[Pipet Devel] New piper version + docs

[Brad Chapman]

Hello all;
    I'm happy to report that I just uploaded a brad new version of 
Piper (with an actual version number--0.0.1, pretty exciting!) to my 
university of Georgia site (http://www.arches.uga.edu/~chapmanb/). 
Sorry for the change of location, but either I can't remeber how to 
ftp to alpha.bioinformatics.org, or it isn't working right now (Gary? 
Is this my fault? Probably :-). This version is quite changed from the 
past ones since we are now using CORBA for communication between the 
user interface and the definition layer. Excitement abounds! This 
change-over has resulted in some loss of functionality from the socket 
version as a result. What works right now is addition, deletion, 
connection and disconnection of loci, basically. The container widget 
stuff hasn't been changed over yet (mainly because I'm not sure how to 
do it with the new system.)
    There are also a ton of other changes, including a switch to use 
the most recent 4DOM. This switch involves a lot of changes in 
namespaces, since 4DOM is going to become the default DOM for python, 
so it has now taken the xml.dom namespace over. So you'll need to have 
this version, and also need to be careful when installing it to blast 
away the PyXML version of xml.dom.
    Thanks to Jeff's keen eye, I also fixed some install bugs (and 
hopefully didn't add any more), and I added an extra target 
--with-piperhome=/a/different/path/to/put/piper, so that people can 
put the libraries in one place and the scripts to run it in another 
(and add version numbers).
    I also updated the dl documentation and added two new docs, "How 
to Plug a Program into Piper" and "How to write a UI for Piper." My 
idea is that we can use these as a starting point to get more docs and 
firm up our ideas about how to do things. In the user interface one, I 
tried to address some of the points Deanne and Jeff raised on the list 
in their disccusion on peep about how to talk to the dl. I would 
really like to hear feedback on these docs so we can make them better. 
These are just my attempts to do this from a marathon session of doc 
writing. The html versions of these docs are in the distribution, and 
pdf versions are at the university of georgia site.
    I'm very excited, as this is taken us much closer to getting 
piper integrated with Overflow--we've even got Overflow node types 
being loaded up (now we just need a little GUI to go with 'em).
    I'd be more than happy to answer any questions about what things I 
did and really look forward to hearing people's feedback. Okay, time 
to get some sleep...

Brad