Mailman 3 January 2015 - yt-dev

Fun with the bitbucket REST API
by Nathan Goldbaum 05 Jan '15

05 Jan '15

Hi all, I'm in the middle of putting together a changelog for the upcoming 3.1 release. Just in case anyone needs to do this in the future, I've put together a quick script that interacts with the bitbucket REST API to generate a summary of all merged pull requests since the release of yt 3.0 on August 4th. The script is here: https://bpaste.net/show/f86b1b4c0326 My plan now is to use the output of this script to manually create a changelog for the docs and release announcement. Hope that's helpful, -Nathan

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Issue #969: Metallicity values reported by LightRay in 3.0 significantly differ from metallicity values in 2.x (yt_analysis/yt)
by Cameron Hummels 05 Jan '15

05 Jan '15

New issue 969: Metallicity values reported by LightRay in 3.0 significantly differ from metallicity values in 2.x https://bitbucket.org/yt_analysis/yt/issue/969/metallicity-values-reported-… Cameron Hummels: I've run into an insidious bug in the LightRay analysis module, wherein metallicity values reported along the light ray in yt 3.0 differ by an OOM with metallicity values reported along the light ray in 2.x. Strangely enough, temperature values between the two versions don't change at all, and density values only change at the <1e-4 level. I have investigated this to some degree and it appears that the bug is confined to the LightRay analysis module, as I'm seeing the same metallicity values for raw ``Ray`` and other data objects between the two versions of yt. The following scripts demonstrate this problem with the enzo_cosmology_plus dataset. Because of the way in which the LightRay object operates, you'll need to run these scripts *inside* the enzo_cosmology_plus directory. For yt-2.x, run this script in the enzo_cosmology_plus directory: http://paste.yt-project.org/show/5323/ With the resulting output: ``` #!python Density: [ 9.97279296e-32 9.20237619e-31] Temperature: [ 1706.254685 75236.83753987] Metallicity: [ 4.96203366e-09 4.62205944e-09] ``` For yt-3.0, run this script in the enzo_cosmology_plus directory: http://paste.yt-project.org/show/5324/ With the resulting output: ``` #!python Density: [ 9.97278399e-32 9.20236791e-31] Temperature: [ 1706.254685 75236.83753987] Metallicity: [ 1.01225503e-10 9.42900276e-11] ```

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3.1 release?
by Cameron Hummels 05 Jan '15

05 Jan '15

Hey everyone, I've seen a lot of PRs get merged in the last few days. So I guess we're gearing up for a 3.1 release? What is the plan for its release? I advocate for having a wait time where no PRs get merged for a while before we release to sort out bugs. I'm personally somewhat hesitant about using yt tip right now for production level analysis after all of those merges, many of which didn't appear to have much review. It was my understanding that we were going to wait to let the dust settle on some things when everyone was back at their desks next week. Either way, I wanted to see what the status of things were with all of the recent activity, since I hadn't heard anything on the list. Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

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Issue #968: FITSImageBuffer notebook raises error in docs build (yt_analysis/yt)
by Nathan Goldbaum 04 Jan '15

04 Jan '15

New issue 968: FITSImageBuffer notebook raises error in docs build https://bitbucket.org/yt_analysis/yt/issue/968/fitsimagebuffer-notebook-rai… Nathan Goldbaum: Here is the error and traceback: ``` #!python --------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-9-ae59799c636e> in <module>() ----> 1 slc2 = yt.SlicePlot(ds2, "z", ["temperature"], width=(500.,"kpc")) 2 slc2.set_log("temperature", True) 3 slc2.show() /Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py in SlicePlot(ds, normal, fields, axis, *args, **kwargs) 1912 del kwargs['north_vector'] 1913 -> 1914 return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) /Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py in __init__(self, ds, axis, fields, center, width, axes_unit, origin, fontsize, field_parameters, window_size, aspect, data_source) 1053 slc = ds.slice(axis, center[axis], field_parameters=field_parameters, 1054 center=center, data_source=data_source) -> 1055 slc.get_data(fields) 1056 PWViewerMPL.__init__(self, slc, bounds, origin=origin, 1057 fontsize=fontsize, fields=fields, /Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py in get_data(self, fields) 620 def get_data(self, fields=None): 621 if self._current_chunk is None: --> 622 self.index._identify_base_chunk(self) 623 if fields is None: return 624 nfields = [] /Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py in index(self) 136 if self._index is not None: 137 return self._index --> 138 self._index = self.ds.index 139 return self._index 140 /Users/goldbaum/Documents/yt-hg/yt/data_objects/static_output.pyc in index(self) 281 oldsettings = np.geterr() 282 np.seterr(all='ignore') --> 283 self.create_field_info() 284 np.seterr(**oldsettings) 285 return self._instantiated_index /Users/goldbaum/Documents/yt-hg/yt/data_objects/static_output.pyc in create_field_info(self) 325 self.filtered_particle_types = [] 326 self.field_info = self._field_info_class(self, self.field_list) --> 327 self.coordinates.setup_fields(self.field_info) 328 self.field_info.setup_fluid_fields() 329 for ptype in self.particle_types: /Users/goldbaum/Documents/yt-hg/yt/geometry/coordinates/spec_cube_coordinates.py in setup_fields(self, registry) 63 def setup_fields(self, registry): 64 if self.ds.no_cgs_equiv_length == False: ---> 65 return super(self, SpectralCubeCoordinateHandler 66 ).setup_fields(registry) 67 for axi, ax in enumerate(self.axis_name): TypeError: must be type, not SpectralCubeCoordinateHandler ``` Responsible: jzuhone

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