[Biopython] Versions of Python 3 to support in Biopython?

[Martin Mokrejs]

Ivan Gregoretti wrote:
> Hi Bow,
> 
> I think that we should drop support for Python 2.x once it is left out
> in favour of Python 3.
> 
> I am not aware of any major linux distrubution that uses Python 3 as
> default. By major linux distribution I mean Debian, Ubuntu, CentOS,
> Fedora and Red Hat Enterprise Linux.
> 
> Out of all the five distributions listed above, most administrators
> use CentOS. Perhaps we should schedule Python v2.x support to be
> dropped when CentOS switches to Python 3. That is likely to happen a
> long time from now.

Hi,
  I don't think 2.x supports needs to be scheduled for the sake of having
a deadline. It is only meaningful to come up with a date
*once the extra development overhead is NOT acceptable anymore*. For sure
by that time the yet to be determined time window will be of some reasonable
width so that people start screaming up. But that is far from today.

  In general, I am very opposed to deprecations of any programming language
API. This just puts a wasteful burden on developers to rewrite their possibly
years working apps just due to API change. Some people even don't want to touch
certains parts of their code. Or they don't have time to do that or stopped
changing their fully working application ... hence why should they re-start
their work if for several years they did NOT need to touch the code? In such
cases when developer does not take an action the API change kills the existing
and working application because people just don't use it anymore on incompatible
systems.

  Seriously, look at mod_python. Clearly, for my purposes mod_python was
and still is just enough, runs on my servers for 8-10 years and I do NOT care
that it is NOW not developed anymore. I do not care about tiny implementation
details which resulted in abandoning of the project because I just do NOT need
those missing features. But, changing my apps, config files, server config files,
re-doing the testing is just a blocker for me. I rather stop upgrading the system
because the transition gives me nothing. And I am not the only one. Look
into comments at https://bugs.gentoo.org/show_bug.cgi?id=343663 and
then poke towards URLs in https://bugs.gentoo.org/show_bug.cgi?id=343663#c6 .
There you can read about mod_python but the homework is where else should you move!

  Similarly, anybody willing to add PHP-5.4 support to EST2uni which was written
for 5.3 (http://cichlid.umd.edu/est2uni/)?

  In summary, somebody should really make a table listing of anticipated 3rd-party
python-based apps which are likely to be imported into python code along biopython.
More pragmatically, somebody please make sure your future decisions are
not conflicting with numpy+matplolib. Personally I want to play in near future
with these to post-process/compile python code (incl. biopython):

http://www.nuitka.net/ (supports 2.5, 2.6, 3.2)
https://github.com/astrand/pyobfuscate
http://python.net/crew/atuining/cx_Freeze (supports 2.3, 2.4, 2.5)
http://bitboost.com/python-obfuscator/manual (supports 2.5, partially 2.6 and 2.7)

  But I have read other answers which landed on the biopython's list meanwhile
and glad to hear from Peter that the original question was really about what 3.x
version should be supported and NOT about stopping certain python 2.x compatibility.
That's good to hear and thanks for keeping the compatibility so far. ;)

Martin