Re: Biopython 1.70 release
Peter Cock <[email protected]> Tue, 11 Jul 2017 10:21:03 +0100
| Newsgroups | gmane.comp.python.bio.devel |
|---|---|
| Message-ID | <CAKVJ-_5oLLx9iaUZRhhF_4Hux6O+_Sey=i0YBaJYuX5Yu==6zA@mail.gmail.com> |
--===============6015339225485877848== Content-Type: multipart/alternative; boundary="089e08223c5cf1e16a055407371d" --089e08223c5cf1e16a055407371d Content-Type: text/plain; charset="UTF-8" Great - I'll delay the PyPI upload and announcement until at least one person confirms the zip/tar-ball works for an install from source. Thanks, Peter On Tue, Jul 11, 2017 at 9:06 AM, Mateusz Korycinski < [email protected]> wrote: > Hi, > > I can also test that on both Mac and Linux. > > Best regards, > Mateusz Korycinski > > Sent with ProtonMail <https://protonmail.com> Secure Email. > > -------- Original Message -------- > Subject: Re: [Biopython-dev] Biopython 1.70 release > Local Time: July 10, 2017 6:56 PM > UTC Time: July 10, 2017 4:56 PM > From: [email protected] > To: Sourav Singh <[email protected]> > Biopython-Dev Mailing List <[email protected]> > > Thanks for the offer Sourav, but Ben Fulton is happy to do > the Windows installers again for Biopython 1.70. > > It would however be great if you could download the zip file > (or tar-ball), and attempt to installing it from source and run > the tests (on Windows, Linux or Mac). > > e.g. > > wget http://biopython.org/DIST/biopython-1.70.zip > unzip biopython-1.70.zip > cd biopython-1.70 > pip install . > cd Tests > python run_tests.py > > Thanks, > > Peter > > On Mon, Jul 10, 2017 at 5:47 PM, Sourav Singh <[email protected]> > wrote: > >> Hello, >> >> I can help with the testing of the gzipped code and creation of Windows >> installers for Biopython 1.70. >> >> Regards, >> >> Sourav >> >> On Jul 10, 2017 9:59 PM, "Peter Cock" <[email protected]> wrote: >> >>> Hi Ben, >>> >>> While in the not too distant future I am hoping to adopt the >>> NumPy approach to building wheels (and installers?) [1], >>> it would be much appreciated if you could make all the >>> Windows installers for Biopython 1.70. >>> >>> (In particular Python 3.6, but if possible also Python 2.7, >>> 3.4 and 3.5 - we no longer support Python 3.3) >>> >>> Now that we have Windows-based continuous integration >>> up and running on AppVeyor [2], I didn't feel it necessary >>> to bother you in advance about running the unit tests. >>> >>> Much obliged, >>> >>> Peter >>> >>> [1] http://mailman.open-bio.org/pipermail/biopython-dev/2017-Jul >>> y/021817.html >>> >>> [2] http://mailman.open-bio.org/pipermail/biopython-dev/2017-Jun >>> e/021797.html >>> https://ci.appveyor.com/project/biopython/biopython/history >>> >>> >>> On Mon, Jul 10, 2017 at 4:43 PM, Peter Cock <[email protected]> >>> wrote: >>> > Hello all, >>> > >>> > I'd like to delay the PyPI upload and official release announcement >>> until >>> > someone else has confirmed they could install this - any volunteers? >>> > >>> > http://biopython.org/DIST/biopython-1.70.tar.gz >>> > http://biopython.org/DIST/biopython-1.70.zip >>> > Checksums: >>> > >>> > $ md5sum biopython-1.70.* >>> > feff7a3e2777e43f9b13039b344e06ff biopython-1.70.tar.gz >>> > 6307ab27c257fe69b9dae4bfc3052f49 biopython-1.70.zip >>> > >>> > $ sha256sum biopython-1.70.