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: sage-6.6
Component: notebook Keywords: days64
Cc: Merged in:
Authors: Volker Braun Reviewers: Eric Gourgoulhon
Report Upstream: N/A Work issues:
Branch: 3fce004 (Commits) Commit: 3fce004fe8a539d2998fff6abcc9b6c14baedd38
Dependencies: #17826 #17234 Stopgaps:

Description (last modified by vbraun)

http://boxen.math.washington.edu/home/vbraun/www/ipython-jsmol.png

Change History (14)

comment:1 Changed 6 years ago by vbraun

  • 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 vbraun

  • Branch set to u/vbraun/jsmol_in_the_ipython_notebook

comment:3 Changed 6 years ago by vbraun

  • Authors set to Volker Braun
  • Commit set to b78260d046fff40e1b672dfc14e680cc3442d61f
  • Description modified (diff)

Last 10 new commits:

​5eb9bc7Merge #17234: Rich output and the IPython Notebook
​706573cMerge in Sage 6.6.beta2
​8f46bc7Merge #17288: MathJax spkg for ipython notebook
​10c8d5dUse the new IPython kernel stuff for Sage
​0dfff38delete the old ipython notebook templates
​e14c533Use local docs, icon
​4748c26Merge #17234: Rich output and the IPython Notebook
​284fd72Merge Trac #17897: Jsonschema package
​af760e2Merge in Sage 6.6.beta3
​b78260dEnable JSmol in the IPython notebook

comment:4 Changed 6 years ago by vbraun

  • Status changed from new to needs_review

comment:5 Changed 6 years ago by egourgoulhon

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 git

  • Commit changed from b78260d046fff40e1b672dfc14e680cc3442d61f to f1968b9e9b367ad40ef9139b46ae4d40900d3ff3

Branch pushed to git repo; I updated commit sha1. New commits:

​f1968b9Merge tag Sage-6.6.rc0 into #17894

comment:7 Changed 6 years ago by vbraun

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 egourgoulhon

  • 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 fbissey

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 vbraun

thanks for noticing, I'll add it here

comment:11 Changed 6 years ago by git

  • 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:

​3fce004use get_ipython_dir

comment:12 Changed 6 years ago by vbraun

  • Status changed from needs_review to positive_review

comment:13 Changed 6 years ago by fbissey

thanks.

comment:14 Changed 6 years ago by vbraun

  • Branch changed from u/vbraun/jsmol_in_the_ipython_notebook to 3fce004fe8a539d2998fff6abcc9b6c14baedd38
  • Resolution set to fixed
  • Status changed from positive_review to closed
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