[Debian-med-packaging] Improving the Gentle package

Tue Jan 1 19:00:22 UTC 2013

Hi!
Sorry for the long delay, but some unexpected events happened which
stopped me from replying faster. Also, there was christmas and
Silvester, so first of all:
  Happy new year to eveeryone!

Now the GENtle part. I now included the mailinglist, so for people who
are interested a very short summary: We are discussing improvements in
GENtle/the GENtle packaging. I started with a request to do some minor
tweaks on the GENtle package, because I always wanted to do that (and
get in touch with the Debian-Med team) and haven't had the time yet.
I'm also in the NM process at time, so I would do this as work-sample
for the NM process.

@Magnus/Steffen: I can imagine packaging GENtle2 and maintaining it -
it works here, but the supported features are quite limited. At time,
I would rather use the original GENtle. Also, GENtle2 is more a
complete rewrite than a successor to the original tool.
Magnus, you said you started porting GENtle to Qt4 - what were the
difficulties, and have you thought about publishing your initial work,
even if it is not working? Maybe others are interested and can help
with that.

For me at time, I can only do very less work, unfortunately. I am busy
with writing exams in January/February and feature/bugfix requests
regarding the Freedesktop projects I'm involved in are piling up here,
and these take priority at time. (but the most time-cosuming tasks are
the exams :P) However, I'll do as much as I can to bring GENtle in an
excellent shape for Debian.
At time, I'm trying to set up the SVN packaging stuff to make changes
on the GENtle packaging and push them back.

Is there a demand for GENtle2 in Debian? (the name is unfortunate, in
case the original GENTle will reach version 2 in future...) If so,
I'll look into it.

Cheers,
   Matthias

P.S: Please keep thijs and Magnus in CC as long as they want to, both
are not subscribed to the list.

