[Numpy-discussion] ticket #842.

Just wanted to bring attention to ticket #842because I think the fix should be pretty easy. I added a comment: The printing inconsistency is a duplicate of #841and has been fixed. What remains odd i

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

On Fri, Jul 18, 2008 at 10:04 PM, Travis E. Oliphant <[EMAIL PROTECTED]> wrote: > Charles R Harris wrote: > > > > > > On Fri, Jul 18, 2008 at 9:15 PM, Travis E. Oliphant > > <[EMAIL PROTECTED] > wrote: > > > > Michael Abbott wrote: > > > Only half of my patch for

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

On Fri, Jul 18, 2008 at 11:35:50PM -0500, Travis E. Oliphant wrote: > > I've attached a test script. > Thank you! It looks like with that added DECREF, the reference count > leak is gone.While it was a minor issue (it should be noted that > reference counting errors on the built-in data-ty

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

> I've attached a test script. Thank you! It looks like with that added DECREF, the reference count leak is gone.While it was a minor issue (it should be noted that reference counting errors on the built-in data-types won't cause issues), it is nice to clean these things up when we can.

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

Charles R Harris wrote: > > > On Fri, Jul 18, 2008 at 9:15 PM, Travis E. Oliphant > <[EMAIL PROTECTED] > wrote: > > Michael Abbott wrote: > > Only half of my patch for this bug has gone into trunk, and > without the > > rest of my patch there remains a lea

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

Charles R Harris wrote: > > > On Fri, Jul 18, 2008 at 9:15 PM, Travis E. Oliphant > <[EMAIL PROTECTED] > wrote: > > Michael Abbott wrote: > > Only half of my patch for this bug has gone into trunk, and > without the > > rest of my patch there remains a lea

[Numpy-discussion] f2py - a recap

Howdy, today's exercise with f2py left some lessons learned, mostly thanks to Robert's excellent help, for which I'm grateful. I'd like to recap here what we have, mostly to decide what changes (if any) should go into numpy to make the experience less "interesting" for future users: - Remove the

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

On Fri, Jul 18, 2008 at 9:30 PM, Travis E. Oliphant <[EMAIL PROTECTED]> wrote: > Charles R Harris wrote: > > > > > > The reference leak seems specific to the float32 and complex64 types > > called with default arguments. > > > > In [1]: import sys, gc > > > > In [2]: t = float32 > > > > In [3]: sy

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

Charles R Harris wrote: > > > On Fri, Jul 18, 2008 at 9:15 PM, Travis E. Oliphant > <[EMAIL PROTECTED] > wrote: > > Michael Abbott wrote: > > Only half of my patch for this bug has gone into trunk, and > without the > > rest of my patch there remains a lea

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

On Fri, Jul 18, 2008 at 9:15 PM, Travis E. Oliphant <[EMAIL PROTECTED]> wrote: > Michael Abbott wrote: > > Only half of my patch for this bug has gone into trunk, and without the > > rest of my patch there remains a leak. > > > Thanks for your work Michael. I've been so grateful to have you and

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

Charles R Harris wrote: > > > The reference leak seems specific to the float32 and complex64 types > called with default arguments. > > In [1]: import sys, gc > > In [2]: t = float32 > > In [3]: sys.getrefcount(dtype(t)) > Out[3]: 4 > > In [4]: for i in range(10) : t(); >...: > > In [5]: sys.g

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

Michael Abbott wrote: > Only half of my patch for this bug has gone into trunk, and without the > rest of my patch there remains a leak. > Thanks for your work Michael. I've been so grateful to have you and Chuck and others looking carefully at the code to fix its problems. In this particu

Re: [Numpy-discussion] Another reference count leak: ticket #848

> Looking at the uses of PyArray_FromAny I can see the motivation for this > design: core/include/numpy/ndarrayobject.h has a lot of calls which take a > value returned by PyArray_DescrFromType as argument. This has prompted me > to take a trawl through the code to see what else is going on, a

Re: [Numpy-discussion] f2py - how to use .pyf files?

