Opened 12 years ago

Closed 10 years ago

#11078 closed defect (fixed)

jmol in the flask notebook

Reported by: Jason Grout Owned by: jason, mpatel, was
Priority: major Milestone: sage-5.2
Component: notebook Keywords: sd31 sd35.5
Cc: Radoslav Kirov, Mike Hansen, Karl-Dieter Crisman 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:

Status badges

Description (last modified by Jason Grout)

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 Grout 11 years ago.

Download all attachments as: .zip

Change History (21)

comment:1 Changed 12 years ago by Karl-Dieter Crisman

Cc: Karl-Dieter Crisman added

comment:2 Changed 12 years ago by Jason Grout

Description: modified (diff)

comment:3 Changed 11 years ago by William Stein

Keywords: sd31 added

comment:4 Changed 11 years ago by Sébastien Labbé

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 11 years ago by Jeroen Demeyer

Milestone: sage-4.8sage-5.0

comment:6 Changed 11 years ago by Jason Grout

Description: modified (diff)

Changed 11 years ago by Jason Grout

Attachment: trac_11078.patch added

comment:7 Changed 11 years ago by Jason Grout

Authors: William Stein, Jonathan Gutow
Reviewers: Jason Grout
Status: newneeds_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.

comment:8 Changed 11 years ago by William Stein

Status: needs_reviewpositive_review

This looks great to me!

comment:9 Changed 11 years ago by Jeroen Demeyer

Dependencies: #11080

comment:10 Changed 11 years ago by Jason Grout

Keywords: sd35.5 added

comment:11 Changed 11 years ago by Jason Grout

Keywords: sd31, sd35.5sd31 sd35.5

comment:12 Changed 11 years ago by Jeroen Demeyer

Milestone: sage-5.0sage-pending

comment:13 Changed 11 years ago by Jeroen Demeyer

Milestone: sage-pendingsage-5.1

comment:14 Changed 11 years ago by Jeroen Demeyer

Milestone: sage-5.1sage-pending

comment:15 Changed 11 years ago by Jeroen Demeyer

Milestone: sage-pendingsage-5.2

comment:16 Changed 10 years ago by Jeroen Demeyer

Merged in: sage-5.2.beta0
Resolution: fixed
Status: positive_reviewclosed

comment:17 Changed 10 years ago by Jeroen Demeyer

Merged in: sage-5.2.beta0
Milestone: sage-5.2sage-pending
Resolution: fixed
Status: closednew

Unmerging this from sage-5.2 due to the serious security issue at #13270.

comment:18 Changed 10 years ago by Jeroen Demeyer

Status: newneeds_review

comment:19 Changed 10 years ago by Jeroen Demeyer

Status: needs_reviewpositive_review

comment:20 Changed 10 years ago by Jeroen Demeyer

Merged in: sage-5.2.beta0
Milestone: sage-pendingsage-5.2
Resolution: fixed
Status: positive_reviewclosed
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