2012/12/12 "Steffen Möller" <steffen_moeller at gmx.de>:
> Hi Magnus,
>
> I have watched your videos and liked their strict focus on single tasks. I just did not manage to do the annotation on my sequence.
>
> Anyway, besides doing some promotion I do not exactly see what Debian could do to help. What comes to mind:
>  * plugin to interact with a tool installed locally (no idea if js allows that) and Debian has many bioinformatics tools
>  * Debian package of your .js files to help others setting it all up
>
> The cloning etc seems missing from the publicly visible parts. I personally would be interested to have a storage format that is kind of human readable and collects the steps that were performed to come up with the final product. Sounds like a nice Bachelor work, possibly.
>
> So, I hope Matthias establishes some direct link with you and ... whenever something gets out, this seems good for everyone.
>
> Many greetings
>
> Steffen
>
> -------- Original-Nachricht --------
>> Datum: Tue, 11 Dec 2012 19:11:33 +0000
>> Von: Magnus Manske <magnusmanske at googlemail.com>
>> An: "Steffen Möller" <steffen_moeller at gmx.de>
>> CC: Andreas Tille <andreas at fam-tille.de>, matthias at tenstral.net, magnusmanske+gentle at googlemail.com, thijs at debian.org
>> Betreff: Re: Improving the Gentle package
>
>> Hi all,
>>
>> I am the original author of GENtle. Just a quick couple of points:
>> * It's wxWidgets, using GTK for Linux
>> * I tried a rewrite using QT and failed horribly due to time constraints
>> * For the same reason, I cannot maintain the current codebase anymore
>>
>> But, fear not, there is hope (kinda;-) !
>>
>> Supported by the good folks at Synbiota, a synthetic biology startup, I
>> have begun a surprisingly successful rewrite of GENtle as a web app, in
>> JavaScript. Yes, seriously.
>> * Try it : http://ec2-23-20-169-157.compute-1.amazonaws.com/dev/ (for the
>> impatient: "File/Open from NCBI"...)
>> * Check out the code, and help out : https://github.com/Synbiota/GENtle2
>>
>> Cheers,
>> Magnus
>>
>>
>>
>>
>> On Tue, Dec 11, 2012 at 9:53 AM, "Steffen Möller"
>> <steffen_moeller at gmx.de>wrote:
>>
>> > Hello,
>> >
>> > > > Thank you for the quick reply!
>> > >
>> > > It would have been the same speed if you would have contacted the
>> > > mailing list and you might have received even more answers.  Feel
>> > > free to post your next mail straight to debian-med at lists.debian.org
>> > > and be aware that I'll most probably will CC my next reply to the
>> > > list (assuming that no private content will be in your mail.)
>> >
>> > ;) sounds familiar.
>> >
>> > > > >> Please read: ... which is maintained by the Debian Med team and
>> in
>> > > the
>> > > > >> case of gentle it happened that Steffen and me did the work.
>> > > > Yep, but from my experience with teams it is always a better idea to
>> > > > directly contact the people who did the work ;-)
>> > >
>> > > I hope we can prove you experience wrong.  Steffen will confirm
>> strongly
>> > > that I have some record of pushing people to discuss in public and
>> from
>> > > my perspective I think it is the best way to go for Free Software.
>> >
>> > I happily confirm Andreas to discuss things openly by default, but he
>> does
>> > not open things when asked not to, which is the important part.
>> >
>> > > > >> I admit Gentle definitely could profit from some enhancement.
>> > > > >
>> > > > > You email's subject line already enthused me. Just, please be
>> aware:
>> > > GENtle is a beast. Coded against some
>> > > > > older version of Qt/KDE, a porting of it all against modern
>> versions
>> > > of the library would be helpful.
>> > > > Isn't GENtle developed using wxWidgets? Porting it to Qt might be
>> > > > helpful, but that would be way out of scope for me ^^
>> > >
>> > > I have not dived into the code but it is definitely not Qt (and
>> Steffen
>> > > most probably does not want you to switch the toolkit).
>> >
>> > Not? Ok, I forgot, then. Sounds likely, given the platform independence
>> > from many years ago.
>> >
>> > > > > Or, just anyone feeling sufficiently competent of the source tree
>> to
>> > > perform some decent communication with
>> > > > > upstream would be much appreciated.
>> > > > Upstream looked dead to me - has the development moved somewhere
>> else,
>> > > probably?
>> > >
>> > > Here you can see the advantages of open discussion.  I asked in public
>> > >
>> > >    https://lists.debian.org/debian-med/2012/08/msg00097.html
>> > >
>> > > and sadly only became a private mail which leaves others in
>> uncertainty.
>> > > Yes, Gentle development has stalled and Magnus is favouring some web
>> > > system now (would have to seek my private mail archive for his
>> response
>> > > but I'm a bit in a hurry.)
>> >
>> > Whatever it is, there are a series of gems in GENtle that would be nice
>> to
>> > be kept.
>> >
>> > > > >> accessing the Vcs would be the most easy way for everybody.  I do
>> > not
>> > > > >> know what Vcs Steffen prefers - at least he started the work in
>> SVN.
>> > > If
>> > > > >> you have some strong preference for Git and this would increase
>> your
