[Biopython-dev] long for longitude in Bio.Phylo and Python 3

[Peter]

On Mon, Jul 26, 2010 at 6:04 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Mon, Jul 26, 2010 at 12:47 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:
>
>> Hi Eric et all,
>>
>> Background: Eric has found a problem in Bio.Phylo with variables, arguments
>> and properties called "long" for longitude which the 2to3 script is wrongly
>> converting into "int", see: http://bugs.python.org/issue2734
>>
>> If the remaining issue with Bug 2734 is fixed, we would still have a
>> problem
>> running the conversion with 2to3 as included with all releases of Python to
>> date (i.e. 2.6, 2.7, 3.1), which would complicate deployment.
>>
>> Eric: It could break backwards compatibility, but would a switch from lat &
>> long to latitude and longitude be the least painful solution? Do you think
>> we could support both names as part of a deprecation cycle?
>>
>> Peter
>>
>
> The names "lat", "long" and "alt" are from the phyloXML spec, so it's
> convenient to keep them the same in Biopython. But I could change them to
> the longer form if that's needed. The parser and serializer assume the
> attribute names match the XML spec in general, and special-case names that
> won't work in Python (like "from").
>
> Deprecation: Since we note in the Tutorial that Bio.Phylo is semi-beta, I'd
> like to use an accelerated deprecation cycle for name changes like this: 1
> transitional release with shims that trigger a warning, then remove the
> shims in the release after that. Is that OK?
>
> I haven't had a chance to try "2to3 --nofix=long" on the entire codebase
> yet.

Assuming that using  "2to3 --nofix=long" on the entire codebase isn't
going to work, then I'm OK with an accelerated deprecation for switching
lat/long in Bio.Phylo.

If "2to3 --nofix=long" doesn't cause us problems elsewhere, that will
be a neater solution.

Peter