[Debian-med-packaging] Bug#730515: cd-hit-est is cdhit-est in Debian [Why?]

[Andreas Tille]

Hi,

any news about the naming cd-hit versus cdhit?  Is the name
intentionally choosen and should be fixed in python-cogent?

Kind regards

        Andreas.

----- Forwarded message from Andreas Tille <andreas at an3as.eu> -----

Date: Tue, 26 Nov 2013 09:25:43 +0100
From: Andreas Tille <andreas at an3as.eu>
To: 730515 at bugs.debian.org, Weizhong Li <liwz at sdsc.edu>
Subject: Bug#730515: cd-hit-est is cdhit-est in Debian [Why?]
X-Debian-PR-Message: followup 730515
X-Debian-PR-Package: src:cd-hit,src:python-cogent
X-Debian-PR-Keywords: 
X-Debian-PR-Source: cd-hit,src:python-cogent

Hi,

as you can read below a Debian user has made some IMHO valid point about
naming inconsistencies in cd-hit.  I think this should be addressed by
the upstream developer and thus I'm forwarding this issue to you with the
kind question, how we should choose some proper naming for the different
tools.  It also might be that we misunderstood something and that your
different naming pattern might have some deeper sense.

Kind regards and thanks for providing cd-hit as free software

     Andreas.

On Mon, Nov 25, 2013 at 04:35:20PM -0800, Don Armstrong wrote:
> Package: src:cd-hit,src:python-cogent
> Control: found -1 cd-hit/4.6.1-2012-08-27-2
> Control: found -1 python-cogent/1.5.3-2
> Severity: normal
> 
> python-cogent refers to cd-hit-est, which I presume is the standard
> upstream naming for cd-hit. However, in Debian, the cd-hit package
> installs cd-hit-est as cdhit-est.
> 
> I don't know which is correct, but either cd-hit or python-cogent should
> be fixed (or both!)
> 
> Secondarily, cd-hit really should decide whether it is called cd-hit or
> cdhit, as it installs some commands called cd-hit and others called
> cdhit:
> 
> /usr/bin/cd-hit-div
> /usr/bin/cdhit-est
> /usr/bin/psi-cd-hit-local
> /usr/bin/cd-hit-2d-para
> /usr/bin/psi-cd-hit-2d
> /usr/bin/psi-cd-hit
> /usr/bin/psi-cd-hit-2d-g1
> /usr/bin/cdhit-454
> /usr/bin/cdhit-2d
> /usr/bin/cdhit-est-2d
> /usr/bin/cd-hit-para
> /usr/bin/cdhit
> 
> -- 
> Don Armstrong                      http://www.donarmstrong.com
> 
> "Do you need [...] [t]ools? Stuff?"
> "Our opponent is an alien starship packed with atomic bombs. [...] We
> have a protractor."
>  -- Neal Stephenson _Anathem_ p320
> 
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> 

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