Re: [Numpy-discussion] proposal: min, max of complex should give warning

2013-12-31 Thread Cera, Tim
I don't work with complex numbers, but just sampling what others do:


Python: no ordering, results in TypeError

Matlab: sorts by magnitude
http://www.mathworks.com/help/matlab/ref/sort.html

R: sorts first by real, then by imaginary
http://stat.ethz.ch/R-manual/R-patched/library/base/html/sort.html

Numpy: sorts first by real, then by imaginary (the documentation link
below calls this sort 'lexicographical' which I don't think is
correct)
http://docs.scipy.org/doc/numpy/reference/generated/numpy.sort.html


I would think that the Matlab sort might be more useful, but easy
enough by using the absolute value.

I think what Numpy does is normal enough to not justify a warning, but
leave this to others because as I pointed out in the beginning I don't
work with complex numbers.

Kindest regards,
Tim
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Re: [Numpy-discussion] PEP8

2013-09-09 Thread Cera, Tim
I made a PR request about supplying a git hooks framework at
https://github.com/numpy/numpy/pull/200.  I asked for it to be closed
because I couldn't easily figure our how to handle x-platform issues.
If you have an answer, what I was working on might be a start.  But
your script is an example of the x-platform challenges since it will
only run on Windows that has a Linux environment installed (Mingw or
the like).

What I have started to use in my projects is 'tox', 'coverage', and
'flake8'.  Really nice stuff.  There is an issue though with the
'flake8' report.  There are only very localized places in a few files
that I want to ignore some portion or other of PEP8, so I don' t
insist that 'flake8' pass, I just ignore the output where I need to
ignore it.  Usually what I want to ignore is the spaces around
brackets and commas in order to line up array values as mentioned in
an earlier post within this thread.  Here is an example of my project
setup based in part on 'cookiecutter' -
https://bitbucket.org/timcera/astronomia/src.  Yes, I use bitbucket -
so sue me.  Magic happens inside the 'tox.ini' file.

I suspect that for numpy, making something like 'flake8' part of the
tests would work better than 'autopep8'.  'autopep8' can be configured
to just report with the --list-fixes option, which would give people a
little more confidence to use it rather that it's primary mission as
an editor.  Another plug for 'flake8'; it can be configured on a file
by file basis to ignore particular errors or warnings, and exits with
an error status if the file doesn't pass.

I do think the idea has merit, but this entire process would be a lot
of work and I am not stepping forward to do it.  At this point I
simply have to say that I am a 'balcony muppet'.  Much thanks to Josef
for the reminder about where I learned my curmudgeony ways.  Those
guys made the show!

Kindest regards,
Tim

On Mon, Sep 9, 2013 at 12:08 PM, Blake Griffith
blake.a.griff...@gmail.com wrote:
 I think a good solution would to use add a git_hooks directory with a
 pre-commit git hook along with an git hook installation script. And a note
 should be added to DEV_README.txt suggesting installing the git hooks for
 pep8 compatibility. I personally use this as a pre-commit

 #!/bin/sh

 FILES=$(git diff --cached --name-status | grep -v ^D | awk '$1 $2 { print
 $2}' | grep -e .py$)
 if [ -n $FILES ]; then
 pep8 -r $FILES
 fi

 which is from here: https://gist.github.com/lentil/810399#comment-303703


 On Mon, Sep 9, 2013 at 10:54 AM, Nathaniel Smith n...@pobox.com wrote:

 On Mon, Sep 9, 2013 at 3:29 PM, Charles R Harris
 charlesr.har...@gmail.com wrote:
 
 
 
  On Mon, Sep 9, 2013 at 8:12 AM, Richard Hattersley
  rhatters...@gmail.com
  wrote:
 
   Something we have done in matplotlib is that we have made PEP8 a part
   of
   the tests.
 
  In Iris and Cartopy we've also done this and it works well. While we
  transition we have an exclusion list (which is gradually getting
  shorter).
  We've had mixed experiences with automatic reformatting, so prefer to
  keep
  the human in the loop.
 
 
  I agree with keeping a human in the loop, the script would be intended
  to
  get things into the right neighborhood, the submitter would have to
  review
  the changes after. If the script isn't too strict there will be than one
  way
  to do some things and those bits would rely on the good taste of the
  coder.