On Fri, Jul 18, 2008 at 5:20 PM, Fernando Perez <[EMAIL PROTECTED]> wrote: > On Fri, Jul 18, 2008 at 5:15 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > >> Probably. What other options would you need, though? If everything is >> accessible from setup.cfg, I'd rather just remove the argument. I just

Re: [Numpy-discussion] [matplotlib-devel] Matplotlib and latest numpy

On Fri, Jul 18, 2008 at 7:14 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > On Fri, Jul 18, 2008 at 19:07, Robert Kern <[EMAIL PROTECTED]> wrote: > > > The code generation logic in numpy does not know anything about > > "build_ext --inplace" (which is a distutils feature that develop > > invokes). T

Re: [Numpy-discussion] [matplotlib-devel] Matplotlib and latest numpy

On Fri, Jul 18, 2008 at 08:14:00PM -0500, Robert Kern wrote: > > The code generation logic in numpy does not know anything about > > "build_ext --inplace" (which is a distutils feature that develop > > invokes). That's it. This problem has always existed for all versions > > of numpy whether you us

Re: [Numpy-discussion] [matplotlib-devel] Matplotlib and latest numpy

On Fri, Jul 18, 2008 at 19:07, Robert Kern <[EMAIL PROTECTED]> wrote: > The code generation logic in numpy does not know anything about > "build_ext --inplace" (which is a distutils feature that develop > invokes). That's it. This problem has always existed for all versions > of numpy whether you

Re: [Numpy-discussion] f2py - how to use .pyf files?

On Fri, Jul 18, 2008 at 5:15 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > Probably. What other options would you need, though? If everything is > accessible from setup.cfg, I'd rather just remove the argument. I'd be OK with that too, and simply telling people to ship a companion setup.cfg. It's

Re: [Numpy-discussion] f2py - how to use .pyf files?

On Fri, Jul 18, 2008 at 19:04, Fernando Perez <[EMAIL PROTECTED]> wrote: > On Fri, Jul 18, 2008 at 4:47 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > >> For publicly distributed packages, it does go against the grain. Never >> hard-code the compiler! Use a setup.cfg file, instead. > > Quite all righ

Re: [Numpy-discussion] [matplotlib-devel] Matplotlib and latest numpy

On Fri, Jul 18, 2008 at 19:02, Charles R Harris <[EMAIL PROTECTED]> wrote: > > On Fri, Jul 18, 2008 at 5:53 PM, Robert Kern <[EMAIL PROTECTED]> wrote: >> >> On Fri, Jul 18, 2008 at 18:49, Gael Varoquaux >> <[EMAIL PROTECTED]> wrote: >> > On Fri, Jul 18, 2008 at 06:44:21PM -0500, Robert Kern wrote:

Re: [Numpy-discussion] f2py - how to use .pyf files?

On Fri, Jul 18, 2008 at 4:47 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > For publicly distributed packages, it does go against the grain. Never > hard-code the compiler! Use a setup.cfg file, instead. Quite all right. But this was for in-house code where a group has agreed to all use the same c

Re: [Numpy-discussion] [matplotlib-devel] Matplotlib and latest numpy

On Fri, Jul 18, 2008 at 5:53 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > On Fri, Jul 18, 2008 at 18:49, Gael Varoquaux > <[EMAIL PROTECTED]> wrote: > > On Fri, Jul 18, 2008 at 06:44:21PM -0500, Robert Kern wrote: > >> It's not a setuptools issue at all. "build_ext --inplace" just doesn't > >> ins

Re: [Numpy-discussion] [matplotlib-devel] Matplotlib and latest numpy

On Fri, Jul 18, 2008 at 18:49, Gael Varoquaux <[EMAIL PROTECTED]> wrote: > On Fri, Jul 18, 2008 at 06:44:21PM -0500, Robert Kern wrote: >> It's not a setuptools issue at all. "build_ext --inplace" just doesn't >> install header files. > > Does that mean that python setup.py develop should be banned

Re: [Numpy-discussion] [matplotlib-devel] Matplotlib and latest numpy

On Fri, Jul 18, 2008 at 06:44:21PM -0500, Robert Kern wrote: > It's not a setuptools issue at all. "build_ext --inplace" just doesn't > install header files. Does that mean that python setup.py develop should be banned for numpy? If so I consider it a setuptools issue: one more caveat to learn abo

Re: [Numpy-discussion] f2py - how to use .pyf files?

