Opened 6 years ago
Closed 6 years ago
#17894 closed enhancement (fixed)
JSMol in the IPython notebook
Reported by:  vbraun  Owned by:  

Priority:  major  Milestone:  sage6.6 
Component:  notebook  Keywords:  days64 
Cc:  Merged in:  
Authors:  Volker Braun  Reviewers:  Eric Gourgoulhon 
Report Upstream:  N/A  Work issues:  
Branch:  3fce004 (Commits, GitHub, GitLab)  Commit:  3fce004fe8a539d2998fff6abcc9b6c14baedd38 
Dependencies:  #17826 #17234  Stopgaps: 
Description (last modified by )
Change History (14)
comment:1 Changed 6 years ago by
 Component changed from PLEASE CHANGE to notebook
 Dependencies set to #17826 #17234
 Type changed from PLEASE CHANGE to enhancement
comment:2 Changed 6 years ago by
 Branch set to u/vbraun/jsmol_in_the_ipython_notebook
comment:3 Changed 6 years ago by
 Commit set to b78260d046fff40e1b672dfc14e680cc3442d61f
 Description modified (diff)
comment:4 Changed 6 years ago by
 Status changed from new to needs_review
comment:5 Changed 6 years ago by
That's nice!
However, when I click on the right button to get the jsmol menu, I cannot access to submenus (e.g. zoom). This is with Sage 6.6.rc0.
Also, there was a small conflict in src/sage/repl/ipython_kernel/install.py when merging into Sage 6.6.rc0 (instance.install_spec()
> instance._install_spec()
and instance.symlink_resources()
> instance._symlink_resources()
)
comment:6 Changed 6 years ago by
 Commit changed from b78260d046fff40e1b672dfc14e680cc3442d61f to f1968b9e9b367ad40ef9139b46ae4d40900d3ff3
Branch pushed to git repo; I updated commit sha1. New commits:
f1968b9  Merge tag Sage6.6.rc0 into #17894

comment:7 Changed 6 years ago by
I don't think the menu is possible. In the current ipython notebook, everything must be embedded in the cell output. But jsmol has no interface to pass the menu in, it insists on loading it in a separate request.
comment:8 Changed 6 years ago by
 Keywords days64 added
 Reviewers set to Eric Gourgoulhon
 Status changed from needs_review to positive_review
OK I see. Anyway, it is already very nice to have interactive 3D plots in the ipython notebook. Thank you for this work!
comment:9 Changed 6 years ago by
Wish I had noticed earlier you had another instance of os.environ[IPYTHONDIR]
in there before it was positively reviewed. Expect a follow up ticket normalizing it to get_ipython_dir
.
comment:10 Changed 6 years ago by
thanks for noticing, I'll add it here
comment:11 Changed 6 years ago by
 Commit changed from f1968b9e9b367ad40ef9139b46ae4d40900d3ff3 to 3fce004fe8a539d2998fff6abcc9b6c14baedd38
 Status changed from positive_review to needs_review
Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:
3fce004  use get_ipython_dir

comment:12 Changed 6 years ago by
 Status changed from needs_review to positive_review
comment:13 Changed 6 years ago by
thanks.
comment:14 Changed 6 years ago by
 Branch changed from u/vbraun/jsmol_in_the_ipython_notebook to 3fce004fe8a539d2998fff6abcc9b6c14baedd38
 Resolution set to fixed
 Status changed from positive_review to closed
Last 10 new commits:
Merge #17234: Rich output and the IPython Notebook
Merge in Sage 6.6.beta2
Merge #17288: MathJax spkg for ipython notebook
Use the new IPython kernel stuff for Sage
delete the old ipython notebook templates
Use local docs, icon
Merge #17234: Rich output and the IPython Notebook
Merge Trac #17897: Jsonschema package
Merge in Sage 6.6.beta3
Enable JSmol in the IPython notebook