Mailman 3 May 2015 - yt-dev

PR Triage at 2:30 EDT
by John Zuhone 29 May '15

29 May '15

Here is the Google Hangout link. See you there! JAZ https://plus.google.com/hangouts/_/gqfrtqetougg32becy54yupqqia <https://plus.google.com/hangouts/_/gqfrtqetougg32becy54yupqqia>

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Going over pull requests (Friday?)
by John Zuhone 29 May '15

29 May '15

Hi all, I sent this email yesterday, but I heard from a few of you it went straight into spam, so I’m trying again. My apologies if you’ve seen it twice. Anyone interested in a PR triage tomorrow (now Friday)? Any time works for me. Sorry about the late notice. If you’re interested, reply back with a time. If I get at least a few people interested I’ll set up a hangout. Best, John Z _______________________________________________ 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 Triage tomorrow?
by John Zuhone 28 May '15

28 May '15

Hi all, Anyone interested in a PR triage tomorrow? Any time from 11 am to 1 pm EDT works for me, as well as 3:30 pm EDT onward after that. Sorry about the late notice. If you’re interested, reply back with a time. If I get at least a few people interested I’ll set up a hangout in the morning. Best, John Z _______________________________________________ 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 #1028: Add test for loading gadget binary data via yt.load() (yt_analysis/yt)
by Nathan Goldbaum 21 May '15

21 May '15

New issue 1028: Add test for loading gadget binary data via yt.load() https://bitbucket.org/yt_analysis/yt/issue/1028/add-test-for-loading-gadget… Nathan Goldbaum: Following up on [PR 1591](https://bitbucket.org/yt_analysis/yt/pull-request/1591/gadget-raw-bin…, we should add tests to verify that _is_valid for gadget binary works going forward. _______________________________________________ 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 #1027: yt.load_particles cannot find newly derived fields (yt_analysis/yt)
by Benjamin Thompson 20 May '15

20 May '15

New issue 1027: yt.load_particles cannot find newly derived fields https://bitbucket.org/yt_analysis/yt/issue/1027/ytload_particles-cannot-fin… Benjamin Thompson: This script. ``` #!python import numpy as np import yt from yt.units.yt_array import YTArray from yt.units import kiloparsec, Msun, kilometer, second, Gyr def _do_magick(field, data): rv = data[("all","particle_birth_epoch")] * 10.0 return rv n_data = 3000 sim_data_verb = {"particle_mass": YTArray(np.random.rand(n_data) * 1000,"Msun"), "particle_position_x": YTArray(np.random.rand(n_data),"kpc"), "particle_position_y": YTArray(np.random.rand(n_data),"kpc"), "particle_position_z": YTArray(np.random.rand(n_data),"kpc"), "particle_velocity_x": YTArray(np.random.rand(n_data), "kpc/s"), "particle_velocity_y": YTArray(np.random.rand(n_data), "kpc/s"), "particle_velocity_z": YTArray(np.random.rand(n_data), "kpc/s"), "particle_mass_birth_epoch": YTArray(np.random.rand(n_data), "Msun"), "particle_birth_epoch": YTArray(np.random.rand(n_data), "Gyr"), "particle_metallicity": YTArray(np.random.rand(n_data),"dimensionless") } bbox = yt.YTArray(np.array([[0,1],[0,1],[0,1]]),"kpc") ds = yt.load_particles(sim_data_verb, length_unit=kiloparsec, mass_unit=Msun, time_unit=second, bbox=bbox, n_ref=256) ds.add_field(name = ('all','particle_birth_epoch_two'),function=_do_magick, units="Gyr") ad = ds.all_data() print ds.derived_field_list print ad[('all','particle_birth_epoch_two')] ``` returns this error File "yt_example2.py", line 35, in <module> print ad[('all','particle_birth_epoch_two')] File "/home/ben/.local/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 246, in __getitem__ f = self._determine_fields([key])[0] File "/home/ben/.local/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 541, in _determine_fields raise YTFieldTypeNotFound(ftype) yt.utilities.exceptions.YTFieldTypeNotFound: Could not find field 'all'. It seems as though it cannot find the newly derived field _______________________________________________ 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 #1026: yt.load_particles cannot handle multiple types of dictionary fields. (yt_analysis/yt)
by Benjamin Thompson 18 May '15