 So if I understand right, the goal is to have some script that
 developers can run before (or after) submitting a PR, like
   tools/autopep8-my-changes numpy/
 that will fix up their changes, but leave the rest of numpy alone?

 And the proposed mechanism is to come up with a combination of changes
 to the numpy source and an autopep8 configuration such that
   autopep8 --our-config numpy/
 becomes a no-op, and then we can use this as an implementation of
 tools/autopep8-my-changes?

 If that's right then my feeling is that the goal seems worthwhile but
 the approach seems difficult and unlikely to survive for long. As soon
 as someone overrides autopep8 once, we either have to disable the rule
 for the whole project or keep overriding it manually forever. You're
 already suggesting taking out the spaces-around-arithmetic rule, which
 strikes me as one of the most useful -- sure, it gets things wrongs
 sometimes, but I feel like we're constantly reviewing PRs where
 all*the*(arithmetic+is)-written**like*this.

 Maybe a better approach would be to spend that time hacking up some
 script that uses git and autopep8 together to run autopep8 over all
 and only those lines which the current branch has actually touched?
 It's pretty easy to parse 'git diff' output to get a list of all line
 numbers which have been modified, and then we could run autopep8 over
 the modified files and pull out only those changes which touch those
 lines.

 -n

 P.S.: definitely [:, :, 2]
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Re: [Numpy-discussion] (no subject)

2013-09-03 Thread Cera, Tim
 I am trying to take the rfft of a numpy array, like this:
 my_rfft = numpy.fft.rfft(my_numpy_array)

 and replace the amplitudes that can be obtained with:

 my_amplitudes = numpy.abs(my_rfft)

 with amplitudes from an arbitrary numpy array's rFFT, which is to then be
 converted back using numpy.fft.irfft .  Alternately, some future plans will
 involve having to modify individual array element amplitudes directly based
 on other parameters.  I would think that modifying and re-synthesizing
 signals using FFT is a fairly common use-case, but my attempts at Googling
 example code have been fruitless.

I have FFT transform filter in my tidal analysis package.   See
http://sourceforge.net/apps/mediawiki/tappy/index.php?title=CompareTidalFilters
for a comparison and short description.

See my function below.  My earlier self made some poor variable name
choices.  The 'low_bound' variable is actually where frequencies
greater are set to zero ('factor[freq  low_bound] = 0.0'), then
factor is ramped from 0 at 'low_bound' to 1 at 'high_bound'.  To
filter out tidal signals if your water elevations are hourly then
'low_bound' = 1/30.0 and 'high_bound' = 1/40.0.  Having this gradual
change in the frequency domain rather than an abrupt change makes a
better filter.

def fft_lowpass(nelevation, low_bound, high_bound):
  Performs a low pass filter on the nelevation series.
 low_bound and high_bound specifies the boundary of the filter.
 
 import numpy.fft as F
 if len(nelevation) % 2:
 result = F.rfft(nelevation, len(nelevation))
 else:
 result = F.rfft(nelevation)
 freq = F.fftfreq(len(nelevation))[:len(nelevation)/2]
 factor = np.ones_like(result)
 factor[freq  low_bound] = 0.0

 sl = np.logical_and(high_bound  freq, freq  low_bound)

 a = factor[sl]
 # Create float array of required length and reverse
 a = np.arange(len(a) + 2).astype(float)[::-1]

 # Ramp from 1 to 0 exclusive
 a = (a/a[0])[1:-1]

 # Insert ramp into factor
 factor[sl] = a

 result = result * factor
 print 'result=', len(result)
 relevation = F.irfft(result, len(nelevation))
 print 'result=', len(relevation)
 return relevation


Kindest regards,
Tim
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[Numpy-discussion] Strange behavior with boolean slices...

2013-08-25 Thread Cera, Tim
I have done this before, but am now really confused.

Created an array 'day' specifying the 'f' type

In [29]: day
Out[29]: array([ 5.,  5.], dtype=float32)

# Have a mask...
In [30]: mask
Out[30]: array([ True, False], dtype=bool)

# So far, so good...
In [31]: day[mask]
Out[31]: array([ 5.], dtype=float32)

In [32]: day[mask] = 10

# What?
In [33]: day
Out[33]: array([ 10.,  10.], dtype=float32)


So I created an integer array 'a'

In [38]: a
Out[38]: array([11,  1])

In [39]: a[mask]
Out[39]: array([11])

In [40]: a[mask] = 12

# This is what I expect.
In [41]: a
Out[41]: array([12,  1])

Am I missing something?  Is this supposed to happen?

