Gentoo Archives: gentoo-science

From: Steven Trogdon <strogdon@×××××.edu>
To: gentoo-science <gentoo-science@l.g.o>
Subject: [gentoo-science] sage-notebook & jmol
Date: Mon, 14 Jun 2010 19:15:38
Message-Id: 1276542835.6175.0@ledaig
Hello,

I believe Jmol is the default Sage 3D viewer. However, it seems to be  
broken from the notebook. A

	sphere()

from the sage prompt works as expected but not so from the notebook.  
Here I get that the problem is in locating the JmolApplet class. It  
appears that sagenb is coded to look in the data directory under sagenb  
for package data, i.e. relative to the python tree in  
site-packages/sagenb/data. After opening the notebook the contents of  
the directory can be viewed by pointing one's browser to

	http://localhost:8000/java/

In particular the notebook seems to look in  
site-packages/sagenb/data/jmol for the JmolApplet class data which was  
removed with the advent of the sage-on-gentoo package,  
sci-chemistry/jmol. Now here I'm able to get Jmol to work from the  
notebook if I create either of the symlinks,

	site-packages/sagenb/data/jmol ->  
/usr/share/webapps/jmol/11.6.16/htdocs
or
	site-packages/sagenb/data/jmol -> /var/www/localhost/htdocs/jmol

There should be a better way to do this but I'm unable to find a way to  
get the sagenb package to access external data other than through a  
symlink. If the first of the above is done then a version bump of jmol  
will require a new sage-notebook install! There is also an "appletweb"  
directory that's present under sagenb/data/jmol and I was curious as to  
whether it's needed? Is it perhaps a carry-over from the older  
Sage-provided jmol stuff?

Steve

Replies

Subject Author
Re: [gentoo-science] sage-notebook & jmol "François Bissey" <f.r.bissey@×××××××××.nz>
Re: [gentoo-science] sage-notebook & jmol "François Bissey" <f.r.bissey@×××××××××.nz>