Mailman 3 August 2013 - yt-dev

Issue #626: Deprecate neighbour finding methods in halo_objects.HaloList (yt_analysis/yt)
by Kacper Kowalik Aug. 14, 2013

Aug. 14, 2013

New issue 626: Deprecate neighbour finding methods in halo_objects.HaloList https://bitbucket.org/yt_analysis/yt/issue/626/deprecate-neighbour-finding-… Kacper Kowalik: There are two methods in the basic `HaloList` class: `nearest_neighbors_3D` and `nearest_neighbors_2D` that invoke unknown function `buildKdHyperRectTree`. It looks like they rely on external dependency that's no longer shipped with *yt* or they are rotten code. Could we raise some exception at the beginning of those methods … [View More]

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Issue #625: Website should have a way to download the install script using curl (yt_analysis/yt)
by Nathan Goldbaum Aug. 14, 2013

Aug. 14, 2013

New issue 625: Website should have a way to download the install script using curl https://bitbucket.org/yt_analysis/yt/issue/625/website-should-have-a-way-to… Nathan Goldbaum: Since `wget` is not included on OS X, we should either use `curl` instead of `wget` in the 'get yt' section, or suggest an alternate `curl`-based solution if the user doesn't have wget.

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My yt roadmap for next few months
by Matthew Turk Aug. 14, 2013

Aug. 14, 2013

Hi all, I wanted to update everyone on where things stand on my end, now that I am back online. These are the yt-specific issues I am targeting for the next few weeks or months: Short term: * Reliability and resiliency of yt 3.0. This includes things like error checking, failure modes, and so on. Currently, there are a number of ways to simply fail during loading of datasets like RAMSES, Gadget, etc, and I want to fix that. * Other showstopping 3.0 stuff (specifically ARTIO stuff and … [View More]

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proposal to replace enzo_tiny_cosmology data
by Britton Smith Aug. 14, 2013

Aug. 14, 2013

Hi all, I would like to propose that we replace the enzo_tiny_cosmology dataset that we store for various examples with one that has a few more physics modules enabled. Hilary Egan has issued PRs to yt and yt-doc for a very nice set of absorption line fitting tools. The recipe provided works really well with a small cosmology simulation, but the ones we have up now are missing some key physics (H/He chemistry and a UV background) that make the output from the recipe look quite poor. We have … [View More]

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RFC: using only explicit imports in core yt
by Kacper Kowalik Aug. 14, 2013

Aug. 14, 2013

Hi, I'd like to discuss deprecating glob imports in yt-3.0. Initial work has been done in PR68 [1]. Main rationale is that '*' confuses all python static checkers and obscures bugs that otherwise would be trivial to find. I understand that it's onerous and the very reason yt.funcs exists is to make devs' live more convenient and allow to easily grab everything that's defined there. However, using said yt.funcs as an example, it's worth noticing that there are not many modules that grab more … [View More]

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Issue #624: PR#54 broke projections in RAMSES in yt-3.0 (yt_analysis/yt)
by nickolas1 Aug. 12, 2013

Aug. 12, 2013

New issue 624: PR#54 broke projections in RAMSES in yt-3.0 https://bitbucket.org/yt_analysis/yt/issue/624/pr-54-broke-projections-in-r… nickolas1: For revisions post-Octree diet, in projections it appears that alternating rows are shifted in alternating directions, and the shift seems to be equal to the cell size at the smallest refinement level. This is subtle if you have several levels of refinement, but it is obvious once individual cells are resolved in the image. Attached are two … [View More]

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Issue #623: OffAxisSlicePlot error in RAMSES (yt_analysis/yt)
by Kyle Stewart Aug. 9, 2013