Version 1.7.1.

Kindest regards,
Tim
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Re: [Numpy-discussion] Strange behavior with boolean slices...

2013-08-25 Thread Cera, Tim
Figured it out.  I created 'day' as a broadcast array.  Does this
catch other people?  Basically changing day[0] would change the entire
'day' array.  I guess all other elements of the day array are views of
day[0].  Made a copy and everything works as expected.

Kindest regards,
Tim

On Sun, Aug 25, 2013 at 8:44 PM, Eric Firing efir...@hawaii.edu wrote:
 On 2013/08/25 2:30 PM, Cera, Tim wrote:
 I have done this before, but am now really confused.

 Created an array 'day' specifying the 'f' type

 In [29]: day
 Out[29]: array([ 5.,  5.], dtype=float32)

 # Have a mask...
 In [30]: mask
 Out[30]: array([ True, False], dtype=bool)

 # So far, so good...
 In [31]: day[mask]
 Out[31]: array([ 5.], dtype=float32)

 In [32]: day[mask] = 10

 # What?
 In [33]: day
 Out[33]: array([ 10.,  10.], dtype=float32)

 I'm not getting that with 1.7.0:
 In [2]: np.__version__
 Out[2]: '1.7.0'

 In [3]: mask = np.array([True, False], dtype=bool)

 In [4]: day = np.array([5, 5], dtype=np.float32)

 In [5]: day
 Out[5]: array([ 5.,  5.], dtype=float32)

 In [6]: mask
 Out[6]: array([ True, False], dtype=bool)

 In [7]: day[mask]
 Out[7]: array([ 5.], dtype=float32)

 In [8]: day[mask] = 10

 In [9]: day
 Out[9]: array([ 10.,   5.], dtype=float32)

 Eric




 So I created an integer array 'a'

 In [38]: a
 Out[38]: array([11,  1])

 In [39]: a[mask]
 Out[39]: array([11])

 In [40]: a[mask] = 12

 # This is what I expect.
 In [41]: a
 Out[41]: array([12,  1])

 Am I missing something?  Is this supposed to happen?

 Version 1.7.1.

 Kindest regards,
 Tim
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Re: [Numpy-discussion] Strange behavior with boolean slices...

2013-08-25 Thread Cera, Tim
Pardon the noise.  The behavior is described right there in the
documentation of broadcast_arrays.

Kindest regards,
Tim

On Sun, Aug 25, 2013 at 8:53 PM, Cera, Tim t...@cerazone.net wrote:
 Figured it out.  I created 'day' as a broadcast array.  Does this
 catch other people?  Basically changing day[0] would change the entire
 'day' array.  I guess all other elements of the day array are views of
 day[0].  Made a copy and everything works as expected.

 Kindest regards,
 Tim

 On Sun, Aug 25, 2013 at 8:44 PM, Eric Firing efir...@hawaii.edu wrote:
 On 2013/08/25 2:30 PM, Cera, Tim wrote:
 I have done this before, but am now really confused.

 Created an array 'day' specifying the 'f' type

 In [29]: day
 Out[29]: array([ 5.,  5.], dtype=float32)

 # Have a mask...
 In [30]: mask
 Out[30]: array([ True, False], dtype=bool)

 # So far, so good...
 In [31]: day[mask]
 Out[31]: array([ 5.], dtype=float32)

 In [32]: day[mask] = 10

 # What?
 In [33]: day
 Out[33]: array([ 10.,  10.], dtype=float32)

 I'm not getting that with 1.7.0:
 In [2]: np.__version__
 Out[2]: '1.7.0'

 In [3]: mask = np.array([True, False], dtype=bool)

 In [4]: day = np.array([5, 5], dtype=np.float32)

 In [5]: day
 Out[5]: array([ 5.,  5.], dtype=float32)

 In [6]: mask
 Out[6]: array([ True, False], dtype=bool)

 In [7]: day[mask]
 Out[7]: array([ 5.], dtype=float32)

 In [8]: day[mask] = 10

 In [9]: day
 Out[9]: array([ 10.,   5.], dtype=float32)

 Eric




 So I created an integer array 'a'

 In [38]: a
 Out[38]: array([11,  1])

 In [39]: a[mask]
 Out[39]: array([11])

 In [40]: a[mask] = 12

 # This is what I expect.
 In [41]: a
 Out[41]: array([12,  1])

 Am I missing something?  Is this supposed to happen?