On Fri, Jul 18, 2008 at 18:35, Fernando Perez <[EMAIL PROTECTED]> wrote: > On Fri, Jul 18, 2008 at 4:26 PM, Robert Kern <[EMAIL PROTECTED]> wrote: >> On Fri, Jul 18, 2008 at 18:19, Fernando Perez <[EMAIL PROTECTED]> wrote: >>> On Fri, Jul 18, 2008 at 3:53 PM, Robert Kern <[EMAIL PROTECTED]> wrote:

Re: [Numpy-discussion] [matplotlib-devel] Matplotlib and latest numpy

On Fri, Jul 18, 2008 at 5:44 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > On Fri, Jul 18, 2008 at 18:40, Gael Varoquaux > <[EMAIL PROTECTED]> wrote: > > On Sat, Jul 19, 2008 at 01:25:51AM +0200, Gael Varoquaux wrote: > >> Am I wrong, or does matploib not build with current numpy svn? > > > > OK, F

Re: [Numpy-discussion] [matplotlib-devel] Matplotlib and latest numpy

On Fri, Jul 18, 2008 at 18:40, Gael Varoquaux <[EMAIL PROTECTED]> wrote: > On Sat, Jul 19, 2008 at 01:25:51AM +0200, Gael Varoquaux wrote: >> Am I wrong, or does matploib not build with current numpy svn? > > OK, Fernando told me that matplotlib builds fine with latest numpy on his > box so Ienquir

Re: [Numpy-discussion] [matplotlib-devel] Matplotlib and latest numpy

On Sat, Jul 19, 2008 at 01:25:51AM +0200, Gael Varoquaux wrote: > Am I wrong, or does matploib not build with current numpy svn? OK, Fernando told me that matplotlib builds fine with latest numpy on his box so Ienquired a bit more. The problem is that the build of matplotlib tries to include a hea

Re: [Numpy-discussion] f2py - how to use .pyf files?

On Fri, Jul 18, 2008 at 4:26 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > On Fri, Jul 18, 2008 at 18:19, Fernando Perez <[EMAIL PROTECTED]> wrote: >> On Fri, Jul 18, 2008 at 3:53 PM, Robert Kern <[EMAIL PROTECTED]> wrote: >> >>> You still need "-m text2", I believe. >> >> Right, thanks. But it sti

Re: [Numpy-discussion] f2py - how to use .pyf files?

On Fri, Jul 18, 2008 at 18:19, Fernando Perez <[EMAIL PROTECTED]> wrote: > On Fri, Jul 18, 2008 at 3:53 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > >> You still need "-m text2", I believe. > > Right, thanks. But it still doesn't quite work. Consider a makefile with > > lib: seglib.so > > seglib.

Re: [Numpy-discussion] f2py - how to use .pyf files?

On Fri, Jul 18, 2008 at 3:53 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > You still need "-m text2", I believe. Right, thanks. But it still doesn't quite work. Consider a makefile with lib: seglib.so seglib.so: Text2.f90 f2py -c --fcompiler=gnu95 -m seglib Text2.f90 pyf: Text2.f90

Re: [Numpy-discussion] integer array creation oddity

2008/7/18 Suchindra Sandhu <[EMAIL PROTECTED]>: > Can someone please explain to me this oddity? > > In [1]: import numpy as n > > In [8]: a = n.array((1,2,3), 'i') > > In [9]: type(a[0]) > Out[9]: There's more than one int32 type lying around. Rather, compare *dtypes*: In [19]: a.dtype == np.in

Re: [Numpy-discussion] f2py - how to use .pyf files?

