Mailman 3 September 2014 - yt-dev

Issues to Trello?
by Matthew Turk Sept. 30, 2014

Sept. 30, 2014

Hi all, What would you all think of having new issues reported to Trello? I would worry about issues then being updated in two places (or one instead of two), but it feels like Trello is just a way more natural fit for how we work than the BB issue tracker. Maybe I'm wrong on that... Anyway, we can have them forwarded via email, or use one of the connectors out there to have them go there. But maybe it would just fragment things. -Matt

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Splitting a compound unit into its atoms
by John ZuHone Sept. 30, 2014

Sept. 30, 2014

This should be obvious to me, but I can't seem to figure it out. Is there a way to take a compound units expression like: dyne*cm**2/g**2 and split it into its constituent parts, so that I have a list like this: [dyne, cm, g] and maybe even containing the information about the powers?

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yt-3.0 two heads
by Michael Zingale Sept. 30, 2014

Sept. 30, 2014

At the moment, in the yt repo, we have two heads on the yt-3.0 branch -- is that what we want? I try merging them in my local copy and it doesn't go cleanly. -- 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

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Issue #914: draw_domain with specified north_vector (yt_analysis/yt)
by Sam Skillman Sept. 30, 2014

Sept. 30, 2014

New issue 914: draw_domain with specified north_vector https://bitbucket.org/yt_analysis/yt/issue/914/draw_domain-with-specified-n… Sam Skillman: Seems to be broken for non-cubical domains. Will update with an example when I get a chance. Something is either transposed or not done correctly during the projection Responsible: samskillman

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Bitbucket/hg documentation PR
by Nathan Goldbaum Sept. 29, 2014

Sept. 29, 2014

Hi all, Chris Malone just opened a pull request to improve our documentation of PR workflows on bitbucket, particularly how to have multiple simultaneous pull requests open. https://bitbucket.org/yt_analysis/yt/pull-request/1227/docs-on-handling-mul… The PR looks good to me right now, but I'd very much appreciate it if an hg novice could look it over and point out anything that's confusing. Thanks for your help! -Nathan

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Issue #913: Field generation issue is breaking fit_spectrum.py (yt_analysis/yt)
by Nathan Goldbaum Sept. 29, 2014

Sept. 29, 2014

New issue 913: Field generation issue is breaking fit_spectrum.py https://bitbucket.org/yt_analysis/yt/issue/913/field-generation-issue-is-br… Nathan Goldbaum: >From the latest docs build (http://tests.yt-project.org/job/yt-docs-3.0/333/): ``` #!python traceback Traceback (most recent call last): File "helper_scripts/run_recipes.py", line 75, in <module> RES.get() File "/home/xarth/yt-x86_64/lib/python2.7/multiprocessing/pool.py", line 558, in get raise self._value Exception: Traceback (most recent call last): File "helper_scripts/run_recipes.py", line 40, in run_receipe File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/doc/source/cookbook/simple_slice_with_multiple_fields.py", line 8, in <module> width = (800.0, 'kpc')).save() File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/visualization/plot_window.py", line 1842, in SlicePlot return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/visualization/plot_window.py", line 1014, in __init__ slc.get_data(fields) File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.py", line 602, in get_data self.index._identify_base_chunk(self) File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.py", line 129, in index self._index = self.ds.index File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/static_output.py", line 279, in index self.create_field_info() File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/static_output.py", line 334, in create_field_info self.field_info.load_all_plugins() File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/fields/field_info_container.py", line 228, in load_all_plugins self.find_dependencies(loaded) File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/fields/field_info_container.py", line 241, in find_dependencies deps, unavailable = self.check_derived_fields(loaded) File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/fields/field_info_container.py", line 310, in check_derived_fields fd = fi.get_dependencies(ds = self.ds) File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/fields/derived_field.py", line 158, in get_dependencies e[self.name] File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/fields/field_detector.py", line 113, in __missing__ vv = finfo(self) File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/fields/derived_field.py", line 184, in __call__ dd = self._function(self, data) File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/doc/source/cookbook/fit_spectrum.py", line 12, in _OVI_number_density return data['H_number_density']*2.0 File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/fields/field_detector.py", line 93, in __missing__ finfo = self.ds._get_field_info(*field) File "/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/static_output.py", line 482, in _get_field_info raise YTFieldNotFound((ftype, fname), self) YTFieldNotFound: Could not find field '('all', 'H_number_density')' in sloshing_nomag2_hdf5_plt_cnt_0150. in module: simple_slice_with_multiple_fields ```

