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Sagemath 8.1 windows: Impossible to export jmol figure from Jupyter while it works with former notebook.

asked 2018-03-02 01:02:30 +0200

c05772 gravatar image

updated 2019-01-09 17:55:48 +0200

FrédéricC gravatar image

After installing sagemath 8.1 for windows I try to save as a jmol file a 3D figure and as shown on the figure that I cannot upload :-( [I do not have the 60 points required, a figure is worth a thousand words, too bad!].

So I load 2 shells: one running "jupyter notebook", the other running "notebook()" in both shell I try the MWE:

show(G,figsize=(5,5),title="Sample Figure",aspect_ratio=1);

On both, I right click on the jmol figure,then on File, in both cases 'File->' becomes red but only in the old notebook() I get the sub menu (Load Save Export) and the subsubmenus. With jupyter, I get nothing and cannot export.

Worse even in a console, I cannot get the jmol figure executed, neither exported.

I jumped to 61 points overnight, so here is the picture:image description

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Do you know what kernel you're running in jupyter? There should be a label in the top right of the window.

j.c. gravatar imagej.c. ( 2018-03-02 18:48:19 +0200 )edit

I now believe you're running into this issue:

j.c. gravatar imagej.c. ( 2018-03-02 19:02:56 +0200 )edit

The kernel in both cases in SageMath 8.1, don't forget that this is the windows edition and the program is launched through the standard windows shortcut created at installation time.

c05772 gravatar imagec05772 ( 2018-03-02 20:22:32 +0200 )edit

Yes, I was mistaken about what your problem was initially.

j.c. gravatar imagej.c. ( 2018-03-02 20:28:04 +0200 )edit

It might be a bug/problem with your web browser. You haven't mentioned what browser you're using.

Iguananaut gravatar imageIguananaut ( 2018-03-22 11:44:49 +0200 )edit

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answered 2018-03-02 05:26:29 +0200

j.c. gravatar image

updated 2018-03-02 20:46:50 +0200

I can confirm that there is an issue here with SageMath and jupyter but I don't have any solution, unfortunately.

I just tested jmol in sage -n jupyter on macOS and see the same thing that you do where the submenus are unable to be displayed. I believe we are running into this previous issue.

the following is probably not relevant

You could also try installing the SageMath kernel into jupyter by following the instructions here, with appropriate modifications for Windows. Note that this requires more fiddling and you might find that interact elements don't work by default.

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Yes but what is surprising is that the export is working with the old notebook() format: same kernel, same windows installation, same shortcut. And by the way this remark may help to find why jupyter is not fully working.

c05772 gravatar imagec05772 ( 2018-03-02 20:27:02 +0200 )edit

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Asked: 2018-03-02 01:02:30 +0200

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Last updated: Mar 02 '18