Mailman 3 December 2014 - yt-dev

Tables in the docs
by John ZuHone 13 Dec '14

13 Dec '14

Hi all, I don’t get it—any way I attempt to make a table in the docs, using every reST directive I can think of, results in a table that spans the entire web browser width. I’ve got my latest changes in this commit: https://bitbucket.org/jzuhone/yt-3.x/commits/7982e5ebf83d24df03da91c07712e5… <https://bitbucket.org/jzuhone/yt-3.x/commits/7982e5ebf83d24df03da91c07712e5…> Could someone help me figure out what the heck is going on? Thanks, John Z

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Issue #955: Off axis slices returning incorrect results (yt_analysis/yt)
by Nathan Goldbaum 12 Dec '14

12 Dec '14

New issue 955: Off axis slices returning incorrect results https://bitbucket.org/yt_analysis/yt/issue/955/off-axis-slices-returning-in… Nathan Goldbaum: See this notebook: http://nbviewer.ipython.org/gist/ngoldbaum/cd93390ce85ed9ccac24 Either the off-axis slice is zoomed in way too far, or it is simply returning junk data. When I alter the notebook to use the Enzo `IsolatedGalaxy` dataset, I get sensible results. However, with the FLASH `GasSloshing` data I get similar nonsense results. _______________________________________________ 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 #954: Poor quality text when saving as eps; bounding box issues when saving as ps (yt_analysis/yt)
by Daniel Fenn 11 Dec '14

11 Dec '14

New issue 954: Poor quality text when saving as eps; bounding box issues when saving as ps https://bitbucket.org/yt_analysis/yt/issue/954/poor-quality-text-when-savin… Daniel Fenn: Running the attached script gives two output files--one is eps, and the other ps. The eps version has very poor-quality text. The ps version has better text, but the bounding box appears to be incorrect in its horizontal dimensions, as it cuts off axis and colorbar labels. Responsible: jwise77

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Issue #953: Unassigned variable being referenced when trying to save slice plot as eps using eps.single_plot (yt_analysis/yt)
by Daniel Fenn 11 Dec '14

11 Dec '14

New issue 953: Unassigned variable being referenced when trying to save slice plot as eps using eps.single_plot https://bitbucket.org/yt_analysis/yt/issue/953/unassigned-variable-being-re… Daniel Fenn: Running the attached script will throw an error stating that _p1 hasn't been assigned. Looking at the code, _p1 is only conditionally assigned; in this case, self.canvas=None, so the assignment isn't happening. When this is fixed, I believe there will still be an error in axis_box_yt() in the file eps_writer.py. The trouble comes from the line _xrange = (0, width * plot.ds[units]) This throws a key error. Responsible: jwise77

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Issue #952: loading hierarchy before parallel_objects causes barrier mismatch (yt_analysis/yt)
by smoh 11 Dec '14

11 Dec '14

New issue 952: loading hierarchy before parallel_objects causes barrier mismatch https://bitbucket.org/yt_analysis/yt/issue/952/loading-hierarchy-before-par… smoh: Loading hierarchy before entering parallel_objects causes barrier mismatch and the process hangs indefinitely. Everything goes well when all cpus are running the operation, but this happens when some of the cpus are idle. Here's the minimal example that produces the problem in yt 2.6 when run with -np 2. Out of three objects, the process hangs when the third projection is finished and a barrier is opened. ``` from yt.config import ytcfg ytcfg['yt', 'loglevel'] = '1' from yt.mods import * import numpy as np cs = np.random.rand(3, 3) def do(c, pf): cube = pf.h.region(c, c-0.1, c+0.1) proj = pf.h.proj(2, 'Density', source=cube) def do_parallel(pf): pf.h for c in parallel_objects(cs): do(c, pf) if __name__ == '__main__': pf = load('../../enzo_tiny_cosmology/DD0046/DD0046') do_parallel(pf) ``` Looking at the log, it seems that the number of barriers opened is very different depending on whether pf.h is called before parallel_objects or not. If it is called, a barrier is opened many times, and always opened after one projection is finished. If not, it is only called once on each cpu when all objects allocated to it is processed (which seems natural) _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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Nightly binary builds
by John ZuHone 11 Dec '14

11 Dec '14

Hi all, I set it up for my own use (having a fresh install to test my Julia wrapper against), but in case anyone is interested, I’ve set up nighty builds for Linux x86_64 and Windows x86_64 on Binstar: http://binstar.org/jzuhone/yt/files <http://binstar.org/jzuhone/yt/files> It takes the current source code from Bitbucket (from yt_analysis) and builds a binary that can be installed using Anaconda. Best, John

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Is Pluto an active frontend?
by Matthew Turk 09 Dec '14

09 Dec '14

Hi all, I seem to recall we had pluto working again. But, it's commented out in yt/frontends/api.py. Is that by design? -Matt

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Issue #951: FITSImageBuffer error in docs build (yt_analysis/yt)
by Nathan Goldbaum 09 Dec '14

09 Dec '14

New issue 951: FITSImageBuffer error in docs build https://bitbucket.org/yt_analysis/yt/issue/951/fitsimagebuffer-error-in-doc… Nathan Goldbaum: This is coming from the `FITSImageBuffer` notebook in the latest docs build: ``` #!python %matplotlib inline import yt from yt.utilities.fits_image import FITSImageBuffer, FITSSlice, FITSProjection INFO:root:Cell returned INFO:root:Running cell: ds = yt.load("MHDSloshing/virgo_low_res.0054.vtk", parameters={"length_unit":(1.0,"Mpc"), "mass_unit":(1.0e14,"Msun"), "time_unit":(1.0,"Myr")}) INFO:root:Cell returned INFO:root:Running cell: prj = yt.ProjectionPlot(ds, "z", ["temperature"], weight_field="density", width=(500.,"kpc")) prj.show() INFO:root:Cell returned INFO:root:Running cell: prj_fits = FITSProjection(ds, "z", ["temperature"], weight_field="density") INFO:root:Cell raised uncaught exception: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-4-429a440945f9> in <module>() ----> 1 prj_fits = FITSProjection(ds, "z", ["temperature"], weight_field="density") /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/utilities/fits_image.pyc in __init__(self, ds, axis, fields, center, width, weight_field, image_res, **kwargs) 472 prj = ds.proj(fields[0], axis, weight_field=weight_field, **kwargs) 473 w, frb = construct_image(prj, center=dcenter, width=width, --> 474 image_res=image_res) 475 super(FITSProjection, self).__init__(frb, fields=fields, wcs=w) 476 for i, field in enumerate(fields): /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/utilities/fits_image.pyc in construct_image(data_source, center, width, image_res) 356 w.wcs.cdelt = cdelt 357 w.wcs.crval = crval --> 358 w.wcs.cunit = cunit 359 w.wcs.ctype = ctype 360 return w, frb /home/xarth/yt-x86_64/lib/python2.7/site-packages/astropy-0.4.dev8348-py2.7-linux-x86_64.egg/astropy/units/core.pyc in __call__(self, s, represents, format, namespace, doc, parse_strict) 1715 .format(s, format_clause, six.text_type(e))) 1716 if parse_strict == 'raise': -> 1717 raise ValueError(msg) 1718 elif parse_strict == 'warn': 1719 warnings.warn(msg, UnitsWarning) ValueError: 'code_length' did not parse as fits unit: At col 0, Unit u'code_length' not supported by the FITS standard. ``` Responsible: jzuhone

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yt Community Survey
by Cameron Hummels 08 Dec '14

08 Dec '14

Fellow yt users: We at the yt development team want to make yt better for you, the user. We have prepared a short survey to gain your valuable feedback to help us understand what is working in yt and what is not. Could you please spare 2 minutes to fill out our survey below? We plan to collect responses and make available a selection of results by December 10, so please let us know what you think at the following URL: http://goo.gl/forms/hRNryOWTPO On behalf of the yt development team, Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

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Nominate Suoqing Ji to be a project member
by Nathan Goldbaum 08 Dec '14

08 Dec '14

Hi all, I'd like to nominate Suoqing Ji to be a yt project member. Suoqing has been making tons of great contributions recently, and I think giving him commit rights on the bitbucket repository is more than justified. -Nathan

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