On Fri, Jul 18, 2008 at 17:39, Fernando Perez <[EMAIL PROTECTED]> wrote: > Howdy, > > again f2py... Since I can't seem to figure out how to pass the > --fcompiler option to f2py via setup.py/distutils, I decided to just > do things for now via a plain makefile. But I'm struggling here too. > The

Re: [Numpy-discussion] numpy.loadtext() fails with dtype + usecols

On Fri, Jul 18, 2008 at 4:16 PM, Ryan May <[EMAIL PROTECTED]> wrote: > Hi, > > I was trying to use loadtxt() today to read in some text data, and I had a > problem when I specified a dtype that only contained as many elements as in > columns in usecols. The example below shows the problem: > > im

[Numpy-discussion] f2py - how to use .pyf files?

Howdy, again f2py... Since I can't seem to figure out how to pass the --fcompiler option to f2py via setup.py/distutils, I decided to just do things for now via a plain makefile. But I'm struggling here too. The problem is this: the call f2py -c --fcompiler=gfortran -m text2 Text2.f90 works pe

Re: [Numpy-discussion] building a better OSX install for 1.1.1

On Fri, Jul 18, 2008 at 3:17 PM, Christopher Burns <[EMAIL PROTECTED]> wrote: > Sorry Russell, I was a bit brief before. > > Installer.app checks for a system requirement when the user installs > numpy. I build numpy using bdist_mpkg against the python.org version of > python (MacPython). If a u

[Numpy-discussion] numpy.loadtext() fails with dtype + usecols

Hi, I was trying to use loadtxt() today to read in some text data, and I had a problem when I specified a dtype that only contained as many elements as in columns in usecols. The example below shows the problem: import numpy as np import StringIO data = '''STID RELH TAIR JOE 70.1 25.3 BOB 60

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

On Fri, Jul 18, 2008 at 2:41 PM, Charles R Harris <[EMAIL PROTECTED]> wrote: There are actually two bugs here which is confusing things. Bug 1) Deleting a numpy scalar doesn't decrement the descr reference count. Bug 2) PyArray_Return decrements the reference to arr, which in turn correctly decr

[Numpy-discussion] integer array creation oddity

Hi, Can someone please explain to me this oddity? In [1]: import numpy as n In [8]: a = n.array((1,2,3), 'i') In [9]: type(a[0]) Out[9]: In [10]: type(a[0]) == n.int32 Out[10]: False When I create an array with 'int', 'int32' etc it works fine What is the type of 'i' and what is n.int0? Th

[Numpy-discussion] f2py_options in setup.py

Howdy, setup.py files with calls like f2py_options = ['--fcompiler=gfortran'], ... when building the extension object used to work. But now I'm trying the same thing with some f90 code and when running the build, it doesn't seem to go through to f2py: maqroll[felipe_fortr

[Numpy-discussion] building a better OSX install for 1.1.1

Sorry Russell, I was a bit brief before. Installer.app checks for a system requirement when the user installs numpy. I build numpy using bdist_mpkg against the python.org version of python (MacPython). If a user tries to install numpy and they _do not_ have this version of python installed, Insta

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

On Fri, Jul 18, 2008 at 12:03 PM, Charles R Harris < [EMAIL PROTECTED]> wrote: > > > Simpler test case: > > import sys, gc > import numpy as np > > def main() : > t = np.dtype(np.float32) > print sys.getrefcount(t) > for i in range(100) : > np.float32() > gc.collect()

Re: [Numpy-discussion] 1.1.0 OSX Installer Fails Under 10.5.3?

In article <[EMAIL PROTECTED]>, "Christopher Burns" <[EMAIL PROTECTED]> wrote: > I've been using bdist_mpkg to build the OSX Installer. I'd like to update > the requirement documentation for the 1.1.1 release candidate to say > "MacPython from python.org" instead of "System Python". bdist_mpkg

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

On Fri, Jul 18, 2008 at 5:15 AM, Michael Abbott <[EMAIL PROTECTED]> wrote: > I'm afraid this is going to be a long one, and I don't see any good way to > cut down the quoted text either... > > Charles, I'm going to plea with you to read what I've just written and > think about it. I'm trying to m

Re: [Numpy-discussion] RFC: A (second) proposal for implementing some date/time types in NumPy