>> > > > >> productivity you should talk to Steffen whether he might mind
>> some
>> > > move.
>> > > > >> I'm personally not very skilled with Git but I'm constantly
>> learning
>> > > and
>> > > > >> the usual packaging tasks are perfectly fine for me in either SVN
>> or
>> > > > >> Git.
>> > > > I love Git and I am much more experienced in using a Git workflow
>> than
>> > > > using SVN - but I don't want to add limitations to anyone of you by
>> > > > forcing someone to use Git. I also don't know if your team has
>> policy
>> > > > for VCS.
>> > > > So, for me I am fine with SVN too (there are enough docs on how to
>> > > > handle Debian packages with it).
>> > >
>> > > Both is possible:
>> > >
>> > >    http://debian-med.alioth.debian.org/docs/policy.html
>> > >
>> > > Ping Steffen: Waht do you think about a Git move?
>> >
>> > I will not be contributing to the effort myself in any near future. You
>> > decide. Just be aware that one easily loses the oversight of what is
>> > important - git vs svn is not important as long as you are alone with
>> the
>> > project IMHO.
>> >
>> > For mere Debian packaging, Svn I consider superior to git. For upstream
>> > development, I use git.
>> >
>> > > > > [...]
>> > > > > There is plenty of easier stuff you could help out with.
>> > > > Yep, but I am explicitly not planning to do a rewrite of GENtle :P
>> > > > What I have in mind is stuff like adding a desktop file,
>> > >
>> > > This could be easily done in the Debian package.
>> >
>> > Do not move to git just for that or more of such kind of things.
>> >
>> > > > killing some
>> > > > pointless buttons, maybe fixing a dialog (depends on where the issue
>> > > > is) and removing the debug messages. (Debug messages in
>> message-boxes
>> > > > (!) - everytime I want to import a database, I have to click a
>> > > > thousant times on useless dialog boxes)
>> > >
>> > > You could also do this via patches inside the Debian package but in
>> this
>> > > case I would strongly recommend talking to upstream to work in the
>> > > original SVN (or convert it to Git and become upstream yourself.)  The
>> > > thing is that there are other distributions than Debian which might
>> also
>> > > try to package.  Having a consistent upstream with as less patches as
>> > > possible seems to be reasonable.
>> >
>> > Andreas' suggestion sounds good to me.
>> >
>> > > > > If you are much into nucleic acid analysis and want to think more
>> > > about preparing for wet lab experiments, I
>> > > > > suggest starting with PerlPrimer. It communicates with Ensembl,
>> but
>> > > Ensembl is much of a moving target, so it needs frequent updates.
>> Charles
>> > > <Plessy at debian.org> may have additional packages coming to mind. There
>> > is now
>> > > a new version of autodock out, which would be a straight forward easy
>> > > start, for instance.
>> > > > ><
>> > > > In sense of packaging work, I already have many things to maintain,
>> > > > e.g. I develop the whole PackageKit stack (package management
>> daemon)
>> > > > for Debian, which requires a lot of attention and much upstream
>> work.
>> > > > But I'll take a look at it - this whole "do some work at Debian"
>> part
>> > > > is a bit fuzzy in the NM process. But since many people at the lab
>> > > > asked me about some minor improvements in GENtle, which annoyed me
>> > > > too, I thought it might be a good starting point.
>> > >
>> > > +1
>> >
>> > Excellent. Also good to hear that you have local users. We have just
>> one,
>> > and he boots into Windows to use it since it is just slightly more
>> stable
>> > over there.
>> >
>> > > > > Definitely, please go for it, but do not render it an intrinsic
>> part
>> > > of your development towards a Debian
>> > > > > Maintainer/Developer. Let it be some spare time fun project. For
>> the
>> > > DM/DD applications it is more the number of packages that you are
>> > > maintaining and the experience you gained through that than the nitty
>> > gritty of an
>> > > individual package that counts.
>> > > > ><
>> > > > I already have experience with super-complex packages - I brought
>> the
>> > > > projectM packaging back to life, which was hell when I started the
>> > > > work. Now it works great, thanks to some changes I did together with
>> > > > upstream. :)
>> > >
>> > > Sounds good.
>> >
>> > Good!
>> >
>> > > > I definitely want to join your team,
>> > >
>> > > I just added ximion-guest to Debian Med team.
>> >
>> > Welcome.
>> >
>> > [..]
>> >
>> > > > Some information which might be interesting to you is that I am part
>> > > > of the local iGEM (Synthetic Biology competition) team of my
>> > > > university - that is the stuff we use GENtle for, and it works okay
>> > > > for most of the stuff.
>> > >
>> > > Good to know.  If you know other stuff that might be interesting just
>> > > let us know (for sure via list ;-).)
>> >
>> > This is excellent. I tried for long to get my folks over here
>> (clinicians)
>> > interested in that. Whatever software you use in that context, please
>> bring
>> > it to Debian. Also please consider to write
>> > something about it in wiki.debian.org.
>> >
>> > Many thanks and greeting
>> >
>> > Steffen
>> >
>> >