Mailman 3 April 2015 - yt-dev

Issue #1017: Streamlines crashes with python 3 (yt_analysis/yt)
by Jill Naiman 28 Apr '15

28 Apr '15

New issue 1017: Streamlines crashes with python 3 https://bitbucket.org/yt_analysis/yt/issue/1017/streamlines-crashes-with-py… Jill Naiman: I'm on version: Version = 3.2-dev Changeset = 39f9c8e0e97c+ yt And I built thinks with python 3. Code is here: http://paste.yt-project.org/show/5529/ Error is: ``` RuntimeError Traceback (most recent call last) /Users/jillnaiman1/astroblend-dev/exampleScripts/streamlines6.py in <module>() 23 pos = c+pos_dx 24 ---> 25 streamlines = Streamlines(ds,pos,'velocity_x', 'velocity_y', 'velocity_z', length=1.0) 26 27 /Users/jillnaiman1/yt-x86_64/lib/python3.4/site-packages/yt-3.2dev-py3.4-macosx-10.10-x86_64.egg/yt/visualization/streamlines.py in __init__(self, ds, positions, xfield, yfield, zfield, volume, dx, length, direction, get_magnitude) 118 if volume is None: 119 volume = AMRKDTree(self.ds) --> 120 volume.set_fields([self.xfield,self.yfield,self.zfield],[False,False,False], False) 121 volume.join_parallel_trees() 122 self.volume = volume /Users/jillnaiman1/yt-x86_64/lib/python3.4/site-packages/yt-3.2dev-py3.4-macosx-10.10-x86_64.egg/yt/utilities/amr_kdtree/amr_kdtree.py in set_fields(self, fields, log_fields, no_ghost) 168 self.brick_dimensions = [] 169 bricks = [] --> 170 for b in self.traverse(): 171 bricks.append(b) 172 self.bricks = np.array(bricks) /Users/jillnaiman1/yt-x86_64/lib/python3.4/site-packages/yt-3.2dev-py3.4-macosx-10.10-x86_64.egg/yt/utilities/amr_kdtree/amr_kdtree.py in traverse(self, viewpoint) 182 def traverse(self, viewpoint=None): 183 for node in kd_traverse(self.tree.trunk, viewpoint=viewpoint): --> 184 yield self.get_brick_data(node) 185 186 def slice_traverse(self, viewpoint = None): /Users/jillnaiman1/yt-x86_64/lib/python3.4/site-packages/yt-3.2dev-py3.4-macosx-10.10-x86_64.egg/yt/utilities/amr_kdtree/amr_kdtree.py in get_brick_data(self, node) 269 dds = [] 270 for i, field in enumerate(self.fields): --> 271 vcd = grid.get_vertex_centered_data(field, smoothed=True, no_ghost=self.no_ghost).astype('float64') 272 if self.log_fields[i]: vcd = np.log10(vcd) 273 dds.append(vcd) /Users/jillnaiman1/yt-x86_64/lib/python3.4/site-packages/yt-3.2dev-py3.4-macosx-10.10-x86_64.egg/yt/data_objects/grid_patch.py in get_vertex_centered_data(self, field, smoothed, no_ghost) 277 new_field, output_left) 278 else: --> 279 cg = self.retrieve_ghost_zones(1, field, smoothed=smoothed) 280 np.add(new_field, cg[field][1: ,1: ,1: ], new_field) 281 np.add(new_field, cg[field][:-1,1: ,1: ], new_field) /Users/jillnaiman1/yt-x86_64/lib/python3.4/site-packages/yt-3.2dev-py3.4-macosx-10.10-x86_64.egg/yt/data_objects/grid_patch.py in retrieve_ghost_zones(self, n_zones, fields, all_levels, smoothed) 254 level, new_left_edge, 255 field_parameters = field_parameters, --> 256 **kwargs) 257 else: 258 cube = self.ds.covering_grid(level, new_left_edge, /Users/jillnaiman1/yt-x86_64/lib/python3.4/site-packages/yt-3.2dev-py3.4-macosx-10.10-x86_64.egg/yt/data_objects/construction_data_containers.py in __init__(self, *args, **kwargs) 811 self.ds.domain_dimensions.astype("float64")) 812 self.global_endindex = None --> 813 YTCoveringGridBase.__init__(self, *args, **kwargs) 814 self._final_start_index = self.global_startindex 815 /Users/jillnaiman1/yt-x86_64/lib/python3.4/site-packages/yt-3.2dev-py3.4-macosx-10.10-x86_64.egg/yt/data_objects/construction_data_containers.py in __init__(self, level, left_edge, dims, fields, ds, num_ghost_zones, use_pbar, field_parameters) 487 self.ds.domain_left_edge)/self.dds).astype('int64') 488 self._setup_data_source() --> 489 self.get_data(fields) 490 491 @property /Users/jillnaiman1/yt-x86_64/lib/python3.4/site-packages/yt-3.2dev-py3.4-macosx-10.10-x86_64.egg/yt/data_objects/construction_data_containers.py in get_data(self, fields) 570 fill, gen, part, alias = self._split_fields(fields_to_get) 571 if len(part) > 0: self._fill_particles(part) --> 572 if len(fill) > 0: self._fill_fields(fill) 573 for a, f in sorted(alias.items()): 574 self[a] = f(self) /Users/jillnaiman1/yt-x86_64/lib/python3.4/site-packages/yt-3.2dev-py3.4-macosx-10.10-x86_64.egg/yt/data_objects/construction_data_containers.py in _fill_fields(self, fields) 849 chunk.ires, domain_dims, self.ds.refine_by) 850 if level == 0 and tot != 0: --> 851 raise RuntimeError 852 self._update_level_state(ls) 853 for name, v in zip(fields, ls.fields): RuntimeError: ``` _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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Issue #1016: Particle callback doesn't handle quantities correctly (yt_analysis/yt)
by Nathan Goldbaum 28 Apr '15

28 Apr '15

New issue 1016: Particle callback doesn't handle quantities correctly https://bitbucket.org/yt_analysis/yt/issue/1016/particle-callback-doesnt-ha… Nathan Goldbaum: The following test script: ``` #!python import yt from yt.units import Mpc ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') p = yt.SlicePlot(ds, 2, 'density') p.annotate_particles(0.3*Mpc) p.save() ``` errors out with the following traceback: ``` #!python Traceback (most recent call last): File "test.py", line 7, in <module> p.save() File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_container.py", line 74, in newfunc args[0].run_callbacks() File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 1003, in run_callbacks sys.exc_info()[2]) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 999, in run_callbacks callback(cbw) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_modifications.py", line 1440, in __call__ reg = self._get_region((x0,x1), (y0,y1), plot.data.axis, data) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_modifications.py", line 1472, in _get_region LE[zax] = data.center[zax].ndarray_view() - self.width*0.5 File "/Users/goldbaum/Documents/yt-hg/yt/units/yt_array.py", line 750, in __rsub__ lo = sanitize_units_add(self, left_object, "subtraction") File "/Users/goldbaum/Documents/yt-hg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) yt.utilities.exceptions.YTPlotCallbackError: annotate_particles callback failed with the following error: The subtraction operator for YTArrays with units (Mpc) and (1) is not well defined. ``` _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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Fwd: [astropy-dev] Astropy Community Code of Conduct
by Britton Smith 28 Apr '15

28 Apr '15

Hi everyone, I think this is something we should consider adopting as well in yt. Britton ---------- Forwarded message ---------- From: Thomas Robitaille <thomas.robitaille(a)gmail.com> Date: Tue, Apr 28, 2015 at 10:11 AM Subject: [astropy-dev] Astropy Community Code of Conduct To: astropy-dev <astropy-dev(a)googlegroups.com> Hi everyone, During the "Python in Astronomy" workshop in Leiden last week, a number of participants decided to get together to write a code of conduct for the Astropy project. We now have a final draft ready, and would like to solicit feedback on this version, which you can find here: https://docs.google.com/document/d/1yLObQMqP66x6MNuHXFpW_4dLPBtNp--9BHxfG8Y… Please let us know by the end of this week if you have any comments! You can make use of the commenting functionality in Google Docs, but please don't use the 'suggested edits' functionality since that will make it harder to read for others. We plan to extend this code of conduct beyond simply the Astropy community, to e.g. the new Python users in Astronomy Facebook group [1], and future Python in Astronomy meetings, but having it as the Astropy community code of conduct for now would be a good place to start. Thanks! Tom [1] https://www.facebook.com/groups/1596306890613995/ -- You received this message because you are subscribed to the Google Groups "astropy-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to astropy-dev+unsubscribe(a)googlegroups.com. For more options, visit https://groups.google.com/d/optout. _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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New code frontend
by Nicola Clementel 27 Apr '15

27 Apr '15

Dear yt developer, I would like to use yt to visualise the output from the SimpleX radiative transfer code. Due to the "Voroni-Delaunay" unstructured grid use in the code the output ‘cells’ are tetrahedra. >From a firs look into the code and in the documentation, I was not able to find if this kind of unstructured grid are already supported in yt or if something similar is under development. If one of the other code have something similar already implemented that I can use as guideline it would be incredibly helpful! Thanks, Nicola Clementel _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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PR hangout
by Matthew Turk 27 Apr '15

27 Apr '15

Hi all, I've set up a hangout tomorrow to go over the PRs. Feel free to come if you can, and don't worry if you can't! https://plus.google.com/events/ctlh4pjafe9cfhep1qurr191g6k -Matt _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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Issue #1015: Invalid read-in objects default to DataSeries (yt_analysis/yt)
by Adam Ginsburg 26 Apr '15

26 Apr '15

New issue 1015: Invalid read-in objects default to DataSeries https://bitbucket.org/yt_analysis/yt/issue/1015/invalid-read-in-objects-def… Adam Ginsburg: The `time_series.DataSeries` reader is meant to take filenames, afaict, but instead it accepts anything: ``` In [4]: yt.load([object, object]) Out[4]: <yt.data_objects.time_series.DatasetSeries at 0x10cd60810> ``` _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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Updated install script
by Nathan Goldbaum 24 Apr '15

24 Apr '15

Hi all, Kacper just updated the install script stack. It'd be great if people on diverse environments could give it a try and let us know on the pull request if they run into issues. https://bitbucket.org/yt_analysis/yt/pull-request/1562/update-yts-dependenc… -Nathan _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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Issue #1014: annotate velocity in on-cubic datasets (yt_analysis/yt)
by Anonymous 20 Apr '15

20 Apr '15

New issue 1014: annotate velocity in on-cubic datasets https://bitbucket.org/yt_analysis/yt/issue/1014/annotate-velocity-in-on-cub… Anonymous: It looks like the annotate_velocity method on SlicePlots selects a number of points uniformly distributed in the x and y coordinates but this does not work well for slices where one of the dimensions is much larger than the other. Is it possible to scale the number of displayed arrows with the size of each axis of the domain? _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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Issue #1013: Consider using __numpy_ufunc__ from numpy 1.10 for YTArray (yt_analysis/yt)
by Nathan Goldbaum 20 Apr '15

20 Apr '15

New issue 1013: Consider using __numpy_ufunc__ from numpy 1.10 for YTArray https://bitbucket.org/yt_analysis/yt/issue/1013/consider-using-__numpy_ufun… Nathan Goldbaum: This new hook in ndarray's subclassing machinery may help us avoid a significant amount of boilerplate in the definition of YTArray. In addition, it may also allow us to fix currently un-resolveable issues with subclassing ndarray, e.g. this example: ``` #! >>> import numpy as np >>> from yt.units import g >>> a = np.array([1,2,3]) >>> print a*g [ 1. 2. 3.] g a*g returns a YTArray, an ndarray subclass that knows about units. "plain" ndarrays are treated as unitless arrays. >>> print g 1.0 g >>> a *= g >>> print a array([1, 2, 3]) I don't seem to have a way to override this behavior, since this invokes __imul__ in the ndarray class rather than __rmul__ in my subclass >>> a = [1,2,3] >>> print a*g [ 1. 2. 3.] g >>> a *= g >>> a YTArray([ 1., 2., 3.]) g Things behave correctly when I use lists rather than ndarray. ``` Unfortunately this is blocked until numpy 1.10 is released. We will also need to be careful to not break compatibility with older versions of numpy, and be sure to not make the code paths followed in different numpy versions different. _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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Issue #1012: FixedResolutionBuffer with non-unit aspect ratios fails (yt_analysis/yt)
by Anonymous 20 Apr '15

20 Apr '15

New issue 1012: FixedResolutionBuffer with non-unit aspect ratios fails https://bitbucket.org/yt_analysis/yt/issue/1012/fixedresolutionbuffer-with-… Anonymous: Attempting to use to_frb with more than one dimension fails. Failures seem to be related to yt trying to parse iterable arguments as numbers with units. ``` #!python >>> proj = ds.proj("density","z") >>> Delta = (0.1,'code_length') >>> dx = (1./512,'code_length') >>> frb=proj.to_frb(Delta,dx) works great! >>> frb=proj.to_frb( [Delta, Delta],[dx,dx]) raceback (most recent call last): File "<stdin>", line 1, in <module> File "tmp.py", line 22, in <module> frb=proj.to_frb( [Delta, Delta],[dx,dx]) File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/data_containers.py", line 909, in to_frb width = self.ds.quan(w, input_units = u) File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/units/yt_array.py", line 1153, in __new__ raise RuntimeError("YTQuantity values must be numeric") RuntimeError: YTQuantity values must be numeric Also I tried using a ds.arr: >>> Delta = ds.arr([0.1,0.1],'code_length') >>> dx = ds.arr([1./512, 1./512], 'code_length') >>> frb=proj.to_frb( Delta, dx) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "tmp.py", line 26, in <module> frb=proj.to_frb( Delta, dx) File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/data_containers.py", line 909, in to_frb width = self.ds.quan(w, input_units = u) File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/units/yt_array.py", line 1155, in __new__ dtype=dtype) File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/units/yt_array.py", line 308, in __new__ input_array.units = Unit(input_units, registry=registry) File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/units/unit_object.py", line 169, in __new__ % (unit_expr, type(unit_expr))) yt.units.unit_object.UnitParseError: Unit representation must be a string or sympy Expr. 0.1 code_length has type <class 'yt.units.yt_array.YTQuantity'>. ``` _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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yt-dev April 2015