On Mon, Feb 10, 2014 at 11:16 AM, Alexander Belopolsky ndar...@mac.com wrote:
On Sun, Feb 9, 2014 at 4:59 PM, alex argri...@ncsu.edu wrote:
On the other hand, it really needs to be deprecated.
While numpy.matrix may have its problems, a NEP should list a better
rationale than the above to
On Feb 11, 2014 3:23 AM, Alan G Isaac alan.is...@gmail.com wrote:
On 2/10/2014 7:39 PM, Pauli Virtanen wrote:
The issue here is semantics for basic linear algebra operations, such as
matrix multiplication, that work for different matrix objects, including
ndarrays.
I'll see if I can
Alan G Isaac alan.isaac at gmail.com writes:
[clip]
Here, quacking is behaving like an ndarray (in your view,
as I understand it) when asked. But how do we ask?
Your view (if I understand) is we ask via the operations
supported by ndarrays. But maybe that is the wrong way
for the library to
My 2pc:
I personally hardly ever use matrix, even in linear algebra dense code. It
can be nice though, to use matrix semantics within a restricted scope. When
I first came to numpy, the ability to choose linear algebra versus array
semantics seemed like a really neat thing to me; though in
Pauli Virtanen p...@iki.fi wrote:
It is not a good thing that there is no well defined
domain specific language for matrix algebra in Python.
Perhaps Python should get some new operators?
__dot__
__cross__
__kronecker__
Obviously, using them in real Python code would require unicode.
;-)
Sturla Molden sturla.molden at gmail.com writes:
Pauli Virtanen pav at iki.fi wrote:
It is not a good thing that there is no well defined
domain specific language for matrix algebra in Python.
Perhaps Python should get some new operators?
It might still be possible to advocate for this in
februari 2014 12:47
To: numpy-discussion@scipy.org
Subject: Re: [Numpy-discussion] deprecate numpy.matrix
Sturla Molden sturla.molden at gmail.com writes:
Pauli Virtanen pav at iki.fi wrote:
It is not a good thing that there is no well defined domain
specific language for matrix algebra in Python
Pauli Virtanen p...@iki.fi wrote:
[1] http://fperez.org/py4science/numpy-pep225/numpy-pep225.html
I have to agree with Robert Kern here. One operator that we can (ab)use for
matrix multiplication would suffice.
Sturla
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Hi,
On Tue, Feb 11, 2014 at 4:16 AM, Jacco Hoekstra - LR
j.m.hoeks...@tudelft.nl wrote:
For our students, the matrix class is really appealing as we use a lot of
linear algebra and expressions with matrices simply look better with an
operator instead of a function:
x=A.I*b
looks
On Tue, Feb 11, 2014 at 11:25 AM, Matthew Brett matthew.br...@gmail.comwrote:
Hi,
On Tue, Feb 11, 2014 at 4:16 AM, Jacco Hoekstra - LR
j.m.hoeks...@tudelft.nl wrote:
For our students, the matrix class is really appealing as we use a lot
of linear algebra and expressions with matrices
Hi,
On Tue, Feb 11, 2014 at 8:55 AM, josef.p...@gmail.com wrote:
On Tue, Feb 11, 2014 at 11:25 AM, Matthew Brett matthew.br...@gmail.com
wrote:
Hi,
On Tue, Feb 11, 2014 at 4:16 AM, Jacco Hoekstra - LR
j.m.hoeks...@tudelft.nl wrote:
For our students, the matrix class is really
On Tue, Feb 11, 2014 at 8:25 AM, Matthew Brett matthew.br...@gmail.comwrote:
Anyway, I would say that there is a clear use for the matrix class:
readability of linear algebra code and hence a lower chance of errors, so
higher productivity.