* >>> > 4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b >>> > biopython-1.70.tar.gz >>> > 34312ce899f6c3fc9dea77ca997f9a8c228043d05284a0653577594aeb119d4f >>> > biopython-1.70.zip >>> > >>> > These are from this tagged commit on the main repository: >>> > >>> > https://github.com/biopython/biopython/tree/biopython-170 >>> > https://github.com/biopython/biopython/commit/4d01a84f0aa8f9 >>> 1863075f7f0f074b4b69e53959 >>> > >>> > The revised documentation is already live: >>> > >>> > http://biopython.org/DIST/docs/api/ >>> > http://biopython.org/DIST/docs/tutorial/Tutorial.pdf >>> > http://biopython.org/DIST/docs/tutorial/Tutorial.html >>> > etc >>> > >>> > Peter >>> > >>> > On Mon, Jul 10, 2017 at 2:19 PM, Peter Cock <[email protected]> >>> wrote: >>> >> Thanks everyone who helped recently with resolving >>> >> open issues and pull requests - especially Eric who >>> >> did lots last week. >>> >> >>> >> I'm going to try the release this afternoon, so please >>> >> consider the mast branch frozen for the time being. >>> >> >>> >> Thanks, >>> >> >>> >> Peter >>> _______________________________________________ >>> Biopython-dev mailing list >>> [email protected] >>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev >>> >> --089e08223c5cf1e16a055407371d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr">Great - I'll delay the PyPI upload and announcement un= til<div>at least one person confirms the zip/tar-ball works for an</div><di= v>install from source.</div><div><br></div><div>Thanks,<br><div><br></div><= div>Peter</div></div></div><div class=3D"gmail_extra"><br><div class=3D"gma= il_quote">On Tue, Jul 11, 2017 at 9:06 AM, Mateusz Korycinski <span dir=3D"= ltr"><<a href=3D"mailto:[email protected]" target=3D"_blank">mko= [email protected]</a>></span> wrote:<br><blockquote class=3D"gmail_= quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1= ex"><div>Hi,<br></div><div><br></div><div>I can also test that on both Mac = and Linux.</div><div><br></div><div class=3D"m_-8982021536014373528protonma= il_signature_block"><div class=3D"m_-8982021536014373528protonmail_signatur= e_block-user"><div>Best regards,<br></div><div>Mateusz Korycinski<br></div>= </div><div><br></div><div class=3D"m_-8982021536014373528protonmail_signatu= re_block-proton">Sent with <a href=3D"https://protonmail.com" target=3D"_bl= ank">ProtonMail</a> Secure Email.<br></div></div><div><br></div><blockquote= class=3D"m_-8982021536014373528protonmail_quote" type=3D"cite"><span class= =3D""><div>-------- Original Message --------<br></div><div>Subject: Re: [B= iopython-dev] Biopython 1.70 release<br></div></span><div><div class=3D"h5"= ><div>Local Time: July 10, 2017 6:56 PM<br></div><div>UTC Time: July 10, 20= 17 4:56 PM<br></div><div>From: <a href=3D"mailto:[email protected]"= target=3D"_blank">[email protected]</a><br></div><div>To: Sourav S= ingh <<a href=3D"mailto:[email protected]" target=3D"_blank">ssou= [email protected]</a>><br></div><div>Biopython-Dev Mailing List <<= a href=3D"mailto:[email protected]" target=3D"_blank">biop= [email protected]<wbr>bio.org</a>><br></div><div><br></div><div di= r=3D"ltr"><div>Thanks for the offer Sourav, but Ben Fulton is happy to do<b= r></div><div>the Windows installers again for Biopython 1.70.<br></div><div= ><br></div><div>It would however be great if you could download the zip fil= e<br></div><div>(or tar-ball), and attempt to installing it from source and= run<br></div><div>the tests (on Windows, Linux or Mac).<br></div><div><br>= </div><div>e.g.<br></div><div><br></div><div>wget=C2=A0<a href=3D"http://bi= opython.org/DIST/biopython-1.70.zip" rel=3D"noreferrer nofollow noopener" t= arget=3D"_blank">http://biopython.org/<wbr>DIST/biopython-1.70.zip</a><br><= /div><div>unzip biopython-1.70.zip<br></div><div>cd biopython-1.70<br></div= ><div>pip install .