[Biopython-dev] Optimization of PDBParser and friends

[João Rodrigues]

Guys,

Looks great, I will try to 'cherry pick' that branch and merge it with
mine. I have to solve some issues with the tests, but it seems to be a
straightforward change.

Cheers,

João
No dia 4 de Set de 2012 15:37, "Wibowo Arindrarto" <w.arindrarto at gmail.com>
escreveu:

> On Tue, Sep 4, 2012 at 2:16 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> >
> > On Tue, Sep 4, 2012 at 7:11 AM, Wibowo Arindrarto
> > <w.arindrarto at gmail.com> wrote:
> > > Hi Peter, João,
> > >
> > > Just a little FYI. I ran into the OrderedDict issue when I started
> > > writing
> > > SearchIO a few months ago as well, so I added an OrderedDict
> > > implementation
> > > in Bio._py3k
> > >
> > > (
> https://github.com/bow/biopython/commit/34f873b2d21136487a0b925be898c52daa0cc61c
> ).
> > >
> > > The code is from the ordereddict module from PyPI at that time. I
> > > haven't
> > > checked if it's the same as the one shown in the link (there may have
> > > been
> > > some updates), but it seems to work fine up to now.
> > >
> > > Hope this is useful :),
> > > Bow
> >
> > Given the OrderedDict will be useful for Bio.PDB and Bow's SearchIO,
> > that seems quite a good case for including it. How does this look
> > (on the 'od' branch in my repository)?
> >
> >
> >
> https://github.com/peterjc/biopython/commit/52b011aa8ddce06e636de776d8cea8e62845853f
> >
> > This differs from Bow's version in that I put the module in as a separate
> > file (Bio/_ordereddict.py), and that it will prefer the ordereddict
> > package
> > if already installed (e.g. from PyPI).
> >
> > Peter
>
> Hi Peter,
>
> This looks good. I like the 'ordereddict' module import check prior to
> using our bundled version.
>
> One more thing I would suggest is about the namespace. I feel that in
> the future, we may run into similar issues (non-Python3 compatibility
> issues) since Python2.7 deprecation is still a long way. Perhaps
> create a new subpackage in the root folder (maybe Bio._compat, but I
> don't have a strong preference), to keep code like this in one place?
> Or we could even put Bio._py3k under this subpackage and have one
> central place for compatibility-related code? This would prevent
> further root namespace clutter.
>
> regards,
> Bow
>