Yes, but it looks like there are not any developers
On Tue, Feb 11, 2014 at 12:14 PM, Chris Barker chris.bar...@noaa.govwrote:
On Tue, Feb 11, 2014 at 8:25 AM, Matthew Brett matthew.br...@gmail.comwrote:
Anyway, I would say that there is a clear use for the matrix class:
readability of linear algebra code and hence a lower chance of errors,
On Tue, Feb 11, 2014 at 12:14 PM, Chris Barker chris.bar...@noaa.gov wrote:
On Tue, Feb 11, 2014 at 8:25 AM, Matthew Brett matthew.br...@gmail.com
wrote:
Anyway, I would say that there is a clear use for the matrix class:
readability of linear algebra code and hence a lower chance of
On Tue, Feb 11, 2014 at 12:05 PM, Matthew Brett matthew.br...@gmail.com wrote:
Hi,
On Tue, Feb 11, 2014 at 8:55 AM, josef.p...@gmail.com wrote:
On Tue, Feb 11, 2014 at 11:25 AM, Matthew Brett matthew.br...@gmail.com
wrote:
Hi,
On Tue, Feb 11, 2014 at 4:16 AM, Jacco Hoekstra - LR
11.02.2014 21:20, alex kirjoitti:
[clip]
In the spirit of offsetting this bias and because this thread is
lacking in examples of projects that use numpy.matrix, here's another
data point: cvxpy (https://github.com/cvxgrp/cvxpy) is a serious
active project that supports the numpy.matrix
Hi,
On Tue, Feb 11, 2014 at 11:40 AM, Pauli Virtanen p...@iki.fi wrote:
11.02.2014 21:20, alex kirjoitti:
[clip]
In the spirit of offsetting this bias and because this thread is
lacking in examples of projects that use numpy.matrix, here's another
data point: cvxpy
On Sun, Feb 9, 2014 at 4:59 PM, alex argri...@ncsu.edu wrote:
Hello list,
I wrote this mini-nep for numpy but I've been advised it is more
appropriate for discussion on the list.
The ``numpy.matrix`` API provides a low barrier to using Python
for linear algebra, just as the pre-3 Python
On 2/9/2014 5:55 PM, alex wrote:
I'm working on the same kinds of problems in scipy development
(functions involving sparse matrices and abstract linear operators)
And how is numpy's matrix object getting in your way?
Your initial post simply treated the desirability of
deprecation as a given
On Sun, Feb 9, 2014 at 4:59 PM, alex argri...@ncsu.edu wrote:
On the other hand, it really needs to be deprecated.
While numpy.matrix may have its problems, a NEP should list a better
rationale than the above to gain acceptance.
Personally, I decided not to use numpy.matrix in production code
On Mon, Feb 10, 2014 at 10:09 AM, Alan G Isaac alan.is...@gmail.com wrote:
On 2/9/2014 5:55 PM, alex wrote:
I'm working on the same kinds of problems in scipy development
(functions involving sparse matrices and abstract linear operators)
And how is numpy's matrix object getting in your
On Mon, Feb 10, 2014 at 11:16 AM, Alexander Belopolsky ndar...@mac.com wrote:
On Sun, Feb 9, 2014 at 4:59 PM, alex argri...@ncsu.edu wrote:
On the other hand, it really needs to be deprecated.
While numpy.matrix may have its problems, a NEP should list a better
rationale than the above to
Scipy sparse uses matrices - I was under the impression that scipy sparse only
works with matrices or have things moved on?
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On Mon, Feb 10, 2014 at 11:27 AM, josef.p...@gmail.com wrote:
How do we calculate the diagonal of the hat matrix without using N by N
matrices?
Not sure if this was a rhetorical question or what, but this seems to work
leverages = np.square(scipy.linalg.qr(X, mode='economic')[0]).sum(axis=1)
Yes, but these will be scipy.sparse matrices, nothing to do with numpy
(dense) matrices.
Cheers,
Matthieu
2014-02-10 Dinesh Vadhia dineshbvad...@hotmail.com:
Scipy sparse uses matrices - I was under the impression that scipy sparse
only works with matrices or have things moved on?
On Mon, Feb 10, 2014 at 12:02 PM, Matthieu Brucher
matthieu.bruc...@gmail.com wrote:
Yes, but these will be scipy.sparse matrices, nothing to do with numpy
(dense) matrices.
Unfortunately when scipy.sparse matrices interact with dense ndarrays
(e.g., sparse matrix * dense vector), then you
On Mon, Feb 10, 2014 at 12:16 PM, Nathaniel Smith n...@pobox.com wrote:
On Mon, Feb 10, 2014 at 12:02 PM, Matthieu Brucher
matthieu.bruc...@gmail.com wrote:
Yes, but these will be scipy.sparse matrices, nothing to do with numpy
(dense) matrices.
