This the readme file for users of PIPRes.  CIPRes developers should consult the DevReadme.txt file.

PIPRes is (will be) a collection of python modules for performing phylogenetic analyses in the CIPRes system.
See LICENSE.txt and LGPL.txt for licensing information.

Installation:
From the PIPRes root directory type the command:
	
	python setup.py build
	
to build the package or 
	
	python setup.py install 
	
to install.

================================================================================
Testing
================================================================================
The script PIPRes/scripts/run_pipres_tests.py recursively looks for test files (by traversing dierectories that start with test and looking for files with names that start with test). So if you go to $PIPRES_ROOT (the directory that is 
the parent of PIPRes) and run this script, you will run all of the PIPRes tests.  Tests in the test_cipres directory rely on CIPRES functionality, so a registry must be running.

I ususally:
	1. Launch a terminal:
		cd $CIPRES_SVN_ROOT
		ant runRegistry
	2. Launch another terminal:
		cd $PIPRES_ROOT
		python PIPRes/scripts/run_pipres_tests.py
	3. Kill the terminals
If the tests all pass you'll see a message like:
============================================================================
Failed  0 test scripts.
Passed  18 test scripts
OK


At the end of the output in the second terminal (the one you launched PIPRes/scripts/run_pipres_tests.py from).