Mailman 3 December 2015 - yt-dev

REQ: Cool results
by Matthew Turk 31 Dec '15

31 Dec '15

Hi folks, Next week I'm giving a talk at AAS about yt. One thing I'd really like to do is showcase some of the cool results that folks have used yt to generate. The slides are due Wednesday, but I'm probably going to put the finishing touches on Monday or Tuesday. The time slot is quite short, but if you have some cool results you're proud of, or that you want to have shown during a talk like that, I'd be mighty obliged if you would consider emailing them to me at matthewturk(a)gmail.com, along with how you'd like them to be cited or credited. Thanks! -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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Analysis module review process
by Matthew Turk 31 Dec '15

31 Dec '15

Hi everyone, Before writing this up in the YTEP, I wanted to get a sense of people's feelings on lowering the barrier to entry for changes to analysis modules. Often these are maintained by a smaller number of people and don't touch much of the rest of the code, so changes can be hard to get pushed through. An alternate thing we could try out would be spinning these out into their own packages, which we could provide helpers or hooks to download and install. A big advantage to having them in the main repo is that then everything comes in the box. [+-][01] on reducing review overhead for analysis modules? _______________________________________________ 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 #1151: unity_registry.lut is not JSON serializable (yt_analysis/yt)
by Robert Thompson 29 Dec '15

29 Dec '15

New issue 1151: unity_registry.lut is not JSON serializable https://bitbucket.org/yt_analysis/yt/issues/1151/unity_registrylut-is-not-j… Robert Thompson: This issue comes up if one wants to save/load the unity registry. Right now I am using pickle.dumps() but this has an obvious issue with the string changes from py2 to py3 and they would not be compatible. Responsible: ngoldbaum _______________________________________________ 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 #1150: difficulty importing yt (yt_analysis/yt)
by dan mckeown 26 Dec '15

26 Dec '15

New issue 1150: difficulty importing yt https://bitbucket.org/yt_analysis/yt/issues/1150/difficulty-importing-yt dan mckeown: upon attempting to import yt using canopy I encounter the following error: AttributeError: 'module' object has no attribute 'utilities' I noticed the following lines in the terminal: File "__init__.pxd", line 155, in init yt.utilities.lib.misc_utilities (build/src.macosx-10.6-intel-2.7/yt/utilities/lib/misc_utilities.c:16424) I have a much later version of osx than 10.6, is this perhaps the reason? _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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unstructured mesh
by Matthew Turk 22 Dec '15

22 Dec '15

Woo! Congrats to Andrew Myers and Allyson Julian on getting the unstructed mesh work in! http://bitbucket.org/yt_analysis/yt/pull-request/1778 -Matt

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Issue #1149: RuntimeError when defining a derived gradient field (2D cartesian data) (yt_analysis/yt)
by Suoqing Ji 19 Dec '15

19 Dec '15

New issue 1149: RuntimeError when defining a derived gradient field (2D cartesian data) https://bitbucket.org/yt_analysis/yt/issues/1149/runtimeerror-when-defining… Suoqing Ji: Script: ``` #!python import yt from yt.fields.derived_field import ValidateSpatial import numpy as np @yt.derived_field(name='gradx_velocity_x', units='1/code_time', validators = [ValidateSpatial(1, ['velocity_x'])]) def _gradx_velocity_x(field,data): sl_left = slice(None, -2, None) sl_right = slice(2, None, None) div_fac = 2.0 ds = div_fac * data['dx'].flat[0] f = data["velocity_x"][sl_right,1:-1,1:-1]/ds f -= data["velocity_x"][sl_left ,1:-1,1:-1]/ds new_field = np.zeros(data["velocity_x"].shape, dtype='float64') new_field = data.ds.arr(new_field,'1/code_time') new_field[1:-1,1:-1,1:-1] = f return new_field ds = yt.load('thermal_instab_hdf5_chk_0050') ds.periodicity = (True, True, True) slc = yt.SlicePlot(ds, 'z', 'gradx_velocity_x') slc.save() ``` Error: ``` #!python Traceback (most recent call last): File "slice.py", line 22, in <module> slc = yt.SlicePlot(ds, 'z', 'gradx_velocity_x') File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1859, in SlicePlot return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1235, in __init__ slc.get_data(fields) File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data self._generate_fields(fields_to_generate) File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields fd = self._generate_field(field) File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field tr = self._generate_fluid_field(field) File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 323, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 352, in _generate_spatial_fluid gz[field][ngz:-ngz, ngz:-ngz, ngz:-ngz], File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__ self.get_data(f) File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 614, in get_data if len(fill) > 0: self._fill_fields(fill) File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 907, in _fill_fields raise RuntimeError RuntimeError ``` However, when I commented out the lines of ```raise RuntimeError```, the script works fine and produces reasonable result.

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PR Triage Hangout
by Hilary Egan 18 Dec '15

18 Dec '15

Hi all, Here's the link to tomorrows PR triage hangout. https://plus.google.com/events/c2nl75lj8g8e4ohl93of147d2og?ghf=3049771 -Hilary -- Hilary Egan Astrophysical and Planetary Science Department University of Colorado Boulder

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What would be useful for coarse-grained indexing?
by Matthew Turk 10 Dec '15

10 Dec '15

Hi all, In this PR I've tried to instigate a discussion of what would be useful for a coarse-grained index of datasets: https://bitbucket.org/yt_analysis/yt/pull-requests/1902/rfc-yt-search-comma… For the "minimum representation" object, we use: ("dimensionality", "refine_by", "domain_dimensions", "current_time", "domain_left_edge", "domain_right_edge", "unique_identifier", "current_redshift", "output_hash", "cosmological_simulation", "omega_matter", "omega_lambda", "hubble_constant", "name") Is this sufficient, or should we add/remove things? We likely want to remove the cosmological ones from non-cosmo sims (and leave them in for cosmo sims) but otherwise, is there anything else we should include? -Matt

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YTEP-0028: proposal for adding the capability to switch between different unit systems
by John A ZuHone 09 Dec '15

09 Dec '15

Hello all, I’ve just submitted a PR for adding the capability to switch between different systems of units in yt (e.g., cgs, MKS, galactic, etc.): https://bitbucket.org/yt_analysis/ytep/pull-requests/58/adding-ytep-0028-fo… I and others have already put in most of the work for this functionality, which will be submitted as a new PR to the codebase soon. Please read the YTEP for an overview of the proposal, and leave comments and suggestions. Best, John Z

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Unstructured mesh pull request needs reviewers
by Nathan Goldbaum 09 Dec '15

09 Dec '15

Hi all, I think the big unstructured mesh pull request, which includes a lot of cool new stuff, is ready to be merged in. However, it's a big PR, we definitely need at least two more people to carefully look it over. If you have some time, it would be great if we could get some attention on the PR. https://bitbucket.org/yt_analysis/yt/pull-requests/1778/more-unstructured-m… -Nathan

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