#9238: J. Gutow's update to Jmol in the notebook...
---------------------------------------------------------------+------------
Reporter: gutow |
Owner: gutow
Type: enhancement |
Status: needs_review
Priority: major |
Milestone: sage-4.7.2
Component: notebook |
Keywords: sd31
Work_issues: |
Upstream: N/A
Reviewer: Jason Grout, Karl-Dieter Crisman, William Stein |
Author: Jonathan Gutow
Merged: |
Dependencies:
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Description changed by gutow:
Old description:
> Ready for testing.
>
> For inclusion in new Flask notebook see [http://code.google.com/r/gutow-
> flask/ enhanced Jmol in Flask]. Note that all fixes and enhancements to
> the Jmol interface from SageDays 31 are in the Flask version and not this
> ticket. The Jmol changes for the Flask notebook should be included in the
> Flask spkg soon. See #11080.
>
> Setting this up on your own copy of Sage requires two steps. Starting
> with a clean Sage 4.6.2 (for 4.7+ skip step 1): [[BR]]
>
> 1. Patch for Jmol at the command line (not for 4.7+). See
> [http://trac.sagemath.org/sage_trac/ticket/9232 #9232].
> 1. Apply the .spkg to get the new Jmol ` ./sage -f
> "http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.6.spkg"`
> 1. Apply the following patches in order (not necessary for Flask):
> [attachment:trac_9238_interactive_js.patch], [attachment:trac_9238-add-
> help.patch] , [attachment:trac_9238_jmol_lib_async.patch],
> [attachment:trac_9238_memory_IE.patch] and
> [attachment:trac_9238_nice_IE_warnings.patch]. These are best applied
> using the hg_sagenb.apply(...) command within sage.
> 1. Apply the patch (not necessary for 4.7+)
> [attachment:Trac_9238_script_extension.patch] using the
> hg_sage.apply(...) command within sage. Exit sage and run a ` ./sage
> -b`.
>
> I have addressed the following issues (let me know if I've missed
> anything): [[BR]]
>
> * Addition of the ability to hide the "advanced controls".
> * Fix so that the advanced controls are hidden when the applet is asleep
> (no accidental calls to nonexistent applets).
> * Fix to issue of not properly loading all applets when a worksheet
> with a lot of applets is reopened (please check this one carefully).
> * Fixes to vocabulary and labels to make things clearer.
> * Hidden the div with the State in it. (Still there b/c I hope to be
> able to recreate the way the user left it on close, rather than starting
> fresh each time.)
> * Fix to loading pages with many Jmols hanging. (FF on MacOS just
> doesn't work reliably or reproducibly so I put up a warning and suggest
> they switch to Chrome).
> * Workaround for bug in MacOS Safari that causes hang when trying to get
> a static image to sleep an applet if more than 9 applets in a worksheet
> (I believe this is a memory leak problem).
> * Tested extensively on Linux with FF and Chromium and on MacOS with
> Safari, Chrome and FF. Works well with both linux browsers and with
> Chrome on MacOS. MacOS/Safari is usable, MacOS FF is not.
> * Lowered memory requirements for Jmol. This improves performance in
> Safari for many applets.
> * Many advanced controls do not work with IE/win. Provide warning and
> suggest using Chrome, which does work. Those that fail do so quietly.
> Sleeping and controlling function color do work.
>
> Happy testing and thank you to those who do test!
New description:
Ready for testing.
For inclusion in new Flask notebook see [http://code.google.com/r/gutow-
flask/ enhanced Jmol in Flask]. Note that all fixes and enhancements to
the Jmol interface from SageDays 31 are in the Flask version and not this
ticket. The Jmol changes for the Flask notebook should be included in the
Flask spkg soon. See #11080.
Setting this up on your own copy of Sage requires two steps. Starting
with a clean Sage 4.6.2 (for 4.7+ skip step 1): [[BR]]
1. Patch for Jmol at the command line (not for 4.7+). See
[http://trac.sagemath.org/sage_trac/ticket/9232 #9232].
1. Apply the .spkg to get the new Jmol ` ./sage -f
"http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.6.spkg"`
1. Apply the following patches in order (not necessary for Flask):
[attachment:trac_9238_interactive_js.patch], [attachment:trac_9238-add-
help.patch] , [attachment:trac_9238_jmol_lib_async.patch],
[attachment:trac_9238_memory_IE.patch] and
[attachment:trac_9238_nice_IE_warnings.patch]. These are best applied
using the hg_sagenb.apply(...) command within sage.
1. Apply the patch (not necessary for 4.7+)
[attachment:Trac_9238_script_extension.patch] using the hg_sage.apply(...)
command within sage. Exit sage and run a ` ./sage -b`.
I have addressed the following issues (let me know if I've missed
anything): [[BR]]
* Addition of the ability to hide the "advanced controls".
* Fix so that the advanced controls are hidden when the applet is asleep
(no accidental calls to nonexistent applets).
* Fix to issue of not properly loading all applets when a worksheet with
a lot of applets is reopened (please check this one carefully).
* Fixes to vocabulary and labels to make things clearer.
* Hidden the div with the State in it. (Still there b/c I hope to be
able to recreate the way the user left it on close, rather than starting
fresh each time.)
* Fix to loading pages with many Jmols hanging. (FF on MacOS just doesn't
work reliably or reproducibly so I put up a warning and suggest they
switch to Chrome).
* Workaround for bug in MacOS Safari that causes hang when trying to get
a static image to sleep an applet if more than 9 applets in a worksheet (I
believe this is a memory leak problem).
* Tested extensively on Linux with FF and Chromium and on MacOS with
Safari, Chrome and FF. Works well with both linux browsers and with
Chrome on MacOS. MacOS/Safari is usable, MacOS FF is not.
* Lowered memory requirements for Jmol. This improves performance in
Safari for many applets.
* Many advanced controls do not work with IE/win. Provide warning and
suggest using Chrome, which does work. Those that fail do so quietly.
Sleeping and controlling function color do work.
Happy testing and thank you to those who do test!
'''Note''': as the Flask switch over appears to be delayed we are working
on incorporating the SageDays31 enhancements into this ticket. They are
not yet in. These .spkgs will not work with #11503 which changes where
Jmol is installed. Look for fix early Sept. 2011.
--
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/9238#comment:169>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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