yt-dev August 2013

yt-dev@python.org

15 participants
47 discussions

Issue #626: Deprecate neighbour finding methods in halo_objects.HaloList (yt_analysis/yt)
by Kacper Kowalik 14 Aug '13

14 Aug '13

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 marking them for removal or should they be revived? Responsible: brittonsmith

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Issue #625: Website should have a way to download the install script using curl (yt_analysis/yt)
by Nathan Goldbaum 14 Aug '13

14 Aug '13

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 14 Aug '13

14 Aug '13

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 other Oct/Particle changes) * Narrative notebooks regarding 3.0 usage * IO enhancements for patch-based codes Medium term: * Substantial effort on unit tests throughout the 3.0 codebase * SPH smoothing, which includes a) generalizing octrees to enable >2 zones in each direction b) searching for neighbor particles at level > L and c) generalizing the smoothing functions sufficiently to enable greater fleixbility for application of kernels and neighbor particle selection. (n.b., a working preliminary smoothing implementation can be found in my "smoothing" bookmark, but it has a way to go!) * Some solicitations of community input, specifically as related to "code liasons" and addressing issues of branding (i.e., "analysis" over "viz") and reaching out into specific simulation code communities (for some of our flagship codes, we're not even mentioned on the code website!) * Concluding the BSD relicense * Diving into the unit handling system from Nathan & Casey Things I cannot prioritize at the moment, but which I have not forgotten: * Narrative docs for 3.0 (docstrings will continue to be added) * Boxlib refactor * Python 3 support (the only remaining task is to change how our metaclasses are handled, which I am somewhat reluctant to do; we may simply want to use a more advanced 2to3-type converted) * Clump finding in 3.0 * Cactus data -Matt

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proposal to replace enzo_tiny_cosmology data
by Britton Smith 14 Aug '13

14 Aug '13

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 been able to make a very nice looking recipe using the same enzo_tiny_cosmology parameter file with these additions, which do not add significantly to the overall size of the dataset. Additionally, none of the existing recipes that use this data will change. I think there will also probably be more analysis_modules coming in the future that will benefit from using a slightly more sophisticated example dataset. Can we get a +/-1 on replacement? Britton

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RFC: using only explicit imports in core yt
by Kacper Kowalik 14 Aug '13

14 Aug '13

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 than 2-3 methods from it. That allows me to hope that in the end it won't be such a great PITA... Cheers, Kacper [1] https://bitbucket.org/yt_analysis/yt-3.0/pull-request/68/

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Issue #624: PR#54 broke projections in RAMSES in yt-3.0 (yt_analysis/yt)
by nickolas1 12 Aug '13

12 Aug '13

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 outputs of a low res single-level run using these commands: pf = load('output_00001/info_00001.txt') p = ProjectionPlot(pf,2,'Density') p.save() using revisions 559bca4 (merging PR#54) and 596e053, a few days prior to that merge. (More recent revisions show the same problem). I've used ProjectionPlot for simplicity, but plotting with a projection using to_frb shows the same thing.

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Issue #623: OffAxisSlicePlot error in RAMSES (yt_analysis/yt)
by Kyle Stewart 09 Aug '13

09 Aug '13

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 --------------------------------------------------------------------------- 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' ```

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Issue #622: problem with covering_grid for Nyx data sets (yt_analysis/yt)
by Anonymous 08 Aug '13

08 Aug '13

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 values 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt : [ERROR ] 2013-08-08 14:39:24,635 Covering problem: 16777216 cells are uncovered Traceback (most recent call last): File "/usr/users/wschmid2/scripts/spect_demo.py", line 59, in <module> velx_hat = na.fft.fftn( cg['xmom']/cg['density'] )/cg['xmom'].size File "/home/uni05/wschmid2/yt-i686/src/yt-hg/yt/data_objects/data_containers.py", line 332, in __getitem__ self.get_data(key) File "/home/uni05/wschmid2/yt-i686/src/yt-hg/yt/data_objects/data_containers.py", line 3776, in get_data raise KeyError(n_bad) KeyError: 16777216 With an older version of yt (8dce70a9c689 from April), which happened to be installed on one of the machines I am using for data analysis, I don't have this problem (after I made the fix in yt/frontends/nyx/data_structures.py suggested by Nathan) and the script runs through. The data set loaded by the script isn't too big, so I could share it if you don't have some Nyx data available. Just let me know. Cheers, Wolfram

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Issue #621: Need better documentation on how to use cut regions in the docs (yt_analysis/yt)
by Cameron Hummels 07 Aug '13

07 Aug '13

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 so people could find it easier.

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Issue #620: yt 2.5.4 does not install (missing data_objects/tests directory) (yt_analysis/yt)
by astrofrog 06 Aug '13

06 Aug '13

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/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 ```

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yt-dev August 2013