jmol in the flask notebook

[jasongrout]

The attached patch solves an issue with jmol finding the right .jmol.zip file in the new flask notebook. This patch should only be applied after the notebook is moved to a flask notebook.

The patch should replace the following line in sage/plot/plot3d/base.pyx

f.write('set defaultdirectory "%s"\n' % archive_name)

with

import sagenb
f.write('set defaultdirectory "cells/%s/%s"\n' % (sagenb.notebook.interact.SAGE_CELL_ID, archive_name))

Depends on #11080

CC: @rkirov @mwhansen @kcrisman

Component: notebook

Keywords: sd31 sd35.5

Author: William Stein, Jonathan Gutow

Reviewer: Jason Grout

Merged: sage-5.2.beta0

Issue created by migration from https://trac.sagemath.org/ticket/11078

[jasongrout]

Description changed:

--- 
+++ 
@@ -12,3 +12,5 @@
 f.write('set defaultdirectory "cells/%s/%s"\n' % (sagenb.notebook.interact.SAGE_CELL_ID, archive_name))
 ```
 
+Note: I haven't actually attached a patch since I hope that we can incorporate the new Jmol in, which would conflict with the patch (but would not conflict with the actual changes on this ticket).
+

[williamstein]

Changed keywords from none to sd31

[seblabbe]

comment:4

This week, I compiled sage-4.7.1.rc0 and installed the new flask Sage notebook following instructions from : http://code.google.com/r/rkirov-flask/. I also followed the section Adding stock Jmol plus the patch trac_11078.patch. This made Jmol to work from the notebook : Great!

But, from the command line, with the patch trac_11078.patch a command like sphere() opens Jmol but Jmol stays all black. I had to mimic the modifications done in #11503 on the same file sage/plot/plot3d/base.pyx to make Jmol works properly from the command line.

Sébastien

[jasongrout]

Description changed:

--- 
+++ 
@@ -12,5 +12,3 @@
 f.write('set defaultdirectory "cells/%s/%s"\n' % (sagenb.notebook.interact.SAGE_CELL_ID, archive_name))
 ```
 
-Note: I haven't actually attached a patch since I hope that we can incorporate the new Jmol in, which would conflict with the patch (but would not conflict with the actual changes on this ticket).
-

[jasongrout]

Author: William Stein, Jonathan Gutow

[jasongrout]

comment:7

Attachment: trac_11078.patch.gz

I updated the patch with the changes from #11503. With the flask notebook, sphere() works both from the command line and from the notebook.

I'm setting as needs review to have one other person double-check this patch works as intended, though I guess I might qualify as the only needed reviewer. Basically, what I did here was just rebase the patch at #11503.