Thanks Nat. I have ipython with my usual python build, yet libtbx.ipython does not exist. I've tried libtbx.refresh, and this doesn't give me anything. What should I re-configure with libtbx.configure? If I can get this working I'll create and share an IPython notebook to demonstrate a use case for it. Cheers, Oli On Mon, Sep 8, 2014 at 1:45 PM, Nathaniel Echols wrote:

On Mon, Sep 8, 2014 at 1:19 PM, Oliver Zeldin wrote:

...

Has anyone tried to get IPython working with cctbx?

I'd really like to be able to use IPython notebooks for examples/tutorials/documented experiments, and was wondering if anyone else had thought the same thing.

Apparently Ralf did this years ago: if you have IPython installed with the Python that you're using, then re-running the configuration (or libtbx.refresh) will result in a command named "libtbx.ipython" being created. I confirmed that this does in fact seem to work, although since I've never used Ipython I'm not sure what to expect.

If this is something that would be generally useful we could add it to the dependencies build script (and the new improved plus bundles, which I will be sending an email about RSN).

-Nat

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

Nothing (it works). Further bits and bobs (my python is installed via Homebrew) $python

...

...

import IPython IPython.__file__ '/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/__init__.pyc'

Also how I normally launch IPython: $ cat `which IPython` #!/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python # -*- coding: utf-8 -*- 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()) On Mon, Sep 8, 2014 at 2:01 PM, Nathaniel Echols wrote:

On Mon, Sep 8, 2014 at 1:58 PM, Oliver Zeldin wrote:

...

I have ipython with my usual python build, yet libtbx.ipython does not exist. I've tried libtbx.refresh, and this doesn't give me anything. What should I re-configure with libtbx.configure?

What happens when you run this?

python -c "import IPython"

-Nat

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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

Working now. I have no idea what just happened. That is odd in the extreme... On Mon, Sep 8, 2014 at 2:15 PM, Nathaniel Echols wrote:

Try editing libtbx/env_config.py and replace lines 1676-7:

try: import IPython except ImportError: return

with simply "import IPython", then run libtbx.refresh and see what happens.

-Nat

On Mon, Sep 8, 2014 at 2:09 PM, Oliver Zeldin wrote:

...

Nothing (it works).

Further bits and bobs (my python is installed via Homebrew)

$python

...

...

...

import IPython IPython.__file__

'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/__init__.pyc'

Also how I normally launch IPython: $ cat `which IPython`

#!/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python

# -*- coding: utf-8 -*- 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())

On Mon, Sep 8, 2014 at 2:01 PM, Nathaniel Echols wrote:

...

On Mon, Sep 8, 2014 at 1:58 PM, Oliver Zeldin wrote:

...

I have ipython with my usual python build, yet libtbx.ipython does not exist. I've tried libtbx.refresh, and this doesn't give me anything. What should I re-configure with libtbx.configure?

What happens when you run this?

python -c "import IPython"

-Nat

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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

On Mon, Sep 8, 2014 at 2:32 PM, Oliver Zeldin 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

Agreed. This would be a simple and useful thing to add to the builds. Oliver, it should work fine if you install it into cctbx's python interpreter. Can you "import IPython" ? Ian On Mon, Sep 8, 2014 at 1:58 PM, Oliver Zeldin wrote:

Thanks Nat.

I have ipython with my usual python build, yet libtbx.ipython does not exist. I've tried libtbx.refresh, and this doesn't give me anything. What should I re-configure with libtbx.configure?

If I can get this working I'll create and share an IPython notebook to demonstrate a use case for it.

Cheers,

Oli

On Mon, Sep 8, 2014 at 1:45 PM, Nathaniel Echols wrote:

...

On Mon, Sep 8, 2014 at 1:19 PM, Oliver Zeldin wrote:

...

Has anyone tried to get IPython working with cctbx?

I'd really like to be able to use IPython notebooks for examples/tutorials/documented experiments, and was wondering if anyone else had thought the same thing.

Apparently Ralf did this years ago: if you have IPython installed with the Python that you're using, then re-running the configuration (or libtbx.refresh) will result in a command named "libtbx.ipython" being created. I confirmed that this does in fact seem to work, although since I've never used Ipython I'm not sure what to expect.

If this is something that would be generally useful we could add it to the dependencies build script (and the new improved plus bundles, which I will be sending an email about RSN).

-Nat

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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

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