Mailman 3 September 2013 - yt-dev

Issue #655: EnzoSimulationTimeSeries fails when there are no time outputs. (yt_analysis/yt)
by Britton Smith Sept. 9, 2013

Sept. 9, 2013

New issue 655: EnzoSimulationTimeSeries fails when there are no time outputs. https://bitbucket.org/yt_analysis/yt/issue/655/enzosimulationtimeseries-fai… Britton Smith: If dtDataDump is set to 0, the time_outputs list does not get defined. Responsible: brittonsmith

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Pull request validation
by Matthew Turk Sept. 7, 2013

Sept. 7, 2013

Hi all, Kacper just issued a PR to update YTEP-0007: https://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0007.html Pull requests are now automatically validated, and a robot will leave comments to let you know if it's good to merge. As an example, yt-fido just told us: https://bitbucket.org/yt_analysis/yt/pull-request/588/move-bundled-software… This is pretty awesome. Kacper, I think I speak for everyone when I say that we're all looking forward to the next stage of development, where your robots will begin issuing pull requests. -Matt

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Issue #654: deposit *_count fails in artio (yt_analysis/yt)
by Sam Leitner Sept. 6, 2013

Sept. 6, 2013

New issue 654: deposit *_count fails in artio https://bitbucket.org/yt_analysis/yt/issue/654/deposit-_count-fails-in-artio Sam Leitner: For the following script applied to a DM-only ARTIO fileset ``` #!python from yt.mods import * pf = load("/home/sleitner/run1/refall2/out/agora.nb_a0.2504.art") sl = SlicePlot(pf, 'z', ('deposit', 'all_count')) ``` I get the following Traceback ``` #!python File "temp.py", line 3, in <module> sl = SlicePlot(pf, 'z', ('deposit', 'all_count')) File "/scratch/midway/sleitner/yt-3.0/yt/visualization/plot_window.py", line 1293, in __init__ slc.get_data(fields) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/data_containers.py", line 533, in get_data self._generate_fields(fields_to_generate) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/data_containers.py", line 549, in _generate_fields self.field_data[field] = self._generate_field(field) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/data_containers.py", line 226, in _generate_field tr = self._generate_fluid_field(field) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/data_containers.py", line 243, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/data_containers.py", line 253, in _generate_spatial_fluid for i,chunk in enumerate(self.chunks(field, "spatial", ngz = 0)): File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/data_containers.py", line 453, in chunks self.get_data(fields) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/data_containers.py", line 533, in get_data self._generate_fields(fields_to_generate) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/data_containers.py", line 549, in _generate_fields self.field_data[field] = self._generate_field(field) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/data_containers.py", line 226, in _generate_field tr = self._generate_fluid_field(field) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/data_containers.py", line 245, in _generate_fluid_field rv = finfo(gen_obj) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/field_info_container.py", line 498, in __call__ dd = self._function(self, data) File "/scratch/midway/sleitner/yt-3.0/yt/data_objects/particle_fields.py", line 74, in particle_count d = data.deposit(pos, method = "count") File "/scratch/midway/sleitner/yt-3.0/yt/frontends/artio/data_structures.py", line 178, in deposit f64 = [np.array(f, dtype="float64") for f in fields] TypeError: 'NoneType' object is not iterable ```

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Issue #653: Several data objects do not have docstring entries in the API docs (yt_analysis/yt)
by Nathan Goldbaum Sept. 6, 2013

Sept. 6, 2013

New issue 653: Several data objects do not have docstring entries in the API docs https://bitbucket.org/yt_analysis/yt/issue/653/several-data-objects-do-not-… Nathan Goldbaum: We rely on the docstrings somewhat to provide information beyond __init__ signatures on [this](http://yt-project.org/docs/2.5/analyzing/objects.html#available-objec… page. Several entries do not have links to the API docs because those objects have not been explicitly added. In particular, * AMRBooleanRegionBase * ExtractedRegionBase * AMRFixedResCuttingPlaneBase * AMRFixedResProjectionBase * AMRInclindedBoxBase * AMRPeriodicRegionBase * AMRQuadTreeProjBase * AMRRegionStrictBase

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Issue #652: add_quantity fails silently if no combine_function is given (yt_analysis/yt)
by J.S. Oishi Sept. 6, 2013

Sept. 6, 2013

New issue 652: add_quantity fails silently if no combine_function is given https://bitbucket.org/yt_analysis/yt/issue/652/add_quantity-fails-silently-… J.S. Oishi: If you add a new derived quantity but forget to give the `combine_function` keyword arg, no error is given, but the field is not added to the list of available derived quantities.

