#9232: jmol on commandline broken
------------------------------------------------+---------------------------
Reporter: vbraun | Owner: gutow
Type: defect | Status: needs_review
Priority: major | Milestone: sage-4.7
Component: graphics | Keywords:
Author: Jonathan Gutow | Upstream: N/A
Reviewer: Jason Grout, Karl-Dieter Crisman | Merged:
Work_issues: |
------------------------------------------------+---------------------------
Old description:
> I can't see Graphics3d objects on the command line. For example,
> {{{
> sage: sphere()
> sage:
> }}}
> The command returns without starting jmol or producing any other
> graphical output.
>
> Strangely enough, I can start jmol from the sage command line:
> {{{
> ----------------------------------------------------------------------
> | Sage Version 4.4.3, Release Date: 2010-06-04 |
> | Type notebook() for the GUI, and license() for information. |
> ----------------------------------------------------------------------
> sage: !jmol
> splash_image=jar:file:/home/vbraun/opt/sage-hg/local/lib/python2.6/site-
> packages/sagenb-0.8-py2.6.egg/sagenb/data/jmol/Jmol.jar!/org/openscience/jmol/images/Jmol_splash.jpg
> history file is /home/vbraun/.jmol/history
> using Smarter Model Adapter
> (C) 2008 Jmol Development
> Jmol Version 11.6.16 2008-11-24 13:39
> java.vendor:Sun Microsystems Inc.
> java.version:1.6.0_18
> os.name:Linux
> memory:9.8/21.1
> useCommandThread: false
> User macros dir: /home/vbraun/.jmol/macros
> exists: false
> isDirectory: false
> }}}
>
> The following also works and shows a tachyon-generated plot:
> {{{
> sphere(viewer='tachyon')
> }}}
>
> More verbosity:
> {{{
> sage: sphere(verbosity=99)
> Traceback (most recent call last):
> File "/home/vbraun/Sage/sage/local/bin/sage-pypkg-location", line 3, in
> <module>
> from pkg_resources import Requirement, working_set
> zipimport.ZipImportError: can't decompress data; zlib not available
> Jmol.jar not found
> }}}
>
> For the record, I'm running Fedora 13 x86_64
New description:
I can't see Graphics3d objects on the command line. For example,
{{{
sage: sphere()
sage:
}}}
The command returns without starting jmol or producing any other graphical
output.
Strangely enough, I can start jmol from the sage command line:
{{{
----------------------------------------------------------------------
| Sage Version 4.4.3, Release Date: 2010-06-04 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
sage: !jmol
splash_image=jar:file:/home/vbraun/opt/sage-hg/local/lib/python2.6/site-
packages/sagenb-0.8-py2.6.egg/sagenb/data/jmol/Jmol.jar!/org/openscience/jmol/images/Jmol_splash.jpg
history file is /home/vbraun/.jmol/history
using Smarter Model Adapter
(C) 2008 Jmol Development
Jmol Version 11.6.16 2008-11-24 13:39
java.vendor:Sun Microsystems Inc.
java.version:1.6.0_18
os.name:Linux
memory:9.8/21.1
useCommandThread: false
User macros dir: /home/vbraun/.jmol/macros
exists: false
isDirectory: false
}}}
The following also works and shows a tachyon-generated plot:
{{{
sphere(viewer='tachyon')
}}}
More verbosity:
{{{
sage: sphere(verbosity=99)
Traceback (most recent call last):
File "/home/vbraun/Sage/sage/local/bin/sage-pypkg-location", line 3, in
<module>
from pkg_resources import Requirement, working_set
zipimport.ZipImportError: can't decompress data; zlib not available
Jmol.jar not found
}}}
For the record, I'm running Fedora 13 x86_64
----
Install
[http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.5.spkg
this spkg] and apply ''only''
[attachment:trac_9232_plot3d_base_pyx.patch].
--
Comment(by kcrisman):
> 1. The correct menu is much shorter in the notebook than in the
application launched from the command line. The application launched from
the command line uses the default menu. I'll look into making them match.
Well, no need on this ticket!
As for this, the '''first patch only''' suffices to fix the command line
problem, and the notebook still works right.
So I would say that the second patch is ''not'' relevant to this ticket,
esp. given its problems with import (which I am looking into - I think has
to do with HG not applying some things correctly because of perceived line
endings. Look at the view of the attachment on this ticket, and look at
the lines with `bond100` and `bond150` and note the weirdness there. It
looks like
{{{
bond100 | 0.10 √Ö = wireframe .1
}}}
instead of angstroms like I think it's supposed to
{{{
bond100 | 0.10 Å = wireframe .1
}}}
No wonder it's not applying, since it's not being interpreted right.
Anyway, not relevant for the ticket.
> 1. Apply the patches in #9238 to see the updated notebook Jmol
interface.
As I thought - thanks, not relevant for reviewing this.
> 1. The .spkg problem is odd. I've got no errors ever. I just use
./sage -f "<web address of patch>".
Yes, that is what should work. Since this isn't an spkg that would
actually ever exist, it's not a problem, I hope.
> 1. The patch with the problem with the .mnu file means redoing it
against a 4.6.2 that had the .mnu file in the repo. For some reason the
version I got for ubuntu 10.04 lts did not.
See above.
I get the following issue as well.
{{{
rm:
/Users/.../sage-4.7.alpha2-jmol/devel/sagenb/sagenb/data/jmol/LICENSE.txt:
No such file or directory
}}}
So was there not a license before? Apparently not - I can confirm that in
an install that does not have the new Jmol. So it's not a big deal, but
at any rate you didn't have to put that in the script.
Otherwise I think this is ready to go. It would be nice to have someone
on a system where command line plotting did ''not'' work before to try
this. Volker, du bist ja bei Sage Days 29, oder? Probierst du es mal
aus?
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/9232#comment:21>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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