[Biopython-dev] biopython-1.51 test log, sage inclusion

[Marshall Hampton]

On Mon, 17 Aug 2009, Peter wrote:
> On Mon, Aug 17, 2009 at 5:28 PM, Peter<biopython at maubp.freeserve.co.uk> wrote:
>>
>> The others are all ImportErrors (e.g. cannot import name _CKDTree)
>> I rather suspect you are running the test suite BEFORE compiling
>> the C extensions, and that this may similarly affect Bio.Restriction.
>
> Also this line is interesting - it suggest you have not installed NumPy,
> or not told sage is is a dependency?

> test_Cluster ... skipping. If you want to use Bio.Cluster, install
> NumPy first and then reinstall Biopython

Numpy is included in Sage, so I guess there is some sort of path problem. 
I'll give it another look.

> P.S. Why does this page talk about Biopython version "4.2b"?
> http://wiki.sagemath.org/Sage_Spkg_Tracking
>
> Peter
>

I have no idea, that was simply wrong.  I have corrected that wiki page.

Thanks for the feedback!
Marshall Hampton