Update notebook to utilize pure javascript JSmol for default live 3-D

gutow commented 10 years ago

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:

Update Sage with #17020
Download the repackaged Jmol from the link provide in #17020 and save the package in the "upstream" directory of your sage install.
run sage -f jmol to install the new jmol.
If you don't have it yet, update Sage with #16911 or just use this branch that Volker has merged with that one.
Same with #16396 if you want to build doc correctly.
Update Sage with the branch here
Put the new upstream package into SAGE_ROOT/upstream
Do sage -f sagenb-0.11.0
Test!
For testing, #17170 is also advised, since without it display in the notebook does not work properly.

Depends on #17020

Upstream: Reported upstream. Developers acknowledge bug.

CC: @kcrisman @novoselt @strogdon @jasongrout @fchapoton

Component: notebook

Keywords: Jmol 3D 3-D

Author: Jonathan Gutow, Volker Braun

Branch: a4c94cd

Reviewer: Steven Trogdon, Karl-Dieter Crisman, Jonathan Gutow

Issue created by migration from https://trac.sagemath.org/ticket/16004

gutow commented 10 years ago

Description changed:

--- 
+++ 
@@ -2,7 +2,7 @@

 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 appear 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. 
+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.

gutow commented 10 years ago

Description changed:

--- 
+++ 
@@ -6,4 +6,6 @@

 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](https://github.com/sagemath/sage-prod/issues/16003). 
+*This requires installation of an updated Jmol.spkg.  See ticket [16003](https://github.com/sagemath/sage-prod/issues/16003).
+
+Sorry for the github commit, but I could not get a notebook branch working in Sage.

gutow commented 10 years ago

Description changed:

--- 
+++ 
@@ -9,3 +9,4 @@
 *This requires installation of an updated Jmol.spkg.  See ticket [16003](https://github.com/sagemath/sage-prod/issues/16003).

 Sorry for the github commit, but I could not get a notebook branch working in Sage. 
+https://github.com/gutow/sagenb/commit/7ce561653aa3ffbb28eb36f487be381227018958

gutow commented 10 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,4 @@
-The notebook needs updates to utilize a pure javascript version of Jmol by default for live 3-D.
+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.

kcrisman commented 10 years ago

Changed dependencies from 16003 to #16003

kcrisman commented 10 years ago

Description changed:

--- 
+++ 
@@ -9,4 +9,5 @@
 *This requires installation of an updated Jmol.spkg.  See ticket [16003](https://github.com/sagemath/sage-prod/issues/16003).

 Sorry for the github commit, but I could not get a notebook branch working in Sage. 
-https://github.com/gutow/sagenb/commit/7ce561653aa3ffbb28eb36f487be381227018958
+* https://github.com/gutow/sagenb/commit/c730aa4cf563c51e7f1f8ca92899bf515d365030
+* https://github.com/gutow/sagenb/commit/7ce561653aa3ffbb28eb36f487be381227018958

gutow commented 10 years ago

comment:9

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?

gutow commented 10 years ago

comment:10

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.

gutow commented 10 years ago

comment:11

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.

novoselt commented 10 years ago

comment:12

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

And perhaps Jason can provide some insight in jquery problems?

jasongrout commented 10 years ago

comment:13

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.

jasongrout commented 10 years ago

comment:14

https://github.com/sagemath/sagecell/blob/master/static/jquery-ui/css/sagecell/jquery-ui-1.10.2.custom.min.css, which points to this theme

gutow commented 10 years ago

Description changed:

--- 
+++ 
@@ -11,3 +11,4 @@
 Sorry for the github commit, but I could not get a notebook branch working in Sage. 
 * https://github.com/gutow/sagenb/commit/c730aa4cf563c51e7f1f8ca92899bf515d365030
 * https://github.com/gutow/sagenb/commit/7ce561653aa3ffbb28eb36f487be381227018958
+* https://github.com/gutow/sagenb/commit/0242d2f495e4be79090e4aae83b4dade1d9a0f26

gutow commented 10 years ago

comment:16

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:)

gutow commented 10 years ago

comment:17

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

kcrisman commented 10 years ago

comment:18

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)?

kcrisman commented 10 years ago

Description changed:

--- 
+++ 
@@ -6,7 +6,7 @@

 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](https://github.com/sagemath/sage-prod/issues/16003).
+*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. 
 * https://github.com/gutow/sagenb/commit/c730aa4cf563c51e7f1f8ca92899bf515d365030

kcrisman commented 10 years ago

comment:20

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

Is this fixed in https://github.com/gutow/sagenb/commit/7aacbfa3957f237edbea448d492f7c2b7d34cec2 ?

kcrisman commented 10 years ago

comment:21

I think that creating a new branch inside sagenb is now not possible with the new layout (not directly git-related). One has to even figure out where sagenb lives... annoying. So to test this one really needs a new sagenb spkg to download, or create one. Harrumph.

strogdon commented 10 years ago

comment:22

Unless I've missed something it would seem that a new sagenb spkg is needed. The problem is the upstream sagenb-0.10.8.2 tarball is a tarball of tarballs. And it is the sagenb sub-tarball that has to be modified. Now I was able to generate patches that could be applied directly to the local/lib/python2.7/site-packages/sagenb-0.10.8.2-py2.7.egg folder by cloning https://github.com/gutow/sagenb. It seems that there are a couple more commits needed than listed above. But generating these patches is a lot of work! I'm able to see the icons and to turn on 3-D which is very, very slow. However, I see no way to evaluate an individual cell.

kcrisman commented 10 years ago

comment:23

Actually, ppurka has a good solution for this at this sage-devel thread. At least I assume it works - I can't check right this second.

$ cd ~/sagenb/sagenb
$ rm flask_version
$ mv ../flask_version .
$ cd ~/sage/local/lib/python/site-packages/sagenb-0.10.8.2-py2.7.egg
$ mv sagenb{,-0.10.8.2}
$ ln -s ~/sagenb/sagenb .

gutow commented 10 years ago

Description changed:

--- 
+++ 
@@ -12,3 +12,17 @@
 * https://github.com/gutow/sagenb/commit/c730aa4cf563c51e7f1f8ca92899bf515d365030
 * https://github.com/gutow/sagenb/commit/7ce561653aa3ffbb28eb36f487be381227018958
 * https://github.com/gutow/sagenb/commit/0242d2f495e4be79090e4aae83b4dade1d9a0f26
+ *https://github.com/gutow/sagenb/commit/7aacbfa3957f237edbea448d492f7c2b7d34cec2
+
+How to test:
+1. Clone the git repository https://githum.com/gutow/sagenb to anywhere convenient on your system.
+2. Do the following to make sage use the new repository.
+
+```
+$cd SAGE_ROOT/local/lib/python/site-packages/sagenb-0.10.8.2-py2.7.egg
+$mv sagenb sagenb_old
+$ln -s sagenb <path to the sagenb directory inside your new repository> 
+```
+
+In my case the symlink looks like 
+`ln -s sagenb ~/git/sagenb/sagenb `

gutow commented 10 years ago

comment:24

I'm updating the instructions above to include a fix that leaves the sagenb egg unchanged and allows you to work with multiple notebook development repositories.

To answer another question above the very latest commit to the repository does include the path fixes for jquery-ui images.

gutow commented 10 years ago

Description changed:

--- 
+++ 
@@ -12,7 +12,7 @@
 * https://github.com/gutow/sagenb/commit/c730aa4cf563c51e7f1f8ca92899bf515d365030
 * https://github.com/gutow/sagenb/commit/7ce561653aa3ffbb28eb36f487be381227018958
 * https://github.com/gutow/sagenb/commit/0242d2f495e4be79090e4aae83b4dade1d9a0f26
- *https://github.com/gutow/sagenb/commit/7aacbfa3957f237edbea448d492f7c2b7d34cec2
+* https://github.com/gutow/sagenb/commit/7aacbfa3957f237edbea448d492f7c2b7d34cec2

 How to test:
 1. Clone the git repository https://githum.com/gutow/sagenb to anywhere convenient on your system.

gutow commented 10 years ago

comment:26

At this point I have not got the option to run the java applet working cleanly. I can do it by manually screwing with things, but I am still working on it. I have not figured out how to modify the templates so that it will not use java applets without the user specifically requesting it. Because of how evil certain browsers/OS combinations have got about using java applets, we do not want that to ever be the default, even though it is better.

