Re: Background needed for developing BioPython

--===============8810198276877956368==
Content-Type: multipart/alternative; boundary="001a1143d6ee72adce05549c9e8e"

--001a1143d6ee72adce05549c9e8e
Content-Type: text/plain; charset="UTF-8"

Thank you for the expansive list. I guess I will start by going through the
tutorial to look for errors. Testing does look like the best way to get to
know the code base.

On Jul 17, 2017 3:21 AM, "Peter Cock" <[email protected]> wrote:

Hi Jennifer,

Hello and welcome.

You certainly could help out even with minimal biological
knowledge. Where you might best help will depend on
your interests and experience.

If you have particular experience with the joys of unicode
encodings, recently we've found a few more problems
lurking in our code tests only exposed under unusual
locales, where real world data files have non-ASCII
characters (usually people's names):

https://github.com/biopython/biopython/issues/1321
https://github.com/biopython/biopython/issues/1320

One practical option would be working though the tutorial
with the latest Biopython and flagging any code snippets
which don't work, or typos. That would also give you some
idea of the breadth of the code base (although not all of
Biopython is covered in the Tutorial).

There are also on going efforts to better follow the PEP8
and PEP257 standards (although we don't want to break
backwards compatibility so things like existing mixed
case module names persist).

https://github.com/biopython/biopython/issues/1170

Related to that, we're also slowly getting our docstrings
into proper RST markup, with a view to replacing epydoc
with something more modern for making the API docs:

https://github.com/biopython/biopython/issues/1221
https://github.com/biopython/biopython/issues/906

Right now I've been working on compiled wheel files
to help with Biopython installation - with that done we
should review all our installation instructions, refocusing
some of the compiler centric material for developers
only etc,

https://github.com/biopython/biopython/issues/1296
https://github.com/biopython/biopython/issues/1295

Note we're asking all new contributors to dual license
their contributions under both the Biopython License
Agreement and the BSD 3-Clause License:

https://github.com/biopython/biopython/issues/898

Regards,

Peter

On Mon, Jul 17, 2017 at 1:45 AM, Jennifer Sweezey <[email protected]>
wrote:
> I am a Python developer with an M.S and 7+ yrs of experience in software
> design\management. I find bioinformatics and genomics fascinating and
really
> want to get involved but I have no biology background whatsoever. Can I
> really contribute to a project like BioPython without the requisite bio
> background?  If so, where do I start?
>
> Thanks!
>
> _______________________________________________
> Biopython-dev mailing list
> [email protected]
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev

--001a1143d6ee72adce05549c9e8e
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

<div dir=3D"auto"><div>Thank you for the expansive list. I guess I will sta=
rt by going through the tutorial to look for errors. Testing does look like=
 the best way to get to know the code base.<br><div class=3D"gmail_extra"><=
br><div class=3D"gmail_quote">On Jul 17, 2017 3:21 AM, &quot;Peter Cock&quo=
t; &lt;<a href=3D"mailto:[email protected]">[email protected]=
om</a>&gt; wrote:<br type=3D"attribution"><blockquote class=3D"quote" style=
=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Jenni=
fer,<br>
<br>
Hello and welcome.<br>
<br>
You certainly could help out even with minimal biological<br>
knowledge. Where you might best help will depend on<br>
your interests and experience.<br>
<br>
If you have particular experience with the joys of unicode<br>
encodings, recently we&#39;ve found a few more problems<br>
lurking in our code tests only exposed under unusual<br>
locales, where real world data files have non-ASCII<br>
characters (usually people&#39;s names):<br>
<br>
<a href=3D"https://github.com/biopython/biopython/issues/1321" rel=3D"noref=
errer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/issues=
/1321</a><br>
<a href=3D"https://github.com/biopython/biopython/issues/1320" rel=3D"noref=
errer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/issues=
/1320</a><br>
<br>
One practical option would be working though the tutorial<br>
with the latest Biopython and flagging any code snippets<br>
which don&#39;t work, or typos. That would also give you some<br>
idea of the breadth of the code base (although not all of<br>
Biopython is covered in the Tutorial).<br>
<br>
There are also on going efforts to better follow the PEP8<br>
and PEP257 standards (although we don&#39;t want to break<br>
backwards compatibility so things like existing mixed<br>
case module names persist).<br>
<br>
<a href=3D"https://github.com/biopython/biopython/issues/1170" rel=3D"noref=
errer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/issues=
/1170</a><br>
<br>
Related to that, we&#39;re also slowly getting our docstrings<br>
into proper RST markup, with a view to replacing epydoc<br>
with something more modern for making the API docs:<br>
<br>
<a href=3D"https://github.com/biopython/biopython/issues/1221" rel=3D"noref=
errer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/issues=
/1221</a><br>
<a href=3D"https://github.com/biopython/biopython/issues/906" rel=3D"norefe=
rrer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/issues/=
906</a><br>
<br>
Right now I&#39;ve been working on compiled wheel files<br>
to help with Biopython installation - with that done we<br>
should review all our installation instructions, refocusing<br>
some of the compiler centric material for developers<br>
only etc,<br>
<br>
<a href=3D"https://github.com/biopython/biopython/issues/1296" rel=3D"noref=
errer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/issues=
/1296</a><br>
<a href=3D"https://github.com/biopython/biopython/issues/1295" rel=3D"noref=
errer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/issues=
/1295</a><br>
<br>
Note we&#39;re asking all new contributors to dual license<br>
their contributions under both the Biopython License<br>
Agreement and the BSD 3-Clause License:<br>
<br>
<a href=3D"https://github.com/biopython/biopython/issues/898" rel=3D"norefe=
rrer" target=3D"_blank">https://github.com/biopython/<wbr>biopython/issues/=
898</a><br>
<br>
Regards,<br>
<br>
Peter<br>
<div class=3D"elided-text"><br>
On Mon, Jul 17, 2017 at 1:45 AM, Jennifer Sweezey &lt;<a href=3D"mailto:jen=
@jensweezey.com">[email protected]</a>&gt; wrote:<br>
&gt; I am a Python developer with an M.S and 7+ yrs of experience in softwa=
re<br>
&gt; design\management. I find bioinformatics and genomics fascinating and =
really<br>
&gt; want to get involved but I have no biology background whatsoever. Can =
I<br>
&gt; really contribute to a project like BioPython without the requisite bi=
o<br>
&gt; background?=C2=A0 If so, where do I start?<br>
&gt;<br>
&gt; Thanks!<br>
&gt;<br>
</div>&gt; ______________________________<wbr>_________________<br>
&gt; Biopython-dev mailing list<br>
&gt; <a href=3D"mailto:[email protected]">Biopython-dev@ma=
ilman.open-<wbr>bio.org</a><br>
&gt; <a href=3D"http://mailman.open-bio.org/mailman/listinfo/biopython-dev"=
 rel=3D"noreferrer" target=3D"_blank">http://mailman.open-bio.org/<wbr>mail=
man/listinfo/biopython-dev</a><br>
</blockquote></div><br></div></div></div>

--001a1143d6ee72adce05549c9e8e--

--===============8810198276877956368==
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
--===============8810198276877956368==--