Re: [Biopython] Planning Biopython 1.87
Peter Cock <[email protected]> Mon, 30 Mar 2026 12:39:49 +0100
| Newsgroups | gmane.comp.python.bio.general |
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| Message-ID | <CAKVJ-_5fYyU85vPMsCfDSArBtfKL6h7Xqmu6cpVu0wPnWL+ktw@mail.gmail.com> |
--===============5531194047333625473== Content-Type: multipart/alternative; boundary="000000000000a1b278064e3c4fd4" --000000000000a1b278064e3c4fd4 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Nearly done, up on PyPI now. The packaging changes mean a bunch of weird errors from the build and upload process if the tooling isn't all up to date. https://pypi.org/project/biopython/1.87/ Peter On Thu, Mar 19, 2026 at 9:38=E2=80=AFAM Peter Cock <[email protected]= om> wrote: > I made that change last week, and have just tested the wheel building: > https://github.com/biopython/biopython-wheels/actions > > Other than the loss of Intel macOS wheels (as the runners we used to use > have been retired), that all looks good. > > I propose to do the Biopython 1.87 release today/tomorrow, and so ask > those with merge permissions to hold off till that's done. > > Thank you, > > Peter > > > Peter > > > > On Wed, Mar 4, 2026 at 11:13=E2=80=AFAM Peter Cock <p.j.a.cock@googlemail= .com> > wrote: > > > > We're still blocking on a NumPy 2.4 incompatibility: > > https://github.com/biopython/biopython/issues/5135 > > > > I am strongly leaning to the quick fix of changing the failing test in > > #5161 (with the possibility of a better fix late), but want a consesus > > or at least another voice in favour. If anyone using the vector > > classes in Bio.PDB had some input that would be useful. > > > > Peter > > > > On Fri, Jan 23, 2026 at 10:11=E2=80=AFAM Peter Cock <p.j.a.cock@googlem= ail.com> > wrote: > > > > > > Also https://github.com/biopython/biopython/issues/5109 which Michiel > has been working on. > > > > > > Peter > > > > > > On Wed, Jan 21, 2026 at 2:29=E2=80=AFPM Peter Cock <p.j.a.cock@google= mail.com> > wrote: > > >> > > >> Dear Biopythoneers, > > >> > > >> I think once the following are resolved (they have pull requests), w= e > should do the next release: > > >> > > >> * NumPy 2.4 compatibility > > >> https://github.com/biopython/biopython/issues/5135 > > >> > > >> * Using pyproject.toml rather than setup.py > > >> https://github.com/biopython/biopython/pull/5142 > > >> > > >> Ideally sooner rather than later as the PDB _ATOM_FORMAT_STRING > glitch introduced in Biopython 1.86 seems to be hitting a lot of people: > > >> https://github.com/biopython/biopython/issues/5097 > > >> > > >> Is there anything else you think is urgent enough to wait on? > > >> > > >> Thanks, > > >> > > >> Peter > --000000000000a1b278064e3c4fd4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Nearly done, up on PyPI now. The packaging changes me= an a bunch of weird errors from the build and upload process if the tooling= isn't all up to date.</div><div><br></div><div><a href=3D"https://pypi= .org/project/biopython/1.87/">https://pypi.org/project/biopython/1.87/</a><= /div><div><br></div><div>Peter</div><div><br></div></div><br><div class=3D"= gmail_quote gmail_quote_container"><div dir=3D"ltr" class=3D"gmail_attr">On= Thu, Mar 19, 2026 at 9:38=E2=80=AFAM Peter Cock <<a href=3D"mailto:p.j.= [email protected]">[email protected]</a>> wrote:<br></div><b= lockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-le= ft:1px solid rgb(204,204,204);padding-left:1ex">I made that change last wee= k, and have just tested the wheel building:<br> <a href=3D"https://github.com/biopython/biopython-wheels/actions" rel=3D"no= referrer" target=3D"_blank">https://github.com/biopython/biopython-wheels/a= ctions</a><br> <br> Other than the loss of Intel macOS wheels (as the runners we used to use<br= > have been retired), that all looks good.<br> <br> I propose to do the Biopython 1.87 release today/tomorrow, and so ask<br> those with merge permissions to hold off till that's done.<br> <br> Thank you,<br> <br> Peter<br> <br> <br> Peter<br> <br> <br> <br> On Wed, Mar 4, 2026 at 11:13=E2=80=AFAM Peter Cock <<a href=3D"mailto:p.= [email protected]" target=3D"_blank">[email protected]</a>>= ; wrote:<br> ><br> > We're still blocking on a NumPy 2.4 incompatibility:<br> > <a href=3D"https://github.com/biopython/biopython/issues/5135" rel=3D"= noreferrer" target=3D"_blank">https://github.com/biopython/biopython/issues= /5135</a><br> ><br> > I am strongly leaning to the quick fix of changing the failing test in= <br> > #5161 (with the possibility of a better fix late), but want a consesus= <br> > or at least another voice in favour. If anyone using the vector<br> > classes in Bio.PDB had some input that would be useful.<br> ><br> > Peter<br> ><br> > On Fri, Jan 23, 2026 at 10:11=E2=80=AFAM Peter Cock <<a href=3D"mai= lto:[email protected]" target=3D"_blank">[email protected]<= /a>> wrote:<br> > ><br> > > Also <a href=3D"https://github.com/biopython/biopython/issues/510= 9" rel=3D"noreferrer" target=3D"_blank">https://github.com/biopython/biopyt= hon/issues/5109</a> which Michiel has been working on.<br> > ><br> > > Peter<br> > ><br> > > On Wed, Jan 21, 2026 at 2:29=E2=80=AFPM Peter Cock <<a href=3D= "mailto:[email protected]" target=3D"_blank">p.j.a.cock@googlemail.= com</a>> wrote:<br> > >><br> > >> Dear Biopythoneers,<br> > >><br> > >> I think once the following are resolved (they have pull reque= sts), we should do the next release:<br> > >><br> > >> * NumPy 2.4 compatibility<br> > >>=C2=A0 =C2=A0 <a href=3D"https://github.com/biopython/biopytho= n/issues/5135" rel=3D"noreferrer" target=3D"_blank">https://github.com/biop= ython/biopython/issues/5135</a><br> > >><br> > >> * Using pyproject.toml rather than setup.py<br> > >>=C2=A0 =C2=A0 <a href=3D"https://github.com/biopython/biopytho= n/pull/5142" rel=3D"noreferrer" target=3D"_blank">https://github.com/biopyt= hon/biopython/pull/5142</a><br> > >><br> > >> Ideally sooner rather than later as the PDB _ATOM_FORMAT_STRI= NG glitch introduced in Biopython 1.86 seems to be hitting a lot of people:= <br> > >> <a href=3D"https://github.com/biopython/biopython/issues/5097= " rel=3D"noreferrer" target=3D"_blank">https://github.com/biopython/biopyth= on/issues/5097</a><br> > >><br> > >> Is there anything else you think is urgent enough to wait on?= <br> > >><br> > >> Thanks,<br> > >><br> > >> Peter<br> </blockquote></div> --000000000000a1b278064e3c4fd4-- --===============5531194047333625473== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Biopython mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biopython --===============5531194047333625473==--