DependencyManagement

TableOfContents([2])

Proposal

Add a build process to Cytoscape, to streamline builds for both developers and users.

Biological Questions / Use Cases

• Many users like specific plugins or have a paper referencing a specific version of Cytoscape and plugin. Builds of the old Cytoscape’s with the plugins that were compatible at the time would make reproducing results from these papers far simpler.
• Simplify library updating/clean up by not keeping all required libraries in the repository
• Tracking a library version would also be simpler and again easier to update
• Core libraries can be built and put in a maven type repository with versioning, again to make it easy to update/clean the libraries through the build process rather than subversion
• Also could be used for creating some generic "skins" for Cytoscape (not user specific necessarily)

General Notes

Maven can utilize ant build scripts so this would use what we currently have and add more control to the libraries. Single "pom" file can handle checking out the most recent code from the repository and building it, streamlining the process for users who don't want to pick their way through subversion in order to create a local build for plugin development.

Requirements

• 1 month FTE

Deferred Items

Open Issues

Backward Compatibility

References

http://maven.apache.org/

Comments

DanielAbel - 8/5/2007

I would like to add a usecase which should be made much easier with such a refactor. For testing / debugging purposes, it is really usefull if one can edit _any_ .java file, whether in a plugin, a coreplugin, core cytoscape or a core library, run an automated build process, and get everything rebuilt. This should be a trivial process. However, currently it is not. I had to severly edit the build.xml files to tie the seperate build.xml files together, copy the produced .jar files in the right place, etc. As far as I could see, there is currently no fully automated build process, despite the fact that everything uses ant. The seperate ant builds are not connected together.

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