Re: Planning to drop Python 2 support by 2020?

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Thanks Andrew,

I think we are agreed about dropping Python 2.7 support by 2020, although
please do comment on the Biopython 2 thread as well.

I will prepare a pull request adding the 2020 language to the README.rst
and NEWS.rst files, and once that's merged we can ask to be added to
http://www.python3statement.org/

Peter

On Mon, Jun 26, 2017 at 5:46 AM, Andrew Guy <[email protected]>
wrote:

> Hi all,
>
> Just wanted to add my thoughts as someone who is a relatively new user of
> Biopython (last ~3 years) and Python in general.
>
> I thankfully started with Python 3.x when I was first learning, and have
> never needed to use Python 2.7 (that I can recall) other than to check
> backwards compatibility for code I've written - the bulk of the big Pytho=
n
> scientific modules (e.g. Numpy, Scipy, scikit-learn) are all Python 3
> compatible. To add to this, using a virtual environment (e.g. pip
> virtualenv) to manage dependencies is something that everyone should be
> doing, and I don't think it's asking too much to require this if anyone
> wants to use an older compute cluster and a new version of Biopython.
>
> To add to sentiments that have been expressed a few times already, I also
> think it would be wonderful to be able to use some of the newer Python
> features in the code base going forward, especially if there is talk of
> moving to a new Biopython 2.x version.
>
> I'll add my vote to* a)* moving to Python 3.x for Biopython 2.x and* b)*
> keep a Biopython 1.x version that supports *critical* bug fixes but is
> otherwise considered to be unsupported. I think the move to Biopython 2.x
> would mark an excellent point from which to drop Python 2.x. Old
> scripts/programs will still use the final 1.x release, whereas code that
> uses the new API will be written with Python 3.x in mind.
>
> Regards,
>
> Andrew
>
> On 26 June 2017 at 11:51, Jo=C3=A3o Rodrigues <j.p.g.l.m.rodrigues@gmail.=
com>
> wrote:
>
>> As we say in Portuguese, 'this discussion grew a beard'. Tiago, you are
>> absolutely right.
>> =E2=80=8B
>> I'll say it again. My opinion is that we should move to Python 3.x for
>> Biopython 2.x *but* keep a version of Biopython 1.x that we support for
>> critical bug fixes for those users stuck with Python 2.x (for whatever
>> reason).
>>
>> I think we should focus on other topics such as modularity. What do the
>> proponents of the said modularity say about it? What are its advantages?=
 I
>> personally think a big disadvantage is that with one package install you
>> get a wide array of tools for a variety of subjects. With a constellatio=
n
>> of modules you might end up with an up-to-date core and an out-of-date l=
one
>> module somewhere, which makes things much much harder not only to mainta=
in
>> but also to debug in case of issues.
>>
>> (I have the impression I'm of the youngest here and already this guy
>> <https://en.wikipedia.org/wiki/The_Old_Man_of_Restelo>)
>>
>> _______________________________________________
>> Biopython-dev mailing list
>> [email protected]
>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>>
>
>
>
> --
> *Andrew Guy*
> PhD Student
> *Burnet Institute*
> T +613 9282 2346 <+613+9282+2346>
> M +614 1987 2670 <+614+1987+2670>
> E [email protected]
> W burnet.edu.au <http://www.burnet.edu.au/>
> The Macfarlane Burnet Institute for Medical Research and Public Health Lt=
d,
> 85 Commercial Road, Melbourne, VIC 3004, Australia
> ABN 49 007 349 984
>
> Equity through better health
> <https://www.burnet.edu.au/system/asset/file/2392/BURNET_2020_-_web_versi=
on.pdf>
>
> _______________________________________________
> Biopython-dev mailing list
> [email protected]
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>

