Scientific Computing with NumPy

Discussion in 'Python' started by mclaugb, Feb 6, 2006.

  1. mclaugb

    mclaugb Guest

    Has anyone recompiled the Scientific Computing package using NumPy instead
    of Numeric?
    I need a least squares algorithm and a Newton Rhaphson algorithm which is
    contained in Numeric but all the documentation out there says that Numeric
    is crap and all code should be using NumPy.
    Thanks,
    Bryan
    mclaugb, Feb 6, 2006
    #1
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  2. mclaugb

    linda.s Guest

    On 2/6/06, mclaugb <> wrote:
    > Has anyone recompiled the Scientific Computing package using NumPy instead
    > of Numeric?
    > I need a least squares algorithm and a Newton Rhaphson algorithm which is
    > contained in Numeric but all the documentation out there says that Numeric
    > is crap and all code should be using NumPy.
    > Thanks,
    > Bryan
    >
    >
    > --
    > http://mail.python.org/mailman/listinfo/python-list
    >

    what is the relationship between Numeric and Numpy?
    linda.s, Feb 6, 2006
    #2
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  3. mclaugb

    mclaugb Guest

    This page documents the differences. It seems that NumPy is supported and
    more recent.
    http://numeric.scipy.org/


    "linda.s" <> wrote in message
    news:...
    On 2/6/06, mclaugb <> wrote:
    > Has anyone recompiled the Scientific Computing package using NumPy instead
    > of Numeric?
    > I need a least squares algorithm and a Newton Rhaphson algorithm which is
    > contained in Numeric but all the documentation out there says that Numeric
    > is crap and all code should be using NumPy.
    > Thanks,
    > Bryan
    >
    >
    > --
    > http://mail.python.org/mailman/listinfo/python-list
    >

    what is the relationship between Numeric and Numpy?
    mclaugb, Feb 6, 2006
    #3
  4. mclaugb

    Brendan Guest

    As of version 0.4.x, Scipy exclusively uses the newer NumPy module
    instead of the older Numeric module. The confusion is inevitable in
    this time of transition, but their intent is to standardize on one
    array package.

    Brendan
    --
    Brendan Simons



    mclaugb wrote:
    > This page documents the differences. It seems that NumPy is supported and
    > more recent.
    > http://numeric.scipy.org/
    >
    >
    > "linda.s" <> wrote in message
    > news:...
    > On 2/6/06, mclaugb <> wrote:
    > > Has anyone recompiled the Scientific Computing package using NumPy instead
    > > of Numeric?
    > > I need a least squares algorithm and a Newton Rhaphson algorithm which is
    > > contained in Numeric but all the documentation out there says that Numeric
    > > is crap and all code should be using NumPy.
    > > Thanks,
    > > Bryan

    > what is the relationship between Numeric and Numpy?
    Brendan, Feb 6, 2006
    #4
  5. mclaugb

    mclaugb Guest

    Is Scipy the same thing as ScientificPython?
    I am confused if SciPy is just the new version. they appear to be separate
    things.
    Bryan

    "Brendan" <> wrote in message
    news:...
    > As of version 0.4.x, Scipy exclusively uses the newer NumPy module
    > instead of the older Numeric module. The confusion is inevitable in
    > this time of transition, but their intent is to standardize on one
    > array package.
    >
    > Brendan
    > --
    > Brendan Simons
    >
    >
    >
    > mclaugb wrote:
    >> This page documents the differences. It seems that NumPy is supported
    >> and
    >> more recent.
    >> http://numeric.scipy.org/
    >>
    >>
    >> "linda.s" <> wrote in message
    >> news:...
    >> On 2/6/06, mclaugb <> wrote:
    >> > Has anyone recompiled the Scientific Computing package using NumPy
    >> > instead
    >> > of Numeric?
    >> > I need a least squares algorithm and a Newton Rhaphson algorithm which
    >> > is
    >> > contained in Numeric but all the documentation out there says that
    >> > Numeric
    >> > is crap and all code should be using NumPy.
    >> > Thanks,
    >> > Bryan

    >> what is the relationship between Numeric and Numpy?