Replying to @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)?

kcrisman commented 10 years ago

comment:27

Replying to @gutow:

At this point I have not got the option to run the java applet working cleanly. I can do it by manually screwing with things, but I am still working on it. I have not figured out how to modify the templates so that it will not use java applets without the user specifically requesting it. Because of how evil certain browsers/OS combinations have got about using java applets, we do not want that to ever be the default, even though it is better.

Well, for instance, could one just hack into Sage itself... after all, one would want to be able to set viewer= whatever, including both jsmol and jmol. What happens with viewer='jmol' with your branch? (I'm trying to set it up but this is an incredibly busy week on campus for me, so I'm not sure how much progress I'll make.) At the least, one would want to just be able to add this to plots to get the Java.

In fact,

sage: from sage.plot.plot3d.base import SHOW_DEFAULTS
sage: SHOW_DEFAULTS['viewer'] = 'jmol'

should be possible then. But I don't know whether that would tie in with your changes thus far.

gutow commented 10 years ago

comment:28

All seems to work on my test server. I need some reviewers testers now.

gutow commented 10 years ago

Description changed:

--- 
+++ 
@@ -13,6 +13,7 @@
 * https://github.com/gutow/sagenb/commit/7ce561653aa3ffbb28eb36f487be381227018958
 * https://github.com/gutow/sagenb/commit/0242d2f495e4be79090e4aae83b4dade1d9a0f26
 * https://github.com/gutow/sagenb/commit/7aacbfa3957f237edbea448d492f7c2b7d34cec2
+* https://github.com/gutow/sagenb/commit/62a3775979c93b09def7487f9c4599554098b5c6

 How to test:
 1. Clone the git repository https://githum.com/gutow/sagenb to anywhere convenient on your system.

kcrisman commented 10 years ago

Description changed:

--- 
+++ 
@@ -16,7 +16,7 @@
 * https://github.com/gutow/sagenb/commit/62a3775979c93b09def7487f9c4599554098b5c6

 How to test:
-1. Clone the git repository https://githum.com/gutow/sagenb to anywhere convenient on your system.
+1. Clone the git repository https://github.com/gutow/sagenb to anywhere convenient on your system.
 2. Do the following to make sage use the new repository.

kcrisman commented 10 years ago

comment:30

I think it should be

$ln -s <path to the sagenb directory inside your new repository> sagenb

not

$ln -s sagenb <path to the sagenb directory inside your new repository>

am I right?

kcrisman commented 10 years ago

Description changed:

--- 
+++ 
@@ -22,7 +22,7 @@

$cd SAGE_ROOT/local/lib/python/site-packages/sagenb-0.10.8.2-py2.7.egg $mv sagenb sagenb_old -$ln -s sagenb +$ln -s sagenb


 In my case the symlink looks like

kcrisman commented 10 years ago

comment:31

Okay, I got it working. Preliminary thoughts:

Snappier than advertised. But SO SLOW with lots of points; a sparse vector field or basic plot is not so horrible. Of course, so was the Java version...
The load 3d live button is precisely what the doctor ordered.
Is it possible that inside interacts the load 3d live button doesn't work (that is, interacts are always live?) Or is it possible that you can only turn that button on, but not off (counter the expectation when clicking it)? I observed some unusual behavior, but maybe it was just something dumb I did.
How do you turn a plot "off" if there are too many open? (Or is that not a problem like it was with the sleeping Java applets?)
I see no way to get the things I used to with right-click (like stereo glasses, color, axes, whatever). Does jsmol just not have that?
The icon for activating the plot is ... not obvious. I still really find the auto-disable piece annoying, and I know that some people have just hacked that away, though I also know I won't convince you otherwise ;-)
Please remove the icons for new cells. They are cute, and probably an improvement in some ways, but it should really be orthogonal to this issue. There's enough moving parts to think about as it is. Especially since the blue bars have been the way to make new cells for many years! That's a pretty big change.
I figure out what strogdon is talking about. Try activating a jsmol, and then move it around a bit, and then try clicking in a cell without clicking alllll the way on the right to "lose focus" from the jsmol. (This is a problem anyway, of having to go all the way to the right to scroll - not limited to jsmol, though, threejs in the cell server has this problem as well.) You won't be able to, at least often not; you have to somehow get off focus and there is some timing delay.
I also haven't tried all the zillions of options out there for 3d plots to see if it still obeys them all, but presumably if it's pretty similar to jmol it will do fine.
Does it require WebGL turned on? I think not, but I'm not sure.