Unfortunately when scipy.sparse matrices
On Mon, Feb 10, 2014 at 7:00 PM, alex argri...@ncsu.edu wrote:
On Mon, Feb 10, 2014 at 11:27 AM, josef.p...@gmail.com wrote:
How do we calculate the diagonal of the hat matrix without using N by N
matrices?
Not sure if this was a rhetorical question or what, but this seems to work
On Mon, Feb 10, 2014 at 2:03 PM, eat e.antero.ta...@gmail.com wrote:
Rhetorical or not, but FWIW I'll prefer to take singular value decomposition
(u, s, vt= svd(x)) and then based on the singular values s I'll estimate a
numerically feasible rank r. Thus the diagonal of such hat matrix would be
On Mon, Feb 10, 2014 at 9:08 PM, alex argri...@ncsu.edu wrote:
On Mon, Feb 10, 2014 at 2:03 PM, eat e.antero.ta...@gmail.com wrote:
Rhetorical or not, but FWIW I'll prefer to take singular value
decomposition
(u, s, vt= svd(x)) and then based on the singular values s I'll estimate
a
Hi,
On Mon, Feb 10, 2014 at 6:26 AM, Nathaniel Smith n...@pobox.com wrote:
On Sun, Feb 9, 2014 at 4:59 PM, alex argri...@ncsu.edu wrote:
Hello list,
I wrote this mini-nep for numpy but I've been advised it is more
appropriate for discussion on the list.
The ``numpy.matrix`` API provides
On Mon, Feb 10, 2014 at 2:12 PM, eat e.antero.ta...@gmail.com wrote:
On Mon, Feb 10, 2014 at 9:08 PM, alex argri...@ncsu.edu wrote:
On Mon, Feb 10, 2014 at 2:03 PM, eat e.antero.ta...@gmail.com wrote:
Rhetorical or not, but FWIW I'll prefer to take singular value
decomposition
(u, s,
Hi,
On Mon, Feb 10, 2014 at 11:44 AM, josef.p...@gmail.com wrote:
On Mon, Feb 10, 2014 at 2:12 PM, eat e.antero.ta...@gmail.com wrote:
On Mon, Feb 10, 2014 at 9:08 PM, alex argri...@ncsu.edu wrote:
On Mon, Feb 10, 2014 at 2:03 PM, eat e.antero.ta...@gmail.com wrote:
Rhetorical or
On Mon, Feb 10, 2014 at 10:09 AM, Alan G Isaac alan.is...@gmail.com wrote:
On 2/9/2014 5:55 PM, alex wrote:
I'm working on the same kinds of problems in scipy development
(functions involving sparse matrices and abstract linear operators)
And how is numpy's matrix object getting in your
On Mon, Feb 10, 2014 at 2:49 PM, Matthew Brett matthew.br...@gmail.comwrote:
Hi,
On Mon, Feb 10, 2014 at 11:44 AM, josef.p...@gmail.com wrote:
On Mon, Feb 10, 2014 at 2:12 PM, eat e.antero.ta...@gmail.com wrote:
On Mon, Feb 10, 2014 at 9:08 PM, alex argri...@ncsu.edu wrote:
On Mon, Feb 10, 2014 at 2:49 PM, Matthew Brett matthew.br...@gmail.comwrote:
Hi,
On Mon, Feb 10, 2014 at 11:44 AM, josef.p...@gmail.com wrote:
On Mon, Feb 10, 2014 at 2:12 PM, eat e.antero.ta...@gmail.com wrote:
On Mon, Feb 10, 2014 at 9:08 PM, alex argri...@ncsu.edu wrote:
Hi,
On Mon, Feb 10, 2014 at 7:09 AM, Alan G Isaac alan.is...@gmail.com wrote:
[snip]
Just to forestall the usual just start them with arrays, eventually they'll
be grateful reply, I would want to hear that suggestion only from someone
who has used it successfully with undergraduates in the
On 2/10/2014 3:04 PM, Matthew Brett wrote:
I teach psychologists and neuroscientists mainly
I must suspect that notebook was not for
**undergraduate** psychology students.
At least, not the ones I usually meet.
