Mailman 3 September 2013 - yt-dev

Issue #651: EnzoSimulationTimeSeries fails when par file line has more than one "=" sign. (yt_analysis/yt)
by Britton Smith Sept. 6, 2013

Sept. 6, 2013

New issue 651: EnzoSimulationTimeSeries fails when par file line has more than one "=" sign. https://bitbucket.org/yt_analysis/yt/issue/651/enzosimulationtimeseries-fai… Britton Smith: When a line in an enzo parameter file has more than one equal sign, you get the following when trying to load a SimulationTimeSeries: Traceback (most recent call last): File "lc.py", line 15, in <module> time_data=False) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/… [View More]

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Issue #650: load helper should fallback to test_data_dir (yt_analysis/yt)
by Kacper Kowalik Sept. 6, 2013

Sept. 6, 2013

New issue 650: load helper should fallback to test_data_dir https://bitbucket.org/yt_analysis/yt/issue/650/load-helper-should-fallback-… Kacper Kowalik: This is related to [PR99](https://bitbucket.org/yt_analysis/yt-doc/pull-request/99/adding-color…. I've initially wanted to as @chummels to modify his `cmap_images.py` script as follows: ``` #!diff --- a/cmap_images.py +++ b/cmap_images.py @@ -1,8 +1,9 @@ from yt.mods import * import matplotlib.cm as cm - +import os # Load the dataset. -… [View More]

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Issue #649: PlotWindow should have toggles for the annotated axes and colorbar (yt_analysis/yt)
by Nathan Goldbaum Sept. 6, 2013

Sept. 6, 2013

New issue 649: PlotWindow should have toggles for the annotated axes and colorbar https://bitbucket.org/yt_analysis/yt/issue/649/plotwindow-should-have-toggl… Nathan Goldbaum: Something like this: ``` p = ProjectionPlot(pf, 2, 'Density') p.toggle_axes() p.save() ``` for a PlotCollection-like experience. Or, ``` p = ProjectionPlot(pf, 2, ['Density', 'Temperature']) p.toggle_colorbar() p.save() ``` to remove the colorbar but leave the annotated axes. Responsible: ngoldbaum

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Issue #648: yt stats -o is broken (yt_analysis/yt)
by Nathan Goldbaum Sept. 5, 2013

Sept. 5, 2013

New issue 648: yt stats -o is broken https://bitbucket.org/yt_analysis/yt/issue/648/yt-stats-o-is-broken Nathan Goldbaum: Using IsolatedGalaxy: ``` ○ yt stats -o out.txt IsolatedGalaxy/galaxy0030/galaxy0030 yt : [INFO ] 2013-09-05 14:06:55,302 Parameters: current_time = 0.00600002000283 yt : [INFO ] 2013-09-05 14:06:55,302 Parameters: domain_dimensions = [32 32 32] yt : [INFO ] 2013-09-05 14:06:55,305 Parameters: domain_left_edge = [ 0. 0. 0.] yt : … [View More][INFO ] 2013-09-05 14:06:55,305 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2013-09-05 14:06:55,305 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2013-09-05 14:06:55,324 Getting the binary hierarchy Parsing Hierarchy100% |||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt : [INFO ] 2013-09-05 14:06:55,357 Gathering a field list (this may take a moment.) yt : [INFO ] 2013-09-05 14:06:55,469 Adding unknown field SFR_Density to list of fields yt : [INFO ] 2013-09-05 14:06:55,469 Adding unknown field Forming_Stellar_Mass_Density to list of fields yt : [INFO ] 2013-09-05 14:06:55,469 Adding unknown field Galaxy1Colour to list of fields yt : [INFO ] 2013-09-05 14:06:55,469 Adding unknown field kphHeI to list of fields yt : [INFO ] 2013-09-05 14:06:55,469 Adding unknown field MBHColour to list of fields yt : [INFO ] 2013-09-05 14:06:55,469 Adding unknown field Phi_pField to list of fields yt : [INFO ] 2013-09-05 14:06:55,469 Adding unknown field Galaxy2Colour to list of fields yt : [INFO ] 2013-09-05 14:06:55,470 Adding unknown field Average_creation_time to list of fields yt : [INFO ] 2013-09-05 14:06:55,470 Adding unknown field gammaHI to list of fields yt : [INFO ] 2013-09-05 14:06:55,470 Adding unknown field kphHI to list of fields yt : [INFO ] 2013-09-05 14:06:55,470 Adding unknown field kphHeII to list of fields yt : [INFO ] 2013-09-05 14:06:55,470 Adding unknown field Star_Particle_Density to list of fields yt : [INFO ] 2013-09-05 14:06:55,470 Adding unknown field PhiField to list of fields level # grids # cells # cells^3 ---------------------------------------------- 0 1 32768 31 1 8 34304 32 2 8 181888 56 3 8 646968 86 4 15 947856 98 5 51 874128 95 6 18 786328 92 7 28 446776 76 8 36 209400 59 ---------------------------------------------- 173 4160416 t = 6.00002000e-03 = 1.39768066e+16 s = 4.42898275e+08 years Smallest Cell: Width: 1.221e-04 1 Width: 1.221e-04 aye Width: 1.221e-04 unitary Width: 1.221e-04 Mpc Width: 1.221e-04 mpc Width: 1.221e-01 kpc Width: 1.221e+02 pc Width: 2.518e+07 au Width: 5.416e+09 rsun Width: 2.341e+15 miles Width: 3.767e+15 km Width: 3.767e+20 cm Traceback (most recent call last): File "/Users/goldbaum/yt-conda/bin/yt", line 6, in <module> sys.exit(run_main()) File "/Users/goldbaum/yt-conda/lib/python2.7/site-packages/yt/utilities/command_line.py", line 1696, in run_main args.func(args) File "/Users/goldbaum/yt-conda/lib/python2.7/site-packages/yt/utilities/command_line.py", line 97, in run self(args) File "/Users/goldbaum/yt-conda/lib/python2.7/site-packages/yt/utilities/command_line.py", line 1602, in __call__ "%s (%0.5e years): %0.5e at %s\n" % (pf, t, v, c)) UnboundLocalError: local variable 'v' referenced before assignment ``` [View Less]

