gutow
commented
14 years ago Attachment: Jmol javascript updates.zip
jmol notebook javascript updates
Closed gutow closed 12 years ago
gutow
commented
14 years ago Attachment: Jmol javascript updates.zip
jmol notebook javascript updates
jasongrout
commented
14 years ago Did you update the version of jmol in Sage as well?
gutow
commented
14 years ago 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
commented
14 years ago 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:
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
commented
14 years ago 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
commented
14 years ago 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
commented
14 years ago 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:
That zip file has a lot of __MACOSX and .DS_Store files...
gutow
commented
14 years ago Replying to @jasongrout:
That zip file has a lot of __MACOSX and .DS_Store files...
Oops...It will still work, but I will clean it up and post an update later today. People can try it with this, but look for a clean file tomorrow.
Jonathan
jasongrout
commented
14 years ago If you replace the existing jmol directory with the above zip, then you delete the "jmol" file inside that directory, which is necessary for the spkg to work. The jmol file is:
#!/bin/sh
#JMOL_HOME=`dirname "$0"`
JMOL_HOME="`"$SAGE_LOCAL"/bin/sage-pypkg-location sagenb`""/sagenb/data/jmol"
# Collect -D & -m options as java arguments
command=java
while [ `echo $1 | egrep '^-D|^-m' | wc -l` != 0 ]; do
command="$command $1"
shift
done
if [ -f ./Jmol.jar ] ; then
jarpath=./Jmol.jar
elif [ -f $JMOL_HOME/Jmol.jar ] ; then
jarpath=$JMOL_HOME/Jmol.jar
elif [ -f /usr/share/jmol/Jmol.jar ] ; then
jarpath=/usr/share/jmol/Jmol.jar
else
echo Jmol.jar not found
exit
fi
$command -Xmx512m -jar $jarpath $@
Is that file still needed? I think it probably makes jmol work from the command line for us.
gutow
commented
14 years ago Hmmm...good eye! I think you are correct. I have never used Jmol from the command line. It does look like the application is used. I can certainly include that in the package as well as the shell script. I thought that was the old Jmol linux shell script...I didn't even look inside....My bad. When I clean things up I will get the necessary files for command line back in there. I will do that this evening. Let me know if you notice anything else.
Jonathan Replying to @jasongrout:
If you replace the existing jmol directory with the above zip, then you delete the "jmol" file inside that directory, which is necessary for the spkg to work. The jmol file is:
#!/bin/sh #JMOL_HOME=`dirname "$0"` JMOL_HOME="`"$SAGE_LOCAL"/bin/sage-pypkg-location sagenb`""/sagenb/data/jmol" # Collect -D & -m options as java arguments command=java while [ `echo $1 | egrep '^-D|^-m' | wc -l` != 0 ]; do command="$command $1" shift done if [ -f ./Jmol.jar ] ; then jarpath=./Jmol.jar elif [ -f $JMOL_HOME/Jmol.jar ] ; then jarpath=$JMOL_HOME/Jmol.jar elif [ -f /usr/share/jmol/Jmol.jar ] ; then jarpath=/usr/share/jmol/Jmol.jar else echo Jmol.jar not found exit fi $command -Xmx512m -jar $jarpath $@Is that file still needed? I think it probably makes jmol work from the command line for us.
jasongrout
commented
14 years ago I've make a new sagenb-0.8.p3.spkg file that includes Jonathan's changes above (as an applied mercurial patch), plus the new jmol. So to test this, all a person should have to do is:
sage -f http://sage.math.washington.edu/home/jason/sagenb-0.8.p3.spkgIt seems to work pretty well for me. I wish the default was Medium Size instead of "small"
gutow
commented
14 years ago Let's take some votes on the default size. The problem with medium is that some people are still using screens as small as 800 x 600. A 400 x 400 applet is likely to use more screen space than the user has allotted to the browser. Maybe we should add a place where the user can set the default Jmol size in their notebook preferences? At present it is just a variable set when jmol_lib.js is loaded. We could certainly set it somewhere else in the web page.