Aug. 9, 2013

New issue 623: OffAxisSlicePlot error in RAMSES https://bitbucket.org/yt_analysis/yt/issue/623/offaxissliceplot-error-in-ra… Kyle Stewart: I get an error about "size" being undefined when I try to plot an OffAxisSlicePlot in RAMSES: ``` #!python In [53]: p = OffAxisSlicePlot(pf, [0,1,0], "Density", center=center) yt : [INFO ] 2013-08-09 12:40:35,697 xlim = -0.500000 0.500000 yt : [INFO ] 2013-08-09 12:40:35,697 ylim = -0.500000 0.500000 ------------------------------------------------… [View More]--------------------------- AttributeError Traceback (most recent call last) /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/scripts/iyt in <module>() ----> 1 p = OffAxisSlicePlot(pf, [0,1,0], "Density", center=center) /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_window.pyc in __init__(self, pf, normal, fields, center, width, axes_unit, north_vector, fontsize, field_parameters) 1445 PWViewerMPL.__init__(self, cutting, bounds, fields=fields, 1446 origin='center-window',periodic=False, -> 1447 oblique=True, fontsize=fontsize) 1448 self.set_axes_unit(axes_unit) 1449 /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_window.pyc in __init__(self, *args, **kwargs) 787 self._font_properties = FontProperties(size=font_size, fname=font_path) 788 self._font_color = None --> 789 PWViewer.__init__(self, *args, **kwargs) 790 791 def _setup_origin(self): /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_window.pyc in __init__(self, *args, **kwargs) 589 if self._plot_type is None: 590 self._plot_type = kwargs.pop("plot_type") --> 591 PlotWindow.__init__(self, *args,**kwargs) 592 self._axes_unit_names = None 593 self._callbacks = [] /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_window.pyc in __init__(self, data_source, bounds, buff_size, antialias, periodic, origin, oblique, window_size) 309 self.window_size = window_size 310 self.antialias = antialias --> 311 self.set_window(bounds) # this automatically updates the data and plot 312 self.origin = origin 313 if self.data_source.center is not None and oblique == False: /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_window.pyc in newfunc(*args, **kwargs) 85 args[0]._data_valid = False 86 args[0]._plot_valid = False ---> 87 args[0]._recreate_frb() 88 if args[0]._initfinished: 89 args[0]._setup_plots() /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_window.pyc in _recreate_frb(self) 362 periodic=self._periodic) 363 if old_fields is None: --> 364 self._frb._get_data_source_fields() 365 else: 366 for key in old_fields: self._frb[key] /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/fixed_resolution.pyc in _get_data_source_fields(self) 150 for f in fields: 151 if f not in exclude and f[0] not in self.data_source.pf.particle_types: --> 152 self[f] 153 154 def _get_info(self, item): /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/fixed_resolution.pyc in __getitem__(self, item) 459 indices = np.argsort(self.data_source['dx'])[::-1] 460 buff = _MPL.CPixelize( self.data_source['x'], self.data_source['y'], self.data_source['z'], --> 461 self.data_source['px'], self.data_source['py'], 462 self.data_source['pdx'], self.data_source['pdy'], self.data_source['pdz'], 463 self.data_source.center, self.data_source._inv_mat, indices, /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 195 if f not in self.field_data: 196 if f in self._container_fields: --> 197 self.field_data[f] = self._generate_container_field(f) 198 return self.field_data[f] 199 else: /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/data_objects/selection_data_containers.pyc in _generate_container_field(self, field) 449 y = self._current_chunk.fcoords[:,1] - self.center[1] 450 z = self._current_chunk.fcoords[:,2] - self.center[2] --> 451 tr = np.zeros(self.size, dtype='float64') 452 tr += x * self._x_vec[0] 453 tr += y * self._x_vec[1] AttributeError: 'YTCuttingPlane' object has no attribute 'size' ``` [View Less]

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Issue #622: problem with covering_grid for Nyx data sets (yt_analysis/yt)
by Anonymous Aug. 8, 2013

Aug. 8, 2013

New issue 622: problem with covering_grid for Nyx data sets https://bitbucket.org/yt_analysis/yt/issue/622/problem-with-covering_grid-f… Anonymous: Hi, this is triggered by a discussion with Nathan. I have troubles with reading in Nyx data with covering_grid up to a certain level (0 or higher, it doesn't matter). My script is attached (it's actually for the computation of power spectra). With the current (yesterday's) development version of yt I get the following error: Searching grids for … [View More]

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Issue #621: Need better documentation on how to use cut regions in the docs (yt_analysis/yt)
by Cameron Hummels Aug. 7, 2013

Aug. 7, 2013

New issue 621: Need better documentation on how to use cut regions in the docs https://bitbucket.org/yt_analysis/yt/issue/621/need-better-documentation-on… Cameron Hummels: There is a small patch on how to do it buried in there: http://yt-project.org/doc/api/generated/yt.data_objects.data_containers.AMR… But one has to know that it is called a "cut region" (cutting region doesn't bring it up in search), and it would be better to have a full description of it in a narrative format elsewhere … [View More]

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Issue #620: yt 2.5.4 does not install (missing data_objects/tests directory) (yt_analysis/yt)
by astrofrog Aug. 6, 2013

Aug. 6, 2013

New issue 620: yt 2.5.4 does not install (missing data_objects/tests directory) https://bitbucket.org/yt_analysis/yt/issue/620/yt-254-does-not-install-miss… astrofrog: I tried installing yt 2.5.4 using the tarball from PyPI but I get the following error: ``` Traceback (most recent call last): File "setup.py", line 280, in <module> setup_package() File "setup.py", line 275, in setup_package 'build_src': my_build_src, 'install_data': my_install_data}, File "/opt/local/… [View More]Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 231, in configuration config.add_subpackage('yt', 'yt') File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage caller_level = 2) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage caller_level = caller_level + 1) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "yt/setup.py", line 11, in configuration config.add_subpackage('data_objects') File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage caller_level = 2) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage caller_level = caller_level + 1) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "yt/data_objects/setup.py", line 12, in configuration config.add_subpackage("tests") File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage caller_level = 2) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 965, in get_subpackage caller_level = caller_level+1) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 744, in __init__ raise ValueError("%r is not a directory" % (package_path,)) ValueError: 'yt/data_objects/tests' is not a directory ``` [View Less]

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