 Version 1.7.1.

 Kindest regards,
 Tim
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Re: [Numpy-discussion] Deprecation of financial routines

2013-08-19 Thread Cera, Tim
On Mon, Aug 19, 2013 at 2:37 AM, Juan Luis Cano juanlu...@gmail.com wrote:

 As now master is open for 1.9, following the discussion opened here

 https://github.com/numpy/numpy/issues/2880

 it was suggested that we deprecate and eventually remove the financial
 functions in NumPy, because they pollute the main namespace and some are
 unimplemented. We could put them in a separate package, in case it
 doesn't exist yet. Nathaniel Smith and Ralf Gommers already gave +1, and
 Charles Harris suggested bringing this up in the mailing list.

When I was initially working with the docs it galled me to find
documented, but unimplemented financial functions.  I spent the time
to implement all of the unimplemented functions. As an example see
https://github.com/numpy/numpy/pull/190.  I just glanced through the
code and all functions are there, implemented and documented, so I
don't know where that comment came from in
https://github.com/numpy/numpy/issues/2880.  Definitely in 1.7.

About whether they should stay or go, I vote 0.  I see financial
functions as an absolute requirement in engineering (though often
engineers allow financial optimization and decisions to default to
others, IMO a big mistake).  Financial analysis in science?  Probably
not so much, which is my guess as to why the discussion was brought
up.

Since I wrote a couple of the financial functions, you would think I
might vote -1 to deprecation, but the reason I wrote the functions was
to remove the NotImplemented errors.  They really bothered me.  I
thought that if the functions were already included in numpy, they
must be useful to someone.  For me, typically I do any financial work
in a spreadsheet - that is why I vote 0.

Kindest regards,
Tim
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Re: [Numpy-discussion] Is there a way to reset an accumulate function?

2012-10-24 Thread Cera, Tim
On Wed, Oct 24, 2012 at 4:47 AM, Robert Kern robert.k...@gmail.com wrote:

 How about this?


 def nancumsum(x):
 nans = np.isnan(x)
 x = np.array(x)
 x[nans] = 0
 reset_idx = np.zeros(len(x), dtype=int)
 reset_idx[nans] = np.arange(len(x))[nans]
 reset_idx = np.maximum.accumulate(reset_idx)
 cumsum = np.cumsum(x)
 cumsum = cumsum - cumsum[reset_idx]
 return cumsum


Thank you for putting in the time to look at this.

It doesn't work for the first group of numbers if x[0] is non-zero.  Could
perhaps concatenate a np.nan at the beginning to force a reset and adjust
the returned array to not include the dummy value...

def nancumsum(x):
x = np.concatenate(([np.nan], x))
nans = np.isnan(x)
x = np.array(x)
x[nans] = 0
reset_idx = np.zeros(len(x), dtype=int)
reset_idx[nans] = np.arange(len(x))[nans]
reset_idx = np.maximum.accumulate(reset_idx)
cumsum = np.cumsum(x)
cumsum = cumsum - cumsum[reset_idx]
return cumsum[1:]

 a
array([  4.,   1.,   2.,   0.,  18.,   5.,   6.,   0.,   8.,   9.],
dtype=float32)

If no np.nan, then 'nancumsum' and 'np.cumsum' should be the same...

 np.cumsum(a)
array([  4.,   5.,   7.,   7.,  25.,  30.,  36.,  36.,  44.,  53.],
dtype=float32)

 nancumsum(a)
array([  4.,   5.,   7.,   7.,  25.,  30.,  36.,  36.,  44.,  53.])

 a[3] = np.nan

 np.cumsum(a)
array([  4.,   5.,   7.,  nan,  nan,  nan,  nan,  nan,  nan,  nan],
dtype=float32)

 nancumsum(a)
array([  4.,   5.,   7.,   0.,  18.,  23.,  29.,  29.,  37.,  46.])

