Milestones for Biopython 1.78 - black style & no alphabets

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Hello all,

Last week at the BCC2020 CoFest thanks to multiple new contributors
we finished applying the black Python coding style to the remaining test
cases in Biopython. We now use this style for all our code.

Also, this has more impact for end users, we have now REMOVED the
Bio.Alphabet module.

In many cases, the alphabet can simply be ignored and removed from scripts.
In a few cases, you may need to specify the "molecule_type" as an annotation
on a SeqRecord for your script to work correctly. We are collating examples
on
https://github.com/biopython/biopython/issues/3156 (content likely to be
moved
to a more permanent location later).

You can read about or hear me talking briefly about this in the 5 minute
"Biopython Project Update 2020" talk given at BCC2020:

https://f1000research.com/slides/9-790

https://bcc2020.sched.com/event/coLV/biopython-project-update-2020

Kind regards,

Peter

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<div dir=3D"ltr"><span style=3D"color:rgb(38,40,42);font-family:&quot;Helve=
tica Neue&quot;,Helvetica,Arial,sans-serif;font-size:13px">Hello all,</span=
><div style=3D"color:rgb(38,40,42);font-family:&quot;Helvetica Neue&quot;,H=
elvetica,Arial,sans-serif;font-size:13px"><br></div><div style=3D"color:rgb=
(38,40,42);font-family:&quot;Helvetica Neue&quot;,Helvetica,Arial,sans-seri=
f;font-size:13px">Last week at the BCC2020 CoFest thanks to multiple new co=
ntributors</div><div style=3D"color:rgb(38,40,42);font-family:&quot;Helveti=
ca Neue&quot;,Helvetica,Arial,sans-serif;font-size:13px">we finished applyi=
ng the black Python coding style to the remaining=C2=A0test</div><div style=
=3D"color:rgb(38,40,42);font-family:&quot;Helvetica Neue&quot;,Helvetica,Ar=
ial,sans-serif;font-size:13px">cases in Biopython. We now use this style fo=
r all our code.</div><div style=3D"color:rgb(38,40,42);font-family:&quot;He=
lvetica Neue&quot;,Helvetica,Arial,sans-serif;font-size:13px"><br></div><di=
v style=3D"color:rgb(38,40,42);font-family:&quot;Helvetica Neue&quot;,Helve=
tica,Arial,sans-serif;font-size:13px">Also, this has more impact for end us=
ers, we have now=C2=A0REMOVED the</div><div style=3D"color:rgb(38,40,42);fo=
nt-family:&quot;Helvetica Neue&quot;,Helvetica,Arial,sans-serif;font-size:1=
3px">Bio.Alphabet module.</div><div style=3D"color:rgb(38,40,42);font-famil=
y:&quot;Helvetica Neue&quot;,Helvetica,Arial,sans-serif;font-size:13px"><br=
></div><div style=3D"color:rgb(38,40,42);font-family:&quot;Helvetica Neue&q=
uot;,Helvetica,Arial,sans-serif;font-size:13px">In many cases, the alphabet=
 can simply be ignored and removed from scripts.</div><div style=3D"color:r=
gb(38,40,42);font-family:&quot;Helvetica Neue&quot;,Helvetica,Arial,sans-se=
rif;font-size:13px">In a few cases, you may need to specify the &quot;molec=
ule_type&quot; as an annotation</div><div style=3D"color:rgb(38,40,42);font=
-family:&quot;Helvetica Neue&quot;,Helvetica,Arial,sans-serif;font-size:13p=
x">on a SeqRecord for your script to work correctly. We are collating examp=
les on<br></div><div style=3D"color:rgb(38,40,42);font-family:&quot;Helveti=
ca Neue&quot;,Helvetica,Arial,sans-serif;font-size:13px"><a rel=3D"nofollow=
" href=3D"https://github.com/biopython/biopython/issues/3156" target=3D"_bl=
ank">https://github.com/biopython/biopython/issues/3156</a>=C2=A0(content l=
ikely to be moved</div><div style=3D"color:rgb(38,40,42);font-family:&quot;=
Helvetica Neue&quot;,Helvetica,Arial,sans-serif;font-size:13px">to a more p=
ermanent location later).</div><div style=3D"color:rgb(38,40,42);font-famil=
y:&quot;Helvetica Neue&quot;,Helvetica,Arial,sans-serif;font-size:13px"><br=
></div><div style=3D"color:rgb(38,40,42);font-family:&quot;Helvetica Neue&q=
uot;,Helvetica,Arial,sans-serif;font-size:13px"><div>You can read about or =
hear me talking briefly about this in the 5 minute</div><div>&quot;Biopytho=
n Project Update 2020&quot; talk given at BCC2020:</div><div><br></div><div=
><a rel=3D"nofollow" href=3D"https://f1000research.com/slides/9-790" target=
=3D"_blank">https://f1000research.com/slides/9-790</a><br></div><div><br></=
div><div><a rel=3D"nofollow" href=3D"https://bcc2020.sched.com/event/coLV/b=
iopython-project-update-2020" target=3D"_blank">https://bcc2020.sched.com/e=
vent/coLV/biopython-project-update-2020</a></div></div><div style=3D"color:=
rgb(38,40,42);font-family:&quot;Helvetica Neue&quot;,Helvetica,Arial,sans-s=
erif;font-size:13px"><br></div><div style=3D"color:rgb(38,40,42);font-famil=
y:&quot;Helvetica Neue&quot;,Helvetica,Arial,sans-serif;font-size:13px">Kin=
d regards,</div><div style=3D"color:rgb(38,40,42);font-family:&quot;Helveti=
ca Neue&quot;,Helvetica,Arial,sans-serif;font-size:13px"><br></div><div sty=
le=3D"color:rgb(38,40,42);font-family:&quot;Helvetica Neue&quot;,Helvetica,=
Arial,sans-serif;font-size:13px">Peter</div></div>

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