Harris wrote:
>> On Thu, Oct 30, 2008 at 5:19 AM, Jan-Willem van de Meent <
>>
>> [EMAIL PROTECTED]> wrote:
>> > Dear all,
>> >
>> > This is my first post to this list. I am having perf
a generic name for a group of methods. For Monte Carlo
Markov Chain sampling, you can eg. see PyMC [1]. I believe there are also
other packages implementing these methods and written in Python.
.. [1] http://code.google.com/p/pymc/
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nually, so Python
2.3 programs will try to look modules in your local/ 2.5 site-packages.
autosummary_generate.py above probably runs under Python 2.3 -- you
should be able to fix this by changing "python" to "python2.5" on the
first line of autosummary_generate.py, o
7;s possible to fix them
using this:
http://docs.scipy.org/numpy/
http://docs.scipy.org/numpy/docs/numpy.matlib.zeros/
http://docs.scipy.org/numpy/docs/numpy.matlib.ones/
The changes will propagate from there eventually to SVN, alongside all
other documentation improveme
Wed, 12 Nov 2008 10:57:59 -0600, Ryan May wrote:
[clip: numpy doc editor]
> Great, can someone get me edit access?
Done.
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Thu, 13 Nov 2008 20:31:05 +0100, Nils Wagner wrote:
[clip]
> make html in numpy-docs works for me now, but make html in scipy-docs
> failed
Yep, there was bad Latex in the docstrings of cluster.hierarchy, which
made sphinx.ext.pngmath to crash. I've fixed the docstrings now.
Pauli
_
Fri, 14 Nov 2008 08:42:08 +0100, Nils Wagner wrote:
[clip]
> Is this source outdated
> svn co http://svn.python.org/projects/doctools/trunk sphinx-trunk ?
I believe it's outdated.
> I mean can I still use it or should I switch to
>
> hg clone http://bitbucket.org/birkenfeld/sphinx
>
> Is it pos
Fri, 14 Nov 2008 14:13:31 +0100, Nils Wagner wrote:
[clip]
> I got a copy of utf8.def
> ftp://ftp.mpi-sb.mpg.de/pub/tex/mirror/ftp.dante.de/pub/tex/macros/
latex/contrib/t2/etc/utf-8/utf-8.def
>
> Where should I store that file ?
See Damian's mail first -- if you have to just to install some pack
hould be trivial
to rig up a cron job that runs whenever there are new revisions in SVN,
so let's put this in the todo list.
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Thu, 27 Nov 2008 01:13:19 -0500, Pierre GM wrote:
[clip]
> Pauli, do you think you could put your numpyext in the doc/ directory as
> well ?
Yes, Numpy SVN would probably be a more natural place for the stuff.
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es. By default
> the data-type is determined from the objects returned from the iterator.
>
> ---> 20 z = fromiter (y)
>
> TypeError: function takes at least 2 arguments (1 given)
The docstring is correct in 1.2.1 and in the documentation; I suppose you
have an
tput of linear congruental
generators has serial correlations. At least according to wikipedia,
these are negligible in Mersenne twister's output.
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; may be initialized the same way, though.
The RandomState object handling numpy.random.random is created (and
seeded) at import time. So, an identical generator should be shared by
all processes after that.
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getpid()
return np.random.random(x)
and note the output
Hi, I'm 16197
Hi, I'm 16198
Hi, I'm 16199
Hi, I'm 16199
[ 0.58175647 0.16293922 0.30488182 0.67367263]
[ 0.58175647 0.16293922 0.30488182 0.67367263]
[ 0.58175647 0.16293922 0.30488182 0.673672
he examples. So the options were either to implement some magic to
skip offending doctest lines, or to not use doctest markup for plots.
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put the source for the documentation to the documentation
tarball, and distribute the built HTML+whatever documentation in a
separate package.
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Sun, 21 Dec 2008 13:05:57 +0100, Ondrej Certik wrote:
> On Sat, Dec 20, 2008 at 3:02 PM, Pauli Virtanen wrote:
>> Sat, 20 Dec 2008 20:15:43 +0900, David Cournapeau wrote:
>>> On Sat, Dec 20, 2008 at 7:43 PM, Ondrej Certik
>>> wrote:
>>>> Just to make it
stuff targeted at
developers (eg. ufuncs.txt), and miscellaneous stuff for users (eg.
cython/, swig/) that should eventually be added as a part of the main
documentation.
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Mon, 22 Dec 2008 00:30:55 +0900, David Cournapeau wrote:
> On Sun, Dec 21, 2008 at 11:42 PM, Pauli Virtanen wrote:
>> Sun, 21 Dec 2008 22:48:41 +0900, David Cournapeau wrote: [clip]
>>> Is everything under trunk/doc necessary to build the doc ? Or only
>>> a
&g
s) allows one to avoid the need
for special-casing any subsequent code for axis=None.