Jonathan Replying to @jasongrout:
It seems to work pretty well for me. I wish the default was Medium Size instead of "small"
jasongrout
commented
14 years ago gutow
commented
14 years ago The link to jmol.zip now leads to a clean zip archive (no .DS_Store files), with the jmol file (shell script) and the Jmol.jar application file.
Jason, I also wonder about your spkg name. Wasn't the .py2.6 indicative of the python version?
Jonathan
jasongrout
commented
14 years ago Where is there a missing .py2.6? I don't think I deleted anything with that name.
It's possible that whatever you are seeing happens at install time, rather in the source of the spkg, but I'm not sure what file you're talking about.
gutow
commented
14 years ago I'm talking about this: sagenb-0.8.p3.spkg ^^ In the download of sage 4.4.3 that I was looking at the notebook is included as an .egg in the directory structure. I think I am confused by the .egg name versus the naming of the .spkg. The .egg name is:
sagenb-0.8-py2.6.egg ^^^ Since I've never built an egg or an spkg, I'm not sure of the significance.
Jonathan
Replying to @jasongrout:
Where is there a missing .py2.6? I don't think I deleted anything with that name.
It's possible that whatever you are seeing happens at install time, rather in the source of the spkg, but I'm not sure what file you're talking about.
jasongrout
commented
14 years ago Ah. What I did is create a new spkg, like in sage/spkg/standard/sagenb-0.8.p2.spkg. When it installs into the python directory (using the "sage -f" command), the py2.6 egg stuff will be taken care of.
gutow
commented
14 years ago Jason,
Once you've incorporated the new jmol.zip file, I suggest you update the description to include instructions on using your .spkg to test right near the top. Or are your and I the only two who are going to look at this?
Jonathan
kcrisman
commented
14 years ago No, you won't - pesky "someone else has already edited this page"!!!
Jonathan,
Sweet. Great work!
Some comments upon a very small amount of testing (which is all I have time for right now). I apologize for their telegraphic nature.
Popup 3dviewer is great.
Functions tab did not immediately have something in it, I had to click "request...", which is nonintuitive. I understand if that step is necessary, but the message could be better; as it is, the person using it wouldn't necessarily realize that this would give mesh etc. info for each object (nice to do it separately, so so so nice).
Colorpicker in Functions tab: awesome.
Initial size Small might be good for iPhone (if Jmol even works there?) but is a little on the small side for normal laptop/PC web browsing. Can the browsing thing be detected for this?
There is an awful lot of space given to the info, not so much to the actual graphic. Would it be possible to put that stuff below the image as opposed to on the right? In fact, that stuff should not necessarily resize with the graphic...
State is cool for those of us who might want to access it, but it should default (when clicked upon) to creating a slider or something, or "click here for full" or something like that. Otherwise the potential for really upsetting work flow is there, it changes the window size so much.
Sleep/Wake works great, might be nice to CSS those words into something less \texttt{}-ish. Note that "Arbitrarily resizable in own window Get static image to save" looks like one command; maybe some
Didn't break any old worksheets, though they all have this new little Jmol double window now, which makes sense.
This may be unrelated, but the axes seem to be in the wrong spots, at least in
var('y')
P=plot3d(x^2+y^2,(x,-3,3),(y,-3,3))
Q=plot3d(sin(x^2+y^2),(x,-3,3),(y,-3,3))
show(P+Q)I did not get to test having billions of applets open at the same time, unfortunately, but will be happy to do so if no one else can over the next week or two.
One really interesting thing is this. We had complaints about the snappiness of 3D interacts recently, but now I get almost instantaneous recomputation with 'small', which is great. However
TypeError: Result of expression '(stateStr.match(re_modelinline))' [null] is not an object.occurs if I change the size in an interact, and then move the slider. Obviously, other things don't stay the same with an interact - say if I change one function to green, it goes back to blue after moving the slider, but there shouldn't be the error message (ideally).
