Here's an example of an IPython notebook for CCTBX:

http://nbviewer.ipython.org/github/zeldebeest/public-notebooks/blob/master/Clustering_basic.ipynb

Basically, it combines a notebook and an interactive python environment. Awesome times for command-line based analysis sessions, so you can keep track of everything you do, and easily share your work.



On Mon, Sep 8, 2014 at 2:36 PM, Nathaniel Echols <nechols@lbl.gov> wrote:
On Mon, Sep 8, 2014 at 2:32 PM, Oliver Zeldin <zeldin@stanford.edu> wrote:
Now.. can we make it take arguments from the command line? This way we can do things like

$libtbx.ipython notebook --matplotib

(or whatever)

For reference, the default ipython launcher does:

import re
import sys

from IPython import start_ipython

if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
    sys.exit(start_ipython())

Ralf's launcher (libtbx/command_line/ipython_shell_start.py) is from 2007 and I don't know of anyone else using it, so feel free to modify it if you think it could be made more useful.

-Nat

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--
Dr. Oliver B. Zeldin
Brunger Group
Stanford University