Re: Package available (was Re: Micro Manager)
On Thu, Nov 3, 2011 at 5:14 PM, Mark Longair
> 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 !
> 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...
> * The source of all these plugins (with widely different or
> undetermined licenses) have ended up mixed into one
> repository. In building Debian packages I have to split the
> build products from this one source tree into separate
> packages, and for each package try to work out the authors
> and licenses. There has been an attempt to keep a track of
> the licenses for each plugin in the LICENSES file, but this
> isn't designed to be machine readable or easily mappable to
> the build products, so this is painstaking manual work.
> Those plugins that I haven't yet classified in this way just
> go into a "plugin soup" package called fiji-plugins, which
> currently has 82 jar files. The amount of work involved in
> going through these remaining plugins would be quite
ok point taken.
> * 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 ?
> * 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
Tell me about it ;) see:
Any help is welcome :)
> 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
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.