[Biojava-l] Problems (slight) with the Biojava code in CVS

[Michael L. Heuer]

All,

> Better yet, it would be nice to clean up the cvs repository and/or
> define a module so that a checkout results in a single, well formed
> source tree.

I would second this suggestion -- a cvs repository can become a nightmare
without a decent module file identifying the projects and subprojects.  

I would also like to suggest that all code contributed to the biojava
repository should use fully-qualified package names adhering to Sun's
package naming recommendations, ie.  org.biojava.myproject.xxx

This leads to a consistent folder heirarchy in all of the src directories.
Proper package names can even be set in IDL-generated code (idl2java has
a command line argument to set the package name, for instance).

Finally, I recommend taking a look at using the cross-platform build tool
ant, which is part of the Apache Jakarta project.  Ant uses a simple 
XML-based build file format, is easily extensible, and frankly, is much
more efficient than the build scripts currently in cvs.

Ant is available for download at:

http://jakarta.apache.org/ant/
http://jakarta.apache.org/builds/tomcat/nightly/ant.zip


If anyone is interested, I can post the ant build.xml file I created for
biojava-live.

   michael