[yt-users] phase plot and time series

[Nathan Goldbaum]

I think I see what broke: you shouldn't be doing "yt update --all", since
you didn't install using the install script.

Instead, you should do the following:

$ conda uninstall yt
$ cd nobackupnfs2/mruszkow/yt/
$ hg pull https://bitbucket.org/yt_analysis/yt
$ hg update yt
$ python setup.py develop

This assumes that nobackupnfs2/mruszkow/yt/ is a clone of the yt mercurial
repository and you have all of yt's hard dependencies installed (numpy,
matplotlib, and cython).

On Sun, Feb 28, 2016 at 6:04 PM, Mateusz Ruszkowski <mateuszr at umich.edu>
wrote:

>
>
>
>    Hi Britton et al.,
>
> Thanks very much. This is very useful!
>
> I have a somewhat unrelated technical question. I just attempted to
> upgrade yt to the latest dev version and yt stopped working for me (i.e.,
> yt script derails in the first couple of lines). Details are below.
> Presumably the problem stems from the fact that the upgrade did not fully
> complete. Could I get some help with this?
>
>    Thanks,
>      Mateusz
>
>
> % yt update --all
>
> yt module located at:
>     /nobackupnfs2/mruszkow/yt
>
> The current version and changeset for the code is:
>
> ---
> Version = 3.3-dev
> Changeset = 96e7ac3e7175 (yt) tip development
> ---
>
> This installation CAN be automatically updated.
> Updating the repository
> Updated successfully.
> Could not determine when yt stack was last updated.
>
> We will now attempt to update the yt stack located at:
> Traceback (most recent call last):
>   File "/nobackupnfs2/mruszkow/miniconda3/bin/yt", line 9, in <module>
>     load_entry_point('yt==3.3.dev0', 'console_scripts', 'yt')()
>   File "/nobackupnfs2/mruszkow/yt/yt/utilities/command_line.py", line
> 1095, in run_main
>     print()
>   File "/nobackupnfs2/mruszkow/yt/yt/utilities/command_line.py", line 89,
> in run
>     class YTCommand(object):
>   File "/nobackupnfs2/mruszkow/yt/yt/utilities/command_line.py", line
> 1033, in __call__
>     os.environ["YT_DEST"], "src", "yt-supplemental")
>   File "/nobackupnfs2/mruszkow/yt/yt/utilities/command_line.py", line 321,
> in _update_yt_stack
>     def _get_yt_stack_date():
>   File "/nobackupnfs2/mruszkow/miniconda3/lib/python3.4/os.py", line 633,
> in __getitem__
>     raise KeyError(key) from None
> KeyError: 'YT_DEST'
>
>
> % python profiles.py
> Traceback (most recent call last):
>   File "profiles.py", line 2, in <module>
>     import yt
>   File "/nobackupnfs2/mruszkow/yt/yt/__init__.py", line 123, in <module>
>     from yt.data_objects.api import \
>   File "/nobackupnfs2/mruszkow/yt/yt/data_objects/api.py", line 16, in
> <module>
>     from .grid_patch import \
>   File "/nobackupnfs2/mruszkow/yt/yt/data_objects/grid_patch.py", line 19,
> in <module>
>     from yt.data_objects.data_containers import \
>   File "/nobackupnfs2/mruszkow/yt/yt/data_objects/data_containers.py",
> line 51, in <module>
>     from yt.utilities.parallel_tools.parallel_analysis_interface import \
>   File
> "/nobackupnfs2/mruszkow/yt/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> line 32, in <module>
>     from yt.utilities.lib.quad_tree import \
> ImportError: No module named 'yt.utilities.lib.quad_tree'
>
>
>
> > On Feb 28, 2016, at 12:19 PM, Britton Smith <brittonsmith at gmail.com>
> wrote:
> >
> > Hi Mateusz,
> >
> > Below is a reasonably simple way that someone might do something like
> this.  This makes use of some newer functionality that currently only
> exists in the development branch, so you would have to update to that to
> use it.  This results in the following plot:
> > http://i.imgur.com/Qlgg6sV.png
> >
> > To do this, I first made some profiles over a time-series of datasets
> with the following script:
> > http://paste.yt-project.org/show/6278/
> >
> > The last line is the new functionality, which saves all of the compiled
> profile data in a way that it can be reloaded as a yt dataset.  You can see
> more information about that here:
> > http://yt-project.org/docs/dev/analyzing/saving_data.html
> >
> > Now, yt is awfully close to being able to plot this itself, but not
> quite there yet, so I plotted this using matplotlib.  The plotting script
> is here:
> > http://paste.yt-project.org/show/6279/
> >
> > At the top of that script, you can see how I get access to the data that
> was saved by the first script.  All that needs to be done is to call
> yt.load with the file that was created and the data fields are all
> accessible with full unit support through ds.data.  So, for example,
> ds.data["density"].
> >
> > I hope this is helpful.
> >
> > Britton
> >
> > On Sat, Feb 27, 2016 at 2:44 AM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
> > While I think this is a really cool idea, I don't think this is possible
> within yt right now. Britton Smith might know a trick to do this though...
> >
> > On Fri, Feb 26, 2016 at 3:59 PM, Mateusz Ruszkowski <mateuszr at umich.edu>
> wrote:
> >
> >    Hi,
> >
> > Is there a simple way in yt to generate a "phase plot" of the gas
> density, with time and radius on the axes, using a time series of data
> files?
> >
> >    Thanks,
> >       Mateusz
> >
> >
> >
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
> _______________________________________________
> 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/20160228/ca05a5b9/attachment.html>