Hope this helps! Actually, it's fairly comparable to the current setup, so probably we could get it in sooner rather than later. Especially if you have any thoughts on the "viewer" thing - to me, this would be by far the easiest way to switch back and forth between functionality.

Once this has been tested enough and the "right" commits used, I think that you can just do a pull request to sagenb on github with your branch for this. Yay! Thanks for what is clearly very good hard work.

gutow commented 10 years ago

comment:32

Replying to @kcrisman:

Okay, I got it working. Preliminary thoughts:

Snappier than advertised. But SO SLOW with lots of points; a sparse vector field or basic plot is not so horrible. Of course, so was the Java version...

The load 3d live button is precisely what the doctor ordered.

Thought this is what people were asking for.

Is it possible that inside interacts the load 3d live button doesn't work (that is, interacts are always live?) Or is it possible that you can only turn that button on, but not off (counter the expectation when clicking it)? I observed some unusual behavior, but maybe it was just something dumb I did.

I believe I wrote the code so that if that box is checked all Jmol/JSmols will load live. If it is not checked they should not load live. I am not aware of anything interacts do that should force a live load.

How do you turn a plot "off" if there are too many open? (Or is that not a problem like it was with the sleeping Java applets?)

Turning them off is presently not possible. For the javascript version (JSmol) I do not think it will matter as long as you do not have the ones you are not interacting with doing things that require continuous computations like spinning or running an animation (something Jmol/JSmol can do, but Sage presently does not generate the input for).

I see no way to get the things I used to with right-click (like stereo glasses, color, axes, whatever). Does jsmol just not have that?

Right-click still brings up a menu. For the time being I've left the default Jmol menu as it provides access to some file writing features. You were not able to get it? I'll look into that.

The icon for activating the plot is ... not obvious. I still really find the auto-disable piece annoying, and I know that some people have just hacked that away, though I also know I won't convince you otherwise ;-)

It is just the default image (a standard stock "play" icon) stored in the JSmol tree. If we can come up with something better it can be replaced.

Please remove the icons for new cells. They are cute, and probably an improvement in some ways, but it should really be orthogonal to this issue. There's enough moving parts to think about as it is. Especially since the blue bars have been the way to make new cells for many years! That's a pretty big change.

I agree that it would be nice to separate this "big" change in the interface out. Unfortunately, I really could not get the old key+click actions to work with the new jquery that is required to support JSmol. Unless somebody else can make it work without breaking JSmol these icons are going to be part of this change. I'm open to suggestions on exactly how things should look, but built it using the standard jquery-ui tools that are part of sagenb.

I figure out what strogdon is talking about. Try activating a jsmol, and then move it around a bit, and then try clicking in a cell without clicking alllll the way on the right to "lose focus" from the jsmol. (This is a problem anyway, of having to go all the way to the right to scroll - not limited to jsmol, though, threejs in the cell server has this problem as well.) You won't be able to, at least often not; you have to somehow get off focus and there is some timing delay.

I'll play with this. Haven't noticed it, at least not anymore than most GUI based software.

I also haven't tried all the zillions of options out there for 3d plots to see if it still obeys them all, but presumably if it's pretty similar to jmol it will do fine.

If it worked in Jmol it works in JSmol as JSmol is just just cross compiled to javascript. There have been some minor oddities, but the demands of the X-ray crystallography users are much more severe than what is usually being done here. I think Bob Hanson and the others working on the conversion between Java and Javascript have found most of problems by now. The chemistry community has been replacing java applet only versions with this for 9-12 months now.

Does it require WebGL turned on? I think not, but I'm not sure.

I have set it up to use HTML5 only. WebGL support exists, but has problems with transparency and other such things.

Hope this helps! Actually, it's fairly comparable to the current setup, so probably we could get it in sooner rather than later. Especially if you have any thoughts on the "viewer" thing - to me, this would be by far the easiest way to switch back and forth between functionality.

I'll keep working on this. I think if I can get it working cleanly in the GUI, it will be easy to couple it to the viewer option.

Once this has been tested enough and the "right" commits used, I think that you can just do a pull request to sagenb on github with your branch for this. Yay! Thanks for what is clearly very good hard work.

kcrisman commented 10 years ago

comment:33

The load 3d live button is precisely what the doctor ordered.