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Issue #912: Be careful about "thermal energy" uses in yt (yt_analysis/yt)
by Chris Malone Sept. 29, 2014

Sept. 29, 2014

New issue 912: Be careful about "thermal energy" uses in yt https://bitbucket.org/yt_analysis/yt/issue/912/be-careful-about-thermal-ene… Chris Malone: This came up in the comments of a PR. In essence, @mzingale summarized the issue quite well: "I'm a little concerned about the name thermal energy. We don't necessarily have thermal energy easily available [in Maestro]. We have internal energy, or gas energy, but when we are very degenerate, the internal energy is not thermal, so the name thermal energy is misleading and perhaps dangerous. Since this is a yt convention, maybe for these codes we should return an error if thermal energy is requested and perhaps we can define a more code-agnostic general name for the gas internal energy that can be used in situations where thermal energy is wrong."

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Issue #911: Enable the same projection "methods" for OffAxisProjectionPlot as available for ProjectionPlot (yt_analysis/yt)
by Cameron Hummels Sept. 28, 2014

Sept. 28, 2014

New issue 911: Enable the same projection "methods" for OffAxisProjectionPlot as available for ProjectionPlot https://bitbucket.org/yt_analysis/yt/issue/911/enable-the-same-projection-m… Cameron Hummels: Right now, OffAxisProjectionPlot only allows weighted and unweighted 'integration' plots, but not 'sum' or 'mip' plots in the same way that ProjectionPlot does.

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Issue #910: It is too hard to find the examples for loading different kinds of data. (yt_analysis/yt)
by Britton Smith Sept. 25, 2014

Sept. 25, 2014

New issue 910: It is too hard to find the examples for loading different kinds of data. https://bitbucket.org/yt_analysis/yt/issue/910/it-is-too-hard-to-find-the-e… Britton Smith: It needs to be easier to find this page: http://yt-project.org/doc/examining/loading_data.html This either needs to be put on the top level of the docs or even linked to directly from the home page.

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Issue #909: calculate_isocontour_flux function raises error in parallel analysis interface (yt_analysis/yt)
by Nathan Goldbaum Sept. 24, 2014

Sept. 24, 2014

New issue 909: calculate_isocontour_flux function raises error in parallel analysis interface https://bitbucket.org/yt_analysis/yt/issue/909/calculate_isocontour_flux-fu… Nathan Goldbaum: The following test script: ``` import yt ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') dd = ds.all_data() dd.calculate_isocontour_flux('density', 1e-23, 'x-velocity', 'y-velocity', 'z-velocity', 'density') ``` raises the following error: ``` #!python AttributeError Traceback (most recent call last) /home/goldbaum/Documents/yt-hg/yt/mods.pyc in <module>() ----> 1 dd.calculate_isocontour_flux('density', 1e-23, 'x-velocity', 'y-velocity', 'z-velocity', 'density') /home/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.pyc in calculate_isocontour_flux(self, field, value, field_x, field_y, field_z, fluxing_field) 1106 """ 1107 flux = 0.0 -> 1108 for g in self._get_grid_objs(): 1109 flux += self._calculate_flux_in_grid(g, field, value, 1110 field_x, field_y, field_z, fluxing_field) /home/goldbaum/Documents/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.pyc in _get_grid_objs(self) 1065 if self._distributed: 1066 return ParallelObjectIterator(self, True, attr='_grids') -> 1067 return ObjectIterator(self, True, attr='_grids') 1068 1069 def get_dependencies(self, fields): /home/goldbaum/Documents/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.pyc in __init__(self, pobj, just_list, attr) 146 gs = getattr(pobj, attr) 147 else: --> 148 gs = getattr(pobj._data_source, attr) 149 if len(gs) == 0: 150 raise YTNoDataInObjectError(pobj) AttributeError: 'YTRegion' object has no attribute '_data_source' ``` I think the parallel analysis interface should be using the chunking system here, but I'm not sure. I also a little mystified why the unit tests for this function didn't pick this up. Responsible: MatthewTurk

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