Re: [matplotlib-devel] 3 test failures

2011-09-18 Thread Jouni K . Seppänen 
Eric Firing  writes:

> image_interp pdf

I bisected this to

79ca159 recover old behavior for 'nearest' interpolation and introduces 'none'. 
close #83

which changes the meaning of "nearest" interpolation but does not change
the corresponding test. I'll send a pull request to fix this soon.

This reminds me: what's the status of the buildbot? Regular buildbot
runs would have caught this much sooner. If I could find some place to
run buildbot, does the git repository contain all the necessary scripts
and configuration or is it more work to set it up?

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[matplotlib-devel] [Basemap] Please explicit mention copyright and license

2011-09-18 Thread Sandro Tosi 
Hello,
I'm packaging basemap for Debian, but as you know, we always have some
problems :)

One important part of Debian packaging is the license/copyright
checks, but for basemap I can't find any explicit indication of them:

for license I have

OSI Approved

that doesn't mean anything (legally speaking): for example, is it BSD
or GPL-3 ? the difference is *huge*

and for copyright I only have the author, but not the years of
validity, except for a single 2006 reference.

Could you please mention them explicitly with the next release of basemap?

Thanks in advance,
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[matplotlib-devel] [Basemap] Don't recompile nad2bin when running setup.py clean

2011-09-18 Thread Sandro Tosi 
Hi,
when running

python setup.py clean

nad2bin is compiled. I've just worked around with the attached patch,
so it would be nice if you can integrate it upstream or come up with a
better solution.

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Re: [matplotlib-devel] [Basemap] Please explicit mention copyright and license

2011-09-18 Thread John Hunter 
On Sun, Sep 18, 2011 at 9:46 AM, Sandro Tosi  wrote:
> Hello,
> I'm packaging basemap for Debian, but as you know, we always have some
> problems :)
>
> One important part of Debian packaging is the license/copyright
> checks, but for basemap I can't find any explicit indication of them:
>
> for license I have
>
>    OSI Approved
>
> that doesn't mean anything (legally speaking): for example, is it BSD
> or GPL-3 ? the difference is *huge*
>
> and for copyright I only have the author, but not the years of
> validity, except for a single 2006 reference.
>
> Could you please mention them explicitly with the next release of basemap?
>
> Thanks in advance,

Take a look at

https://github.com/matplotlib/basemap/blob/master/README

Does this have everything you need?

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Re: [matplotlib-devel] [Basemap] Please explicit mention copyright and license

2011-09-18 Thread Sandro Tosi 
On Sun, Sep 18, 2011 at 16:53, John Hunter  wrote:
> Take a look at
>
> https://github.com/matplotlib/basemap/blob/master/README
>
> Does this have everything you need?

Gaah, I was overwhelmed by the third-party tools copyright/licenses I
missed the basemap ones: thanks John!

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[matplotlib-devel] [Basemap] Add missing shebang in scripts in data/ dir

2011-09-18 Thread Sandro Tosi 
Hello,
there are some scripts in the data/ dir (I'm not even sure they're
needed at all, but they are there) missing the shebang; attached patch
adds it.

Regards,
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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread Fernando Perez 
I'm not sure why, but as of a few weeks ago, with recent builds of
numpy/mpl I always get these warnings:

In [1]: imshow(rand(10,10))
Out[1]: 

In [2]: 
/home/fperez/usr/opt/lib/python2.6/site-packages/matplotlib/colors.py:519:
DeprecationWarning: putmask has been deprecated. Use copyto with
'where' as the mask instead
  np.putmask(xa, xa==1.0, 0.999) #Treat 1.0 as slightly less than 1.
/home/fperez/usr/opt/lib/python2.6/site-packages/matplotlib/colors.py:531:
DeprecationWarning: putmask has been deprecated. Use copyto with
'where' as the mask instead
  np.putmask(xa, xa<0.0, -1)
/home/fperez/usr/opt/lib/python2.6/site-packages/matplotlib/colors.py:535:
DeprecationWarning: putmask has been deprecated. Use copyto with
'where' as the mask instead
  np.putmask(xa, xa>self.N-1, self._i_over)
/home/fperez/usr/opt/lib/python2.6/site-packages/matplotlib/colors.py:536:
DeprecationWarning: putmask has been deprecated. Use copyto with
'where' as the mask instead
  np.putmask(xa, xa<0, self._i_under)


It would be nice to have these gone from master before release.

