[Biopython-dev] Python 2 and 3 migration thoughts

[Peter Cock]

On Mon, Sep 30, 2013 at 12:22 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Assuming my methodology isn't flawed, we're about half way
> in terms of getting every file in Biopython do be dual Python 2
> and Python 3 code:
>
> 262 no change, 290 need fixers
> Troublesome ones at 52.5%

New numbers with Bio._py3k.urllib changes which should
have dropped the number of troublesome files by at most
13 files:

374 no change, 177 need fixers
Troublesome ones 32.1%

I think my markup script is a bit fragile in terms of the exact
sequence of steps with do2to3.py etc. But much better
numbers than Sunday night :)

Revised branch here:
https://github.com/peterjc/biopython/tree/mark2to3a
https://github.com/peterjc/biopython/commit/14f9ff121532ff92ec7bacc1867bdd058a6e8f74

Build and test times on the master vs this branch are
looking a lot better for Python 3 (although the numbers
for different TravisCI runs are not directly comparable),
and there is still a lot of room for improvement:

master:
https://travis-ci.org/biopython/biopython/builds/11965000

branch:
https://travis-ci.org/peterjc/biopython/builds/11968132

So that's good. However, are these urllib import fixes
an acceptable way forwards? Included in the above
branch and here:

https://github.com/peterjc/biopython/tree/urllib
https://github.com/peterjc/biopython/commit/1305387a5d98a5f3c7b83ca3db580b9e63dba851

Thanks,

Peter