[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: Package available (was Re: Micro Manager)


at first thanks to Mark for his detailed and helpful explanation.

On Thu, Nov 03, 2011 at 09:06:46PM +0100, Mathieu Malaterre wrote:
> On Thu, Nov 3, 2011 at 5:14 PM, Mark Longair
> <mark-debianlists@longair.net> wrote:
> [...]
> > It's been a long term aim of mine to get (at least some of) Fiji
> > into Debian, and in fact I've intermittently discussed this with
> > Steffen Möller.
> Ok that's great news !

Yep.  And it also proves my point that discussion things on public
mailing lists makes sense because we can seek for it and refer to it in
the future. :-)
> > Unfortunately, I believe that my current approach to creating
> > the Fiji Debian packages is the wrong one, and it might be worth
> > taking a paragraph or two to explain why.  One of the aims of
> > Fiji was to create an easily installable package which bundled
> > ImageJ with a large number of useful plugins, various JVM-based
> > scripting languages, etc.  Essentially this was achieved by
> > adding the source of all these plugins to the Fiji git
> > repository, with major dependencies being added as submodules in
> > that repository.  This has had the following problems for
> > creating the Debian packages:
> This really looks like debian-med goals for most of its package...

> >  * I've tried as far as possible to replace components from Fiji
> >   with dependencies on existing Debian packages.  However,
> >   whenever developers update libraries in Fiji to versions that
> >   are later than those packaged in Debian, I have to switch
> >   back to creating a Fiji-specific version of that package.
> >   This is the case, for example, with Weka, Jython, jfreechart
> >   and commons-math.
> Did you fill bug reports in debian bts for those issues ?

It might be that it creates to much work for a single person like Mark
to continuosely file bug reports.  I have no idea how frequently these
dependencies are changing and in how far this really influences the
usability of Fiji.  I'd personally say that I would be quite annoyed if
I would continuosely be forced to adapt to new versions of software
because these might change interfaces or whatever.

However, if it turns out that we could spot some specific packages which
are not appropriately maintained inside Debian we could try to take over
team maintenance and take over responsibility on our own to make the
package better usable for the purpose we want to finally approach:
Making the best software for medical care available to our users right
inside Debian.  So Mark, if you say: well, package A, B and C are
usually OK, but package X and Y are constantly lagging behind what I
would need for Fiji, please do not hesitate to pronounce this here.
> >  * The Fiji source tree contains a number of binary jar files
> >   without corresponding source.  The bio-formats submodule is
> >   particularly concerning, since it's an important library in
> >   general for biological image processing, and the source tree
> >   currently bundles 24 jar files which should be external
> >   dependencies.
> Tell me about it ;) see:
> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=641448
> Any help is welcome :)

It would be great if we could (slowly but constantly) iron out such
Dependencies.  Finally we need to figh tthrough this dependency hell if
we want to reach the goal I mentioned above.  So lets try to set
priorities where to start.  If we succeed with this start we might find
more and more helpers who are convinced by our effort.
> > Although it pains me to say so, given the amount of time I've
> > spent on this already, I'm not convinced that trying to build
> > fine-grained packages out of the Fiji source tree is likely to
> > meet the quality requirements for Debian main any time soon.  It
> > would probably be better on building up a similar set of
> > packages based on the existing Debian imagej package, but
> > starting from upstream for each particular plugin.  (Where
> > components only exist in fiji.git I can extra them into a
> > standalone repository with git-subtree.)  Although it would take
> > a long time to build up the same number of plugins as are
> > bundled in Fiji, at least steady progress could be made in
> > introducing useful packages into Debian.  For a number of
> Sound like a plan !

> > packages it doesn't make sense that they should be built out of
> > the Fiji source tree anyway (e.g. bio-formats, RSyntaxTextArea,
> > AutoComplete) since they're generically useful libraries outside
> > context of Fiji.
> How many people are behind the fiji effort ? Are they mostly
> debian-based system users ? Jumping in the debian-med effort is
> relatively easy.

Good questions.  We can not stress frequently enough that in the past it
worked quite good to teach and help interested persons (upstream
developers) to build packages and help them to get it finally to the
official mirror.

> I do not believe debian-med could get even close to the momemtum
> involve in the fiji packaging, since it involve careful review of each
> and every single source code to check licensing issue. But I can
> imagine there is some duplicate work, and we could use some of your
> help, if you wish to jump in.

Full ACK here as well.

Kind regards



Reply to: