Mailman 3 August 2014 - yt-dev

Issue #886: ReadTheDocs docs are still at 2.6 (yt_analysis/yt)
by John ZuHone Aug. 25, 2014

Aug. 25, 2014

New issue 886: ReadTheDocs docs are still at 2.6 https://bitbucket.org/yt_analysis/yt/issue/886/readthedocs-docs-are-still-a… John ZuHone: Not sure if we were planning to update them there or not.

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docker builds
by Matthew Turk Aug. 22, 2014

Aug. 22, 2014

Hi all, I've put a docker repository into yt_analysis/yt-docker . Not 100% sure I've named it all correctly. Anyway, we've also got a group on hub.docker.io, and it's building images as: ytproject/yt-stable ytproject/yt-stable:jiffylab the latter one is for using inside jiffylab. -Matt

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How to install yt 2.6 in a computer without internet?
by Reju Sam John Aug. 21, 2014

Aug. 21, 2014

Dear all, How to install yt 2.6 in a computer without internet? -- Reju Sam John

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Difference between the fields "Mach" and "MachNumber"
by Reju Sam John Aug. 19, 2014

Aug. 19, 2014

Dear all, In one of my user defined field, I have to do a multiplication with Mach number. I found that, I can use both * data["Mach"]* and *data["MachNumber"]. *What is the difference between "Mach" and "MachNumber". Thank you -- Reju Sam John

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Issue #883: 1D Enzo data is incorrectly parsed (yt_analysis/yt)
by Nathan Goldbaum Aug. 19, 2014

Aug. 19, 2014

New issue 883: 1D Enzo data is incorrectly parsed https://bitbucket.org/yt_analysis/yt/issue/883/1d-enzo-data-is-incorrectly-… Nathan Goldbaum: For some reason the on-disk hydrodynamic fields are interpreted as particle fields and given field type 'io' instead of 'enzo'. This uses the attached 1D sod shock dataset. ``` #!python import yt import pprint ds = yt.load('DD0001/data0001') pprint.pprint(ds.field_list) ``` This outputs: ``` #! [('io', 'y-velocity'), ('io', 'x-velocity'), ('io', 'Density'), ('io', 'z-velocity'), ('io', 'TotalEnergy'), ('all', 'z-velocity'), ('all', 'y-velocity'), ('all', 'x-velocity'), ('all', 'TotalEnergy'), ('all', 'Density')] ```

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Issue #882: BoxLib frontend does not deal with 1-d data properly (yt_analysis/yt)
by Michael Zingale Aug. 19, 2014

Aug. 19, 2014

New issue 882: BoxLib frontend does not deal with 1-d data properly https://bitbucket.org/yt_analysis/yt/issue/882/boxlib-frontend-does-not-dea… Michael Zingale: In the BoxLib frontend, around line 572, we do: ``` # Skip timesteps per level header_file.readline() self._header_mesh_start = header_file.tell() header_file.next() next_line = header_file.next() if len(next_line.split()) == 1: coordinate_type = int(next_line) else: coordinate_type = 0 ``` This code is supposed to skip over all the lines the give the timestep per level, but the boxlib format actually writes out the dx's per left here, in the format dx dy dz (level 0) dx dy dz (level 1) ... when it is over, it will print out an integer flag that represents the geometry. But for 1-d, it seems that this `len(next_line.split()) == 1` clause is catching a single dx as the geometry, at we crash. Responsible: mzingale

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Differences between on-axis projections and off-axis projections
by Cameron Hummels Aug. 18, 2014

Aug. 18, 2014

Hey everyone, Now that the righthandedness has gone into the PlotWindow objects, making slices and projections of isolated disk galaxy simulations yields the y-projection having a vertically oriented disk as seen here in an image generated by Mike Butler: http://www.ics.uzh.ch/~butler/Enzo_nofeedback_1000Myr_Sigma.png I suppose we could modify the ProjectionPlot framework to allow a keyword to specify the x-axis and y-axis vectors, but I was just trying to make equivalent projections using the OffAxisProjectionPlot object since that allows for one to explicitly specify a north_vector. Unfortunately, I'm finding some inconsistencies between the ProjectionPlot (on-axis) images and the OffAxisProjectionPlot images (specifying vectors to be on-axis). This simple script demonstrates what I'm talking about: http://paste.yt-project.org/show/5049/ Running this script yields 4 images: off_axis_proj.png - http://i.imgur.com/CKbq5iO.png on_axis_proj.png - http://i.imgur.com/2iBucuv.png off_axis_weighted_proj.png - http://i.imgur.com/RQV2REP.png on_axis_weighted_proj.png - http://i.imgur.com/CNWHyQS.png As you can see, the off_axis_proj is using significantly different limits than the on_axis_proj, which makes me think it isn't doing a true line integral, but I haven't investigated this closely. While the weighted projections are better, they still have slight differences in their limits. Is this expected and I'm just messing something up here, or is this a true bug? Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

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yt 3.0.1 release?
by Nathan Goldbaum Aug. 18, 2014

Aug. 18, 2014

Hi all, There have been a number of bugfixes since the yt 3.0 release - I think it would be a good idea to to issue a minor point release sooner rather than later so these bugfixes can be released to anaconda, pypi, and people who are on the stable branch. +/- 1? -Nathan

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Issue #881: yt is unable to read outputs created by enzo 2.4 (yt_analysis/yt)
by Nathan Goldbaum Aug. 17, 2014

Aug. 17, 2014

New issue 881: yt is unable to read outputs created by enzo 2.4 https://bitbucket.org/yt_analysis/yt/issue/881/yt-is-unable-to-read-outputs… Nathan Goldbaum: As part of the enzo 2.4 release, I was told to increment the VERSION typedef to 2.4: https://bitbucket.org/enzo/enzo-dev/commits/d10fc823d618cd9930b0a44fa09f43d… Unfortunately, this seems to have caused some breakage on the yt side of things. In particular, the `VersionNumber` parameter written to output files is now 2.4. This causes the data dumps to be incorrectly identified as enzo 3.0 outputs, which causes breakage when yt tries to parse the data dumps for active particle parameters. I'm not sure how to fix this without also breaking i/o for enzo 3.0. I've attached a data dump from the MHDCTOrszagTang test. To reproduce, do `yt stats` on the data dump.

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Issue #880: Infinite recursion when plotting unit'd things (yt_analysis/yt)
by Adam Ginsburg Aug. 15, 2014

Aug. 15, 2014

New issue 880: Infinite recursion when plotting unit'd things https://bitbucket.org/yt_analysis/yt/issue/880/infinite-recursion-when-plot… Adam Ginsburg: When attempting to plot a `TransferFunctionHelper`, I ran into an infinite recursion error: ``` tfh.plot(fn='tf.png') File "/Users/adam/anaconda/envs/astropy27/lib/python2.7/site-packages/yt/units/yt_array.py", line 1135, in __new__ if not isinstance(input_scalar, (numeric_type, np.number, np.ndarray)): File "/Users/adam/anaconda/envs/astropy27/python.app/Contents/lib/python2.7/abc.py", line 132, in __instancecheck__ if subclass is not None and subclass in cls._abc_cache: File "/Users/adam/anaconda/envs/astropy27/python.app/Contents/lib/python2.7/_weakrefset.py", line 75, in __contains__ return wr in self.data RuntimeError: maximum recursion depth exceeded in cmp ``` @ngoldbaum tells me this is a matplotlib 1.3.1 issue. Responsible: ngoldbaum

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