Opened 11 years ago

Closed 9 years ago

#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:

Status badges

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 10 years ago.

Download all attachments as: .zip

Change History (21)

comment:1 Changed 11 years ago by kcrisman

  • Cc kcrisman added

comment:2 Changed 11 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 10 years ago by jdemeyer

  • Milestone changed from sage-4.8 to sage-5.0

comment:6 Changed 10 years ago by jason

  • Description modified (diff)

Changed 10 years ago by jason

comment:7 Changed 10 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.

comment:8 Changed 10 years ago by was

  • Status changed from needs_review to positive_review

This looks great to me!

comment:9 Changed 10 years ago by jdemeyer

  • Dependencies set to #11080

comment:10 Changed 10 years ago by jason

  • Keywords sd35.5 added

comment:11 Changed 10 years ago by jason

  • Keywords changed from sd31, sd35.5 to sd31 sd35.5

comment:12 Changed 10 years ago by jdemeyer

  • Milestone changed from sage-5.0 to sage-pending

comment:13 Changed 10 years ago by jdemeyer

  • Milestone changed from sage-pending to sage-5.1

comment:14 Changed 9 years ago by jdemeyer

  • Milestone changed from sage-5.1 to sage-pending

comment:15 Changed 9 years ago by jdemeyer

  • Milestone changed from sage-pending to sage-5.2

comment:16 Changed 9 years ago by jdemeyer

  • Merged in set to sage-5.2.beta0
  • Resolution set to fixed
  • Status changed from positive_review to closed

comment:17 Changed 9 years ago by jdemeyer

  • Merged in sage-5.2.beta0 deleted
  • Milestone changed from sage-5.2 to sage-pending
  • Resolution fixed deleted
  • Status changed from closed to new

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

comment:18 Changed 9 years ago by jdemeyer

  • Status changed from new to needs_review

comment:19 Changed 9 years ago by jdemeyer

  • Status changed from needs_review to positive_review

comment:20 Changed 9 years ago by jdemeyer

  • Merged in set to sage-5.2.beta0
  • Milestone changed from sage-pending to sage-5.2
  • Resolution set to fixed
  • Status changed from positive_review to closed
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