Francesc Alted (el 2008-07-16 a les 18:44:36 +0200) va dir:: > After tons of excellent feedback received for our first proposal about > the date/time types in NumPy Ivan and me have had another brainstorming > session and ended with a new proposal for your consideration. After re-reading the pr

Re: [Numpy-discussion] chararray __mod__ behavior

2008/7/18 Alan McIntyre <[EMAIL PROTECTED]>: > This seems odd to me: > A=np.array([['%.3f','%d'],['%s','%r']]).view(np.chararray) A % np.array([[1,2],[3,4]]) > Traceback (most recent call last): > File "", line 1, in > File "/opt/local/lib/python2.5/site-packages/numpy/core/defchararra

[Numpy-discussion] chararray __mod__ behavior

This seems odd to me: >>> A=np.array([['%.3f','%d'],['%s','%r']]).view(np.chararray) >>> A % np.array([[1,2],[3,4]]) Traceback (most recent call last): File "", line 1, in File "/opt/local/lib/python2.5/site-packages/numpy/core/defchararray.py", line 126, in __mod__ newarr[:] = res ValueE

Re: [Numpy-discussion] Type checking of arrays containing strings

2008/7/18 Arnar Flatberg <[EMAIL PROTECTED]>: > ... and instead of just complaining, I can do something about it :-) Could > you add permissions to me for the documentation editor, username: That's the spirit! You are now added. But I'm worried: I had a bet with Joe that we won't get more than

Re: [Numpy-discussion] Ticket review: #848, leak in PyArray_DescrFromType

I'm afraid this is going to be a long one, and I don't see any good way to cut down the quoted text either... Charles, I'm going to plea with you to read what I've just written and think about it. I'm trying to make the case as clear as I can. I think the case is actually extremely simple: th

Re: [Numpy-discussion] Type checking of arrays containing strings

On Fri, Jul 18, 2008 at 12:38 PM, Arnar Flatberg <[EMAIL PROTECTED]> wrote: > > > On Fri, Jul 18, 2008 at 11:40 AM, Stéfan van der Walt <[EMAIL PROTECTED]> > wrote: > >> 2008/7/18 Arnar Flatberg <[EMAIL PROTECTED]>: >> > I need to check if my array (a) is of type `string`. That is, I dont >> know

Re: [Numpy-discussion] Type checking of arrays containing strings

On Fri, Jul 18, 2008 at 11:40 AM, Stéfan van der Walt <[EMAIL PROTECTED]> wrote: > 2008/7/18 Arnar Flatberg <[EMAIL PROTECTED]>: > > I need to check if my array (a) is of type `string`. That is, I dont know > > the number of characters beforehand, so I cant do a.dtype == '|S*' (* = > > (max) numbe

Re: [Numpy-discussion] Type checking of arrays containing strings

2008/7/18 Arnar Flatberg <[EMAIL PROTECTED]>: > I need to check if my array (a) is of type `string`. That is, I dont know > the number of characters beforehand, so I cant do a.dtype == '|S*' (* = > (max) number of characters) > Looking at my options, I see either a.dtype.kind == 'S' or a.dtype.typ

Re: [Numpy-discussion] interleaved indexing

Hi Amir 2008/7/18 Amir <[EMAIL PROTECTED]>: > A very beginner question about indexing: let x be an array where n = > len(x). I would like to create a view y of x such that: > > y[i] = x[i:i+m,...] for each i and a fixed m << n > > so I can do things like numpy.cov(y). With n large, allocating y i

[Numpy-discussion] Type checking of arrays containing strings

Hi I need to check if my array (a) is of type `string`. That is, I dont know the number of characters beforehand, so I cant do a.dtype == '|S*' (* = (max) number of characters) Looking at my options, I see either a.dtype.kind == 'S' or a.dtype.type == np.string_, might be ok. Are these any of the

[Numpy-discussion] interleaved indexing

A very beginner question about indexing: let x be an array where n = len(x). I would like to create a view y of x such that: y[i] = x[i:i+m,...] for each i and a fixed m << n so I can do things like numpy.cov(y). With n large, allocating y is a problem for me. Currently, I either do for loops in