[Biopython-dev] Updating C extensions to Python 3

[Peter]

On Sat, Dec 25, 2010 at 11:24 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Sat, Dec 18, 2010 at 12:18 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> On Sat, Dec 18, 2010 at 3:20 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>>> Hi everybody,
>>>
>>> I looked at what will be needed to make Biopython's C extensions
>>> ready for Python 3. It doesn't seem too bad, so if there are no
>>> objections then I will go ahead and make the necessary changes
>>> over the next two weeks or so. If you are maintaining one of the
>>> C extensions and would like to make the required changes yourself,
>>> please let us know, then I won't touch those modules.
>>>
>>> Best,
>>> --Michiel.
>>
>> Excellent news :)
>>
>
> Hi Michiel,
>
> I see you've started work on the C extensions for Python 3,
> which is great news.
>
> However, it looks like Python 2.4 and 2.5 have broken
> (on both Linux and Windows, probably on Mac too but
> that build slave is off at the minute):
> http://events.open-bio.org:8010/tgrid
>
> If you can fix Python 2.5 but not Python 2.4, don't
> worry - we've said Biopython 1.57 won't officially
> support Python 2.4 anyway.

I think I've fixed things for both Python 2.4 and 2.5.
It was just using a couple of new definitions added in
Python 2.6 - does this look OK to you?

https://github.com/biopython/biopython/commit/d4eaf57946c7b4c32eca8d18821edf32f83e300d

> There also appears to be a Python 2.7 problem on
> Windows:
> http://events.open-bio.org:8010/builders/Windows%20XP%20-%20Python%202.7/builds/63/steps/compile/logs/warnings%20%2810%29
> http://events.open-bio.org:8010/builders/Windows%20XP%20-%20Python%202.7/builds/63/steps/compile/logs/stdio
>

That one may be more tricky to fix right now - the Win XP
box is on as a buildslave, but I'd have to go into the office
to debug things directly - I don't have remote access. Note
that this is using an MS C compiler on Python 2.7, not
cygwin mingw32 which I think it is setup to use on the
older versions of Python.

Peter