[Biopython-dev] Numeric/numpy

[Peter Cock]

Michiel wrote:
>Peter wrote:
>> I was assuming dual support for both numpy or Numeric for the next
>> release based on code like this:
>>
>> try:
>>     from Numeric import x, y, z
>> except ImportError:
>>     from numpy.oldnumeric import x, y, z
>
> This is the easy part. Keep in mind though that the "from numpy.oldnumeric import x, y, z" approach is only a temporary solution; at some point, the oldnumeric wrapper will disappear from numpy.

Yes, if/when the oldnumeric wrapper goes away we'll have more work to
do.  Something to worry about later.

>> where I assumed the C code would have been decided at
>> compile time.
>
> This is the complicated part; it's not just replacing one #include with another. We'd have to use a bunch of #ifdefs to separate the old code from the new code.
>
> Anyway I was planning to go through the Numerical Python - dependent code to see if any other
> changes are needed. If anybody wants to be able to use the old Numerical Python, please let
> yourself be heard; otherwise I suggest we go directly to NumPy.
>
> --Michiel

That suits me - how about we post something like this on the main
discussion list then?:

Dear all,

As you probably are well aware, Biopython releases to date have used
the now obsolete Numeric python library.  This is no longer being
maintained and has been superseded by the numpy library.  See
http://www.scipy.org/History_of_SciPy for more about details on the
history of numerical python.  Biopython 1.48 should be the last
Numeric only release of Biopython - we have already started moving to
numpy in CVS.

Supporting both Numeric and numpy ought to be fairly straight forward
for the pure python modules in Biopython. However, we also have C code
which must interact with Numeric/numpy, and trying to support both
would be harder.

Would anyone be inconvenienced if the next release of Biopython
supported numpy ONLY (dropping support for Numeric)?  If so please
speak up now - either here or on the development mailing list.
Otherwise, a simple switch from Numeric to numpy will probably be the
most straightforward migration plan.

Thank you,

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