But thank you! This would be a big improvement. Looking forward to being able to evaluate it properly - clearly a big change needs big testing.
jasongrout
commented
14 years ago Description changed:
---
+++
@@ -1,4 +1,14 @@
I believe this drop-in set of javascript files now works. Need testers!
+
+To test, do:
+
+```
+sage -f http://sage.math.washington.edu/home/jason/sagenb-0.8.p3.spkg
+```
+
+(this will overwrite your current sagenb code (but not your worksheets), so you might want to do it in a test Sage installation)
+
+Alternatively, you can use the attached files:
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.
Description changed:
---
+++
@@ -8,7 +8,7 @@
(this will overwrite your current sagenb code (but not your worksheets), so you might want to do it in a test Sage installation)
-Alternatively, you can use the attached files:
+Alternatively, you can use the attached files and jmol.zip:
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.
Replying to @kcrisman:
Sweet. Great work!
Glad you like it.
Some comments upon a very small amount of testing (which is all I have time for right now). I apologize for their telegraphic nature.
Popup 3dviewer is great.
Functions tab did not immediately have something in it, I had to click "request...", which is nonintuitive. I understand if that step is necessary, but the message could be better; as it is, the person using it wouldn't necessarily realize that this would give mesh etc. info for each object (nice to do it separately, so so so nice).
You are correct that I could not originally get the information from Jmol on load because of timing issues. I have an idea about this and will work on it a little. In the meantime, I think you are correct that we need better instructions in this tab.
Colorpicker in Functions tab: awesome.
We use it for other Jmol stuff, but it was originally inspired by the needs of SAGE.
Initial size Small might be good for iPhone (if Jmol even works there?) but is a little on the small side for normal laptop/PC web browsing. Can the browsing thing be detected for this?
I believe we can get the surrounding window size. I will look into that. Maybe it should default to no more than 405 of width or height, whichever is higher?
There is an awful lot of space given to the info, not so much to the actual graphic. Would it be possible to put that stuff below the image as opposed to on the right? In fact, that stuff should not necessarily resize with the graphic...
I can play with the table formatting a little. I don't see any problems off the top of my head with it not resizing. I think underneath is a problem as the applet can be big enough that the controls will be off screen.
State is cool for those of us who might want to access it, but it should default (when clicked upon) to creating a slider or something, or "click here for full" or something like that. Otherwise the potential for really upsetting work flow is there, it changes the window size so much.
Eventually I want it hidden. But I think I can set it up to be scrolling....
Sleep/Wake works great, might be nice to CSS those words into something less \texttt{}-ish. Note that "Arbitrarily resizable in own window Get static image to save" looks like one command; maybe some
useful here?
These are formatting issues that I can deal with easily.
Didn't break any old worksheets, though they all have this new little Jmol double window now, which makes sense.
Good!
This may be unrelated, but the axes seem to be in the wrong spots, at least in
var('y') P=plot3d(x^2+y^2,(x,-3,3),(y,-3,3)) Q=plot3d(sin(x^2+y^2),(x,-3,3),(y,-3,3)) show(P+Q)
That is likely to be a SAGE python bug as Jmol just draws lines where SAGE tells it to. I will double check the parsing, but since the axes look correct for everything I've tried, I'm guessing something funny is passed to Jmol.
I did not get to test having billions of applets open at the same time, unfortunately, but will be happy to do so if no one else can over the next week or two.
One really interesting thing is this. We had complaints about the snappiness of 3D interacts recently, but now I get almost instantaneous recomputation with 'small', which is great.
This is because I switched to using the incrementally loaded applet. Thus only the parts needed are loaded. This significantly reduces load time.