SymPy is great but for those without background
it is at best awkward. It
Hi,
On Mon, Feb 10, 2014 at 12:23 PM, Alan G Isaac alan.is...@gmail.com wrote:
On 2/10/2014 3:04 PM, Matthew Brett wrote:
I teach psychologists and neuroscientists mainly
I must suspect that notebook was not for
**undergraduate** psychology students.
At least, not the ones I usually meet.
On Mon, Feb 10, 2014 at 3:04 PM, Matthew Brett matthew.br...@gmail.comwrote:
Hi,
On Mon, Feb 10, 2014 at 7:09 AM, Alan G Isaac alan.is...@gmail.com
wrote:
[snip]
Just to forestall the usual just start them with arrays, eventually
they'll
be grateful reply, I would want to hear that
On Mon, Feb 10, 2014 at 1:23 PM, Alan G Isaac alan.is...@gmail.com wrote:
On 2/10/2014 3:04 PM, Matthew Brett wrote:
I teach psychologists and neuroscientists mainly
I must suspect that notebook was not for
**undergraduate** psychology students.
At least, not the ones I usually meet.
On Mon, Feb 10, 2014 at 2:36 PM, Matthew Brett matthew.br...@gmail.com wrote:
Hi,
On Mon, Feb 10, 2014 at 6:26 AM, Nathaniel Smith n...@pobox.com wrote:
On Sun, Feb 9, 2014 at 4:59 PM, alex argri...@ncsu.edu wrote:
Hello list,
I wrote this mini-nep for numpy but I've been advised it is more
Hi,
On Mon, Feb 10, 2014 at 12:44 PM, Charles R Harris
charlesr.har...@gmail.com wrote:
On Mon, Feb 10, 2014 at 1:23 PM, Alan G Isaac alan.is...@gmail.com wrote:
On 2/10/2014 3:04 PM, Matthew Brett wrote:
I teach psychologists and neuroscientists mainly
I must suspect that notebook was
Hi,
On Mon, Feb 10, 2014 at 12:39 PM, josef.p...@gmail.com wrote:
On Mon, Feb 10, 2014 at 3:04 PM, Matthew Brett matthew.br...@gmail.com
wrote:
Hi,
On Mon, Feb 10, 2014 at 7:09 AM, Alan G Isaac alan.is...@gmail.com
wrote:
[snip]
Just to forestall the usual just start them with
On Mon, Feb 10, 2014 at 3:45 PM, alex argri...@ncsu.edu wrote:
On Mon, Feb 10, 2014 at 2:36 PM, Matthew Brett matthew.br...@gmail.com
wrote:
Hi,
On Mon, Feb 10, 2014 at 6:26 AM, Nathaniel Smith n...@pobox.com wrote:
On Sun, Feb 9, 2014 at 4:59 PM, alex argri...@ncsu.edu wrote:
Hello
On Mon, Feb 10, 2014 at 3:39 PM, josef.p...@gmail.com wrote:
On Mon, Feb 10, 2014 at 3:04 PM, Matthew Brett matthew.br...@gmail.comwrote:
Hi,
On Mon, Feb 10, 2014 at 7:09 AM, Alan G Isaac alan.is...@gmail.com
wrote:
[snip]
Just to forestall the usual just start them with arrays,
10.02.2014 22:23, Alan G Isaac kirjoitti:
[clip]
As far as I have been able to discern, the underlying
motivation for eliminating the matrix class is that
some developers want to stop supporting in any form
the subclassing of numpy arrays. Do I have that right?
What sparked this discussion
Hi,
On Mon, Feb 10, 2014 at 12:58 PM, josef.p...@gmail.com wrote:
On Mon, Feb 10, 2014 at 3:45 PM, alex argri...@ncsu.edu wrote:
On Mon, Feb 10, 2014 at 2:36 PM, Matthew Brett matthew.br...@gmail.com
wrote:
Hi,
On Mon, Feb 10, 2014 at 6:26 AM, Nathaniel Smith n...@pobox.com wrote:
On 2/10/2014 4:03 PM, Pauli Virtanen wrote:
What sparked this discussion (on Github) is that it is not possible to
write duck-typed code that works correctly for:
Do you mean one must start out with an 'asarray'?
