Opened 11 years ago

Last modified 10 years ago

#11503 closed task

Make new spkg to install Jmol in SAGE_LOCAL/share — at Version 10

Reported by: gutow Owned by: gutow
Priority: major Milestone: sage-5.2
Component: notebook Keywords: sd31 Jmol flask
Cc: rado, fbissey, strogdon Merged in:
Authors: gutow Reviewers:
Report Upstream: N/A Work issues:
Branch: Commit:
Dependencies: flask notebook Stopgaps:

Status badges

Description (last modified by gutow)

In an effort to remove Jmol from the notebook in the Flask notebook it is being moved to SAGE_LOCAL/share. This is based on the logic that the notebook can run without Jmol, but Sage cannot run without either the notebook or Jmol even when using just the command line.

To achieve this relocation of Jmol:

  1. install this .spkg
./sage -f "http://www.uwosh.edu/faculty_staff/gutow/Jmol-12.0.45.p2.spkg

(which lives at this location)

  1. Some patches are necessary to notebook paths and the plot3d code
    1. for flask attachment:trac_11503_path_fix.patch
    2. for plot3d package attachment:trac_11503_cmd_line_fix.patch

Change History (12)

comment:1 Changed 11 years ago by gutow

  • Owner changed from jason, mpatel, was to gutow

Changed 11 years ago by gutow

path fix for flask

comment:2 Changed 11 years ago by gutow

  • Description modified (diff)

Changed 11 years ago by gutow

plot3d command line fix

comment:3 Changed 11 years ago by gutow

  • Description modified (diff)

comment:4 Changed 11 years ago by fbissey

  • Cc fbissey added

comment:5 Changed 11 years ago by kcrisman

  • Description modified (diff)

comment:6 Changed 11 years ago by gutow

  • Description modified (diff)

spkg refactored to better meet Sage standards and remove dead code from spkg-install.

comment:7 Changed 11 years ago by gutow

  • Description modified (diff)
  • Status changed from new to needs_review

comment:8 follow-up: Changed 11 years ago by jhpalmieri

  • Status changed from needs_review to needs_work

Several comments:

  • There are some backup files present: SPKG.txt~ and spkg-install~.
  • As I noted on #11496, you should copy the jmol shell script to SAGE_LOCAL/bin as part of spkg-install.
  • It would be helpful if you could prepare the mercurial repository with the version of hg installed with Sage. When I use the version included with Sage (which is the only version on my computer), I get
    $ hg status
    abort: requirement 'dotencode' not supported!
    
    so I can't check the state of the repo without installing a new version of hg.

comment:9 in reply to: ↑ 8 Changed 11 years ago by gutow

  • Hmm...didn't notice the backup files.  I'll look into that...
  • I could add the Jmol script to the jmol .spkg.  The one that is in there is the generic install not the one for SAGE...It seems reasonable that it should not be tracked by SAGE...I will add the SAGE version as a patch to the .spkg.  Once I get this done, I believe #11496 should be closed, as it will no longer apply...let me know who to notify about that.
  • Not sure if I can manage to successfully backtrack on the Hg repository format.  In order to work with the flask-notebook on my machine, I found I needed a system install of Hg and I got the latest.  Is this going to be a hold up?  Hg has been a real pain compared to the other version control systems I've  used.  Can somebody point out how to do the backtrack cleanly and quickly.  If it takes me a couple of hours to untangle Hg that's more time than it will take me to fix the rest of the .spkg problems and more time than I have for this project at the moment.

Replying to jhpalmieri:

Several comments: - There are some backup files present: SPKG.txt~ and spkg-install~. - As I noted on #11496, you should copy the jmol shell script to SAGE_LOCAL/bin as part of spkg-install. - It would be helpful if you could prepare the mercurial repository with the version of hg installed with Sage. When I use the version included with Sage (which is the only version on my computer), I get $ hg status abort: requirement 'dotencode' not supported! so I can't check the state of the repo without installing a new version of hg.

comment:10 Changed 11 years ago by gutow

  • Description modified (diff)
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