Opened 8 years ago

Last modified 7 years ago

#16004 closed enhancement

Update notebook to utilize pure javascript JSmol for default live 3-D — at Version 19

Reported by: gutow Owned by: gutow
Priority: major Milestone: sage-6.4
Component: notebook Keywords: Jmol 3D 3-D
Cc: kcrisman, novoselt, strogdon, jason, chapoton Merged in:
Authors: gutow Reviewers:
Report Upstream: Reported upstream. Developers acknowledge bug. Work issues:
Branch: Commit:
Dependencies: #16003 Stopgaps:

Status badges

Description (last modified by kcrisman)

The notebook needs updates to utilize a pure javascript version of Jmol by default for live 3-D. This includes changes to make the notebook compatible with the newer jquery-1.9 (some things used in the notebook have been deprecated).

Jmol is cross compiled to java and javascript. Because so many browser/OS combinations now actively try to avoid using java applets, it is necessary to have a pure javascript alternative. This solution provides all the functionality of Jmol, but as expected since javascript is interpreted rather than bytecode ("~3/4" of the way to compiled) the performance when interacting with the plot is slower.

This first implementation removes the user tools that have appeared to the right of the 3-D plot as they need to be rewritten as well. In this first implementation it is not possible to choose to use the java applet instead.

One added feature is a "load 3-D live" check box that can be used to make a worksheet load 3-D plots live when the worksheet is opened. For worksheets with a single interact or only 1-2 plots this should be OK.

*This requires installation of an updated Jmol.spkg. See ticket #16003.

Sorry for the github commit, but I could not get a notebook branch working in Sage.

Change History (19)

comment:1 Changed 8 years ago by gutow

  • Component changed from PLEASE CHANGE to notebook
  • Description modified (diff)

comment:2 Changed 8 years ago by gutow

  • Owner changed from (none) to gutow

comment:3 Changed 8 years ago by gutow

  • Description modified (diff)

comment:4 Changed 8 years ago by gutow

  • Description modified (diff)

comment:5 Changed 8 years ago by gutow

  • Description modified (diff)
  • Status changed from new to needs_review

comment:6 Changed 8 years ago by kcrisman

  • Dependencies changed from 16003 to #16003

comment:7 Changed 8 years ago by kcrisman

  • Cc kcrisman novoselt strogdon added; krisman nosvelt strongdon removed

comment:8 Changed 8 years ago by kcrisman

  • Description modified (diff)

comment:9 follow-up: Changed 8 years ago by gutow

I'm not sure it has to do with this or something broken in my jquery.form.min.js installation, but I can no longer rename worksheets. Does anybody else seeing this or have an idea how this could have anything to do with the changes in this ticket?

comment:10 in reply to: ↑ 9 Changed 8 years ago by gutow

Replying to gutow:

I'm not sure it has to do with this or something broken in my jquery.form.min.js installation, but I can no longer rename worksheets. Does anybody else seeing this or have an idea how this could have anything to do with the changes in this ticket?

I think I've found it. This may be painful. The newer jquery seems to be killing stuff in jquery-ui-1.8.11.custom.js. I will look for a version that is compatible with the newer jquery.

comment:11 Changed 8 years ago by gutow

jquery-ui is definitely out-of-date. The 1.8.11 release is from 2011. Does anybody know what selections need to be made to get the theme for the notebook to look right? I think to get everything working will require updating to the latest 1.10.4.

comment:12 Changed 8 years ago by novoselt

  • Cc jason added

First of all, thanks for all your work on this, Jonathan!

And perhaps Jason can provide some insight in jquery problems?

comment:13 Changed 8 years ago by jason

See my message to sage-devel: https://groups.google.com/d/msg/sage-devel/8zS6qofxxwk/K5LcLsCWBeMJ for the configuration we use in the cell server with jquery-ui 1.10.something.

comment:15 follow-up: Changed 8 years ago by gutow

  • Description modified (diff)

comment:16 in reply to: ↑ 15 Changed 8 years ago by gutow

Replying to gutow: With Jason's directions for building the theme and a little tweaking, I believe I have everything working again along with the javascript 3-D. As a bonus we now how little icons to click on for adding compute and rich-text cells, so forgetful people like me do not have to remember which key-click combinations to use. The real reason for the icons is that I could not get the key combinations to work:)

Last edited 8 years ago by gutow (previous) (diff)

comment:17 Changed 8 years ago by gutow

  • Status changed from needs_review to needs_work

Some jquery-ui image paths broken (probably issue of symlinks)...

comment:18 Changed 8 years ago by kcrisman

Hey, just a quick question as I hopefully will be able to get testing this soon - can the 'load 3-D live" checkbox work just as well with jmol as with jsmol? Also, I presume it will be evident once I finally get it going, but how does one get the Jmol instead of jsmol (say, locally, so that things are snappier)?

comment:19 Changed 8 years ago by kcrisman

  • Description modified (diff)
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