[yt-users] data_source SlicePlot Error

Nathan Goldbaum nathan12343 at gmail.com
Fri Mar 27 22:56:26 PDT 2015 

On Fri, Mar 27, 2015 at 10:41 PM, Andrew James Emerick <aje2123 at columbia.edu
> wrote:

> I feel like I may have just tied myself into a package installation knot...
>
> I decided to try and preempt future headaches by just installing via conda
> ($conda install yt). This ran fine, and I can now run "yt update" without
> getting the error message. So now, for the commands you asked for:
>
> which yt   ->         /home/emerick/anaconda/bin/yt
> which python >     /home/emerick/anaconda/bin/python
> import yt; yt.__file__ -> /home/emerick/code/yt/yt/__init__.pyc
>
> Now, that is somewhat baffling. The final path is the path to the original
> yt installation (installed from source, managed by mercurial) I was using.
> The weird part is that that path is not located in any environment
> variables that I could think of (e.g. $PATH, $PYTHONPATH, $LD_LIBRARY_PATH,
> etc.).
>
> I figured there was a chance it would work now, even given the above, but
> when running the same code as before I get a new error (though I guess
> maybe I shouldn't be surprised): http://paste.yt-project.org/show/5494/
>

This is actually due to a very recent change by Cameron Hummels, who
totally revamped the plot callbacks recently. The annoate_line callback
should take two coordinates and draw a straight line between them.  Take a
look at the dev docs:

http://yt-project.org/docs/dev/visualizing/callbacks.html#overplot-a-straight-line

And the docstring for the callback:

http://yt-project.org/docs/dev/reference/api/generated/yt.visualization.plot_modifications.LinePlotCallback.html#yt.visualization.plot_modifications.LinePlotCallback


>
>
>
> Andrew E.
>
>
> On Sat, Mar 28, 2015 at 12:40 AM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Fri, Mar 27, 2015 at 9:28 PM, Andrew James Emerick <
>> aje2123 at columbia.edu> wrote:
>>
>>> Nathan,
>>>
>>> I can do "import h5py" without issue in a python script, and checked the
>>> "from h5py import _errors" statement that seems to cause the breakage.
>>> Updating via conda didn't fix the issue. I have hdf5 and h5py installed via
>>> conda.
>>>
>>> Doing some more checking it looks like (for whatever reason) when
>>> running "yt update" it is looking for a version of the hdf5 library that I
>>> don't have anywhere. When I did the soft linking of the libhdf5.so that I
>>> do have to the libhdf5.so.6 that it is looking for, it yelled at me saying
>>> it is trying to use the HDF5 version 1.8.4 headers, but can't find the
>>> corresponding libraries. (the most up to date version I have installed is
>>> 1.8.14).
>>>
>>> I guess a workaround would be to get the HDF5 1.8.4 library somewhere,
>>> but I'm still bothered by this...
>>>
>>
>> I'm not sure what's going wrong here.  You shouldn't need to create a
>> softlink and you shouldn't need to install an old version of the hdf5
>> library. It sort of looks like you have the remnants of an old python
>> installation conflicting with your current anaconda installation.
>> Unfortunately it's really hard to debug this sort of thing remotely...
>>
>> Can you paste the output of:
>>
>> $ which yt
>> $ which python
>> $ python -c 'import yt; yt.__file__'
>>
>> I'm looking for yt being installed in a strange place outside of your
>> normal python installation.
>>
>> You could try the yt conda package, installable via "consta install yt",
>> which is newer than the old pre-yt 3.1 development version you had
>> installed.
>>
>> You could also try installing yt from a fresh clone of the yt mercurial
>> repository.  See the instructions here:
>>
>>
>> http://yt-project.org/docs/dev/installing.html#installing-yt-using-pip-or-from-source
>>
>> Finally, you could build a fresh conda package based on the yt mercurial
>> repostiory.  That will require a small modification to the conda recipe to
>> point it at the mercurial repository instead of the release tarball on pypi.
>>
>> Hope you're able to sort this out.
>>
>> -Nathan
>>
>> PS Python packaging is literally the worst.
>>
>>
>>> Thanks again.
>>>
>>>
>>>
>>> Andrew E.
>>>
>>>
>>> On Fri, Mar 27, 2015 at 5:18 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>> On Fri, Mar 27, 2015 at 2:15 PM, Andrew James Emerick <
>>>> aje2123 at columbia.edu> wrote:
>>>>
>>>>> Nathan,
>>>>>
>>>>> Thanks for the response. I have been delinquent in updating yt.
>>>>>
>>>>> Running "yt update", however gives me this error:
>>>>> http://paste.yt-project.org/show/5492/
>>>>>
>>>>> Looks like an issue with finding the libhdf5.so.6 library that I
>>>>> couldn't figure out on my own. I had installed yt from source as to not
>>>>> disturb the python, numpy, hdf5, etc. installations I already had (managed
>>>>> by anaconda). I have libhdf5.so.9 in my LD_LIBRARY_PATH (I already
>>>>> tried soft linking .so.9 as .so.6 .. understandably it threw an error).
>>>>>
>>>>>
>>>> The error is happening when python tries to import h5py.  Can you
>>>> import h5py in a script that doesn't use yt?  How did you install h5py?
>>>>
>>>> $ conda update -f h5py
>>>>
>>>> might fix this.
>>>>
>>>>
>>>>> Have you run across this before?
>>>>>
>>>>>
>>>>>
>>>>> Andrew E.
>>>>>
>>>>> On Fri, Mar 27, 2015 at 1:04 PM, Nathan Goldbaum <
>>>>> nathan12343 at gmail.com> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Mar 27, 2015 at 10:00 AM, Andrew James Emerick <
>>>>>> aje2123 at columbia.edu> wrote:
>>>>>>
>>>>>>> Hello everyone,
>>>>>>>
>>>>>>> I just ran into an error in using "data_source" kwarg with the
>>>>>>> SlicePlot function (error message copied below):
>>>>>>>
>>>>>>> slice = yt.SlicePlot(ds, axis, field, data_source=region)
>>>>>>> File
>>>>>>> "/home/emerick/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/visualization/plot_window.py",
>>>>>>> line 1816, in SlicePlot
>>>>>>>     return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs)
>>>>>>> TypeError: __init__() got an unexpected keyword argument
>>>>>>> 'data_source'
>>>>>>>
>>>>>>> I have no problem doing the above with ProjectionPlot. If anyone
>>>>>>> knows what could be causing this I'd appreciate the help. Otherwise I can
>>>>>>> do some digging into the code myself.
>>>>>>>
>>>>>>>
>>>>>> Hi Andrew,
>>>>>>
>>>>>> This should work, but might not if you haven't updated yt in a
>>>>>> while.  Can you update to the latest development version and try again?
>>>>>>
>>>>>> -Nathan
>>>>>>
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Andrew E.
>>>>>>> --
>>>>>>> Graduate Student
>>>>>>> Columbia University
>>>>>>> Department of Astronomy
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> yt-users mailing list
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>>>>>>>
>>>>>>>
>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Graduate Student
>>>>> Columbia University
>>>>> Department of Astronomy
>>>>>
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>>>>>
>>>>>
>>>>
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>>> --
>>> Graduate Student
>>> Columbia University
>>> Department of Astronomy
>>>
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>
>
> --
> Graduate Student
> Columbia University
> Department of Astronomy
>
> _______________________________________________
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