[Biopython-dev] Versions of numpy/Numeric

[Peter]

> Hi,
> With Numeric 24.2 and Numpy 1.2rc2 installed on linux 64bit and Python
> 2.5.1.

I don't currently have access to a machine with that setup - so this
is very useful.  Thanks!

> python python setup.py test gives several deprecation warnings from
> test_Cluster and test_KDTree but still pass.

Iteresting - these may be deprecations for Numpy 1.2 - if you have the
output handy could you share it?  If its very long, you can just send
it to me off the list (or file a bug with the details).

> test_MarkovModel fails as I found with BioPython 1.48 (Bug 2589). This is
> most likely a 64-bit thing with Python 2.5.
>
> ERROR: test_MarkovModel
>  ----------------------------------------------------------------------
> Traceback (most recent call last):
> ...
> line 276, in _baum_welch_one
> lp_initial[:] = lp_arcout_t[:,0]
>
> I did notice that both test_MarkovModel.py and test_SVDSuperimposer.py have
> first try to import Numeric - as does MarkovModel.py.

Yeah - I'd raised that on the dev list earlier.  Depending on how we
do this, we'll could end up with misleading import failures (an error
about Numeric when we really care about numpy).  If however no-one
objects to completely dropping Numeric for the next release, things
become much simpler.

> However this same bug is still likely since numpy.oldnumeric is used.

If you have both Numeric and numpy installed, this module is probably
using Numeric and thus still fails.  Could you try flipping the
imports round in .../Bio/MarkovModel.py to see if this problem goes
away (i.e. make sure it uses numpy instead of Numeric)?

If the problem is still there, would you mind also trying the work
around you suggested on Bug 2589 please (dropping the [:] from the
left-hand side)?  If that works for you on both numpy and Numeric it
seems a worthwhile change for CVS.

Thanks

Peter