However
TypeError: Result of expression '(stateStr.match(re_modelinline))' [null] is not an object.occurs if I change the size in an interact, and then move the slider. Obviously, other things don't stay the same with an interact - say if I change one function to green, it goes back to blue after moving the slider, but there shouldn't be the error message (ideally).
Is that completely reproducible? I've seen it occasionally when javascript gets executed before the applets are completely loaded. However, I've never seen any ill effects since things get reset later. If it causes problems and you can pin it down, let me know.
Thanks for the initial testing.
Jonathan
kcrisman
commented
14 years ago I want to point out that apparently Jmol won't load from the command line now. I don't have time to revert the spkg right now, but at any rate things like
sage: point3d([0,0,1])doesn't do anything now. No applet, etc.
gutow
commented
14 years ago Please check to see if the following two files are in the directory sage/local/lib/python2.6/site-packages/sagenb-0.8-py2.6.egg/sagenb/data/jmol
Jmol.jar & Jmol (a shell script).
If they are not then try downloading the .spkg again to see if that fixes it.
If the files are there then there is something we don't understand or the path in the Jmol shell script is wrong.
Jonathan
Replying to @kcrisman:
I want to point out that apparently Jmol won't load from the command line now. I don't have time to revert the spkg right now, but at any rate things like
sage: point3d([0,0,1])doesn't do anything now. No applet, etc.
kcrisman
commented
14 years ago Replying to @gutow:
Please check to see if the following two files are in the directory sage/local/lib/python2.6/site-packages/sagenb-0.8-py2.6.egg/sagenb/data/jmol
Jmol.jar & Jmol (a shell script).
Yup, both there (well, Jmol is jmol, but would that make the difference?).
If the files are there then there is something we don't understand or the path in the Jmol shell script is wrong.
I want to emphasize things worked fine from the notebook.
Replying to @kcrisman:
I want to point out that apparently Jmol won't load from the command line now. I don't have time to revert the spkg right now, but at any rate things like
sage: point3d([0,0,1])doesn't do anything now. No applet, etc.
gutow
commented
14 years ago Replying to @kcrisman: I was correct it is a path issue caused by whomever set things up so that sagenb is inside an .egg with sage rather than simply its own directory structure. It works fine if the following replacement is made in the shell file jmol:
JMOL_HOME=""$SAGE_LOCAL"/bin/sage-pypkg-location sagenb""sagenb/data/jmol"
is replaced by
JMOL_HOME=""$SAGE_LOCAL"/bin/sage-pypkg-location sagenb""sagenb-0.8-py2.6.egg/sagenb/data/jmol"
to account for the extra directory level that has been added. Who do I ask about this? I can fix the shell, but I want to make sure that the directory structure is supposed to have the .egg in it.
Yup, both there (well, Jmol is jmol, but would that make the difference?).
If the files are there then there is something we don't understand or the path in the Jmol shell script is wrong.
gutow
commented
14 years ago Jason,
Jmol.jar appears to be missing in the .spkg. The .zip file on my site does have it. You may want to rebuild the .spkg. Maybe I need to learn to do this as well...where do I start?:)
Jonathan
gutow
commented
14 years ago Description changed:
---
+++
@@ -3,20 +3,18 @@
To test, do:
-sage -f http://sage.math.washington.edu/home/jason/sagenb-0.8.p3.spkg +sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkg
-(this will overwrite your current sagenb code (but not your worksheets), so you might want to do it in a test Sage installation)
+or
-Alternatively, you can use the attached files and jmol.zip:
+```
+./sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkg
+```
+depending on your command line syntax.
-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. 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.
+This will change the Jmol files, jmol_lib.js and notebook_lib.js (current as of Sage 4.4.3), so you might want to do it in a test Sage installation.
Adds the following features to the notebook:I've figured out how to make an spkg that only changes the files pertinent to Jmol. Using this .spkg we should be able to test it against different versions of the notebook. The only notebook specific file that is change is notebook_lib.js. If using a notebook with changes to this file since Sage-4.4.3 a merge should be performed rather than a straight .spkg install.