Cheers,

f

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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread John Hunter 
On Sun, Sep 18, 2011 at 1:44 PM, Fernando Perez  wrote:
> I'm not sure why, but as of a few weeks ago, with recent builds of
> numpy/mpl I always get these warnings:
>
> In [1]: imshow(rand(10,10))
> Out[1]: 
>
> In [2]: 
> /home/fperez/usr/opt/lib/python2.6/site-packages/matplotlib/colors.py:519:
> DeprecationWarning: putmask has been deprecated. Use copyto with
> 'where' as the mask instead
>  np.putmask(xa, xa==1.0, 0.999) #Treat 1.0 as slightly less than 1.
> /home/fperez/usr/opt/lib/python2.6/site-packages/matplotlib/colors.py:531:
> DeprecationWarning: putmask has been deprecated. Use copyto with
> 'where' as the mask instead
>  np.putmask(xa, xa<0.0, -1)
> /home/fperez/usr/opt/lib/python2.6/site-packages/matplotlib/colors.py:535:
> DeprecationWarning: putmask has been deprecated. Use copyto with
> 'where' as the mask instead
>  np.putmask(xa, xa>self.N-1, self._i_over)
> /home/fperez/usr/opt/lib/python2.6/site-packages/matplotlib/colors.py:536:
> DeprecationWarning: putmask has been deprecated. Use copyto with
> 'where' as the mask instead
>  np.putmask(xa, xa<0, self._i_under)
>
>
> It would be nice to have these gone from master before release.

I can fix these putmask calls, but strangely I am not seeing the
deprecation warning on numpy and mpl HEAD

  In [1]: print np.__version__
  2.0.0.dev-aded70c

  In [2]: print matplotlib.__version__
  1.1.0

  In [3]: imshow(rand(10,10))
  Out[3]: 


If I do a simple putmask test I also don't get the warning

  In [4]: x = np.random.rand(10)

  In [5]: np.putmask(x, x<0.5, 0)

Do you have some custom warning or error settings turned on/  What
commit of np are you on?

I like how they have the commit hash in the version number; we need that.

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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread John Hunter 
On Sun, Sep 18, 2011 at 1:17 AM, Christoph Gohlke  wrote:

> The master branch builds OK on Windows and so far almost everything
> worked well.
>
> I have trouble receiving the sample_data from github via cbook.py. There
> are frequent HTTP 304 (Not Modified) and 500 (Internal Server Error)
> exceptions and redirection to
> .

I confirmed this on linux and added an issue on github:
https://github.com/matplotlib/matplotlib/issues/478.  I also assigned
a new tag "release_critical" which we should use as we close in on the
release to mark show-stopper issues.  I assigned this to Jouni since
he wrote most of the original implementation.  Jouni, if you can't get
to this let me know and I'll take a look.

JDH

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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread Fernando Perez 
On Sun, Sep 18, 2011 at 12:05 PM, John Hunter  wrote:
> I can fix these putmask calls, but strangely I am not seeing the
> deprecation warning on numpy and mpl HEAD
>
>  In [1]: print np.__version__
>  2.0.0.dev-aded70c
>
>  In [2]: print matplotlib.__version__
>  1.1.0
>
>  In [3]: imshow(rand(10,10))
>  Out[3]: 

Weird, I'm on the same; I just did a clean git pull right before building:

In [1]: np.__version__
Out[1]: '2.0.0.dev-aded70c'

In [2]: matplotlib.__version__
Out[2]: '1.1.0'

(master)dreamweaver[matplotlib]> git log --oneline | head -1
fcc8039 axisartist: implement LocatorDM, LocatorD, LocatorHM, LocatorH
and update FormatterHMS and FormaterDMS


This is on a linux 10.10 box, 64-bit just in case it matters.  I
haven't tested it on 32-bits.  The problem also appears (at least for
me) on my office box that you have access to.

