Ticket #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 | Work issues: | |
| Report Upstream: | N/A | Reviewers: | Jason Grout |
| Authors: | William Stein, Jonathan Gutow | Merged in: | sage-5.2.beta0 |
| Dependencies: | #11080 | Stopgaps: |
Description (last modified by jason) (diff)
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
-
trac_11078.patch
(886 bytes) -
added by jason 17 months ago.
Change History
comment:4 Changed 22 months 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:7 Changed 17 months ago by jason
- Status changed from new to needs_review
- Reviewers set to Jason Grout
- Authors set to William Stein, Jonathan Gutow
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 17 months ago by was
- Status changed from needs_review to positive_review
This looks great to me!
comment:16 Changed 11 months ago by jdemeyer
- Status changed from positive_review to closed
- Resolution set to fixed
- Merged in set to sage-5.2.beta0
comment:17 Changed 10 months ago by jdemeyer
- Status changed from closed to new
- Resolution fixed deleted
- Merged in sage-5.2.beta0 deleted
- Milestone changed from sage-5.2 to sage-pending
Unmerging this from sage-5.2 due to the serious security issue at #13270.
comment:20 Changed 10 months ago by jdemeyer
- Status changed from positive_review to closed
- Resolution set to fixed
- Merged in set to sage-5.2.beta0
- Milestone changed from sage-pending to sage-5.2
