[Biopython-dev] Python 2 and 3 migration thoughts

[Peter Cock]

On Sat, Oct 5, 2013 at 8:02 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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:
>
> https://github.com/peterjc/biopython/tree/mark2to3b
> https://travis-ci.org/peterjc/biopython/builds/12175589
>
> 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:
> https://github.com/biopython/biopython/pull/245
>
> Peter

Incorporating another new feature branch gives:

387 no change, 161 need fixers
Troublesome ones 29.4%

The new batch of 2to3 issues solved is changes to
built in functions like range, zip, map, filter. Branch:
https://github.com/peterjc/biopython/tree/builtins
https://github.com/biopython/biopython/pull/246

Peter