[Biopython-dev] Python 2 and 3 migration thoughts

Peter Cock p.j.a.cock at googlemail.com
Sat Oct 5 19:02:47 UTC 2013

On Mon, Sep 30, 2013 at 5:18 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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 :)

I wasn't using the -B switch in diff until now, that makes
things easier:

383 no change, 171 need fixers
Troublesome ones 30.9%

Revised branch here:


This is rebased on the master where I've also cut down the
number of fixers in use, so together we get a good speed
up for the Python 3 install time.

I've rebased the urllib changes (include in the above
test branch) and made a pull request for comment:


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