[Biopython-dev] Optimization of PDBParser and friends

João Rodrigues anaryin at gmail.com
Fri Sep 7 07:21:56 UTC 2012

Likely true.

I'm writing a txt file with the changes. I don't think they can be merged
easily without breaking a lot of stuff, in particular the removal of
child_list. Therefore, I suggest we write a few deprecation warnings here
and there where affected by the consensual changes we agree on and give a
few releases before we actually merge them.

Also, once I'm happy with the changes, I'll make a new branch to allow
'beta testing' by anyone who wants and write a wiki page on it.


No dia 7 de Set de 2012 04:03, "Peter Cock" <p.j.a.cock at googlemail.com>

> On Thu, Sep 6, 2012 at 2:48 PM, João Rodrigues <anaryin at gmail.com> wrote:
> > Ok, thanks.
> >
> > The modules are littered with set/get methods and adding
> DeprecationWarning
> > to all of them might be a bit too much.. Instead, should we add one
> single
> > warning at the top of the PDBParser, since this is the only obligatory
> > module for Bio.PDB so that everyone gets the warning message once and
> once
> > only? Otherwise I can imagine several warnings popping up everywhere..
> If you use the exact same message, then I think you'll only see the
> warning once. Try it with a couple of the get/set methods to confirm.
> Having the warning happen even if you don't use the get/set seems
> wrong.
> Peter

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