>As mentioned - I put the mavric module under cvs.
>My procedure to start working:
>cd ~/code/work
>setenv CVSROOT ':pserver:thomas@theopenlab.uml.edu:/home/cvs'
>cvs login
>cvs checkout pyphy # that creates ~/code/work/pyphy and
> # ~/code/work/pyphy/mavric
>
>cd pyphy/mavric
> ... start hacking ...
>cvs commit
Hello, I downloaded
http://theopenlab.uml.edu/mavric/mavric-19990428.tar.gz and got the
example scripts to run. By upgrading to linux redhat 6.0 all the
required python related programs were installed. I had to make a
couple trivial changes to get main.py to work.
from mavric.treeUtil import BasicNewickReader, collapseWeakBranches
-> from treeUtil import BasicNewickReader, collapseWeakBranches
and
from mavric.gui import MavApp
-> from gui import MavApp
and in testdi.py
from mavric.dataUtil import ...
-> from dataUtil import ...
It might be worth mentioning in the README what gtest.py and testdi.py
do. An example phylip alignment file in the examples directory would
be good.
I noticed that if you try to collapse a node that is a polytomy the
branch leading to that node disappears and this error is printed:
Traceback (innermost last):
File "/usr/lib/python1.5/site-packages/gtk.py", line 227, in __call__
self.cb(action, _obj2inst(widget))
File "./gui.py", line 46, in _collapseNode
redrawNode(node.back.data['canvasNode'].get_data('node'))
File "./gui.py", line 305, in redrawNode
root = node.findroot()
File "./treeUtil.py", line 121, in findroot
if nptr.isroot: break
AttributeError: 'None' object has no attribute 'isroot'
Traceback (innermost last):
File "/usr/lib/python1.5/site-packages/gtk.py", line 114, in __call__
ret = apply(self.func, a)
File "./events.py", line 9, in branchEvent
root = node.findroot()
File "./treeUtil.py", line 121, in findroot
if nptr.isroot: break
AttributeError: 'None' object has no attribute 'isroot'
So I thought I would download the latest cvs stuff and have a look. I
would like to start using the treeviewer but the example main.py
didn't seem to take quoted taxa names containing space. At least it
had some problems with my trees. I thought this might be pretty easy
to fix. I know c and perl but haven't messed with python nor cvs.
Anyway I have a couple questions about cvs. 1. If 2 people "checkout
pyphy" at the same time and both make changes, how is the second set
of changes incorporated? Will the first get overwritten by the
second? 2. when you "commit" should you be in the directory that you
"checkout pyphy" from? I am asking because the above example suggests
not. I am sure there are several other things I should know, so fill
me in.
By the way, I think this little treeviewer already rules.
Danny Rice