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d. Also, roundtrip tests for repr would be nice to add, if they
aren't there yet, and possibly for str <-> fromstring roundtrip, too.
I'll be almost offline for 1.5 weeks starting now, so if you want to
finish this, go ahead.
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he float
formatting. However, the current formatting of "Inf", "-Inf", "NaN" is OK
as far as C99 is concerned.
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rg/blas/blast-forum/cblas.tgz
So, I think you need to compile it & link it with ACML, and add it in
site.cfg with ACML libs.
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j); cmath:
> (1.31695789692-1.57079632679j)
Same as http://scipy.org/scipy/numpy/ticket/977, fixed in trunk.
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I am disappointed that the docs page renders this suggestion
> invisible.
Fixed, no need to be dissappointed any more. It actually didn't cross my
mind that there was a reason not to link directly to the PDF file, but I
see now that there is.
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make the promise that it shall be found there in the future, too.
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Mon, 02 Feb 2009 18:27:05 -0600, Robert Kern wrote:
> On Mon, Feb 2, 2009 at 18:21, wrote:
>> Hello list.. I've run into two SVD errors over the last few days. Both
>> errors are identical in numpy/scipy.
>>
>> I've submitted a ticket for the 1st problem (numpy ticket #990).
>> Summary is: some b
Wed, 04 Feb 2009 11:04:25 +0900, David Cournapeau wrote:
[clip]
> Talking about the things I have worked on for 1.3, I did not have the
> time to finish everything. The things which I would like to be done
> before a 1.3.0 release are:
> - fix formatting issues that Pauli and me worked on (for loc
oposal was to add the ability to refer to dimensions with
names instead of numbers. This is separate from referring to entries in a
dimension. (Addressing 'columns' by name is already provided by
structured arrays.)
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of some bug (in the new math config system?), or
a glitch in the buildslaves only?
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r `dot` in any way.
On the other hand, `numpy.sum` already has a `dtype` argument that
specifies the accumulator data type. Maybe you can use that?
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> this causes trouble,
Excellent.
I note that we can't test this now on Windows, since the trunk does not
build (because of the atanhf umath build error).
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Sun, 15 Feb 2009 00:57:12 +0900, David Cournapeau wrote:
> On Sun, Feb 15, 2009 at 12:41 AM, Pauli Virtanen wrote:
>> Hi,
>>
>> Sat, 14 Feb 2009 23:38:11 +0900, David Cournapeau wrote:
>>> I've just merged the branch Pauli and me have been working on
&g
Poller.get_new_logentries(self, *a, **kw)
f = open(self.persist_file, 'w')
try:
f.write("%d" % self.last_change)
finally:
f.close()
return r
}}}
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N
Sat, 14 Feb 2009 23:39:32 +0200, Stéfan van der Walt wrote:
> 2009/2/14 Pauli Virtanen :
>> It seems that the buildbot.scipy.org is not picking up the changes in
>> Numpy trunk.
>
> Thanks for the report. I've let the system administrater know.
>
> Once the
Sun, 15 Feb 2009 11:09:20 -0500, josef.pktd wrote:
[clip]
> In my setup the plot directive doesn't create any graphs, it always
> skips plots with the following warning
>
> WARNING:
> C:\Josef\_progs\building\scipy\scipy-trunk-new-r5551\doc\source\tutoria
> l\stats.rst:300: (ERROR/3) Error in "plo
t
> .figure in scipy.css and now the htmlhelp doesn't have a floating text
> anymore.
Yep, IE6 doesn't seem to understand the :after CSS attribute. But it
seems to be added in IE8, if that's any consolation :)
Ah, the joys of HTML/CSS design. I wonder if
).
> Or is there another way to check whether it's a view or a copy?
c.base is a
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Fri, 20 Feb 2009 00:16:42 +0900, David Cournapeau wrote:
[clip]
> Ok, I have started this in the coremath branch - it solves the warning
> issues we got since the merge of formatting stuff. I tested it on Linux,
> windows (both mingw and VS - still need to test on Win64), so I think it
> is good to
t;
> maybe we could change the names, then ? nc is not very clear IMHO (and
> since they were static up to now, we are free to change them I believe).
I think it would make sense to change them to follow C99 function names,
with a npy_ prefix.
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Pauli Virtanen
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the "New item" form:
http://docs.scipy.org/numpy/docs/numpy-docs/user/
No need to add stubs to SVN.
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Tue, 24 Feb 2009 14:04:42 +, Neal Becker wrote:
> Pauli Virtanen iki.fi> writes:
>
> ...
>> One question: doesn't this add one extra function call to all umath
>> functions? Could we do '#define npy_XXX XXX' in the npy_math.h header
>> when the
?
Is float32 still a problem?
(The test passes for me.)
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