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#11078 closed defect (fixed)

jmol in the flask notebook

Reported by:	jason	Owned by:	jason, mpatel, was
Priority:	major	Milestone:	sage-5.2
Component:	notebook	Keywords:	sd31 sd35.5
Cc:	rkirov, mhansen, kcrisman	Merged in:	sage-5.2.beta0
Authors:	William Stein, Jonathan Gutow	Reviewers:	Jason Grout
Report Upstream:	N/A	Work issues:
Branch:		Commit:
Dependencies:	#11080	Stopgaps:

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Description (last modified by jason)

The attached patch solves an issue with jmol finding the right .jmol.zip file in the new flask notebook. This patch should only be applied *after* the notebook is moved to a flask notebook.

The patch should replace the following line in sage/plot/plot3d/base.pyx

f.write('set defaultdirectory "%s"\n' % archive_name)

with

import sagenb
f.write('set defaultdirectory "cells/%s/%s"\n' % (sagenb.notebook.interact.SAGE_CELL_ID, archive_name))

Attachments (1)

trac_11078.patch (886 bytes) - added by jason 9 years ago.

Download all attachments as: .zip

Change History (21)

comment:1 Changed 10 years ago by kcrisman

Cc kcrisman added

comment:2 Changed 10 years ago by jason

Description modified (diff)

comment:3 Changed 10 years ago by was

Keywords sd31 added

comment:4 Changed 10 years ago by slabbe

This week, I compiled sage-4.7.1.rc0 and installed the new flask Sage notebook following instructions from : http://code.google.com/r/rkirov-flask/. I also followed the section Adding stock Jmol plus the patch trac_11078.patch. This made Jmol to work from the notebook : Great!

But, from the command line, with the patch trac_11078.patch a command like sphere() opens Jmol but Jmol stays all black. I had to mimic the modifications done in #11503 on the same file sage/plot/plot3d/base.pyx to make Jmol works properly from the command line.

Sébastien

comment:5 Changed 9 years ago by jdemeyer

Milestone changed from sage-4.8 to sage-5.0

comment:6 Changed 9 years ago by jason

Description modified (diff)

Changed 9 years ago by jason

Attachment trac_11078.patch added

comment:7 Changed 9 years ago by jason

Authors set to William Stein, Jonathan Gutow
Reviewers set to Jason Grout
Status changed from new to needs_review

I updated the patch with the changes from #11503. With the flask notebook, sphere() works both from the command line and from the notebook.

I'm setting as needs review to have one other person double-check this patch works as intended, though I guess I might qualify as the only needed reviewer. Basically, what I did here was just rebase the patch at #11503.