[Biopython-dev] Python 3 status (ignoring our C code and most dependencies)

[Bartek Wilczynski]

On Thu, Sep 9, 2010 at 7:08 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> Hi Bartek, Eric, et al,
>
> Hi,


> I've rerun the test suite on the trunk code, and we have the
> following issues, most of which I'd already noted in this thread:
> http://lists.open-bio.org/pipermail/biopython-dev/2010-July/008079.html
>
> Bartek - I was seeing a couple of issues with Bio.Motif which came
> down to relative import issues, this seems to have fixed things.
> Could you confirm this change looks OK to you?
>
> http://github.com/biopython/biopython/commit/4700d1be7afffe5e06b41df6ee8cc19e68a9a6c1
>
> I have to confess that my knowledge about python 3 is almost non-existent,
so I was not following the messages related to the migration too closely. As
far as I can tell, the changes in the imports are practically purely
syntactic. I don't see possibilities of serious code breakage (the names
which have changed in the Bio.Motif namespaces were introduced recently and
I think any code relying on having Parsers.AlignAce.read inside Bio.Motif
namespace should be reviewed anyway).

Thanks for making the changes (and finishing my removal of Bio.MEME and
Bio.AlignAce - I keep forgetting about those pesky files in the main
biopython dir...)

cheers
Bartek