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yt Strategy Meeting Monday the 22nd
by Matthew Turk Sept. 4, 2013

Sept. 4, 2013

Hi all, I'd like to call a brief, approximately one hour, strategy meeting on Monday, April 22nd at 3PM Eastern. This will cover where yt is at, where we can go, and how things are progressing. Some of this will be dedicated to progress updates (from me and others) as well as soliciting feedback on a number of things. Many other projects -- notably Cactus -- do these on a fixed schedule, so based on the success/failure of this one we can consider having them semi-regularly. The agenda I … [View More]

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Issue #647: Volume Rendering + Log Fields + Zeros (yt_analysis/yt)
by Sam Skillman Sept. 4, 2013

Sept. 4, 2013

New issue 647: Volume Rendering + Log Fields + Zeros https://bitbucket.org/yt_analysis/yt/issue/647/volume-rendering-log-fields-… Sam Skillman: Currently if you have a volume rendering of a field that is done in log-space and there are zeros/negative values in the raw field data, the resulting NaNs contaminate the image, causing most if not all of the rendering to be empty (zeros). Responsible: samskillman

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Issue #646: Trailing Spaces in FLASH datasets carried over to output file names in SlicePlot (yt_analysis/yt)
by James Guillochon Sept. 4, 2013

Sept. 4, 2013

New issue 646: Trailing Spaces in FLASH datasets carried over to output file names in SlicePlot https://bitbucket.org/yt_analysis/yt/issue/646/trailing-spaces-in-flash-dat… James Guillochon: All variables in FLASH are internally represented by a 4 character string, if a variable has less characters, it has trailing spaces, for instance, carbon is "c12 ". When you perform a SlicePlot on one of these variables, the output file is annoyingly named "mysimulation_c12 .png". This is only an issue … [View More]

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Issue #645: Setup script should complain or error out when using intel compilers (yt_analysis/yt)
by Nathan Goldbaum Sept. 4, 2013

Sept. 4, 2013

New issue 645: Setup script should complain or error out when using intel compilers https://bitbucket.org/yt_analysis/yt/issue/645/setup-script-should-complain… Nathan Goldbaum: As noted on the list, when yt is compiled with icc, there are mysterious hangs during some operations. We should be able to detect that and either error out or print a warning rather than silently generate a broken installation.

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Documentation Sprint and Creating BB Issues When You See a Gap
by Cameron Hummels Sept. 3, 2013

Sept. 3, 2013

Hey peeps, After talking with Matt at some length about the yt documentation, we thought it might be a good idea to have a documentation sprint in a few months when we've moved over to yt 3.0 as the focus of our development. The docs in general are good, but there are some gaps here and there with some functionality not present in the documentation. I'm not proposing an entire (or even partial) rewrite of the docs, as I think that would be counterproductive. I'm simply thinking we could … [View More]

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Issue #644: PR 87 causes test failure in test_offaxisprojection (yt_analysis/yt)
by Kacper Kowalik Sept. 3, 2013

Sept. 3, 2013

New issue 644: PR 87 causes test failure in test_offaxisprojection https://bitbucket.org/yt_analysis/yt/issue/644/pr-87-causes-test-failure-in Kacper Kowalik: Revision 3aba7ca1ff0b causes ```` ====================================================================== ERROR: Failure: ValueError (The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()) ---------------------------------------------------------------------- Traceback (most recent call last): … [View More]

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