Thought this is what people were asking for.

Yes, absolutely!

I see no way to get the things I used to with right-click (like stereo glasses, color, axes, whatever). Does jsmol just not have that?

Right-click still brings up a menu. For the time being I've left the default Jmol menu as it provides access to some file writing features. You were not able to get it? I'll look into that.

Yeah. This is on Safari 5, granted, but still... actually, it doesn't work on FF either. I don't know why, other right-clicking seems to be working fine on this computer still.

The icon for activating the plot is ... not obvious. I still really find the auto-disable piece annoying, and I know that some people have just hacked that away, though I also know I won't convince you otherwise ;-)

It is just the default image (a standard stock "play" icon) stored in the JSmol tree. If we can come up with something better it can be replaced.

I think that a word of some kind would be helpful. The image doesn't say much to me, while your previous "live image" or whatever made it very clear. Not everyone will mouse over that icon.

Please remove the icons for new cells. They are cute, and probably an improvement in some ways, but it should really be orthogonal to this issue. There's enough moving parts to think about as it is. Especially since the blue bars have been the way to make new cells for many years! That's a pretty big change.

I agree that it would be nice to separate this "big" change in the interface out. Unfortunately, I really could not get the old key+click actions to work with the new jquery that is required to support JSmol. Unless somebody else can make it work without breaking JSmol these icons are going to be part of this change. I'm open to suggestions on exactly how things should look, but built it using the standard jquery-ui tools that are part of sagenb.

Huh, that is weird. When I start actually reviewing the code changes I'll try to think about that.

Hope this helps! Actually, it's fairly comparable to the current setup, so probably we could get it in sooner rather than later. Especially if you have any thoughts on the "viewer" thing - to me, this would be by far the easiest way to switch back and forth between functionality.

I'll keep working on this. I think if I can get it working cleanly in the GUI, it will be easy to couple it to the viewer option.

That would be very good, providing all available options.

gutow commented 10 years ago

comment:34

Replying to @kcrisman:

I see no way to get the things I used to with right-click (like stereo glasses, color, axes, whatever). Does jsmol just not have that?

Right-click still brings up a menu. For the time being I've left the default Jmol menu as it provides access to some file writing features. You were not able to get it? I'll look into that.

Found the problem, but it's going to be a toughy...relates to the load order of the various js files. It appears a function in jquery clobbers a JSmol function or vice-versa if we switch the load order of the two. I can either get the right-click JSmol menu working or dialogs in Sagenb. I'm consulting with the Jmol/JSmol community on this.

The icon for activating the plot is ... not obvious. I still really find the auto-disable piece annoying, and I know that some people have just hacked that away, though I also know I won't convince you otherwise ;-)

It is just the default image (a standard stock "play" icon) stored in the JSmol tree. If we can come up with something better it can be replaced.

I think that a word of some kind would be helpful. The image doesn't say much to me, while your previous "live image" or whatever made it very clear. Not everyone will mouse over that icon.

Actually, I think the text pops up if you mouse over the whole image. But I see your point. The idea was to make it "youtube-like".

kcrisman commented 10 years ago

comment:35

I see no way to get the things I used to with right-click (like stereo glasses, color, axes, whatever). Does jsmol just not have that?

Right-click still brings up a menu. For the time being I've left the default Jmol menu as it provides access to some file writing features. You were not able to get it? I'll look into that.

Found the problem, but it's going to be a toughy...relates to the load order of the various js files. It appears a function in jquery clobbers a JSmol function or vice-versa if we switch the load order of the two. I can either get the right-click JSmol menu working or dialogs in Sagenb. I'm consulting with the Jmol/JSmol community on this.

Hmm, so the functions happen to be named the same thing?

Okay, I think that if we can fix the following in one way or another, and it otherwise it seems to handle things well, we can probably move to this:

Fix the clobbered function you mention above.
Fix or somehow make the icon here more obvious:

Actually, I think the text pops up if you mouse over the whole image. But I see your point. The idea was to make it "youtube-like".
Find some resolution to the new versus old ways to get new cells, ideally using the old clicking syntax (else a major change in interface).
Getting viewer to work with this so we can provide jmol or jsmol.

I know dealing with these is a lot harder than it seems to me, so hopefully we can find something good. I'm going to also look into the shift-click thing for a minute in the hopes I get lucky...