    >
    mclaugb, Feb 6, 2006
    #5
  6. mclaugb wrote:
    > Is Scipy the same thing as ScientificPython?


    No. They are two separate projects. Scientific Python is still
    Numeric-only. SciPy 0.3.x is Numeric-based and SciPy 0.4.x is NumPy-based.

    The developers for NumPy are also the developers for SciPy (for the most
    part).

    There is a mailing list where
    all of your questions can be answered.
    Travis E. Oliphant, Feb 6, 2006
    #6
  7. mclaugb

    Robert Kern Guest

    mclaugb wrote:
    > Is Scipy the same thing as ScientificPython?
    > I am confused if SciPy is just the new version. they appear to be separate
    > things.


    They are separate projects.

    --
    Robert Kern


    "In the fields of hell where the grass grows high
    Are the graves of dreams allowed to die."
    -- Richard Harter
    Robert Kern, Feb 6, 2006
    #7
  8. mclaugb

    Robert Kern Guest

    mclaugb wrote:
    > Has anyone recompiled the Scientific Computing package using NumPy instead
    > of Numeric?


    What "Scientific Computing" package? I don't know of any package under that
    name. AFAIK, Konrad Hinsen has not yet ported his ScientificPython package to
    numpy, yet.

    scipy 0.4+ is ported to numpy (I recommend using an SVN checkout rather than the
    tarball).

    --
    Robert Kern


    "In the fields of hell where the grass grows high
    Are the graves of dreams allowed to die."
    -- Richard Harter
    Robert Kern, Feb 6, 2006
    #8
  9. mclaugb

    Tim Hochberg Guest

    mclaugb wrote:
    > Is Scipy the same thing as ScientificPython?
    > I am confused if SciPy is just the new version. they appear to be separate
    > things.
    > Bryan


    No, Scientific Python is "a collection of Python modules that are useful
    for scientific computing" written by Konrad Hinsen. I'm not a user, but
    you can find information here:

    http://starship.python.net/~hinsen/ScientificPython/

    SciPy is, I believe, a more recent and more ambitious project. In any
    event it is not directly related to ScientficPython. Information here:

    http://scipy.org/

    Both of these packages are built on top of one of the three extant array
    extensions for Python. To try to clear up some of the confusion around
    those, let me summarize the states of these three packages as I
    understand it:

    Numeric: This is the origingal array package.

    Numarray: This was written as a replacement for Numeric. It has improved
    performance for large arrays. The internals were also simplified and
    many other improvements were made (arrays were subclassable, numeric
    signal handling vastly improved, etc). Unfortunately, a side effect of
    the changes was that small array performance got worse. There was a
    signifigant chunk of the numeric community for whom this was a deal
    breaker and as a result there ended up being a split between the Numeric
    and Numarray communities.

    Numpy: This is a rewrite of Numeric that incorporates most of the
    improvements in Numarray. It is designed to bring the two halves of the
    Python numeric community back together. So far, it seems to have gotten
    a positive reception. It is currently at 0.9.4 and I expect a stable 1.0
    version in relatively short order. If I were starting with Python
    numerics, this is where I would start, although I've yet to start
    converting my Numarray based code over.

    I hope that sheds some light on this.

    regards,

    -tim



    >
    > "Brendan" <> wrote in message
    > news:...
    >
    >>As of version 0.4.x, Scipy exclusively uses the newer NumPy module
    >>instead of the older Numeric module. The confusion is inevitable in
    >>this time of transition, but their intent is to standardize on one
    >>array package.
    >>
    >>Brendan
    >>--
    >>Brendan Simons
    >>
    >>
    >>
    >>mclaugb wrote:
    >>
    >>>This page documents the differences. It seems that NumPy is supported
    >>>and
    >>>more recent.
    >>>http://numeric.scipy.org/
    >>>
    >>>
    >>>"linda.s" <> wrote in message
    >>>news:...
    >>>On 2/6/06, mclaugb <> wrote:
    >>>
    >>>>Has anyone recompiled the Scientific Computing package using NumPy
    >>>>instead
    >>>>of Numeric?
    >>>>I need a least squares algorithm and a Newton Rhaphson algorithm which
    >>>>is
    >>>>contained in Numeric but all the documentation out there says that
    >>>>Numeric
    >>>>is crap and all code should be using NumPy.
    >>>>Thanks,
    >>>>Bryan
    >>>
    >>>what is the relationship between Numeric and Numpy?