Or more than that?
As I detailed in past discussion, the one thing
I really do
On 2/10/2014 4:08 PM, Matthew Brett wrote:
I think the active questions here are:
* Should we collect the discussion in coherent form somewhere?
* Should we add something to the np.matrix docstring and if so what?
* (Pauli's point): to what extent should we try to emulate the np.matrix API.
10.02.2014 23:13, Alan G Isaac kirjoitti:
On 2/10/2014 4:03 PM, Pauli Virtanen wrote:
What sparked this discussion (on Github) is that it is not
possible to write duck-typed code that works correctly for:
Do you mean one must start out with an 'asarray'? Or more than
that?
Starting with
On 2/10/2014 4:28 PM, Pauli Virtanen wrote:
Starting with asarray won't work: sparse matrices are not subclasses
of ndarray.
I was focused on the `matrix` object.
For this object, an initial asarray is all it takes to use array code.
(Or ... not?) And it is a view, not a copy.
I don't have
On Mon, Feb 10, 2014 at 3:47 PM, Matthew Brett matthew.br...@gmail.com wrote:
Hi,
On Mon, Feb 10, 2014 at 12:44 PM, Charles R Harris
charlesr.har...@gmail.com wrote:
On Mon, Feb 10, 2014 at 1:23 PM, Alan G Isaac alan.is...@gmail.com wrote:
On 2/10/2014 3:04 PM, Matthew Brett wrote:
I
On 2/10/2014 4:40 PM, alex wrote:
I really want to remove it
Can you articulate the problem created by its existence
that leads you to this view?
Alan Isaac
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On Mon, Feb 10, 2014 at 2:28 PM, Pauli Virtanen p...@iki.fi wrote:
10.02.2014 23:13, Alan G Isaac kirjoitti:
On 2/10/2014 4:03 PM, Pauli Virtanen wrote:
What sparked this discussion (on Github) is that it is not
possible to write duck-typed code that works correctly for:
Do you mean
Hi,
On Mon, Feb 10, 2014 at 1:52 PM, Charles R Harris
charlesr.har...@gmail.com wrote:
On Mon, Feb 10, 2014 at 2:28 PM, Pauli Virtanen p...@iki.fi wrote:
10.02.2014 23:13, Alan G Isaac kirjoitti:
On 2/10/2014 4:03 PM, Pauli Virtanen wrote:
What sparked this discussion (on Github) is
10.02.2014 23:40, Alan G Isaac kirjoitti:
On 2/10/2014 4:28 PM, Pauli Virtanen wrote:
Starting with asarray won't work: sparse matrices are not
subclasses of ndarray.
I was focused on the `matrix` object. For this object, an initial
asarray is all it takes to use array code. (Or ... not?)
On Mon, Feb 10, 2014 at 4:42 PM, Alan G Isaac alan.is...@gmail.com wrote:
On 2/10/2014 4:40 PM, alex wrote:
I really want to remove it
Can you articulate the problem created by its existence
that leads you to this view?
In my opinion, Pauli has articulated these problems well in this thread.
On Mon, Feb 10, 2014 at 1:13 PM, Alan G Isaac alan.is...@gmail.com wrote:
Do you mean one must start out with an 'asarray'?
Or more than that?
maybe np.asanyarray()
It's nice, at least in principle for duck-typed functions to return the
type they were handed. And this really is the primary
Hi,
On Mon, Feb 10, 2014 at 2:11 PM, Pauli Virtanen p...@iki.fi wrote:
10.02.2014 23:40, Alan G Isaac kirjoitti:
On 2/10/2014 4:28 PM, Pauli Virtanen wrote:
Starting with asarray won't work: sparse matrices are not
subclasses of ndarray.
I was focused on the `matrix` object. For this
On 2/10/2014 5:11 PM, Pauli Virtanen wrote:
The existence of np.matrix messes up the general agreement on ndarray
semantics in Python. The meaning of very basic code such as
A * B
A.sum(0)
A[0]
where A and B are NxN matrices of some sort now depends on the types
of A and
11.02.2014 00:17, Matthew Brett kirjoitti:
[clip]
That is a very convincing argument.