18 May '15

New issue 1026: yt.load_particles cannot handle multiple types of dictionary fields. https://bitbucket.org/yt_analysis/yt/issue/1026/ytload_particles-cannot-han… Benjamin Thompson: yt.load_particles works fine so long as you keep the dictionary fields consistant. For example ``` #!python import numpy as np import yt from yt.units.yt_array import YTArray from yt.units import kiloparsec, Msun, kilometer, second, Gyr n_data = 3000 sim_data_verb = {"particle_mass": YTArray(np.random.rand(n_data) * 1000,"Msun"), "particle_position_x": np.random.rand(n_data), "particle_position_y": np.random.rand(n_data), "particle_position_z": np.random.rand(n_data), "particle_velocity_x": YTArray(np.random.rand(n_data), "kpc/s"), "particle_velocity_y": YTArray(np.random.rand(n_data), "kpc/s"), "particle_velocity_z": YTArray(np.random.rand(n_data), "kpc/s"), "particle_mass_birth_epoch": YTArray(np.random.rand(n_data), "Msun"), "particle_birth_epoch": YTArray(np.random.rand(n_data), "Gyr"), "particle_metallicity": YTArray(np.random.rand(n_data),"dimensionless") } bbox = yt.YTArray(np.array([[0,1],[0,1],[0,1]]),"kpc") ds = yt.load_particles(sim_data_verb, length_unit=kiloparsec, mass_unit=Msun, time_unit=second, bbox=bbox, n_ref=256) ad = ds.all_data() for key in sim_data_verb: print key, ad[key] ``` will work but will return ``` #!python particle_position_z [ 0.2815859 0.38847204 0.22986295 ..., 0.29531876 0.66077444 0.88342952] code_length particle_position_x [ 0.35727259 0.52799574 0.7032232 ..., 0.78598736 0.43919501 0.77617413] code_length particle_position_y [ 0.21314061 0.71663901 0.19971711 ..., 0.41379908 0.20679615 0.26690946] code_length particle_metallicity [ 0.19719678 0.8893857 0.71944182 ..., 0.94147203 0.40978591 0.37535933] dimensionless particle_mass_birth_epoch [ 0.14538698 0.91165767 0.24366002 ..., 0.93701722 0.31856248 0.2815376 ] dimensionless particle_velocity_z [ 1.32970858e+21 2.02143717e+21 8.91082065e+20 ..., 1.45218388e+20 9.72945874e+20 3.02182398e+21] cm/s particle_birth_epoch [ 0.74899177 0.80996651 0.39013562 ..., 0.55047881 0.21678475 0.07351061] dimensionless particle_mass [ 4.94763075e+35 7.77704243e+35 1.12806228e+36 ..., 8.01759848e+35 1.49906294e+36 2.58791744e+35] g particle_velocity_x [ 2.83463595e+21 2.21176517e+21 1.45116224e+21 ..., 1.15946794e+21 2.20856829e+21 1.40417681e+21] cm/s particle_velocity_y [ 3.27195893e+20 1.88669889e+21 3.58577639e+20 ..., 1.01434342e+21 2.92246102e+20 2.07493516e+21] cm/s ``` and e.g particle_mass_birth_epoch will be dimensionless whereas if you were to be consistent with the arrays ``` #!python import numpy as np import yt from yt.units.yt_array import YTArray from yt.units import kiloparsec, Msun, kilometer, second, Gyr n_data = 3000 sim_data_verb = {"particle_mass": YTArray(np.random.rand(n_data) * 1000,"Msun"), "particle_position_x": YTArray(np.random.rand(n_data),"kpc"), "particle_position_y": YTArray(np.random.rand(n_data),"kpc"), "particle_position_z": YTArray(np.random.rand(n_data),"kpc"), "particle_velocity_x": YTArray(np.random.rand(n_data), "kpc/s"), "particle_velocity_y": YTArray(np.random.rand(n_data), "kpc/s"), "particle_velocity_z": YTArray(np.random.rand(n_data), "kpc/s"), "particle_mass_birth_epoch": YTArray(np.random.rand(n_data), "Msun"), "particle_birth_epoch": YTArray(np.random.rand(n_data), "Gyr"), "particle_metallicity": YTArray(np.random.rand(n_data),"dimensionless") } bbox = yt.YTArray(np.array([[0,1],[0,1],[0,1]]),"kpc") ds = yt.load_particles(sim_data_verb, length_unit=kiloparsec, mass_unit=Msun, time_unit=second, bbox=bbox, n_ref=256) ad = ds.all_data() for key in sim_data_verb: print key, ad[key] ``` you get sensible results ``` #!python particle_position_z [ 1.91010138e+21 2.72597553e+21 1.88470277e+20 ..., 1.20441080e+21 2.14680199e+21 5.77431567e+20] cm particle_position_x [ 2.08016250e+21 3.50853505e+20 1.58804046e+21 ..., 1.57472014e+21 3.55352460e+20 2.40592132e+21] cm particle_position_y [ 1.53145514e+21 1.87942152e+21 3.01891288e+21 ..., 1.61942691e+21 1.02154497e+21 2.49263525e+21] cm particle_metallicity [ 0.20026758 0.74414137 0.11611151 ..., 0.71398545 0.9404482 0.12193648] dimensionless particle_mass_birth_epoch [ 0.55149932 0.80309968 0.07713267 ..., 0.16103389 0.85597544 0.55997554] Msun particle_velocity_z [ 1.55542587e+21 2.57960677e+21 2.90400726e+21 ..., 1.90426357e+21 2.94137672e+21 8.78600990e+20] cm/s particle_birth_epoch [ 0.12942072 0.00235603 0.63535871 ..., 0.8858202 0.58461139 0.34462516] Gyr particle_mass [ 1.05296456e+36 1.92696089e+36 3.48006468e+35 ..., 9.26929432e+35 1.86347040e+36 1.21576381e+36] g particle_velocity_x [ 1.01967742e+21 2.38948376e+21 1.83127998e+21 ..., 1.18012037e+20 1.90840829e+21 2.71858174e+21] cm/s particle_velocity_y [ 2.01127183e+20 8.90953057e+20 2.38801554e+21 ..., 1.68662686e+20 3.00596354e+21 4.53271032e+20] cm/s ``` i.e particle_mass_birth_epoch now has dimensions _______________________________________________ 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 #1025: Autoupdate documentation with content of `install_script.sh` (yt_analysis/yt)
by Kacper Kowalik 15 May '15

