J. Gutow's update to Jmol in the notebook...

[gutow]

NOTE: This ticket has been replaced by #12299

Ready for testing.

For inclusion in new Flask notebook see 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):

1. Patch for Jmol at the command line (not for 4.7+). See #9232.
2. Apply the .spkg to get the new Jmol ./sage -f "http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.6.spkg"
3. 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.
4. 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):

• 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: This ticket has been replaced by #12299.

CC: @TimDumol @kcrisman @rkirov

Component: notebook

Keywords: sd31, sd32

Reviewer: Jason Grout, Karl-Dieter Crisman, William Stein, Jonathan Gutow

Issue created by migration from https://trac.sagemath.org/ticket/9238

[gutow]

Attachment: Jmol javascript updates.zip

jmol notebook javascript updates

[jasongrout]

comment:1

Did you update the version of jmol in Sage as well?

[gutow]

comment:2

Replying to @jasongrout:

Did you update the version of jmol in Sage as well?

Jason,

Thanks!!! I forgot about that. Yes, for all of this to work you need to use Jmol 11.8. The latest release. Should I add a .zip of the necessary applet files to the trac?

Jonathan

[gutow]

Description changed:

--- 
+++ 
@@ -1,6 +1,8 @@
 I believe this drop-in set of javascript files now works.  Need testers!
 
 Attached are replacement javascript files for jmol_lib.js and notebook_lib.js, which are located in sagenb/data/sage/js.  Changes to notebook_lib.js are just some added calls to functions in jmol_lib.js to let the javascript know when applets are closed.  The library jmol_lib.js is a complete rewrite.
+
+Also requires latest Jmol version 11.8.
 
 Adds the following features to the notebook:
 

[jasongrout]

comment:4

We should make a new spkg. Is that what you did? If not, then I can try to update the spkg to include the newest jmol if it's just a drop-in replacement for the old java files.

[jasongrout]

comment:5

On the other hand, I didn't realize that jmol was just included in the sagenb spkg, so it'll probably be easier to update. I'm CCing Tim, who has done some of the recent sagenb releases.

Yes, can you attach the updated jmol files as well, then (or if they're more than a megabyte or so, can you post a link to them?)

Thanks for all of this work!

Jason

[gutow]

comment:6

OK, I've posted a .zip archive with all the necessary Jmol stuff. The link is now included in the trac ticket. Sorry I forgot about that.

Jonathan

[gutow]

Description changed:

--- 
+++ 
@@ -2,7 +2,12 @@
 
 Attached are replacement javascript files for jmol_lib.js and notebook_lib.js, which are located in sagenb/data/sage/js.  Changes to notebook_lib.js are just some added calls to functions in jmol_lib.js to let the javascript know when applets are closed.  The library jmol_lib.js is a complete rewrite.
 
-Also requires latest Jmol version 11.8.
+Also requires latest Jmol version 11.8.  To do this download the zipped version of the sagenb/data/jmol directory from this link (3.4 Mb):
+
+http://www.uwosh.edu/faculty_staff/gutow/jmol.zip
+
+Unzip this directory and replace the existing sagenb/data/jmol directory.  I have updated things to the latest version of the jmol applet that loads incrementally and cleaned out many files that were not used.
+
 
 Adds the following features to the notebook:
 

[jasongrout]

comment:7

That zip file has a lot of __MACOSX and .DS_Store files...