<br></div><div>cd Tests<br></div><div>python run_tests.p= y<br></div><div><br></div><div>Thanks,<br></div><div><br></div><div>Peter<b= r></div></div><div class=3D"gmail_extra"><div><br></div><div class=3D"gmail= _quote"><div>On Mon, Jul 10, 2017 at 5:47 PM, Sourav Singh <span dir=3D"ltr= "><<a href=3D"mailto:[email protected]" rel=3D"noreferrer nofollo= w noopener" target=3D"_blank">[email protected]</a>></span> wrote= :<br></div><blockquote style=3D"margin:0 0 0 .8ex;border-left:1px #ccc soli= d;padding-left:1ex" class=3D"gmail_quote"><div dir=3D"auto"><div>Hello,<br>= </div><div dir=3D"auto"><br></div><div dir=3D"auto">I can help with the tes= ting of the gzipped code and creation of Windows installers for Biopython 1= .70.<br></div><div dir=3D"auto"><br></div><div dir=3D"auto">Regards,<br></d= iv><div dir=3D"auto"><br></div><div dir=3D"auto">Sourav<br></div></div><div= class=3D"gmail_extra"><div><br></div><div class=3D"gmail_quote"><div><div = class=3D"m_-8982021536014373528h5">On Jul 10, 2017 9:59 PM, "Peter Coc= k" <<a href=3D"mailto:[email protected]" rel=3D"noreferrer = nofollow noopener" target=3D"_blank">[email protected]</a>> wrot= e:<br></div></div><blockquote style=3D"margin:0 0 0 .8ex;border-left:1px #c= cc solid;padding-left:1ex" class=3D"gmail_quote"><div><div class=3D"m_-8982= 021536014373528h5"><div>Hi Ben,<br></div><div> <br></div><div> While in the= not too distant future I am hoping to adopt the<br></div><div> NumPy appro= ach to building wheels (and installers?) [1],<br></div><div> it would be mu= ch appreciated if you could make all the<br></div><div> Windows installers = for Biopython 1.70.<br></div><div> <br></div><div> (In particular Python 3.= 6, but if possible also Python 2.7,<br></div><div> 3.4 and 3.5 - we no long= er support Python 3.3)<br></div><div> <br></div><div> Now that we have Wind= ows-based continuous integration<br></div><div> up and running on AppVeyor = [2], I didn't feel it necessary<br></div><div> to bother you in advance= about running the unit tests.<br></div><div> <br></div><div> Much obliged,= <br></div><div> <br></div><div> Peter<br></div><div> <br></div><div> [1] <a= rel=3D"noreferrer nofollow noopener" href=3D"http://mailman.open-bio.org/p= ipermail/biopython-dev/2017-July/021817.html" target=3D"_blank">http://mail= man.open-bio.org/pi<wbr>permail/biopython-dev/2017-Jul<wbr>y/021817.html</a= ><br></div><div> <br></div><div> [2] <a rel=3D"noreferrer nofollow noopener= " href=3D"http://mailman.open-bio.org/pipermail/biopython-dev/2017-June/021= 797.html" target=3D"_blank">http://mailman.open-bio.org/pi<wbr>permail/biop= ython-dev/2017-Jun<wbr>e/021797.html</a><br></div><div> <a rel=3D"noreferre= r nofollow noopener" href=3D"https://ci.appveyor.com/project/biopython/biop= ython/history" target=3D"_blank">https://ci.appveyor.com/projec<wbr>t/biopy= thon/biopython/history</a><br></div><div> <br></div><div> <br></div><div> O= n Mon, Jul 10, 2017 at 4:43 PM, Peter Cock <<a href=3D"mailto:p.j.a.cock= @googlemail.com" rel=3D"noreferrer nofollow noopener" target=3D"_blank">p.j= [email protected]</a>> wrote:<br></div><div> > Hello all,<br></d= iv><div> ><br></div><div> > I'd like to delay the PyPI upload and= official release announcement until<br></div><div> > someone else has c= onfirmed they could install this - any volunteers?