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<div dir=3D"ltr">Thanks Andrew,<div><br></div><div>I think we are agreed ab=
out dropping Python 2.7 support by 2020, although</div><div>please do comme=
nt on the Biopython 2 thread as well.</div><div><br></div><div>I will prepa=
re a pull request adding the 2020 language to the README.rst</div><div>and =
NEWS.rst files, and once that&#39;s merged we can ask to be added to</div><=
div><a href=3D"http://www.python3statement.org/">http://www.python3statemen=
t.org/</a>=C2=A0</div><div><br></div><div>Peter</div></div><div class=3D"gm=
ail_extra"><br><div class=3D"gmail_quote">On Mon, Jun 26, 2017 at 5:46 AM, =
Andrew Guy <span dir=3D"ltr">&lt;<a href=3D"mailto:[email protected]=
" target=3D"_blank">[email protected]</a>&gt;</span> wrote:<br><bloc=
kquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #cc=
c solid;padding-left:1ex"><div dir=3D"ltr">Hi all,<div><br></div><div>Just =
wanted to add my thoughts as someone who is a relatively new user of Biopyt=
hon (last ~3 years) and Python in general.</div><div><br></div><div>I thank=
fully started with Python 3.x when I was first learning, and have never nee=
ded to use Python 2.7 (that I can recall) other than to check backwards com=
patibility for code I&#39;ve written - the bulk of the big Python scientifi=
c modules (e.g. Numpy, Scipy, scikit-learn) are all Python 3 compatible. To=
 add to this, using a virtual environment (e.g. pip virtualenv) to manage d=
ependencies is something that everyone should be doing, and I don&#39;t thi=
nk it&#39;s asking too much to require this if anyone wants to use an older=
 compute cluster and a new version of Biopython.</div><div><br></div><div>T=
o add to sentiments that have been expressed a few times already, I also th=
ink it would be wonderful to be able to use some of the newer Python featur=
es in the code base going forward, especially if there is talk of moving to=
 a new Biopython 2.x version.</div><div><br></div><div>I&#39;ll add my vote=
 to<b> a)</b> moving to Python 3.x for Biopython 2.x and<b> b)</b> keep a B=
iopython 1.x version that supports <i>critical</i>=C2=A0bug fixes but is ot=
herwise considered to be unsupported. I think the move to Biopython 2.x wou=
ld mark an excellent point from which to drop Python 2.x. Old scripts/progr=
ams will still use the final 1.x release, whereas code that uses the new AP=
I will be written with Python 3.x in mind.</div><div><br></div><div>Regards=
,</div><div><br></div><div>Andrew</div></div><div class=3D"gmail_extra"><br=
><div class=3D"gmail_quote"><div><div class=3D"h5">On 26 June 2017 at 11:51=
, Jo=C3=A3o Rodrigues <span dir=3D"ltr">&lt;<a href=3D"mailto:j.p.g.l.m.rod=
[email protected]" target=3D"_blank">[email protected]</a><wbr>&=
gt;</span> wrote:<br></div></div><blockquote class=3D"gmail_quote" style=3D=
"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div c=
lass=3D"h5"><div dir=3D"ltr"><div><div>As we say in Portuguese, &#39;this d=
iscussion grew a beard&#39;. Tiago, you are absolutely right.<br>=E2=80=8B<=
br></div>I&#39;ll say it again. My opinion is that we should move to Python=
 3.x for Biopython 2.x *but* keep a version of Biopython 1.x that we suppor=
t for critical bug fixes for those users stuck with Python 2.x (for whateve=
r reason).<br><br></div>I think we should focus on other topics such as mod=
ularity. What do the proponents of the said modularity say about it? What a=
re its advantages? I personally think a big disadvantage is that with one p=
ackage install you get a wide array of tools for a variety of subjects. Wit=
h a constellation of modules you might end up with an up-to-date core and a=
n out-of-date lone module somewhere, which makes things much much harder no=
t only to maintain but also to debug in case of issues. <br><br>(<a href=3D=
"https://en.wikipedia.org/wiki/The_Old_Man_of_Restelo" target=3D"_blank">I =
