[Biopython-dev] Versions of numpy/Numeric

[Peter]

> The not very informative list says it also ''includes a few some minor API
> breakage first scheduled in the 1.1 release"
> http://scipy.org/scipy/numpy/milestone/1.2.0
>
> But this is one of them! There is no message in the numpy 1.1 code. There is
> an email on Jul 13, 2008
> (http://www.nabble.com/Newly-deprecated-API-functions-td18436792.html) that
> notes these are depreciated and will be scheduled removed for Numpy 1.3. So
> rather annoying!

Yes - this does seem annoying :(

> Sorry, I did not realize until I looked that these were 1.2 related. So the
> relevant output is:

So in summary, the warnings from numpy 1.2 were multiple cases of the
following where the old functions will be removed in numpy 1.3:

PyArray_FromDims to PyArray_SimpleNew.
PyArray_FromDimsAndDataAndDescr to PyArray_NewFromDescr

Bio.Cluster will therefore need updating at some point - the next
question is when were PyArray_SimpleNew and PyArray_NewFromDescr
introduced...

>>> test_MarkovModel fails as I found with BioPython 1.48 (Bug 2589). This is
>>> most likely a 64-bit thing with Python 2.5.
>
> Luckily MarkovModel.py is almost self-contained so I used it independently
> of the installation. The test passes as is with numpy and if I drop the [:]
> it passes with both Numeric and numpy import statements.

Great - I've checked that into CVS now.

Thanks,

Peter