Excellent!

Kindest regards,
Tim
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[Numpy-discussion] Is there a way to reset an accumulate function?

2012-10-23 Thread Cera, Tim
I have an array that is peppered throughout in random spots with 'nan'.  I
would like to use 'cumsum', but I want it to reset the accumulation to 0
whenever a 'nan' is encountered.  Is there a way to do this?  Aside from a
loop - which is what I am going to setup here in a moment.

Kindest regards,
Tim
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Re: [Numpy-discussion] [numpy] ENH: Initial implementation of a 'neighbor' calculation (#303)

2012-10-15 Thread Cera, Tim
On Sun, Oct 14, 2012 at 8:24 PM, Zachary Pincus zachary.pin...@yale.eduwrote:

 It would be useful for the author of the PR to post a detailed comparison
 of this functionality with scipy.ndimage.generic_filter, which appears to
 have very similar functionality.


I'll be durned.   I created neighbor because I didn't find what I wanted,
and to find now that I just didn't look in the right place is well ...
 Let's just say that I went for a long run last night.

Searching for ndimage, I found that is has been around a long, long time.
 First in numarray, then moved to scipy.

Really I could only nitpick about minor differences - kinda like a primary
political campaign.  On the face of it though, generic_filter looks better.
 First off it is written in C so likely will be faster and more efficient
memory use.  I didn't look at optimizing neighbor at all and at least my
part of it is pure Python.  Of course for all of the small differences, I
like my choices better.  :-)

I would like to make a mild suggestion.  Emphasis on mild.  Maybe ndimage,
in all or in part, should be brought into (back into?) Numpy and renamed.

About the PR.  Given that the neighbor functionality exists already, I will
close the PR later today.  Move along, nothing to see here...

Side note:  I wrote arraypad with the future idea that it would become
easyish to include that functionality in other places, for example in
neighbor.  A Don't Repeat Yourself idea.  Previously I had only seen
Fortran pad capabilities in some of the Fast Fourier Transform functions.
The generic_filter function includes several padding functions - written in
C.  This means that if arraypad needs be more efficient we have C code to
base a better arraypad.

Another side node:  The measurements functions in ndimage are called zonal
functions in the GIS field.

Kindest regards,
Tim
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Re: [Numpy-discussion] Fwd: [numpy] ENH: Initial implementation of a 'neighbor' calculation (#303)

2012-10-12 Thread Cera, Tim
For the neighbor module, the neighborhood is input specified by the
'weight' array.  All values in the neighborhood are processed by a function.

In the geosciences, ArcGIS is a very important tool and the neighbor module
is very loosely modeled after
http://webhelp.esri.com/arcgisdesktop/9.2/index.cfm?TopicName=An%20overview%20of%20the%20Neighborhood%20tools

If the language is confusing, now is the time to change the names.

Kindest regards,
Tim

On Fri, Oct 12, 2012 at 8:33 AM, Sturla Molden stu...@molden.no wrote:

 On 10.10.2012 15:42, Nathaniel Smith wrote:
  This PR submitted a few months ago adds a substantial new API to numpy,
  so it'd be great to get more review. No-one's replied yet, though...
 
  Any thoughts, anyone? Is it useful, could it be better...?

 Fast neighbor search is what scipy.spatial.cKDTree is designed for.
 There is an brand new version in SciPy master.

 Sturla
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Re: [Numpy-discussion] Fwd: [numpy] ENH: Initial implementation of a 'neighbor' calculation (#303)

2012-10-12 Thread Cera, Tim
If you followed the link
http://webhelp.esri.com/arcgisdesktop/9.2/index.cfm?TopicName=An%20overview%20of%20the%20Neighborhood%20tools
note
that the current neighborhood implementation that we are talking about
implements the ArcGIS 'Focal*' functionality, not the 'Block*' ones.  Note
also that ArcGIS is limited to 2-d, and a 3x3 neighborhood.

Kindest regards,
Tim
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Re: [Numpy-discussion] Fwd: [numpy] ENH: Initial implementation of a 'neighbor' calculation (#303)

2012-10-10 Thread Cera, Tim
On Wed, Oct 10, 2012 at 1:58 AM, Travis E. Oliphant 
notificati...@github.com wrote:

 I'm not sure what to make of no comments on this PR. This seems like a
 useful addition. @timcera https://github.com/timcera are you still
 interested in having this PR merged?