Random request: In this commit it would be helpful to know which of this truly huge commit is just adding the new jquery, and what is something for Sage. There are occasional changes I couldn't figure out if they were not important or if they were quite important, and it is kind of a bomb, by necessity. So any hints on what to focus on there would be very helpful.

kcrisman commented 10 years ago

comment:36

Find some resolution to the new versus old ways to get new cells, ideally using the old clicking syntax (else a major change in

So it seems that this was just some custom thing written way back when.

Currently this stuff is in sagenb/data/jquery/plugins/extendedclick. In fact, it seems to still be there after the update as well, and it's still loaded in base.html. So maybe we can just update it for the new jquery after all...

In fact, Jason has a github repo for this! At the time he updated for a new jquery too. I did try editing things back in Safari's Firebug equivalent, but any clicking at all - even in the compute cells - yielded

TypeError: 'undefined' is not an object (evaluating 'introspect[id].before_replacing_word')

from line 23 of master.js. Not sure if this is related. Anyway, I would be very surprised if one couldn't fix this but I couldn't get the web inspector to allow me to change any of the js files, very annoying.

Or, we could perhaps use this jquery plugin or this javascript thing instead? This link seems less robust but could work too...

gutow commented 10 years ago

comment:37

Random request: In this commit it would be helpful to know which of this truly huge commit is just adding the new jquery, and what is something for Sage. There are occasional changes I couldn't figure out if they were not important or if they were quite important, and it is kind of a bomb, by necessity. So any hints on what to focus on there would be very helpful.

I couldn't seem to update the commit message without redoing the commit. So here's the answer. That commit is just replacing all the old jquery and jquery-ui files. Nothing Sage related. I wonder if we should start handling things like that as upstream packages? A ticket in itself?

Still testing, but believe I have solved the dialog/JSmol popup conflict. There is an alternative JSmol package to avoid these kinds of problems...

Still no luck on getting the cntl-click stuff to work. I suspect it simply will require a careful rewrite of the old code. I'm not convinced that is a good use of anybody's time as we have a functional (and for novices more usable) alternative.

novoselt commented 10 years ago

comment:38

Just to clarify - the problems are only with the mouse use for cells, keyboard commands like Ctrl+Enter, Alt+Enter etc. are still functional, correct?

kcrisman commented 10 years ago

comment:39

Still no luck on getting the cntl-click stuff to work. I suspect it simply will require a careful rewrite of the old code. I'm not convinced that is a good use of anybody's time as we have a functional (and for novices more usable) alternative.

But it's backwards-incompatible, and requires rewriting of the help pages, and so forth. (The page that is linked to "Help" in the notebook.)

Just to clarify - the problems are only with the mouse use for cells, keyboard commands like Ctrl+Enter, Alt+Enter etc. are still functional, correct?

Yes, they appear to. But I don't think there is a way to get a text cell without the mouse - or is there? Also, sometimes one might not want to evaluate the current cell before inserting a new cell - and how would one get a new cell at the top of the page? Things to consider.

gutow commented 10 years ago

comment:40

OK. I think I've fixed the following with the latest commit:

Restored legacy click and shift-click behavior for adding cells to worksheets. This no longer uses the old code but is modern jquery. I have not taken out the old code because I believe it is used for keyboard key combinations as well. Can somebody double check me on this. If I'm wrong we can take it out.
Fixed the conflict between the dialog boxes and the Jmol/JSmol popup menu.

Still to do:

Change icons/wording so making JSmol live is more obvious.
See if I can fix defaults to use wire images during rotation for faster response.
Should I add back the link to help for the 3D viewer?

Can anybody explain in more detail what the strange behavior with the "load live" checkbox was? Karl-Dieter, Thanks for spotting this.

gutow commented 10 years ago

Description changed:

--- 
+++ 
@@ -14,6 +14,7 @@
 * https://github.com/gutow/sagenb/commit/0242d2f495e4be79090e4aae83b4dade1d9a0f26
 * https://github.com/gutow/sagenb/commit/7aacbfa3957f237edbea448d492f7c2b7d34cec2
 * https://github.com/gutow/sagenb/commit/62a3775979c93b09def7487f9c4599554098b5c6
+* https://github.com/gutow/sagenb/commit/c3659b35e3595605cbb01289f1279195cf0b8653