I've have tried to address some of the issues mentioned above. I still suggest installing to a test system. A public example of this will also be available on my server (link to follow, once installed).
Version 1.1 of Jmol for Sage. Install with command
sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkg
or
./sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkg
depending on your command line syntax.
I'm also updating the ticket to show this instead of the first version.
gutow
commented
14 years ago Example worksheet running on my test server is available here:
https://141.233.197.45:4443/home/pub/0/
Note the certificate is self-signed so you will get security warnings. Don't worry about them.
gutow
commented
14 years ago June 28, 2010---My server is down because of a power outage. Hopefully, it wasn't killed and I will have it up again tomorrow.
Jonathan Replying to @gutow:
Example worksheet running on my test server is available here:
https://141.233.197.45:4443/home/pub/0/
Note the certificate is self-signed so you will get security warnings. Don't worry about them.
gutow
commented
14 years ago Server is back up. Replying to @gutow:
June 28, 2010---My server is down because of a power outage. Hopefully, it wasn't killed and I will have it up again tomorrow.
gutow
commented
14 years ago Working with 4.5
gutow
commented
14 years ago There appears to be a javascript issue with the sleeping and waking. Sometimes when an applet is put to sleep the controls lose track of which applet they go with and stop modifying things. I'm working on it. There is probably an indexing error.
jasongrout
commented
14 years ago Thanks. I'm keeping an eye on this; I believe that I now can review it officially relatively quickly (after the bug you mentioned is figured out). So how about after the problem with sleeping/waking is figured out, another call for reviewers is sent to sage-devel, and I'll work on reviewing this more in-depth.
Thanks again for all of your work on this!
jasongrout
commented
14 years ago Author: Jonathan Gutow
gutow
commented
14 years ago Description changed:
---
+++
@@ -3,13 +3,13 @@
To test, do:
-sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkg +sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.1.spkg
or
-./sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkg +./sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.1.spkg
depending on your command line syntax.
@@ -19,7 +19,7 @@
Adds the following features to the notebook:
-1) No more than 8 Jmols will be active at once. This prevents running out of memory. The user is provided with a link to wake up sleeping Jmols that they wish to manipulate. Sleeping Jmols are replaced with a static image.
+1) No more than 5 Jmols will be active at once. This prevents running out of memory. The user is provided with a link to wake up sleeping Jmols that they wish to manipulate. Sleeping Jmols are replaced with a static image.
2) A spin on/off check box is now provided.
Bug fixed. Problem related to how the standard Jmol.js package interprets applet labels of zero. The package version has been updated to 1.1.1. This is fixed above so that nobody will download the wrong one.
jasongrout
commented
14 years ago Thanks! I will try to look at this this next week.
jasongrout
commented
14 years ago CCing kcrisman, as it seems he'd be interested (or at least willing) to look at this as well.
gutow
commented
14 years ago Description changed:
---
+++
@@ -1,4 +1,6 @@
I believe this drop-in set of javascript files now works. Need testers!
+
+NOTE this package is outdated and the trac has moved to the notebook google site. See...
To test, do:
Reviewer: Jason Grout, Karl-Dieter Crisman
kcrisman
commented
14 years ago I tried installing this on a recent alpha of Sage:
Updating sagenb-0.8.10-py2.6.egg
removing old jmol_lib.js and notebook_lib.js…
New jmol_lib.js installed.
New notebook_lib.js installed.
removing Jmol*.jar and support files…
installing Jmol.jar and support files…
New Jmol*.jar and support files installed.
real 0m0.335s
user 0m0.012s
sys 0m0.075s
Successfully installed Jmol_for_SageNoteBook-1.1.1
Now cleaning up tmp files.
Making Sage/Python scripts relocatable...