Yes.

I mentioned in PR comments that the lack of discussion is because my code
engenders speechless awe in anyone who looks at it.  :-)   Of course
speechless awe can come from two different reasons!  Hopefully it is
because my code is so awesome.

Seriously, I really wanted some input, especially after I found
#31https://github.com/numpy/numpy/issues/31
.


On Wed, Oct 10, 2012 at 7:24 AM, Eric Moore notificati...@github.com
 wrote:

 This seems to be trying to solve a very similar problem to 
 #31https://github.com/numpy/numpy/issues/31

Internally I implemented something like rolling window, but I don't return
the windows.  Instead the contents of the windows are used for calculation
of each windows 'central' cell in the results array.

After seeing the rolling window function I thought it might be nice to
bring that out into a callable function, so that similar functionality
would be available.  That particular function isn't useful to me directly,
but perhaps others?

Kindest regards,
Tim
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Re: [Numpy-discussion] Multidimensional neighbours

2012-08-16 Thread Cera, Tim
I have a pull request for a neighborhood function at
https://github.com/numpy/numpy/pull/303 .   I think IMHO it handles these
problems quite handily.  It does rely on my pad routine that is in Numpy
1.7, so you would need to get the 1.7 beta installed or install the
development branch.

For your example you would just create a weight array, and a function that
returns a scalar value from the collected neighborhood values.

Untested, but workflow is something like:

 inputarr = np.random.random(9*9*9)
 inputarr = inputarr.reshape((9,9,9))
 weight = np.ones((3,3,3))
 ans = neighbor(inputarr, weight, np.mean, pad = None)

In place of 'np.mean' you can define your own function - game of life
function for example.

The PR has not had much activity, so if you can review/comment/program that
would be appreciated.

Kindest regards,
Tim
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Re: [Numpy-discussion] Looking for the most important bugs, documentation needs, etc.

2012-07-10 Thread Cera, Tim
 For documentation we have docstrings for each function and tutorial-style
 docs (http://docs.scipy.org/doc/numpy/user/,
 http://scipy-lectures.github.com/intro/numpy/index.html) . All docstrings
 should have clear usage examples, but I'm actually finding it quite hard to
 find functions that don't have any right now. The only one I could dig up
 so quickly is corrcoef(). There must be a few more.


The documentation wiki has a little known feature to list functions that do
not have docstrings and docstrings that do not have examples.

Go to http://docs.scipy.org/numpy/search/ and click on the 'No Examples' or
'No Documentation' links.

Same searches are available with scipy at
http://docs.scipy.org/scipy/search/, which Ralf already pointed out needs
the most work.

Kindest regards,
Tim
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Re: [Numpy-discussion] Meta: help, devel and stackoverflow

2012-06-28 Thread Cera, Tim
Similar to http://scicomp.stackexchange.com there is
http://meta.programmers.stackexchange.com/ intended for programmers.  Darn
it, there are choices involved!

I had proposed http://meta.programmers.stackexchange.com/ on this mailing
list earlier and no-one seemed interested, but maybe now the time is right.

Kindest regards,
Tim
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Re: [Numpy-discussion] Meta: help, devel and stackoverflow

2012-06-28 Thread Cera, Tim
You are correct, I meant  http://programmers.stackexchange.com/

And on a site like stackexchange I could actually edit my post instead of
my mistake being permanent.   :-)

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Tim
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Re: [Numpy-discussion] Meta: help, devel and stackoverflow

2012-06-28 Thread Cera, Tim
A little more research shows that we could have a
http://numpy.stackexchange.com.  The requirements are just to have people
involved. See http://area51.stackexchange.com/faq for more info.

Kindest regards,
Tim
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Re: [Numpy-discussion] Meta: help, devel and stackoverflow

2012-06-28 Thread Cera, Tim
That is really funny.  Looking through the posts, there wasn't any spam
(could have been deleted), but it wasn't used as much as I would think.
 Have to attract people who answer questions.  Early on the registration
seemed to be a problem.

Solace, the software behind ask.scipy.org looks pretty nice, EXCEPT that
the last commit was in 2009.  On the other have it could be that it has
reached perfection.  :-)

Kindest regards,
Tim
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