Re: Planning to drop Python 2 support by 2020?

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I'm in Prague for the pre-BOSC 2017 CodeFest, where quite a few
Biopython contributors are present, and finally wrote this pull request:

https://github.com/biopython/biopython/pull/1333

Peter


On Mon, Jun 26, 2017 at 9:47 AM, Peter Cock <[email protected]>
wrote:

> 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 o=
f
>> 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 Pyth=
on
>> 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 als=
o
>> 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 yo=
u
>>> get a wide array of tools for a variety of subjects. With a constellati=
on
>>> of modules you might end up with an up-to-date core and an out-of-date =
lone
>>> module somewhere, which makes things much much harder not only to maint=
ain
>>> 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
>> Ltd,
>> 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_vers=
ion.pdf>
>>
>> _______________________________________________
>> Biopython-dev mailing list
>> [email protected]
>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>>
>
>

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<div dir=3D"ltr">I&#39;m in Prague for the pre-BOSC 2017 CodeFest, where qu=
ite a few<div>Biopython contributors are present, and finally wrote this pu=
ll request:</div><div><br></div><div><a href=3D"https://github.com/biopytho=
n/biopython/pull/1333">https://github.com/biopython/biopython/pull/1333</a>=
</div><div><br></div><div>Peter<br></div><div><br><div class=3D"gmail_extra=
"><br><div class=3D"gmail_quote">On Mon, Jun 26, 2017 at 9:47 AM, Peter Coc=
k <span dir=3D"ltr">&lt;<a href=3D"mailto:[email protected]" target=
=3D"_blank">[email protected]</a>&gt;</span> wrote:<br><blockquote =
class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px sol=
id rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr">Thanks Andrew,<div><=
br></div><div>I think we are agreed about dropping Python 2.7 support by 20=
20, although</div><div>please do comment on the Biopython 2 thread as well.=
</div><div><br></div><div>I will prepare a pull request adding the 2020 lan=
guage to the README.rst</div><div>and NEWS.rst files, and once that&#39;s m=
erged we can ask to be added to</div><div><a href=3D"http://www.python3stat=
ement.org/" target=3D"_blank">http://www.python3statement.<wbr>org/</a>=C2=
=A0</div><span class=3D"gmail-HOEnZb"><font color=3D"#888888"><div><br></di=
v><div>Peter</div></font></span></div><div class=3D"gmail-HOEnZb"><div clas=
s=3D"gmail-h5"><div class=3D"gmail_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><blockquote class=3D"gmail_quote" style=3D"margin=
:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);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 Biopython (last ~3 years) and P=
ython in general.</div><div><br></div><div>I thankfully started with Python=
 3.x when I was first learning, and have never needed to use Python 2.7 (th=
at I can recall) other than to check backwards compatibility for code I&#39=
;ve written - the bulk of the big Python scientific modules (e.g. Numpy, Sc=
ipy, scikit-learn) are all Python 3 compatible. To add to this, using a vir=
tual environment (e.g. pip virtualenv) to manage dependencies is something =
that everyone should be doing, and I don&#39;t think it&#39;s asking too mu=
ch to require this if anyone wants to use an older compute cluster and a ne=
w version of Biopython.</div><div><br></div><div>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 vers=
ion.</div><div><br></div><div>I&#39;ll add my vote to<b> a)</b> moving to P=
ython 3.x for Biopython 2.x and<b> b)</b> keep a Biopython 1.x version that=
 supports <i>critical</i>=C2=A0bug fixes but is otherwise considered to be =
unsupported. I think the move to Biopython 2.x would mark an excellent poin=
t from which to drop Python 2.x. Old scripts/programs will still use the fi=
nal 1.x release, whereas code that uses the new API will be written with Py=
thon 3.x in mind.</div><div><br></div><div>Regards,</div><div><br></div><di=
v>Andrew</div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quot=
e"><div><div class=3D"gmail-m_-7956034893111808259h5">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.=
[email protected]" target=3D"_blank">[email protected]</a><wb=
r>&gt;</span> wrote:<br></div></div><blockquote class=3D"gmail_quote" style=
=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding=
-left:1ex"><div><div class=3D"gmail-m_-7956034893111808259h5"><div dir=3D"l=
tr"><div><div>As we say in Portuguese, &#39;this discussion grew a beard&#3=
9;. 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 *b=
ut* 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).<br><br></div>I=
 think we should focus on other topics such as modularity. What do the prop=
onents of the said modularity say about it? What are its advantages? I pers=
onally think a big disadvantage is that with one package install you get a =
wide array of tools for a variety of subjects. With a constellation of modu=
les you might end up with an up-to-date core and an out-of-date lone module=
 somewhere, which makes things much much harder not only to maintain but al=
so 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>______________________________<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"gmail-m_-7956034893111808259m_707379=
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d style=3D"font-family:Verdana,Geneva,Tahoma,sans-serif;font-size:12px;line=
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.edu.au/" style=3D"color:rgb(89,111,128);text-decoration:none" target=3D"_b=
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<br>______________________________<wbr>_________________<br>
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[email protected]<wbr>.org</a><br>
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=3D"noreferrer" target=3D"_blank">http://mailman.open-bio.org/ma<wbr>ilman/=
listinfo/biopython-dev</a><br></blockquote></div><br></div>
</div></div></blockquote></div><br></div></div></div>

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