Mailman 3 August 2015 - yt-dev

PR Triage Hangout
by Hilary Egan Aug. 31, 2015

Aug. 31, 2015

Hi all, Last week I said that today would be the first week of changing the scheduled time to Mondays at 2 (EST), but looking at the calendar a little more closely I think we should hold off on switching. We just met a couple days ago on Thursday, and next Monday we will presumably take off given the holiday. That would leave us with quite a stretch in between meetings, so unless there are any strong objections I propose we do a hangout this Thursday (9/3), skip next Monday (9/7), and then meet again the following Monday (9/14). If this is amendable to you all, here's this week's link: https://plus.google.com/b/107728486871834552760/events/caj83u54mic68etgb9of… Thanks! -- Hilary Egan Astrophysical and Planetary Science Department University of Colorado Boulder

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yt 3.2.1?
by Nathan Goldbaum Aug. 31, 2015

Aug. 31, 2015

Hi all, I'd like to do a stable release soonish. I think it should include what's on the stable branch right now along with the pull request I issued today. Does anyone have any pending bugfixes they thing really needs to be in a 3.2.1 release but either hasn't been merged or pull requested yet? Barring any missing bits, I think a good time to do this would be after the PR hangout on Thursday. What do you all think? -Nathan

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Issue #1077: Hotfix existing halo finders to take ptype (yt_analysis/yt)
by Britton Smith Aug. 28, 2015

Aug. 28, 2015

New issue 1077: Hotfix existing halo finders to take ptype https://bitbucket.org/yt_analysis/yt/issues/1077/hotfix-existing-halo-finde… Britton Smith: Responsible: MatthewTurk

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Issue #1076: Add HaloCatalogTimeSeries (yt_analysis/yt)
by Britton Smith Aug. 28, 2015

Aug. 28, 2015

New issue 1076: Add HaloCatalogTimeSeries https://bitbucket.org/yt_analysis/yt/issues/1076/add-halocatalogtimeseries Britton Smith: This is the final component outlined in YTEP-0012.

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Issue #1075: Switch HaloCatalog main loop to loop over io chunks (yt_analysis/yt)
by Britton Smith Aug. 28, 2015

Aug. 28, 2015

New issue 1075: Switch HaloCatalog main loop to loop over io chunks https://bitbucket.org/yt_analysis/yt/issues/1075/switch-halocatalog-main-lo… Britton Smith: The loop over all halos in the HaloCatalog currently requires all processors to have the entire list of halos. This should be changed such that process groups work only on a single io chunk. Currently, only one io chunk exists even when the halo catalog is saved to multiple files. This needs to be reverted to one chunk per file first.

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Issue #1074: LaTeX representations of units are not seriailized (yt_analysis/yt)
by Nathan Goldbaum Aug. 26, 2015

