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

Matthew Pocock mrp@sanger.ac.uk
Wed, 09 Feb 2000 11:40:24 +0000


"Michael L. Heuer" wrote:

> 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.

Quite right. I guess we need modules for each unit people would want to check
out. Where would you slice up the repository? One module would be everything -
biojava-live. Another should be the org.biojava packages, and another the
org.acedb. What else?

> 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 is my fault - the src/GNOME and src/Bio packages (which you may have seen
appear) were a bit of a mistake with idltojava. I will probably blow these
away and put them somewhere helpfull within  the next few days.

> 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.

Pleas tell us more. The scripts under the build directory were realy more for
utility than ease-of-use/extensability. Can you get ant working on the current

If you are willing to contribute the sripts/classes/xml, then mabey you should
get a read/write account at bio.java.org (mail me if you do) - in the mean
time, I can pop things in.

> 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
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