[Biopython-dev] TravisCI BioSQL - TypeError: unhashable type: 'bytearray'

[Peter Cock]

On Thu, Oct 9, 2014 at 10:43 AM, Lluís Revilla <lluis.revilla at gmail.com> wrote:
>
> El dia 08/10/2014 11:38, "Peter Cock" <p.j.a.cock at googlemail.com> va
> escriure:
>
>> It looks like we need one of the developers to try installing this
>> new version locally to reproduce and diagnose the error...

Tiago has been able to reproduce this problem on one of his
Linux machines which is setup as a buildslave, see:

http://testing.open-bio.org/biopython/tgrid
http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.4/builds/193

> I volunteer!!
>
> I have never before installed locally a version from github. Is there any
> tutorial or recommended reading? I would install it on a windows 7 home
> premium 64 bytes operative system, with python 3.3
>
> Lluís

Hi Lluís,

Volunteering is great, but unless this particular problem interests
you there may be some easier bugs/issues you could work on.

You've picked a hard target - compiling on Windows is a pain, and
64 bit Windows especially so (I still only have a 32 bit Windows XP
machine for testing). Tiago has made some notes here:

http://biopython.org/wiki/64-bit_Windows_Biopython

There is further information focused on making a 32 bit version
of Biopython for use with a 32 bit Python (which still should be
possible on 64 bit Windows), but it may be a bit out of date:

http://biopython.org/DIST/docs/install/Installation.html
https://github.com/biopython/biopython/blob/master/Doc/install/Installation.tex

However, BioSQL and most of Biopython doesn't need a C compiler
(which is why most of Biopython works under Jython and PyPy) so
you might be able to avoid that for now. Basically you'd hack setup.py
to set EXTENSIONS = [], much like how setup.py already does this
for Jython or PyPy.

Also are you familiar with git, and have you ever used it on Windows?

For this specific bug you will also need a MySQL database installed,
and the connector-python library. This is available for Python 3.3,
hopefully for both 32 and 64 bit Python (?):
http://dev.mysql.com/downloads/connector/python/

Finally, working out what is wrong will also need some experience of
Python 2 vs 3 and bytes vs unicode.

On the bright side, debugging a problem can be a great way to
learn things...

Regards,

Peter