[yt-users] yt and ipython notebook

[Nathan Goldbaum]

Hi Mark,

Take a look at this issue: https://github.com/ipython/ipython/issues/4177

It looks like updating yt's dependencies left the old version of IPython
behind.  You should be able to get rid of it by doing `pip remove IPython`
and then `pip install IPython`.

That will get you IPython 1.1, which we should also add to the install
script when we add jinja2.

-Nathan


On Wed, Sep 18, 2013 at 2:51 PM, Mark Krumholz <mkrumhol at ucsc.edu> wrote:

>
> On Sep 18, 2013, at 2:42 PM, Matthew Turk wrote:
>
> > Hi Mark,
> >
> > pip install jinja2
> >
> > should fix it.  I think we missed that in our dependency stack, but I
> > will add it to the install script.
> >
> > Thanks for the report!
> >
> > -Matt
>
>
> Hi Matt,
>
> That helps, but still doesn't let me run. I tried your suggestion, and
> jinja2 seems to build, though it throws a bunch of warning messages:
>
> (yt-x86_64)pfe20:hmc3_mhd_lowden mkrumhol$ pip install jinja2
> Downloading/unpacking jinja2
>   Downloading Jinja2-2.7.1.tar.gz (377kB): 377kB downloaded
>   Running setup.py egg_info for package jinja2
>
>     warning: no files found matching '*' under directory 'custom_fixers'
>     warning: no previously-included files matching '*' found under
> directory 'docs/_build'
>     warning: no previously-included files matching '*.pyc' found under
> directory 'jinja2'
>     warning: no previously-included files matching '*.pyc' found under
> directory 'docs'
>     warning: no previously-included files matching '*.pyo' found under
> directory 'jinja2'
>     warning: no previously-included files matching '*.pyo' found under
> directory 'docs'
> Downloading/unpacking markupsafe (from jinja2)
>   Downloading MarkupSafe-0.18.tar.gz
>   Running setup.py egg_info for package markupsafe
>
> Installing collected packages: jinja2, markupsafe
>   Running setup.py install for jinja2
>
>     warning: no files found matching '*' under directory 'custom_fixers'
>     warning: no previously-included files matching '*' found under
> directory 'docs/_build'
>     warning: no previously-included files matching '*.pyc' found under
> directory 'jinja2'
>     warning: no previously-included files matching '*.pyc' found under
> directory 'docs'
>     warning: no previously-included files matching '*.pyo' found under
> directory 'jinja2'
>     warning: no previously-included files matching '*.pyo' found under
> directory 'docs'
>   Running setup.py install for markupsafe
>
>     building 'markupsafe._speedups' extension
>     gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
> -Wstrict-prototypes -fPIC -I/u/mkrumhol/yt-x86_64/include/python2.7 -c
> markupsafe/_speedups.c -o build/temp.linux-x86_64-2.7/markupsafe/_speedups.o
>     gcc -pthread -shared -L/u/mkrumhol/yt-x86_64/lib/
> -L/u/mkrumhol/yt-x86_64/lib64/ -L/u/mkrumhol/yt-x86_64/lib/
> -L/u/mkrumhol/yt-x86_64/lib64/ -L/u/mkrumhol/yt-x86_64/lib/
> -L/u/mkrumhol/yt-x86_64/lib64/ -L/u/mkrumhol/yt-x86_64/lib/
> -L/u/mkrumhol/yt-x86_64/lib64/
> build/temp.linux-x86_64-2.7/markupsafe/_speedups.o -o
> build/lib.linux-x86_64-2.7/markupsafe/_speedups.so
> Successfully installed jinja2 markupsafe
> Cleaning up...
>
>
> So far so good. Then I can then start the ipython notebook and get further
> than I did before, but I again get a crash:
>
> (yt-x86_64)pfe20:hmc3_mhd_lowden mkrumhol$ ipython notebook --no-browser
> --port=51707
> 2013-09-18 14:47:12.782 [NotebookApp] Using existing profile dir:
> u'/home3/mkrumhol/.ipython/profile_default'
> 2013-09-18 14:47:12.956 [NotebookApp] Using MathJax from CDN:
> http://cdn.mathjax.org/mathjax/latest/MathJax.js
> 2013-09-18 14:47:12.998 [NotebookApp] The port 51707 is already in use,
> trying another random port.
> 2013-09-18 14:47:12.998 [NotebookApp] The port 51708 is already in use,
> trying another random port.
> 2013-09-18 14:47:12.998 [NotebookApp] Serving notebooks from local
> directory: /nobackupp8/mkrumhol/hmc3_mhd_lowden
> 2013-09-18 14:47:12.998 [NotebookApp] The IPython Notebook is running at:
> http://127.0.0.1:51709/
> 2013-09-18 14:47:12.999 [NotebookApp] Use Control-C to stop this server
> and shut down all kernels (twice to skip confirmation).
> [NotebookApp] Kernel started: 5434ad94-81be-46ad-80e1-fa9a820411f8
> [NotebookApp] Connecting to: tcp://127.0.0.1:37756
> [NotebookApp] Connecting to: tcp://127.0.0.1:57662
> [NotebookApp] Connecting to: tcp://127.0.0.1:38185
> Traceback (most recent call last):
>   File "<string>", line 1, in <module>
>   File
> "/u/mkrumhol/yt-x86_64/lib/python2.7/site-packages/IPython/zmq/ipkernel.py",
> line 55, in <module>
>     from serialize import serialize_object, unpack_apply_message
>   File
> "/u/mkrumhol/yt-x86_64/lib/python2.7/site-packages/IPython/zmq/serialize.py",
> line 35, in <module>
>     from IPython.utils.pickleutil import can, uncan, canSequence,
> uncanSequence
> ImportError: cannot import name canSequence
>
> --
> Mark Krumholz
>
>
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20130918/32659fbe/attachment.html>