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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/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 158, in __init__ find_outputs=find_outputs) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 44, in __init__ find_outputs=find_outputs) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line 131, in simulation find_outputs=find_outputs) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 81, in __init__ find_outputs=find_outputs) File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/time_series.py", line 343, in __init__ self._parse_parameter_file() File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 273, in _parse_parameter_file param, vals = (i.strip() for i in line.split("=")) ValueError: too many values to unpack Responsible: brittonsmith

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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. -pf = load("IsolatedGalaxy/galaxy0030/galaxy0030") +pf = load(os.path.join(ytcfg.get("yt", "test_data_dir"), + "IsolatedGalaxy/galaxy0030/galaxy0030")) # Create projections using each colormap available. ``` Then I thought that if we could make `load` fallback to that path if `args` doesn't exists, that would come handy for docstrings tests. Responsible: xarthisius

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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 : [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 ```

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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 would like to cover will include: * yt 3.0 status, including near/long term plans for development and support for non-grid codes * Rundown of all YTEPs accepted and outstanding * yt's "presence" on the web * 3.0 paper I will also be soliciting feedback in roundtable style on: * How are we doing? * How is the procedure for code contributions working? * How is the yt "infrastructure" meeting people's needs? (Mailing lists, Bitbucket, etc) * Where are energies being spent that could be better spent elsewhere? If you have either agenda items or discussion items, please reply to this email and suggest them. I think having a large presence at this meeting would be very useful, so if you are able to make it, please try to do so. It'll be held as a google hangout, and I'll send details here when it starts up. If there's a pressing need to reschedule, please write in reply to this email. Thanks, and looking forward to seeing you there, Matt

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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 for element names when using either the 13 or 19 element burn network. Responsible: ngoldbaum

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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 fill in the holes to make sure all of the cool stuff in yt is written up so people know how to use it. Now, I know doc writing is not often fun, but I think this could be really beneficial to our user base, and actually cut down on the amount of time we have to respond to new users on the mailing list and irc (as well as making it easier for people to use yt). What I'm asking from you is if you encounter something that you don't think is well documented in the formal docs (not simply the docstrings), could you take a moment to create a bitbucket issue about it? You don't even have to fix it then, just note it, so we know where to work when we do the sprint in a few months. Anyone else have any other ideas about this? Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

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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): File "/usr/lib64/python2.7/site-packages/nose/loader.py", line 231, in generate for test in g(): File "/home/xarth/codes/yt-3.0/yt/visualization/tests/test_offaxisprojection.py", line 86, in test_write_projection write_projection(image, fn, **wp_kwargs) File "/home/xarth/codes/yt-3.0/yt/visualization/image_writer.py", line 417, in write_projection cbar = fig.colorbar(cax) File "/usr/lib64/python2.7/site-packages/matplotlib/figure.py", line 1394, in colorbar cb = cbar.colorbar_factory(cax, mappable, **kw) File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 1173, in colorbar_factory cb = Colorbar(cax, mappable, **kwargs) File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 854, in __init__ ColorbarBase.__init__(self, ax, **kw) File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 298, in __init__ self.draw_all() File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 319, in draw_all self._process_values() File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 632, in _process_values b = self.norm.inverse(self._uniform_y(self.cmap.N+1)) File "/usr/lib64/python2.7/site-packages/matplotlib/colors.py", line 982, in inverse return vmin * ma.power((vmax / vmin), val) File "/usr/lib64/python2.7/site-packages/numpy/ma/core.py", line 3648, in __mul__ return multiply(self, other) File "/usr/lib64/python2.7/site-packages/numpy/ma/core.py", line 941, in __call__ if m: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() ````

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cell padding in RegionSelector
by Douglas Harvey Rudd Sept. 1, 2013

Sept. 1, 2013

Hi all, Matt and I are finishing up our changes to the selector functions and ran into a feature which may or may not be currently used. In RegionSelector, there is a parameter _dx_pad to allow for cells just outside the selected region to be included. Is anyone using that feature or can it be deprecated? Douglas Rudd Scientific Computing Consultant Research Computing Center drudd(a)uchicago.edu

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