    >>

    >
    >
    Tim Hochberg, Feb 6, 2006
    #9
  10. Tim Hochberg wrote:
    > mclaugb wrote:
    >
    >
    > No, Scientific Python is "a collection of Python modules that are useful
    > for scientific computing" written by Konrad Hinsen. I'm not a user, but
    > you can find information here:
    >
    > http://starship.python.net/~hinsen/ScientificPython/
    >
    > SciPy is, I believe, a more recent and more ambitious project. In any
    > event it is not directly related to ScientficPython. Information here:
    >


    SciPy's been around since 2001. ScientificPython since about 1998, I
    think.

    > Numeric: This is the origingal array package.
    >
    > Numarray: This was written as a replacement for Numeric. It has improved
    > performance for large arrays. The internals were also simplified and
    > many other improvements were made (arrays were subclassable, numeric
    > signal handling vastly improved, etc). Unfortunately, a side effect of
    > the changes was that small array performance got worse. There was a
    > signifigant chunk of the numeric community for whom this was a deal
    > breaker and as a result there ended up being a split between the Numeric
    > and Numarray communities.


    Just to be clear, small array performance was only 1 of the
    "deal-breaker" problems with numarray. Anothber big problem for SciPy
    was that the Numeric C-API was never fully supported (in particular the
    Ufunc C-API). This made it more difficult to convert to numarray.
    Thus, porting never happened. The small-array speed issue just made
    porting that much less enticing.

    >
    > Numpy: This is a rewrite of Numeric that incorporates most of the
    > improvements in Numarray.


    The goal is to incorporate *all* of the improvements (unless being
    written in Python is one of the improvements). If there are missing
    improvements we need to know about them.


    Thanks to Tim for spreading some light on the issue. There will no
    doubt be continued confusion for new users over the coming months.
    Hopefully, with time the confusion will fade as more people use NumPy
    and any remainging issues get resolved.

    -Travis
    Travis E. Oliphant, Feb 6, 2006
    #10
  11. mclaugb

    linda.s Guest

    where to download numpy for Python 2.3 in Mac?
    Thanks!
    Linda
    linda.s, Feb 10, 2006
    #11
  12. mclaugb

    Robert Kern Guest

    linda.s wrote:
    > where to download numpy for Python 2.3 in Mac?


    I don't think anybody has a binary package compiled for you. However, if you
    have gcc installed, numpy should build out-of-box.

    $ tar zcf ~/downloads/numpy-0.9.4.tar.gz
    $ cd numpy-0.9.4
    $ python setup.py build
    $ sudo python setup.py install --install-scripts=/usr/local/bin

    Note: the sudo in that last command is only necessary if your user account does
    not have write access to /usr/local/bin

    --
    Robert Kern


    "In the fields of hell where the grass grows high
    Are the graves of dreams allowed to die."
    -- Richard Harter
    Robert Kern, Feb 10, 2006
    #12
  13. "linda.s" <> writes:

    > where to download numpy for Python 2.3 in Mac?
    > Thanks!
    > Linda


    I don't know if anybody's specifically compiled for 2.3; I think most
    of the developers on mac are using 2.4 :)

    But (assuming you have the developer tools installed) it's really to
    compile: python setup.py build && python setup.py install.

    Do you need Tiger (10.4) or Panther (10.3) compatibility?

    --
    |>|\/|<
    /--------------------------------------------------------------------------\
    |David M. Cooke
    |cookedm(at)physics(dot)mcmaster(dot)ca
    David M. Cooke, Feb 11, 2006
    #13
  14. David M. Cooke <> wrote:

    > "linda.s" <> writes:
    >
    > > where to download numpy for Python 2.3 in Mac?
    > > Thanks!
    > > Linda

    >
    > I don't know if anybody's specifically compiled for 2.3; I think most
    > of the developers on mac are using 2.4 :)


    However, what comes with MacOSX is STILL 2.3 (specifically 2.3.5 with
    Tiger).


