#16004: Update notebook to utilize pure javascript JSmol for default live 3-D
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Reporter: gutow | Owner: gutow
Type: enhancement | Status:
Priority: major | needs_review
Component: notebook | Milestone: sage-6.4
Keywords: Jmol 3D 3-D | Resolution:
Authors: Jonathan Gutow, Volker Braun | Merged in:
Report Upstream: Reported upstream. Developers | Reviewers:
acknowledge bug. | Work issues:
Branch: | Commit:
Dependencies: #17020 | Stopgaps:
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Description changed by gutow:
Old description:
> 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.
>
> 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 #17020.
> Will require a new sagenb release: [INSERT HERE]
>
> How to test:
> 1. Switch Sage to #17020
> 1. Download the repackaged Jmol from the link provide in #17020 and save
> the package in the "upstream" directory of your sage install.
> 1. run `sage -f jmol` to install the new jmol.
> 1. Clone the `new_jmol` branch from the PR to anywhere convenient on your
> system: `git clone https://github.com/vbraun/sagenb.git -b new_jmol`
> 1. From within the sagenb repository run `sage -python setup.py install`
New description:
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.
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 #17020.
Will require a new sagenb release: [INSERT HERE]
How to test:
1. Switch Sage to #17020
1. Download the repackaged Jmol from the link provide in #17020 and save
the package in the "upstream" directory of your sage install.
1. run `sage -f jmol` to install the new jmol.
1. Clone the `new_jmol` branch from the PR to anywhere convenient on your
system: `git clone https://github.com/vbraun/sagenb.git -b new_jmol`
1. Apply the three attached patches to this new sagenb repository.
1. From within the sagenb repository run `sage -python setup.py install`
--
--
Ticket URL: <http://trac.sagemath.org/ticket/16004#comment:85>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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