Re: Deprecating Bio.PDB.PSEA
João Rodrigues <[email protected]> Thu, 27 Jul 2017 17:41:52 +0000
| Newsgroups | gmane.comp.python.bio.devel |
|---|---|
| Message-ID | <CAB=-b2bg1qUNEz5XqTbpR90X+uTuwFBtbJE5f--N4b=qewkKcA@mail.gmail.com> |
--===============4239973817187593644== Content-Type: multipart/alternative; boundary="94eb2c19c74c193b640555501534" --94eb2c19c74c193b640555501534 Content-Type: text/plain; charset="UTF-8" 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 <[email protected]> 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 > <[email protected]> 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 <[email protected] > > > >> 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. > >>> > >>> _______________________________________________ > >>> Biopython-dev mailing list > >>> [email protected] > >>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev > >> > >> _______________________________________________ > >> Biopython-dev mailing list > >> [email protected] > >> http://mailman.open-bio.org/mailman/listinfo/biopython-dev > > > > > > _______________________________________________ > > Biopython-dev mailing list > > [email protected] > > http://mailman.open-bio.org/mailman/listinfo/biopython-dev > _______________________________________________ > Biopython-dev mailing list > [email protected] > http://mailman.open-bio.org/mailman/listinfo/biopython-dev > --94eb2c19c74c193b640555501534 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <p dir=3D"ltr">I'm partially against it. </p> <p dir=3D"ltr">NACCESS is also old software, not updated since forever. Thi= s 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. </p> <br><div class=3D"gmail_quote"><div dir=3D"ltr">A qui, 27/07/2017, 16:08, P= eter Cock <<a href=3D"mailto:[email protected]">p.j.a.cock@googl= email.com</a>> escreveu:<br></div><blockquote class=3D"gmail_quote" styl= e=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Thanks = Patrick,<br> <br> Sourav - If there are no objections, then next week I suggest<br> you make a pull request to do the deprecation.<br> <br> Regards,<br> <br> Peter<br> <br> On Thu, Jul 27, 2017 at 3:30 PM, Patrick Kunzmann<br> <<a href=3D"mailto:[email protected]" target=3D"_blank">padix.klebe= [email protected]</a>> wrote:<br> > There are also no objections from my side. If the algorithm is well<br= > > documented and implementation using numpy arrays is feasible, I might<= br> > integrate it in my onging develoment of a new structure subpackage.<br= > ><br> > Best regards,<br> ><br> > Patrick<br> ><br> ><br> ><br> > On 27.07.2017 10:50, Peter Cock wrote:<br> >><br> >> This came up in discussion on this pull request:<br> >><br> >> <a href=3D"https://github.com/biopython/biopython/pull/1336" rel= =3D"noreferrer" target=3D"_blank">https://github.com/biopython/biopython/pu= ll/1336</a><br> >><br> >> Quoting the tool's README file,<br> >><br> >> "P-SEA is small tool for secondary structure assignment<br> >> from Ca cartesian coordinates of proteins. It reads<br> >> PDB-formatted file and return a file containing : the<br> >> sequence read in one-letter code and the secondary<br> >> structure assigned (a=3Dhelix, b=3Dstrand, c=3Dcoil)."<br> >><br> >> It does compile fine on macOS Sierra, and the readme<br> >> talks about other Unix platforms (HP-UX and IRIX),<br> >> but it does not compile as is on Linux.<br> >><br> >> In either case you get warnings about using the "gets"<b= r> >> function which is not secure.<br> >><br> >> I favour deprecating Bio.PDB.PSEA<br> >><br> >> Peter<br> >><br> >><br> >> On Wed, Jul 26, 2017 at 7:13 PM, Sourav Singh <<a href=3D"mailt= o:[email protected]" target=3D"_blank">[email protected]</a>&= gt;<br> >> wrote:<br> >>><br> >>> Hello,<br> >>><br> >>> As referenced in the subject, I would like to discuss about de= precating<br> >>> Bio.PDB.PSEA<br> >>><br> >>> As referenced in the link here-<br> >>> <a href=3D"ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/prot= ein/p-sea/P-SEA.tar.gz" rel=3D"noreferrer" target=3D"_blank">ftp://ftp.lmcp= .jussieu.fr/pub/sincris/software/protein/p-sea/P-SEA.tar.gz</a><br> >>><br> >>> The last update to the P-SEA package was done in September 199= 6, which<br> >>> makes<br> >>> it really old. I would like to know if the dev community is fi= ne with<br> >>> deprecating the module for future releases of Biopython.<br> >>><br> >>> Regards,<br> >>><br> >>> Sourav<br> >>><br> >>> Sent from my Phone.Excuse any mistakes and brevity.<br> >>><br> >>> _______________________________________________<br> >>> Biopython-dev mailing list<br> >>> <a href=3D"mailto:[email protected]" target= =3D"_blank">[email protected]</a><br> >>> <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biopyt= hon-dev" rel=3D"noreferrer" target=3D"_blank">http://mailman.open-bio.org/m= ailman/listinfo/biopython-dev</a><br> >><br> >> _______________________________________________<br> >> Biopython-dev mailing list<br> >> <a href=3D"mailto:[email protected]" target=3D"_b= lank">[email protected]</a><br> >> <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biopython-= dev" rel=3D"noreferrer" target=3D"_blank">http://mailman.open-bio.org/mailm= an/listinfo/biopython-dev</a><br> ><br> ><br> > _______________________________________________<br> > Biopython-dev mailing list<br> > <a href=3D"mailto:[email protected]" target=3D"_blank= ">[email protected]</a><br> > <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biopython-dev"= rel=3D"noreferrer" target=3D"_blank">http://mailman.open-bio.org/mailman/l= istinfo/biopython-dev</a><br> _______________________________________________<br> Biopython-dev mailing list<br> <a href=3D"mailto:[email protected]" target=3D"_blank">Bio= [email protected]</a><br> <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biopython-dev" rel= =3D"noreferrer" target=3D"_blank">http://mailman.open-bio.org/mailman/listi= nfo/biopython-dev</a><br> </blockquote></div> --94eb2c19c74c193b640555501534-- --===============4239973817187593644== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Biopython-dev mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/biopython-dev --===============4239973817187593644==--