Happy to test further...

f

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[matplotlib-devel] Quantization of normalized float to uint8

2011-09-18 Thread Christoph Gohlke 
Hello,

matplotlib uses int(x*255) or np.array(x*255, np.uint8) to quantize 
normalized floating point numbers x in the range [0.0 to 1.0] to 
integers in the range [0 to 255]. This way only 1.0 is mapped to 255, 
not for example 0.999. Is this really intended or would not the largest 
floating point number below 256.0 be a better scale factor than 255? The 
exact factor depends on the floating point precision (~255.92 for 
np.float32, ~255.93 for np.float16).

Christoph

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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread Eric Firing 
On 09/18/2011 09:24 AM, Fernando Perez wrote:
> On Sun, Sep 18, 2011 at 12:05 PM, John Hunter  wrote:
>> I can fix these putmask calls, but strangely I am not seeing the
>> deprecation warning on numpy and mpl HEAD

putmask was deprecated in favor of copyto only 2 months ago; copyto 
didn't even exist before that. So we certainly can't replace putmask 
with copyto in mpl.

http://currents.soest.hawaii.edu/hgstage/numpy_from_git/rev/26533521322b

Eric


>>
>>   In [1]: print np.__version__
>>   2.0.0.dev-aded70c
>>
>>   In [2]: print matplotlib.__version__
>>   1.1.0
>>
>>   In [3]: imshow(rand(10,10))
>>   Out[3]:
>
> Weird, I'm on the same; I just did a clean git pull right before building:
>
> In [1]: np.__version__
> Out[1]: '2.0.0.dev-aded70c'
>
> In [2]: matplotlib.__version__
> Out[2]: '1.1.0'
>
> (master)dreamweaver[matplotlib]>  git log --oneline | head -1
> fcc8039 axisartist: implement LocatorDM, LocatorD, LocatorHM, LocatorH
> and update FormatterHMS and FormaterDMS
>
>
> This is on a linux 10.10 box, 64-bit just in case it matters.  I
> haven't tested it on 32-bits.  The problem also appears (at least for
> me) on my office box that you have access to.
>
> Happy to test further...
>
> f
>
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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread Fernando Perez 
On Sun, Sep 18, 2011 at 12:41 PM, John Hunter  wrote:
>
> I'm on 11.04, 64 bit also.
>
> What does this give you?
>
>  > ython -c 'import numpy as np; print np.__version__; x =
> np.random.rand(10); np.putmask(x, x<0.5, 0.)'
>
> I only get the version string 2.0.0.dev-aded70c, no warning.

It seems to be python version-dependent, my system python is 2.6 and I
get the warning:

(master)dreamweaver[matplotlib]> python -c 'import numpy as np; print
np.__version__; x = np.random.rand(10); np.putmask(x, x<0.5, 0.)'
2.0.0.dev-aded70c
-c:1: DeprecationWarning: putmask has been deprecated. Use copyto with
'where' as the mask instead

but with 2.7 I don't:

(master)dreamweaver[matplotlib]> python2.7 -c 'import numpy as np;
print np.__version__; x = np.random.rand(10); np.putmask(x, x<0.5,
0.)'
2.0.0.dev-aded70c


Cheers,

f

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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread John Hunter 
> putmask was deprecated in favor of copyto only 2 months ago; copyto
> didn't even exist before that. So we certainly can't replace putmask
> with copyto in mpl.
>
> http://currents.soest.hawaii.edu/hgstage/numpy_from_git/rev/26533521322b


The putmasks in colors.py are simple and could be replaced by a simple
boolean, mask eg replace

  np.putmask(xa, xa==1.0, 0.999) #Treat 1.0 as slightly less than 1.

with

  xa[xa==1.0]  = 0.999 #Treat 1.0 as slightly less than 1.

In quiver.py, there appear to be some broadcasting shape issues that
make this trickier, eg in

short = np.repeat(length < minsh, 8, axis=1)
# Now select X0, Y0 if short, otherwise X, Y
np.putmask(X, short, X0)

Since much of quiver.py is your code I believe Eric, maybe you can
come up with something that doesn't rely on putmasking and just uses
plain vanilla boolean arrays of the right shape?