<br></div><div> ><br><= /div><div> > <a rel=3D"noreferrer nofollow noopener" href=3D"http://biop= ython.org/DIST/biopython-1.70.tar.gz" target=3D"_blank">http://biopython.or= g/DIST/biop<wbr>ython-1.70.tar.gz</a><br></div><div> > <a rel=3D"norefer= rer nofollow noopener" href=3D"http://biopython.org/DIST/biopython-1.70.zip= " target=3D"_blank">http://biopython.org/DIST/biop<wbr>ython-1.70.zip</a><b= r></div><div> > Checksums:<br></div><div> ><br></div><div> > $ md5= sum biopython-1.70.*<br></div><div> > feff7a3e2777e43f9b13039b344e06<wbr= >ff=C2=A0 biopython-1.70.tar.gz<br></div><div> > 6307ab27c257fe69b9dae4b= fc3052f<wbr>49=C2=A0 biopython-1.70.zip<br></div><div> ><br></div><div> = > $ sha256sum biopython-1.70.*<br></div><div> > 4a7c5298f03d1a45523f3= 2bae1fffc<wbr>ff323ea9dce007fb1241af092f5ab2<wbr>e45b<br></div><div> > b= iopython-1.70.tar.gz<br></div><div> > 34312ce899f6c3fc9dea77ca997f9a<wbr= >8c228043d05284a0653577594aeb11<wbr>9d4f<br></div><div> > biopython-1.70= .zip<br></div><div> ><br></div><div> > These are from this tagged com= mit on the main repository:<br></div><div> ><br></div><div> > <a rel= =3D"noreferrer nofollow noopener" href=3D"https://github.com/biopython/biop= ython/tree/biopython-170" target=3D"_blank">https://github.com/biopython/b<= wbr>iopython/tree/biopython-170</a><br></div><div> > <a rel=3D"noreferre= r nofollow noopener" href=3D"https://github.com/biopython/biopython/commit/= 4d01a84f0aa8f91863075f7f0f074b4b69e53959" target=3D"_blank">https://github.= com/biopython/b<wbr>iopython/commit/4d01a84f0aa8f9<wbr>1863075f7f0f074b4b69= e53959</a><br></div><div> ><br></div><div> > The revised documentatio= n is already live:<br></div><div> ><br></div><div> > <a rel=3D"norefe= rrer nofollow noopener" href=3D"http://biopython.org/DIST/docs/api/" target= =3D"_blank">http://biopython.org/DIST/docs<wbr>/api/</a><br></div><div> >= ; <a rel=3D"noreferrer nofollow noopener" href=3D"http://biopython.org/DIST= /docs/tutorial/Tutorial.pdf" target=3D"_blank">http://biopython.org/DIST/do= cs<wbr>/tutorial/Tutorial.pdf</a><br></div><div> > <a rel=3D"noreferrer = nofollow noopener" href=3D"http://biopython.org/DIST/docs/tutorial/Tutorial= .html" target=3D"_blank">http://biopython.org/DIST/docs<wbr>/tutorial/Tutor= ial.html</a><br></div><div> > etc<br></div><div> ><br></div><div> >= ; Peter<br></div><div> ><br></div><div> > On Mon, Jul 10, 2017 at 2:1= 9 PM, Peter Cock <<a href=3D"mailto:[email protected]" rel=3D"no= referrer nofollow noopener" target=3D"_blank">[email protected]</a>= > wrote:<br></div><div> >> Thanks everyone who helped recently wit= h resolving<br></div><div> >> open issues and pull requests - especia= lly Eric who<br></div><div> >> did lots last week.<br></div><div> >= ;><br></div><div> >> I'm going to try the release this afterno= on, so please<br></div><div> >> consider the mast branch frozen for t= he time being.<br></div><div> >><br></div><div> >> Thanks,<br><= /div><div> >><br></div><div> >> Peter<br></div></div></div><div= ><span>______________________________<wbr>_________________<br> Biopython-d= ev mailing list<br> <a href=3D"mailto:[email protected]" r= el=3D"noreferrer nofollow noopener" target=3D"_blank">Biopython-dev@mailman= .open-bio<wbr>.org</a><br> <a rel=3D"noreferrer nofollow noopener" href=3D"= http://mailman.open-bio.org/mailman/listinfo/biopython-dev" target=3D"_blan= k">http://mailman.open-bio.org/ma<wbr>ilman/listinfo/biopython-dev</a></spa= n></div></blockquote></div></div></blockquote></div></div></div></div></blo= ckquote></blockquote></div><br></div> --089e08223c5cf1e16a055407371d-- --===============6015339225485877848== 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 --===============6015339225485877848==--