#9238: J. Gutow's update to Jmol in the notebook...
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   Reporter:  gutow                             |       Owner:  gutow     
       Type:  enhancement                       |      Status:  needs_work
   Priority:  major                             |   Milestone:  sage-4.7  
  Component:  notebook                          |    Keywords:            
     Author:  Jonathan Gutow                    |    Upstream:  N/A       
   Reviewer:  Jason Grout, Karl-Dieter Crisman  |      Merged:            
Work_issues:                                    |  
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Comment(by gutow):

 Replying to [comment:102 kcrisman]:

 > Hmm, those files are not being tracked by HG.  Otherwise any changes
 would be recorded, even binary ones.   But I think that we try not to
 track them because they are all binaries and we can't directly access them
 - hence the new spkg.

 On  my machine I set it up to have hg track those files.  The patch I made
 does list them as being added or changed, but the binaries are not
 included, just the file names.  Thus the patch won't work.  I gather from
 what you are saying, an .spkg is the only way.  I can do that.  It will
 take a little time to reconfigure so that it is only updating the binary
 files.  The rest can be put in as a patch so it will be tracked properly.
 (I'm getting less enthusiastic about hg...svn would  handle this with no
 problem).
 >
 > If the `isosurface fullylit; pmesh o* fullylit; set antialiasdisplay
 on;` stuff is just to fix the lighting in general, we could get that in a
 lot more quickly by simply opening another ticket, since it doesn't
 require a new SageNB package.  I *have* noticed that the top of surfaces
 was not well lit, as opposed to the bottom... but only in the notebook,
 not the command line, weirdly.  That part of this patch fixes that.  Any
 ideas as to what was going on with that?

 There was a bug in the version of Jmol things were originally written for,
 which meant the default lighting was fullylit (despite being documented as
 otherwise).  To update SAGE to a newer Jmol this needs to be accounted
 for.  The fix I put in is temporary.  I would like use a more complete and
 up-to-date file format for the generated .jmol files, but first I want to
 have basic stuff working.  Notebook vs command line depends on which
 version of the jmol_lib.js you have.  This fix is also in there.
 >
 > But anything that is about changing those jmol files would have to be
 another package, though, I guess, because we don't track those files.  Why
 doesn't changing the extension just work 'out of the box'?

 Changing the extension doesn't work out-of-the-box because of bugs in some
 versions of Jmol.  12.0.35 is the first 12.0.x series I could get this
 working with.  There are some newer versions, but the menu system has been
 damaged, so I am avoiding anything newer until we get that fixed.

-- 
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/9238#comment:103>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica, 
and MATLAB

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