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Re: bioinfo package - maintenance of ...

From: Doug Stewart
Subject: Re: bioinfo package - maintenance of ...
Date: Mon, 18 Dec 2017 09:33:44 -0500

On Mon, Dec 18, 2017 at 8:29 AM, Michael D Godfrey <address@hidden> wrote:

On 12/18/2017 10:03 AM, Julien Bect wrote:
Le 18/12/2017 à 10:41, Alois Schloegl a écrit :
On 2017-12-18 09:04, Olaf Till wrote:
On Sun, Dec 17, 2017 at 09:44:17PM +0100, Alois Schloegl wrote:
Dear Octave maintainers,

for several years, the bioinfo package does not have maintainer, I've
been adding three functions, and would like to maintain that package.

However, it is important to me, that this code can be used under matlab
as well, which means coding style that would work only in Octave but not
in Matlab would be a problem, and I could not contribute. Essentially,
I'd need to find or start another repository for maintaining these

Therefore, I'm asking whether it would be ok with you, if I take the
role of a maintainer for the bioinfo package.

Best regards,
FTR, after pointing out that the existing functions of this package
comply with Octave coding style, the following had been my
(unanswered) reply to this request at

https://sourceforge.net/p/octave/package-releases/322/ :

I understand the need for running code both in Octave and in
Matlab. But if the code is to be maintained in collaboration, it can't
be kept in a style which deviates from the standard style of the
collaborating group.

I understand, too, that this removes your motivation to maintain the
code within the bioinfo package. But still, if you are willing to
contribute your new code as it is, GPL3+ licensed, this would be
nice. You could do it at the patch tracker. Since the bioinfo package
is currently comparatively simply structured, others (even me) could
take the task of adapting your code to Octave style. And since making
a bioinfo release is currently also comparatively simple, I can
probably do it myself once I get a hint that it's suitable to make a
new one.

Could you accept this compromise? If yes, do you give me leave to
adapt your current new code and to make a release?

Dear Olaf,

If you insist on a coding style that is incompatible to Mat*ab, I'll
need to setup another repository. My prefered solution would be not
doing that, but maintaining the code within the current repo. Since the
code is licensed with the GPL, the code is Free anyway, so it will not
be a big issue either way. There is "just" the additional effort of
maintaining two code bases - something I'd prefer to avoid.

Still, I'm hoping that it's acceptable to use a compatible coding style
within OF. Since the bioinfo package has no maintainer for several
years, I thought I can contribute here.

My opinion : 1) more maintained OF packages is good ; 2) more Matlab-compatible packages is good.

So I'm all in favour of Alois taking maintenance of this package and making new contributions in a Matlab-compatible style,


I definitely agree with Julien. Having a maintainer is very good. And, the maintainers should have
reasonable freedom to make the choices that work best.


I agree with Michael who agrees with Julien.

I still think we need a 3 tier setup
1) pkgs like control statistics etc that should have strict rules
2) pkgs like this that allows the maintainer more freedom.
3) pkgs that we only link to and the maintainer has full control over.

DASCertificate for 206392

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