[Biopython-dev] Bio.File

[Peter Cock]

Hi Michiel,

Regarding code using Bio.File, which you asked about
deprecating last month:
http://lists.open-bio.org/pipermail/biopython-dev/2011-September/009144.html

I objected at the time because I was using it for the
TogoWS code I was working on,

On Thu, Sep 8, 2011 at 4:25 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
On Wed, Sep 7, 2011 at 3:36 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>> If the server could be relied on to always give an
>>> HTTP error code this wouldn't be needed:
>>>
>>> https://github.com/peterjc/biopython/blob/togows/Bio/TogoWS/__init__.py
>>>
>
> ...
>
> [Some of those TogoWS checks are probably superfluous
> right now, I'm still polishing the error handling - some of
> which will rely on TogoWS itself catching more conditions]

I've updated my TogoWS to rely on the HTTP error codes,
and removed the heuristic error detection which required
Bio.File for the UndoHandle. That seems to be working fine
now.

That leaves Bio/SCOP/__init__.py as the only existing or
imminent code using Bio.File, so if we can sort that out,
we can deprecate Bio.File as you suggested.

Regards,

Peter