    Alex
    Alex Martelli, Feb 11, 2006
    #14
  15. mclaugb

    linda.s Guest

    On 2/10/06, David M. Cooke <> wrote:
    > "linda.s" <> writes:
    >
    > > where to download numpy for Python 2.3 in Mac?
    > > Thanks!
    > > Linda

    >
    > I don't know if anybody's specifically compiled for 2.3; I think most
    > of the developers on mac are using 2.4 :)
    >
    > But (assuming you have the developer tools installed) it's really to
    > compile: python setup.py build && python setup.py install.
    >
    > Do you need Tiger (10.4) or Panther (10.3) compatibility?
    >
    > --
    > |>|\/|<
    > /--------------------------------------------------------------------------\
    > |David M. Cooke

    The confusing thing is python 2.3 comes with mac when you got the
    machine. so we need numpy which is OK with python 2.3. is my
    understanding right?
    Linda
    linda.s, Feb 11, 2006
    #15
  16. mclaugb

    Tariq Guest

    Has anyone been able to successfully install numpy 0.9.4 on python 2.4
    under cygwin?

    I'm getting a few errors, especially while it installs the C source.

    --
    Tariq
    Tariq, Feb 15, 2006
    #16
  17. mclaugb

    Robert Kern Guest

    Tariq wrote:
    > Has anyone been able to successfully install numpy 0.9.4 on python 2.4
    > under cygwin?
    >
    > I'm getting a few errors, especially while it installs the C source.


    I don't know of anyone compiling numpy under cygwin, but we will be happy to
    help you on if you will give us some more
    information like what arguments you gave to the setup script and the exact error
    messages that you are seeing.

    --
    Robert Kern


    "In the fields of hell where the grass grows high
    Are the graves of dreams allowed to die."
    -- Richard Harter
    Robert Kern, Feb 16, 2006
    #17
  18. mclaugb

    kpp9c Guest

    Numeric, Numarray, & Numpy... some one stick a screwdriver in my
    forehead and end the madness that Numeric has become.

    Brilliant programming & an almost essential part of scientific & math
    hacking in python made maddeningly confusing by truly dumb naming
    scheme.

    For crying all night! Numpy was Numeric's nickname!!... choose a new,
    related, but unique name!!!! Holy cow!!! How hard is that? A group of
    folks smart enough to come up with such an amazing piece of software
    can't do better than to avoid this unnecessary confusion?

    only Apple could top naming as retarded as this.

    with 2.3 seconds i came up with this:

    Nappy

    Numeric Array processing in Python

    similar enough to suggest its origins, unique enough to not confuse the
    heck out of everyone...

    I am sure folks can do better, but really!

    <wink>
    kpp9c, Feb 18, 2006
    #18
  19. mclaugb

    Terry Reedy Guest

    "kpp9c" <> wrote in message
    news:...
    > Numeric, Numarray, & Numpy... some one stick a screwdriver in my
    > forehead and end the madness that Numeric has become.


    > For crying all night! Numpy was Numeric's nickname


    Given that NumPy *is* an updated version of Numeric, with the same basic
    interface, I think the name quite appropriate. It also works well as a
    partner for SciPy.

    > with 2.3 seconds i came up with this:
    > Nappy
    > Numeric Array processing in Python


    Nice 8-(). British nanny slang for diaper (napkin).

    tjr
    Terry Reedy, Feb 18, 2006
    #19
  20. mclaugb

    Guest

    Terry Reedy wrote:
    > "kpp9c" <> wrote in message
    > news:...
    > > Numeric, Numarray, & Numpy... some one stick a screwdriver in my
    > > forehead and end the madness that Numeric has become.

    >
    > > For crying all night! Numpy was Numeric's nickname

    >
    > Given that NumPy *is* an updated version of Numeric, with the same basic
    > interface, I think the name quite appropriate. It also works well as a
    > partner for SciPy.


    Which, to make the confusion even worse, is *not* the updated version
    of Scientific Python.

    I'm with the previous author: this naming is a mess.

    -greg
    , Feb 20, 2006
    #20
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