Making script relocatable
Finished installing Jmol_for_SageNoteBook-1.1.1.spkgSo all seemed well. But after ./sage -b, the Jmol applet now seems to be exactly as it was originally. Did I miss something I was supposed to do other than ./sage -f this spkg?
gutow
commented
14 years ago You beat me to finishing the update to the trac ticket. Everything has been moved to the notebook google site. This will not work with the latest release as the location of the notebook code has changed. This .spkg will not properly update 4.6.1.
See http://code.google.com/p/sagenb/issues/detail?id=1 for details of what works with 4.6.1. I will now finish updating this trac.
Sorry, Jonathan Replying to @kcrisman:
I tried installing this on a recent alpha of Sage:
Updating sagenb-0.8.10-py2.6.egg removing old jmol_lib.js and notebook_lib.js… New jmol_lib.js installed. New notebook_lib.js installed. removing Jmol*.jar and support files… installing Jmol.jar and support files… New Jmol*.jar and support files installed. real 0m0.335s user 0m0.012s sys 0m0.075s Successfully installed Jmol_for_SageNoteBook-1.1.1 Now cleaning up tmp files. Making Sage/Python scripts relocatable... Making script relocatable Finished installing Jmol_for_SageNoteBook-1.1.1.spkgSo all seemed well. But after ./sage -b, the Jmol applet now seems to be exactly as it was originally. Did I miss something I was supposed to do other than ./sage -f this spkg?
gutow
commented
14 years ago Description changed:
---
+++
@@ -1,6 +1,8 @@
I believe this drop-in set of javascript files now works. Need testers!
-NOTE this package is outdated and the trac has moved to the notebook google site. See...
+NOTE this package is outdated and the trac has moved to the notebook google site. See http://code.google.com/p/sagenb/issues/detail?id=1 for details.
+
+If you are using <= Sage 4.6 this should still work.
To test, do:
Description changed:
---
+++
@@ -2,7 +2,7 @@
NOTE this package is outdated and the trac has moved to the notebook google site. See http://code.google.com/p/sagenb/issues/detail?id=1 for details.
-If you are using <= Sage 4.6 this should still work.
+If you are using <= Sage 4.5 this should still work.
To test, do:
Thanks for the clarification. I have to say, since your ticket is the only listed 'issue' on that code.google.com site, I am not sure how useful that will be for people to help. Of course, I've been against separating the sagenb out that much, because it becomes too easy to get out of the loop.
I have to say, though it now works, I'm still a little mystified, because the 'click to own 3d window' just gives a blank window (the Jmol doesn't appear, except brief Jmol logo), and if you click 'wake up' when it's already awake, it disappears too. I wonder if they are related.
But this will make it quite easy to review, at any rate, and hopefully that is just something silly I did. This was with 4.6.2.alpha0.
gutow
commented
14 years ago Replying to @kcrisman:
Thanks for the clarification. I have to say, since your ticket is the only listed 'issue' on that code.google.com site, I am not sure how useful that will be for people to help. Of course, I've been against separating the sagenb out that much, because it becomes too easy to get out of the loop.
I sort of wondered about that too, but since that is where the notebook is now hosted, I thought I should move this stuff there.
I have to say, though it now works, I'm still a little mystified, because the 'click to own 3d window' just gives a blank window (the Jmol doesn't appear, except brief Jmol logo), and if you click 'wake up' when it's already awake, it disappears too. I wonder if they are related.
Might be. I can't reproduce it however on 4.6.1. If I click the "Arbitrarily resizable in own window" it works fine from my server. (Safari MacOSX, and FireFox with Linux. There is a problem for logged in users with the way the notebook passes headers for Firefox on MacOS--this is long standing and probably part of Twisted.) If you can send me more specifics I can try to track this down.
But this will make it quite easy to review, at any rate, and hopefully that is just something silly I did. This was with 4.6.2.alpha0.
Thanks for looking at this.
Jonathan
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):
./sage -f "http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.6.spkg"./sage -b.I have addressed the following issues (let me know if I've missed anything):
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