Now that the bulk of the development is moving over to the yt-3.0 branch, I
propose we have the yt-3.0 docs available on the website. Right now, a
yt-3.0 branch exists in the yt-doc repository, but there are very minor
changes in it relative to the yt 2.x documentation. Unfortunately, there
is no public way to view these documentations aside from downloading the
repository and building locally. I think by putting the 3.0 docs on the
webpage, it will make it more likely that people contribute docs when they
contribute new code changes, whereas if we wait too long, the codebase may
get considerably out of sync with the docs.
I think this will only require a slight change to the buildbot targets by
Kacper. What do people think?
University of Arizona
New issue 751: PhasePlot is broken in 3.0
I cannot create PhasePlots in 3.0. The same command works fine in the current stable release.
Here is the traceback I'm seeing:
TypeError Traceback (most recent call last)
<ipython-input-7-db8ac28b5d75> in <module>()
----> 1 plot = PhasePlot(dd, "CellMassMsun", "Radius", "Height")
/home/goldbaum/yt-hg/yt/visualization/profile_plotter.pyc in __init__(self, data_source, x_field, y_field, z_fields, weight_field, x_bins, y_bins, accumulation, fractional, profile, fontsize, font_color, figure_size)
543 weight_field = weight_field,
--> 545 fractional=fractional)
546 self.profile = profile
547 ImagePlotContainer.__init__(self, data_source, profile.field_data.keys(),
/home/goldbaum/yt-hg/yt/data_objects/profiles.pyc in create_profile(data_source, bin_fields, n, weight_field, fields, accumulation, fractional)
998 setattr(obj, "fractional", fractional)
999 if fields is not None:
-> 1000 obj.add_fields(fields)
1001 for field in fields:
1002 if fractional:
/home/goldbaum/yt-hg/yt/data_objects/profiles.pyc in add_fields(self, fields)
758 fields = ensure_list(fields)
759 temp_storage = ProfileFieldAccumulator(len(fields), self.size)
--> 760 for g in parallel_objects(self.data_source._grids):
761 self._bin_grid(g, fields, temp_storage)
762 self._finalize_storage(fields, temp_storage)
/home/goldbaum/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.pyc in parallel_objects(objects, njobs, storage, barrier, dynamic)
431 # If our objects object is slice-aware, like time series data objects are,
432 # this will prevent intermediate objects from being created.
--> 433 oiter = itertools.islice(enumerate(objects), my_new_id, None, njobs)
434 for obj_id, obj in oiter:
435 result_id = obj_id * njobs + my_new_id
TypeError: 'NoneType' object is not iterable
Looking at the traceback, the issue seems to be that the profile code expects there to be a `_grids` attribute attached to data sources.
New issue 748: ColorTransferFunction.sample_colormap has erroneous docstring
As reported on [yt-users ml](http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-December/004535.html) by Mateusz Ruszkowski, current docstring for `ColorTransferFunction.sample_colormap`:
>>> tf = ColorTransferFunction( (-10.0, -5.0) )
>>> tf.sample_colormap(-7.0, 0.01, 'algae')
Traceback (most recent call last):
File "layer_test.py", line 9, in <module>
tf.sample_colormap(-27.0, 0.01, 'algae')
File "yt/visualization/volume_rendering/transfer_functions.py", line 632, in sample_colormap
self.add_gaussian(v, w, [r, g, b, alpha])
File "yt/visualization/volume_rendering/transfer_functions.py", line 404, in add_gaussian
tf.add_gaussian(location, width, v)
File "yt/visualization/volume_rendering/transfer_functions.py", line 81, in add_gaussian
vals = height * np.exp(-(self.x - location)**2.0/width)
TypeError: only integer arrays with one element can be converted to an index
New issue 747: Reason Gui 2D Slice / Plot after update
I recently update YT but now when I run Reason I cannot view slices or plots
> on any datasets.
> I get the following error message:
> Traceback (most recent call last):
> File "/home/ctay6066/yt-x86_64/src/yt-hg/yt/gui/reason/basic_repl.py",
> line 81, in execute
> exec code in self.locals
> File "", line 1, in
> File "/home/ctay6066/yt-x86_64/src/yt-hg/yt/gui/reason/widget_store.py",
> line 70, in create_slice
> setup = False, plot_type='SlicePlot')
> TypeError: __init__() got an unexpected keyword argument 'plot_type'
> Here is some additional info that may be helpful:
> The current version of the code is:
> This installation CAN be automatically updated.
> yt dependencies were last updated on
> Mon Dec 9 21:59:01 EST 2013
>my pastebin link
> Please let me know if you need additional information.
New issue 746: Radius units incorrect in Rockstar frontend
The radius units are supposed to be defined as kpc/h comoving, but printing them out after loading indicates that yt thinks the native units are cm. In fact, I have found that changing the value of r_unit does not actually seem to change the resulting unit system.
New issue 745: Can't pl.plot(YTArray, YTArray)
from yt.mods import *
import matplotlib.pyplot as plt
a = YTArray([1.0,2.0])
Traceback (most recent call last): File "test_plot.py", line 6, in <module>
File "/u/ki/skillman/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 2987, in plot
ret = ax.plot(*args, **kwargs)
File "/u/ki/skillman/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/axes.py", line 4137, in plot
for line in self._get_lines(*args, **kwargs):
File "/u/ki/skillman/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/axes.py", line 317, in _grab_next_args
for seg in self._plot_args(remaining, kwargs):
File "/u/ki/skillman/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/axes.py", line 276, in _plot_args
linestyle, marker, color = _process_plot_format(tup[-1])
File "/u/ki/skillman/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/axes.py", line 80, in _process_plot_format
color = mcolors.colorConverter.to_rgb(fmt)
File "/u/ki/skillman/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/colors.py", line 291, in to_rgb
argl = arg.lower()
AttributeError: 'YTArray' object has no attribute 'lower'
Using .to_ndarray() on a in the plotting call works as expected. pl.plot(a) also works, so I think this must be something about mpl interpreting the second ytarray as a different arg/kwarg.
New issue 744: Standardize geometry selection
Currently, there is some ambiguity in how the lengths are passed in in the selection routines. For the most part, everything is (currently) done correctly in "code_length" units, but this needs to be made explicit.
"code_length" itself is no longer mandated to be a part of the lookup registry. This was to prevent errors. I think that we may eventually want to mandate everything in "unitary", but for now I will attempt to implement in "code_length" in the Cython code.
To complete this, essentially every place in `yt/geometry/selection_routines.pyx` that a geometric ndarray is accessed will need to be converted to "code_length". I am inclined to think that we can use in-place conversions here, to avoid making duplicates of the arrays (which may be large).
I trying to add the metallicity field back to the enzo frontend and am
wondering what field registry it would be appropriate to put it in. Anyone
have any thoughts on this?
Additionally, I noticed that the particle field metallicity_fraction
currently has units of Zsun. As far as I know, this is not correct. I
believe the field is actually unitless and would have to be divided by
~0.02 to be in units of Zsun. How can I set this up correctly to make it
aware of these units?
Should I make a "code_metallicity" unit? This might actually be usable for
the gas metallicity field as well.