Hi Mark, On Thu, Nov 3, 2011 at 5:14 PM, Mark Longair <mark-debianli...@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 ! > 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 > considerable. 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 > dependencies. Tell me about it ;) see: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=641448 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 relatively easy. 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. 2cts -- Mathieu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CA+7wUsys_XBeHXH=ejuvd1duoo5+pm3n9+tw526kgb_vhor...@mail.gmail.com