Re: fiji packages [was Re: debian imagej]
Hi Mark,
On Thu, 30 Apr 2009, Mark Longair wrote:
I should probably say "hello" at this point,
Welcome at the Debian Med mailing list.
since I'm one of
the Fiji developers and I built the debian packages of Fiji that
you can get from http://pacific.mpi-cbg.de/
It is nice to stay in close contact with upstream authors.
Although I think these packages work OK (and it's always nice to
to hear that some people use them!) there are quite a few
reasons why they wouldn't be suitable for Debian main at the
moment:
- We've been working to get rid of, or replace, any remaining
non-DFSG licensed plugins, but there's at least one left.
The bug for tracking this is here:
http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=19
Good to hear that people are busy working to make their product
DFSG-free. Please keep us informed if you are successful.
- At the moment Fiji depends on sun-java6 rather than openjdk.
Any strong reasons for this? I'm just asking because this would
move fiji at best to contrib and if some small patches might
suffice this would be definitely worth the effort.
- The packages are rather large at the moment (about 35MiB).
This is mostly due to bundling various components with Fiji
that could be satisfied as dependencies in Debian, such as
junit, jruby, etc. but I haven't had time to work on
separating those out.
Well, bundling separate third party components is not a good
idea if you are targeting at an official package. This would
have to be sorted out once we might tackle this goal.
- Fiji uses a modified version of ImageJA (which again is
bundled into the fiji package) rather than depending on the
imagej Debian package created by people on this list.
Is there any reason not to use ImageJ? I mean - Debian just
has an old version because of the problem I mentioned in the
beginning of this thread [1] and which did not changed since
March [2]. I would really love to update this version but
I'm just lacking time and knowledge in Java to accomplish this
myself. Currently I do not even have time to contact ImageJ
upstream and I wonder if there is a volunteer to sort out
(perhaps via mail to upstream) this probably easy to fix
regression. BTW, IMHO this is just one SUN Java / Open Java
issue thus fixing this might also in your interest.
If there are other issues than the outdated upstream version
not to use plain ImageJ I wonder whether upstream might not
accept patches from your side.
- One of the aims of Fiji was to make Benjamin Schmid's
Java3D-based 3D viewer plugin work out-of-the-box, since
people often had trouble installing it manually. At the time
when I first made these packages there were no java3d
packages in Debian, but now that these are in sid we should
eventually be able to switch to using those.
This would be great. I'm also a real fan of modularised
packaging. So if fiji might be just a collection of ImageJ
plugins we might split all these plugins into their own
packages which makes them smaller, prevent code duplication
with other third parte projects and enables a smooth integration
step by step into Debian. If I understood your mail correctly
than this would be the best thing to do - but I might be wrong
here if I missinterpreted the role of Fiji.
- I've only built packages for i386 and amd64.
That's no problem. In case we build official packages all
other architectures will be autobuilded ... or might uncover
errors we should fix.
It would be wonderful if we were eventually able to get Fiji
into Debian, but I think there's quite a lot of work to be done
before that could happen.
Well, in this case Fiji is not really special - we have several
projects which just need work. So what do you think about the
following plan:
1. Update ImageJ in Debian to a state, where you can base
your further work on.
a) Update Debian package to latest upstream
b) Apply patche you might need
c) Foreward the patches to upstream to make sure
it gets included in future versions.
2. Start packaging plugins step by step beginning with
the most interesting (regarding user interest) and
which do not show technical or license problems.
P.S. Incidentally, someone mentioned in a previous email on this
list (before I subscribed) that they couldn't find the source
code for Fiji. This has always been available via git (the
recommended method) and as tar.gz or zip archives - hopefully
that should be clear from the web pages. There are also source
archives for the Debian packages.
I just added Fiji to our Debian Med todo list for imaging:
http://debian-med.debian.net/tasks/imaging#fiji
Kind regards and thanks for your input
Andreas.
[1] http://lists.debian.org/debian-med/2009/04/msg00054.html
[2] http://lists.debian.org/debian-med/2009/03/msg00149.html
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