[Biopython-dev] Deprecating Bio.PDB.PSEA

[João Rodrigues]

I'm partially against it.

NACCESS is also old software, not updated since forever. This shouldn't be
a reason for deprecating modules. If the code isn't available anymore, it's
OK, otherwise, people might still use it. I'd send an email to the general
users list asking first.

A qui, 27/07/2017, 16:08, Peter Cock <p.j.a.cock at googlemail.com> escreveu:

> Thanks Patrick,
>
> Sourav - If there are no objections, then next week I suggest
> you make a pull request to do the deprecation.
>
> Regards,
>
> Peter
>
> On Thu, Jul 27, 2017 at 3:30 PM, Patrick Kunzmann
> <padix.kleber at gmail.com> wrote:
> > There are also no objections from my side. If the algorithm is well
> > documented and implementation using numpy arrays is feasible, I might
> > integrate it in my onging develoment of a new structure subpackage.
> >
> > Best regards,
> >
> > Patrick
> >
> >
> >
> > On 27.07.2017 10:50, Peter Cock wrote:
> >>
> >> This came up in discussion on this pull request:
> >>
> >> https://github.com/biopython/biopython/pull/1336
> >>
> >> Quoting the tool's README file,
> >>
> >> "P-SEA is small tool for secondary structure assignment
> >> from Ca cartesian coordinates of proteins. It reads
> >> PDB-formatted file and return a file containing : the
> >> sequence read in one-letter code and the secondary
> >> structure assigned (a=helix, b=strand, c=coil)."
> >>
> >> It does compile fine on macOS Sierra, and the readme
> >> talks about other Unix platforms (HP-UX and IRIX),
> >> but it does not compile as is on Linux.
> >>
> >> In either case you get warnings about using the "gets"
> >> function which is not secure.
> >>
> >> I favour deprecating Bio.PDB.PSEA
> >>
> >> Peter
> >>
> >>
> >> On Wed, Jul 26, 2017 at 7:13 PM, Sourav Singh <ssouravsingh12 at gmail.com
> >
> >> wrote:
> >>>
> >>> Hello,
> >>>
> >>> As referenced in the subject, I would like to discuss about deprecating
> >>> Bio.PDB.PSEA
> >>>
> >>> As referenced in the link here-
> >>>
> ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/P-SEA.tar.gz
> >>>
> >>> The last update to the P-SEA package was done in September 1996, which
> >>> makes
> >>> it really old. I would like to know if the dev community is fine with
> >>> deprecating the module for future releases of Biopython.
> >>>
> >>> Regards,
> >>>
> >>> Sourav
> >>>
> >>> Sent from my Phone.Excuse any mistakes and brevity.
> >>>
> >>> _______________________________________________
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> >>
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> >
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