Aug. 26, 2015

New issue 1074: LaTeX representations of units are not seriailized https://bitbucket.org/yt_analysis/yt/issues/1074/latex-representations-of-u… Nathan Goldbaum: This issue is illustrated by the following example (which needs to happen over the course of two python scripts). save.py: ``` #!python import yt ds = yt.load('enzo_tiny_cosmology/DD0000/DD0000') data = ds.arr([1,2,3], 'Mpccm') data.write_hdf5('my_data') ``` load.py: ``` #!python import yt yt.YTArray.from_hdf5('my_data') ``` This will crash with the following traceback: ``` #!python --------------------------------------------------------------------------- KeyError Traceback (most recent call last) <ipython-input-2-a3d4124ff75c> in <module>() ----> 1 yt.YTArray.from_hdf5('my_data') /Users/goldbaum/Documents/yt-hg/yt/units/yt_array.pyc in from_hdf5(cls, filename, dataset_name) 706 f.close() 707 registry = UnitRegistry(lut=unit_lut, add_default_symbols=False) --> 708 return cls(data, units, registry=registry) 709 710 # /Users/goldbaum/Documents/yt-hg/yt/units/yt_array.pyc in __new__(cls, input_array, input_units, registry, dtype, bypass_validation) 356 # don't handle all the cases here, let the Unit class handle if 357 # it's a str. --> 358 units = Unit(input_units, registry=registry) 359 360 # Attach the units /Users/goldbaum/Documents/yt-hg/yt/units/unit_object.pyc in __new__(cls, unit_expr, base_value, base_offset, dimensions, registry, **assumptions) 202 else: 203 # lookup the unit symbols --> 204 unit_data = _get_unit_data_from_expr(unit_expr, registry.lut) 205 base_value = unit_data[0] 206 dimensions = unit_data[1] /Users/goldbaum/Documents/yt-hg/yt/units/unit_object.pyc in _get_unit_data_from_expr(unit_expr, unit_symbol_lut) 476 # Now for the sympy possibilities 477 if isinstance(unit_expr, Symbol): --> 478 return _lookup_unit_symbol(str(unit_expr), unit_symbol_lut) 479 480 if isinstance(unit_expr, Number): /Users/goldbaum/Documents/yt-hg/yt/units/unit_object.pyc in _lookup_unit_symbol(symbol_str, unit_symbol_lut) 539 sstr = symbol_str 540 latex_symbol_lut[symbol_str] = \ --> 541 latex_symbol_lut[symbol_wo_prefix].replace( 542 '{'+symbol_wo_prefix+'}', '{'+sstr+'}') 543 KeyError: 'pccm' ``` The issue is that the LaTeX version of symbols is saved in a singleton dictionary (`latex_symbol_lut`) which is not persisted between python sessions. Coming units specifically define a special LaTeX represetation, which is not available in the python session for load.py. Annoyingly, it *would* work if load.py were executed in the same python session as save.py, since the singleton dictionary would be populated with the correct values. I think the correct thing to do is to store the LaTeX representations of units in the `UnitRegistry` object itself rather than in a global singleton. Responsible: ngoldbaum

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Merger tree format
by Matthew Turk Aug. 25, 2015

Aug. 25, 2015

Hi all, This looks pretty interesting: http://arxiv.org/abs/1508.05388 -Matt

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Issue #1073: Quickstart notebooks do not work under python3 (yt_analysis/yt)
by Nathan Goldbaum Aug. 25, 2015

Aug. 25, 2015

New issue 1073: Quickstart notebooks do not work under python3 https://bitbucket.org/yt_analysis/yt/issues/1073/quickstart-notebooks-do-no… Nathan Goldbaum: We should write the quickstart notebooks so they work both under python2 and python3 without any modifications. They're mostly there already, just the print statements need to be edited. In general we should probably have a pass over all of the example code in the documentation to ensure it functions under python3. Maybe the easiest way to get a start on this would be to set up doc builds for python3.

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PR to remove reason
by Nathan Goldbaum Aug. 25, 2015

Aug. 25, 2015

Hi all, I've opened a pull request to remove the reason GUI here: https://bitbucket.org/yt_analysis/yt/pull-requests/1719 As I mentioned in my e-mail a couple weeks ago about cleaning up the codebase, most of the functionality provided by reason is currently disabled. It could be re-enabled, but someone would need to commit to maintaining it and go through the work of updating the python side of things to work with the current state of yt. If anyone is invested in the reason gui and thinks my pull request is not the way to go, please feel free to comment on the pull request so we can start a discussion about what to do. Thanks for your time, -Nathan

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Arch Linux Packages
by Stuart Mumford Aug. 25, 2015

Aug. 25, 2015

Hello, I have uploaded new Arch Linux AUR yt packages for both Python 2 and Python 3. https://aur.archlinux.org/packages/python-yt/ https://aur.archlinux.org/packages/python2-yt/ For the Python 2 package I have appended a '2' to all the executable scripts so you can have both Python 2 and Python 3 versions installed along side one another. Any feedback and bug reports are welcome. Sorry it took a while after the 3.2 release, blame my impending release of Thesis 0.1. Stuart

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