[Biopython-dev] Tests in python 3.1.2

Peter biopython at maubp.freeserve.co.uk
Tue Oct 26 21:53:47 UTC 2010

On Tue, Oct 26, 2010 at 9:41 PM, Dragoslav Zaric
<zaricdragoslav at gmail.com> wrote:
> Dear Peter,
> I installed python 3.1.2, than run
> 2to3 -w biopython

Don't do that - see our README file:

2to3 --nofix=long --no-diffs -n -w Bio BioSQL Tests Scripts Doc/examples
2to3 --nofix=long --no-diffs -n -w -d Bio BioSQL Tests Scripts Doc/examples

You have to run 2to3 twice (strange design choice in the tool, this
is once for the code, and again with -d for the doctests which are
code examples within the docstring comments). You also need to
turn off the "long" fixer (otherwise it causes problems in Bio.Phylo).

> and after that
> python3.1 run_tests.py
> I capture screen output in log.txt file that I am sending you in attachment.
> Based on this log, can you advise me which way to go. Fix error one by one,
> or maybe I made mistake in installation/upgrade.

The attachment is too big for the mailing list, so your message was rejected.

I hope that helps.


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