have the impression I&#39;m of the youngest here and already this guy</a>)<=
br></div>
<br></div></div><span class=3D"">______________________________<wbr>_______=
__________<br>
Biopython-dev mailing list<br>
<a href=3D"mailto:[email protected]" target=3D"_blank">Bio=
[email protected]<wbr>.org</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/ma<wbr>ilman/=
listinfo/biopython-dev</a><br></span></blockquote></div><br><br clear=3D"al=
l"><div><br></div>-- <br><div class=3D"m_7073799667050689210gmail_signature=
" data-smartmail=3D"gmail_signature"><div dir=3D"ltr"><table style=3D"font-=
family:Verdana,Geneva,Tahoma,sans-serif;width:1904px"><tbody><tr><td style=
=3D"font-family:Verdana,Geneva,Tahoma,sans-serif;font-size:12px;line-height=
:14.4px"><strong style=3D"color:rgb(189,12,17)">Andrew Guy</strong></td></t=
r><tr><td style=3D"font-family:Verdana,Geneva,Tahoma,sans-serif;font-size:1=
2px;line-height:14.4px"><span style=3D"color:rgb(74,107,126)">PhD Student</=
span></td></tr><tr><td style=3D"font-family:Verdana,Geneva,Tahoma,sans-seri=
f;font-size:12px;line-height:14.4px"><strong style=3D"color:rgb(74,107,126)=
">Burnet Institute</strong></td></tr></tbody></table><br style=3D"color:rgb=
(0,0,0);font-family:Verdana,Geneva,Tahoma,sans-serif;font-size:12px"><table=
 style=3D"font-family:Verdana,Geneva,Tahoma,sans-serif;margin:0px"><tbody><=
tr><td style=3D"font-family:Verdana,Geneva,Tahoma,sans-serif;font-size:12px=
;line-height:14.4px;color:rgb(89,111,128);width:15px">T</td><td style=3D"fo=
nt-family:Verdana,Geneva,Tahoma,sans-serif;font-size:12px;line-height:14.4p=
x"><a href=3D"tel:+613+9282+2346" style=3D"color:rgb(89,111,128);text-decor=
ation:none" target=3D"_blank">+613 9282 2346</a></td></tr><tr><td style=3D"=
font-family:Verdana,Geneva,Tahoma,sans-serif;font-size:12px;line-height:14.=
4px;color:rgb(89,111,128);width:15px">M</td><td style=3D"font-family:Verdan=
a,Geneva,Tahoma,sans-serif;font-size:12px;line-height:14.4px"><a href=3D"te=
l:+614+1987+2670" style=3D"color:rgb(89,111,128);text-decoration:none" targ=
et=3D"_blank">+614 1987 2670</a></td></tr><tr><td style=3D"font-family:Verd=
ana,Geneva,Tahoma,sans-serif;font-size:12px;line-height:14.4px;color:rgb(89=
,111,128);width:15px">E</td><td style=3D"font-family:Verdana,Geneva,Tahoma,=
sans-serif;font-size:12px;line-height:14.4px"><a href=3D"mailto:andrew.guy@=
burnet.edu.au" style=3D"color:rgb(89,111,128);text-decoration:none" target=
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ily:Verdana,Geneva,Tahoma,sans-serif;font-size:12px;line-height:14.4px;colo=
r:rgb(89,111,128);width:15px">W</td><td style=3D"font-family:Verdana,Geneva=
,Tahoma,sans-serif;font-size:12px;line-height:14.4px"><a href=3D"http://www=
.burnet.edu.au/" style=3D"color:rgb(89,111,128);text-decoration:none" targe=
t=3D"_blank">burnet.edu.au</a></td></tr></tbody></table><br style=3D"color:=
rgb(0,0,0);font-family:Verdana,Geneva,Tahoma,sans-serif;font-size:12px"><ta=
ble style=3D"font-family:Verdana,Geneva,Tahoma,sans-serif;width:1904px"><tb=
ody><tr><td style=3D"font-family:Verdana,Geneva,Tahoma,sans-serif;font-size=
:12px;line-height:14.4px;color:rgb(172,166,160)">The Macfarlane Burnet Inst=
itute for Medical Research and Public Health Ltd,<br>85 Commercial Road, Me=
lbourne, VIC 3004, Australia<br><span style=3D"font-size:10px">ABN 49 007 3=
49 984</span><br><br><span style=3D"font-style:italic"><a href=3D"https://w=
ww.burnet.edu.au/system/asset/file/2392/BURNET_2020_-_web_version.pdf" styl=
e=3D"text-decoration:none;color:rgb(172,166,160)" target=3D"_blank">Equity =
through better health</a></span></td></tr></tbody></table></div></div>
</div>
<br>______________________________<wbr>_________________<br>
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.open-<wbr>bio.org</a><br>
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listinfo/biopython-dev</a><br></blockquote></div><br></div>

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