15 May '15

New issue 1025: Autoupdate documentation with content of `install_script.sh` https://bitbucket.org/yt_analysis/yt/issue/1025/autoupdate-documentation-wi… Kacper Kowalik: Update [Getting and Installing](http://yt-project.org/docs/dev/installing.html) with dependencies by parsing `install_script.sh` Responsible: xarthisius _______________________________________________ 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 #1024: Scripts sometimes harmlessly exit with exception (yt_analysis/yt)
by Nathan Goldbaum 14 May '15

14 May '15

New issue 1024: Scripts sometimes harmlessly exit with exception https://bitbucket.org/yt_analysis/yt/issue/1024/scripts-sometimes-harmlessl… Nathan Goldbaum: Sometimes yt scripts will (harmlessly) exit with the following exception: ``` Exception TypeError: "'NoneType' object is not callable" in <function _removeHandlerRef at 0x37b6cf8> ignored ``` This was brought up by @smumford on IRC this morning. I've also seen this too but never dove into why it's happening. _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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Oops
by Michael Zingale 12 May '15

12 May '15

I accidently pushed to the yt_analysis bitbucket instead of my fork -- can anyone let me know how to undo that? -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale _______________________________________________ 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 #1023: slice().to_frb() ignores aspect ratio (yt_analysis/yt)
by maxhutch 11 May '15

11 May '15

New issue 1023: slice().to_frb() ignores aspect ratio https://bitbucket.org/yt_analysis/yt/issue/1023/slice-to_frb-ignores-aspect… maxhutch: `to_frb(width, resolution, height)` ignores height when selecting which data to use for the window. It does, however, produce an FRB with the given resolution, which can have non-unity aspect ratio. In the attached ipynb, the three visualizations *should* be the same (up to an overall rotation). The bug prevents the third visualization from displaying a circle. Responsible: MatthewTurk _______________________________________________ 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 May 2015