Mailman 3 December 2013 - yt-dev

3.0 Documentation
by Cameron Hummels 13 Dec '13

13 Dec '13

Hello everyone, 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? Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

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Issue #751: PhasePlot is broken in 3.0 (yt_analysis/yt)
by Nathan Goldbaum 13 Dec '13

13 Dec '13

New issue 751: PhasePlot is broken in 3.0 https://bitbucket.org/yt_analysis/yt/issue/751/phaseplot-is-broken-in-30 Nathan Goldbaum: I cannot create PhasePlots in 3.0. The same command works fine in the current stable release. Here is the traceback I'm seeing: ``` #!python traceback 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, 544 accumulation=accumulation, --> 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.

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Issue #749: Cannot SlicePlot in yt-3.0 using UnitRefactor on Enzo 2D dataset (yt_analysis/yt)
by Cameron Hummels 13 Dec '13

13 Dec '13

New issue 749: Cannot SlicePlot in yt-3.0 using UnitRefactor on Enzo 2D dataset https://bitbucket.org/yt_analysis/yt/issue/749/cannot-sliceplot-in-yt-30-us… Cameron Hummels: I get a failure when I try to do a SlicePlot on either "density" or "Density" using the new UnitRefactor code in yt 3.0. I'm using a packed HDF5 dataset of a 64^2 KH test output from enzo. The small dataset is available here: http://www.astro.columbia.edu/~chummels/DD0010.tar The script for running it is here: http://paste.yt-project.org/show/4146/ The traceback is here: http://paste.yt-project.org/show/yoWiFunffH8WflwcU7Jz Essentially, it looks like it is bailing in the source here: if any((ftype != "gas" for ftype, fname in fields)): raise NotImplementedError Responsible: MatthewTurk

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Issue #750: Test failure for Profile1D (yt_analysis/yt)
by Kacper Kowalik 13 Dec '13

13 Dec '13

New issue 750: Test failure for Profile1D https://bitbucket.org/yt_analysis/yt/issue/750/test-failure-for-profile1d Kacper Kowalik: Reduced test case: ``` #!python from yt.testing import fake_random_pf from yt.data_objects.profiles import Profile1D pf = fake_random_pf(64, nprocs=8, fields=("Density", "Temperature")) nv = pf.domain_dimensions.prod() dd = pf.h.all_data() (rmi, rma), (tmi, tma) = dd.quantities["Extrema"](["Density", "Temperature"]) p1d = Profile1D(dd, "Density", 8, rmi * 0.9, rma * 1.1, False, weight_field=None) p1d.add_fields(["Ones", "Temperature"]) ``` yields: ``` #!bash Traceback (most recent call last): File "issue.py", line 9, in <module> p1d.add_fields(["Ones", "Temperature"]) File "yt/data_objects/profiles.py", line 760, in add_fields for g in parallel_objects(self.data_source._grids): File "yt/utilities/parallel_tools/parallel_analysis_interface.py", line 433, in parallel_objects oiter = itertools.islice(enumerate(objects), my_new_id, None, njobs) TypeError: 'NoneType' object is not iterable ```

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Issue #748: ColorTransferFunction.sample_colormap has erroneous docstring (yt_analysis/yt)
by Kacper Kowalik 11 Dec '13

11 Dec '13

New issue 748: ColorTransferFunction.sample_colormap has erroneous docstring https://bitbucket.org/yt_analysis/yt/issue/748/colortransferfunctionsample_… Kacper Kowalik: 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`: ```` #!python >>> tf = ColorTransferFunction( (-10.0, -5.0) ) >>> tf.sample_colormap(-7.0, 0.01, 'algae') ```` yields: ```` #!bash 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 ```` Responsible: xarthisius

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Issue #747: Reason Gui 2D Slice / Plot after update (yt_analysis/yt)
by Anonymous 11 Dec '13

11 Dec '13

New issue 747: Reason Gui 2D Slice / Plot after update https://bitbucket.org/yt_analysis/yt/issue/747/reason-gui-2d-slice-plot-aft… Anonymous: 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: > > --- > be524f912750 > --- > > This installation CAN be automatically updated. > yt dependencies were last updated on > Mon Dec 9 21:59:01 EST 2013 > >my pastebin link > http://paste.yt-project.org/show/35x3VUOpItAuLpZgtcBl > > > Please let me know if you need additional information. > Responsible: MatthewTurk

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Issue #746: Radius units incorrect in Rockstar frontend (yt_analysis/yt)
by Britton Smith 10 Dec '13

10 Dec '13

New issue 746: Radius units incorrect in Rockstar frontend https://bitbucket.org/yt_analysis/yt/issue/746/radius-units-incorrect-in-ro… Britton Smith: 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.

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Issue #745: Can't pl.plot(YTArray, YTArray) (yt_analysis/yt)
by Sam Skillman 09 Dec '13

09 Dec '13

New issue 745: Can't pl.plot(YTArray, YTArray) https://bitbucket.org/yt_analysis/yt/issue/745/cant-plplot-ytarray-ytarray Sam Skillman: ``` #!python from yt.mods import * import matplotlib.pyplot as plt a = YTArray([1.0,2.0]) plt.plot(a, a) ``` produces: ``` #!python (yt-x86_64)360Mpc/1024L0:python test_plot.py Traceback (most recent call last): File "test_plot.py", line 6, in <module> plt.plot(a, a) 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. Responsible: ngoldbaum

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Issue #744: Standardize geometry selection (yt_analysis/yt)
by Matthew Turk 06 Dec '13

06 Dec '13

New issue 744: Standardize geometry selection https://bitbucket.org/yt_analysis/yt/issue/744/standardize-geometry-selecti… Matthew Turk: 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). Responsible: MatthewTurk

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unitrefactor: enzo metal fields
by Britton Smith 06 Dec '13

06 Dec '13

Hi all, 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.

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yt-dev December 2013