What would be the problems (apart from code compatibility) in making
scipy.sparse use the ndarray semantics?
I'd estimate the effort it would take to convert scipy.sparse to ndarray
semantics is about a
Hi,
On Mon, Feb 10, 2014 at 2:33 PM, Pauli Virtanen p...@iki.fi wrote:
11.02.2014 00:17, Matthew Brett kirjoitti:
[clip]
That is a very convincing argument.
What would be the problems (apart from code compatibility) in making
scipy.sparse use the ndarray semantics?
I'd estimate the effort
11.02.2014 00:31, Alan G Isaac kirjoitti:
On 2/10/2014 5:11 PM, Pauli Virtanen wrote:
The existence of np.matrix messes up the general agreement on ndarray
semantics in Python. The meaning of very basic code such as
A * B
A.sum(0)
A[0]
where A and B are NxN matrices of some
On Mon, Feb 10, 2014 at 6:29 PM, Pauli Virtanen p...@iki.fi wrote:
11.02.2014 00:31, Alan G Isaac kirjoitti:
On 2/10/2014 5:11 PM, Pauli Virtanen wrote:
The existence of np.matrix messes up the general agreement on ndarray
semantics in Python. The meaning of very basic code such as
On Mon, Feb 10, 2014 at 6:39 PM, josef.p...@gmail.com wrote:
On Mon, Feb 10, 2014 at 6:29 PM, Pauli Virtanen p...@iki.fi wrote:
11.02.2014 00:31, Alan G Isaac kirjoitti:
On 2/10/2014 5:11 PM, Pauli Virtanen wrote:
The existence of np.matrix messes up the general agreement on ndarray
11.02.2014 01:39, josef.p...@gmail.com kirjoitti:
[clip]
Almost all the code in scipy.stats and statsmodels starts with np.asarray.
The numpy doc standard has the term `array_like` to indicate things that
can be converted to a usable object by ndasarray.
ducktyping could be restricted to a
On Mon, Feb 10, 2014 at 5:39 PM, Pauli Virtanen p...@iki.fi wrote:
11.02.2014 01:39, josef.p...@gmail.com kirjoitti:
[clip]
Almost all the code in scipy.stats and statsmodels starts with
np.asarray.
The numpy doc standard has the term `array_like` to indicate things that
can be converted
On Mon, Feb 10, 2014 at 6:11 PM, Charles R Harris charlesr.har...@gmail.com
wrote:
On Mon, Feb 10, 2014 at 5:39 PM, Pauli Virtanen p...@iki.fi wrote:
11.02.2014 01:39, josef.p...@gmail.com kirjoitti:
[clip]
Almost all the code in scipy.stats and statsmodels starts with
np.asarray.
On 2/10/2014 7:39 PM, Pauli Virtanen wrote:
The issue here is semantics for basic linear algebra operations, such as
matrix multiplication, that work for different matrix objects, including
ndarrays.
I'll see if I can restate my suggestion in another way,
because I do not feel you are
Hello list,
I wrote this mini-nep for numpy but I've been advised it is more
appropriate for discussion on the list.
The ``numpy.matrix`` API provides a low barrier to using Python
for linear algebra, just as the pre-3 Python ``input`` function
and ``print`` statement provided low barriers to
On 2/9/2014 4:59 PM, alex wrote:
The ``numpy.matrix`` API provides a low barrier to using Python
for linear algebra, just as the pre-3 Python ``input`` function
and ``print`` statement provided low barriers to using Python for
automatically evaluating input and for printing output.
On the
On Sun, Feb 9, 2014 at 5:12 PM, Alan G Isaac wrote:
On 2/9/2014 4:59 PM, alex wrote:
The ``numpy.matrix`` API provides a low barrier to using Python
for linear algebra, just as the pre-3 Python ``input`` function
and ``print`` statement provided low barriers to using Python for
Hi,
On Sun, Feb 9, 2014 at 2:55 PM, alex argri...@ncsu.edu wrote:
On Sun, Feb 9, 2014 at 5:12 PM, Alan G Isaac wrote:
On 2/9/2014 4:59 PM, alex wrote:
The ``numpy.matrix`` API provides a low barrier to using Python
for linear algebra, just as the pre-3 Python ``input`` function
and
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