JDH

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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread Eric Firing 
On 09/18/2011 09:54 AM, John Hunter wrote:
>> putmask was deprecated in favor of copyto only 2 months ago; copyto
>> didn't even exist before that. So we certainly can't replace putmask
>> with copyto in mpl.
>>
>> http://currents.soest.hawaii.edu/hgstage/numpy_from_git/rev/26533521322b
>
>
> The putmasks in colors.py are simple and could be replaced by a simple
> boolean, mask eg replace
>
>np.putmask(xa, xa==1.0, 0.999) #Treat 1.0 as slightly less than 1.
>
> with
>
>xa[xa==1.0]  = 0.999 #Treat 1.0 as slightly less than 1.
>
> In quiver.py, there appear to be some broadcasting shape issues that
> make this trickier, eg in
>
>  short = np.repeat(length<  minsh, 8, axis=1)
>  # Now select X0, Y0 if short, otherwise X, Y
>  np.putmask(X, short, X0)
>
> Since much of quiver.py is your code I believe Eric, maybe you can
> come up with something that doesn't rely on putmasking and just uses
> plain vanilla boolean arrays of the right shape?

I really don't want to mess with this now; putmask was used because it 
is *much* faster than boolean indexing (after I supplied the 
fast_putmask code to numpy back in 2007).  And I did that because it 
removed a genuine, significant bottleneck in mpl.  Now, with Mark 
Wiebe's modifications to numpy, putmask is obsolete.  His copyto is as 
fast, and boolean indexing might even be good enough now.  But the next 
mpl release is not targeted at numpy 2.0.  It will be used with older 
versions as well, and probably most often.

We will need to deal with the deprecation of putmask, but this is not 
the time to do it, unless there is a way to do it that does *not* change 
the present actual *use* of putmask, but merely tells numpy to shut up 
about it.  I don't know why it is complaining; I don't think that it is 
normal procedure to start issuing warnings the minute a replacement 
(copyto) appears.

We are trying to get a release out without introducing major breakage. 
It is a bad time to muck around with internals like the use of putmask.

Eric

>
> JDH


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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread Eric Firing 
On 09/18/2011 09:54 AM, John Hunter wrote:
>> putmask was deprecated in favor of copyto only 2 months ago; copyto
>> didn't even exist before that. So we certainly can't replace putmask
>> with copyto in mpl.
>>
>> http://currents.soest.hawaii.edu/hgstage/numpy_from_git/rev/26533521322b
>
>
> The putmasks in colors.py are simple and could be replaced by a simple
> boolean, mask eg replace
>
>np.putmask(xa, xa==1.0, 0.999) #Treat 1.0 as slightly less than 1.
>
> with
>
>xa[xa==1.0]  = 0.999 #Treat 1.0 as slightly less than 1.
>
> In quiver.py, there appear to be some broadcasting shape issues that
> make this trickier, eg in
>
>  short = np.repeat(length<  minsh, 8, axis=1)
>  # Now select X0, Y0 if short, otherwise X, Y
>  np.putmask(X, short, X0)
>
> Since much of quiver.py is your code I believe Eric, maybe you can
> come up with something that doesn't rely on putmasking and just uses
> plain vanilla boolean arrays of the right shape?
>
> JDH

John,

There is a way to deal with this now: define our own copyto which uses 
np.copyto if it exists, and falls back on putnav otherwise.  I think 
this can be done with reasonable safety and no loss of performance.  The 
only question is where to put our copyto.  I think a new compat.py would 
make sense as a home for this sort of version compatibility interface 
code.  We may need a lot more in the future as numpy evolves.

Eric

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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread Eric Firing 
On 09/18/2011 09:46 AM, Fernando Perez wrote:
> On Sun, Sep 18, 2011 at 12:41 PM, John Hunter  wrote:
>>
>> I'm on 11.04, 64 bit also.
>>
>> What does this give you?
>>
>>   >  ython -c 'import numpy as np; print np.__version__; x =
>> np.random.rand(10); np.putmask(x, x<0.5, 0.)'
>>
>> I only get the version string 2.0.0.dev-aded70c, no warning.
>
> It seems to be python version-dependent, my system python is 2.6 and I
> get the warning:
>
> (master)dreamweaver[matplotlib]>  python -c 'import numpy as np; print
> np.__version__; x = np.random.rand(10); np.putmask(x, x<0.5, 0.)'
> 2.0.0.dev-aded70c
> -c:1: DeprecationWarning: putmask has been deprecated. Use copyto with
> 'where' as the mask instead
>
> but with 2.7 I don't:
>
> (master)dreamweaver[matplotlib]>  python2.7 -c 'import numpy as np;
> print np.__version__; x = np.random.rand(10); np.putmask(x, x<0.5,
> 0.)'
> 2.0.0.dev-aded70c

Right.

http://docs.python.org/dev/whatsnew/2.7.html explains the change in 
handling DeprecationWarning.

