Re: Ideas for Biopython 2.0

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It can see plenty of issues where it could help. In my specific case all
the PopGen code is stopped for 10 years because I would need to write very
fast code (say in Cython). This would be an extension module, not a core
module because it would impart a very big dependency on the system.

Modules would allow a core with very strict policies and dependencies _but_
extensions that could be way more relaxed.

It would also lower the barrier of entry for new content. Everyone could
publish an extension. If the extension would survive time (which most do
not - creating a maintenance burden in the core) then it could eventually
be made a core extension. Now the policy in practice is to add very little
innovation out of the fear that it will become stagnant and not-supported
by the main author (say after publication). An extension system would
accommodate both innovation whereas preserving the core quality.

Currently we have a gigantic monolith that in practice imposes very
conservative technologies and changes. I suspect that is why we do not see
anything really exciting with Biopython for the better part of the last
decade,

On 28 June 2017 at 04:25, Michiel de Hoon <[email protected]> wrote:

> I agree with Joao here. I don't see an immediate and overriding problem
> that modularity would solve, and I can see many drawbacks.
>
> Best,
> -Michiel
>
>
> On Monday, June 26, 2017 11:03 AM, Jo=C3=A3o Rodrigues <
> [email protected]> wrote:
>
>
> Copied from the other thread where I mistakenly posted:
>
> 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 constellation
> of modules you might end up with an up-to-date core and an out-of-date lo=
ne
> module somewhere, which makes things much much harder not only to maintai=
n
> but also to debug in case of issues.
>
>
> _______________________________________________
> Biopython-dev mailing list
> [email protected]
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>
>
>


--=20
Tiago Antao
Scientific and HPC programmer
http://tiago.org
https://github.com/tiagoantao/

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<div dir=3D"ltr">It can see plenty of issues where it could help. In my spe=
cific case all the PopGen code is stopped for 10 years because I would need=
 to write very fast code (say in Cython). This would be an extension module=
, not a core module because it would impart a very big dependency on the sy=
stem.<div><br></div><div>Modules would allow a core with very strict polici=
es and dependencies _but_ extensions that could be way more relaxed.</div><=
div><br></div><div>It would also lower the barrier of entry for new content=
. Everyone could publish an extension. If the extension would survive time =
(which most do not - creating a maintenance burden in the core) then it cou=
ld eventually be made a core extension. Now the policy in practice is to ad=
d very little innovation out of the fear that it will become stagnant and n=
ot-supported by the main author (say after publication). An extension syste=
m would accommodate both innovation whereas preserving the core quality.=C2=
=A0<br></div><div><br></div><div>Currently we have a gigantic monolith that=
 in practice imposes very conservative technologies and changes. I suspect =
that is why we do not see anything really exciting with Biopython for the b=
etter part of the last decade,</div></div><div class=3D"gmail_extra"><br><d=
iv class=3D"gmail_quote">On 28 June 2017 at 04:25, Michiel de Hoon <span di=
r=3D"ltr">&lt;<a href=3D"mailto:[email protected]" target=3D"_blank">mjld=
[email protected]</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quote" =
style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><di=
v><div style=3D"color:#000;background-color:#fff;font-family:Helvetica Neue=
,Helvetica,Arial,Lucida Grande,sans-serif;font-size:10px"><div id=3D"m_4366=
980446051291029yui_3_16_0_1_1498644225839_45791" dir=3D"ltr"><span id=3D"m_=
4366980446051291029yui_3_16_0_1_1498644225839_45863">I agree with Joao here=
. I don&#39;t see an immediate and overriding problem that modularity would=
 solve, and I can see many drawbacks.</span></div><div dir=3D"ltr"><span id=
=3D"m_4366980446051291029yui_3_16_0_1_1498644225839_45863"><br></span></div=
><div dir=3D"ltr"><span id=3D"m_4366980446051291029yui_3_16_0_1_14986442258=
39_45863">Best,</span></div><div dir=3D"ltr"><span id=3D"m_4366980446051291=
029yui_3_16_0_1_1498644225839_45863">-Michiel</span></div> <div class=3D"m_=
4366980446051291029qtdSeparateBR"><br><br></div><div class=3D"m_43669804460=
51291029yahoo_quoted" style=3D"display:block"> <div style=3D"font-family:He=
lvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif;font-size:10px"> <div=
 style=3D"font-family:HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida G=
rande,sans-serif;font-size:16px"><span class=3D""> <div dir=3D"ltr"><font s=
ize=3D"2" face=3D"Arial"> On Monday, June 26, 2017 11:03 AM, Jo=C3=A3o Rodr=
igues &lt;<a href=3D"mailto:[email protected]" target=3D"_blank=
">[email protected]</a><wbr>&gt; wrote:<br></font></div>  <br><=
br> </span><div class=3D"m_4366980446051291029y_msg_container"><span class=
=3D""><div id=3D"m_4366980446051291029yiv5820356184"><div><div dir=3D"ltr">=
Copied from the other thread where I mistakenly posted:<br clear=3D"none"><=
br clear=3D"none">I think we should focus on other topics such as=20
modularity. What do the proponents of the said modularity say about it?=20
What are its advantages? I personally think a big disadvantage is that=20
with one package install you get a wide array of tools for a variety of=20
subjects. With a constellation of modules you might end up with an=20
up-to-date core and an out-of-date lone module somewhere, which makes=20
things much much harder not only to maintain but also to debug in case=20
of issues. <div class=3D"m_4366980446051291029yiv5820356184yqt2693074091" i=
d=3D"m_4366980446051291029yiv5820356184yqtfd23041"><br clear=3D"none"><br c=
lear=3D"none"></div></div><div class=3D"m_4366980446051291029yiv5820356184y=
qt2693074091" id=3D"m_4366980446051291029yiv5820356184yqtfd49977">
</div></div></div></span><span class=3D""><div class=3D"m_43669804460512910=
29yqt2693074091" id=3D"m_4366980446051291029yqtfd49057">___________________=
___________<wbr>_________________<br clear=3D"none">Biopython-dev mailing l=
ist<br clear=3D"none"><a shape=3D"rect" href=3D"mailto:Biopython-dev@mailma=
n.open-bio.org" target=3D"_blank">[email protected]<wbr>bio.org</=
a><br clear=3D"none"><a shape=3D"rect" href=3D"http://mailman.open-bio.org/=
mailman/listinfo/biopython-dev" target=3D"_blank">http://mailman.open-bio.o=
rg/<wbr>mailman/listinfo/biopython-dev</a></div><br><br></span></div>  </di=
v> </div>  </div></div></div></blockquote></div><br><br clear=3D"all"><div>=
<br></div>-- <br><div class=3D"gmail_signature" data-smartmail=3D"gmail_sig=
nature"><div dir=3D"ltr">Tiago Antao<div>Scientific and HPC programmer</div=
><div><a href=3D"http://tiago.org" target=3D"_blank">http://tiago.org</a></=
div><div><a href=3D"https://github.com/tiagoantao/" target=3D"_blank">https=
://github.com/tiagoantao/</a><br></div></div></div>
</div>

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