 How to test:
 1. Clone the git repository https://github.com/gutow/sagenb to anywhere convenient on your system.
@@ -26,4 +27,4 @@

In my case the symlink looks like -ln -s sagenb ~/git/sagenb/sagenb +ln -s ~/git/sagenb/sagenb sagenb

strogdon commented 10 years ago

comment:41

There are certain situations, and I haven't been able to isolate the sequence of things, where I'm unable to evaluate a cell - both with the mouse and from the keyboard. At these times I'm also unable to rename the worksheet. When renaming the worksheet does work the Rename worksheet dialog box is partially "covered" by any graphics image in the worksheet. And by moving the dialog box around (this requires a little work) it can be made to disappear "behind" a graphics image leaving the worksheet in a "frozen" state.

gutow commented 10 years ago

comment:42

Replying to @strogdon:

There are certain situations, and I haven't been able to isolate the sequence of things, where I'm unable to evaluate a cell - both with the mouse and from the keyboard. At these times I'm also unable to rename the worksheet.

I am not seeing this. I'm going to need more help reproducing this.

When renaming the worksheet does work the Rename worksheet dialog box is partially "covered" by any graphics image in the worksheet. And by moving the dialog box around (this requires a little work) it can be made to disappear "behind" a graphics image leaving the worksheet in a "frozen" state.

Thanks. Got it. Had a problem with z-index settings. I will include this fix in my next commit.

kcrisman commented 10 years ago

comment:43

I was planning to get to this yesterday but other things intervened. So not having tried the latest commits (and it sounds like others are still coming), I think that only the icons/wording change is 100% necessary, as the js was faster with normal plot_points than I thought (still not horrible but okay), though that was not exhaustive testing.

However, if you have any way to attack the "viewer" issue to allow jmols that would be really useful.

gutow commented 10 years ago

comment:44

Replying to @strogdon:

There are certain situations, and I haven't been able to isolate the sequence of things, where I'm unable to evaluate a cell - both with the mouse and from the keyboard. At these times I'm also unable to rename the worksheet.

Does this problem only occur when using interacts? I found an interact that has controls below where the applet is drawn and am seeing some funny things about who gets the click. I've also seen an issue with interacts not moving out of the way to show the evaluate button. That is probably a css issue that is separate from Jmol/JSmol.

gutow commented 10 years ago

comment:45

Note to testers. You may want to update the Jmol installation spkg #16003, because I have updated to the latest stable Jmol/JSmol and updated the popup menu to include file and image save/download from within the active 3-D view.

gutow commented 10 years ago

Description changed:

--- 
+++ 
@@ -15,6 +15,7 @@
 * https://github.com/gutow/sagenb/commit/7aacbfa3957f237edbea448d492f7c2b7d34cec2
 * https://github.com/gutow/sagenb/commit/62a3775979c93b09def7487f9c4599554098b5c6
 * https://github.com/gutow/sagenb/commit/c3659b35e3595605cbb01289f1279195cf0b8653
+* https://github.com/gutow/sagenb/commit/2e4fd33d6ad88485b9c80e508917ccc976878561

 How to test:
 1. Clone the git repository https://github.com/gutow/sagenb to anywhere convenient on your system.

gutow commented 10 years ago

comment:46

Latest commit includes fixes to hidden rename dialog, some click on image to activate instructions and some speed improvements.

There is definitely a problem with interacts that have controls below the active 3-D image. I am presently stumped as to what is going on. Any clues from what people are seeing would be welcome.

strogdon commented 10 years ago

comment:47

Replying to @gutow:

Replying to @strogdon:

There are certain situations, and I haven't been able to isolate the sequence of things, where I'm unable to evaluate a cell - both with the mouse and from the keyboard. At these times I'm also unable to rename the worksheet.

Does this problem only occur when using interacts? I found an interact that has controls below where the applet is drawn and am seeing some funny things about who gets the click. I've also seen an issue with interacts not moving out of the way to show the evaluate button. That is probably a css issue that is separate from Jmol/JSmol.

This issue from my end is not associated with using interacts. I haven't isolated the exact sequence to reproduce it. But I have seen it on two occasions. Now I'm testing on top of the develop branch. So there could be some irregularity in switching to my testing branch that includes the newer jmol.

sagemath / sage

Update notebook to utilize pure javascript JSmol for default live 3-D #16004