Eric

>
>
> Cheers,
>
> f
>
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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread John Hunter 
On Sun, Sep 18, 2011 at 4:02 PM, Eric Firing  wrote:
> There is a way to deal with this now: define our own copyto which uses
> np.copyto if it exists, and falls back on putnav otherwise.  I think this
> can be done with reasonable safety and no loss of performance.  The only
> question is where to put our copyto.  I think a new compat.py would make
> sense as a home for this sort of version compatibility interface code.  We
> may need a lot more in the future as numpy evolves.

We used to put these in cbook I believe; eg functions that existed in
python2.3 that we wanted to use but weren't defined in python2.2 which
we supported.  We could prefix them with a leading underscore to steer
users away from them

def _copyto(...):
   # temporary function to use numpy's copyto if it is defined, else
putmask; this function will be deprecated when we support only numpy
2.0 and later
   ...

I'd be in favor of doing this, because deprecations warnings are a nuisance.

JDH

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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread Fernando Perez 
On Sun, Sep 18, 2011 at 2:02 PM, Eric Firing  wrote:
> There is a way to deal with this now: define our own copyto which uses
> np.copyto if it exists, and falls back on putnav otherwise.  I think
> this can be done with reasonable safety and no loss of performance.  The
> only question is where to put our copyto.  I think a new compat.py would
> make sense as a home for this sort of version compatibility interface
> code.  We may need a lot more in the future as numpy evolves.

If you want to just silence this particular warning, it can be done
with this code:

import warnings
warnings.filterwarnings('ignore', 'putmask has been deprecated',
DeprecationWarning)

That would be enough to keep numpy quiet about this for now...

Cheers,

f

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Re: [matplotlib-devel] Quantization of normalized float to uint8

2011-09-18 Thread Eric Firing 
On 09/18/2011 09:30 AM, Christoph Gohlke wrote:
> Hello,
>
> matplotlib uses int(x*255) or np.array(x*255, np.uint8) to quantize
> normalized floating point numbers x in the range [0.0 to 1.0] to
> integers in the range [0 to 255]. This way only 1.0 is mapped to 255,
> not for example 0.999. Is this really intended or would not the largest
> floating point number below 256.0 be a better scale factor than 255? The
> exact factor depends on the floating point precision (~255.92 for
> np.float32, ~255.93 for np.float16).
>
> Christoph

Christoph,

It's a reasonable question; but do you have use cases in mind where it 
actually makes a difference?

The simple scaling with truncation is used in many places, both in the 
python and the c++ code.

Eric

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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread Eric Firing 
On 09/18/2011 11:15 AM, John Hunter wrote:
> On Sun, Sep 18, 2011 at 4:02 PM, Eric Firing  wrote:
>> There is a way to deal with this now: define our own copyto which uses
>> np.copyto if it exists, and falls back on putnav otherwise.  I think this
>> can be done with reasonable safety and no loss of performance.  The only
>> question is where to put our copyto.  I think a new compat.py would make
>> sense as a home for this sort of version compatibility interface code.  We
>> may need a lot more in the future as numpy evolves.
>
> We used to put these in cbook I believe; eg functions that existed in
> python2.3 that we wanted to use but weren't defined in python2.2 which
> we supported.  We could prefix them with a leading underscore to steer
> users away from them
>
> def _copyto(...):
> # temporary function to use numpy's copyto if it is defined, else
> putmask; this function will be deprecated when we support only numpy
> 2.0 and later
> ...
>
> I'd be in favor of doing this, because deprecations warnings are a nuisance.
>
> JDH

See
https://github.com/matplotlib/matplotlib/pull/480

Eric

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Re: [matplotlib-devel] release: stalled again?

2011-09-18 Thread Jouni K . Seppänen 
John Hunter  writes:

> I confirmed this on linux and added an issue on github:
> https://github.com/matplotlib/matplotlib/issues/478.  

Pull request #479 fixes the immediate problem, but for the long term we
should fix the handling of redirection in get_sample_data.

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