yt-dev February 2017

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ANN: yt 3.3.4 released
by Nathan Goldbaum 13 Feb '17

13 Feb '17

We are proud to announce the release of yt 3.3.4! yt (http://yt-project.org) is an open-source, community-developed toolkit for analysis and visualization of volumetric data of all types, with a particular emphasis on astrophysical and nuclear engineering simulations. yt 3.3.4 is officially the "Happy 10th Birthday to yt!" release. Version 3.3.4 is a regularly scheduled bugfix release including fixes for a number of issues reported since the release of yt 3.3.3. We urge all users to update to the latest version. If your python installation is managed via conda, update following: $ conda update -c conda-forge yt If your python installation is managed via pip, update following: $ pip install -U yt Finally, if you manage your yt installation by running out of a clone of the yt mercurial repository, update following: $ yt update We would like to thank the following people for their contributions to this release: Corentin Cadiou Nathan Goldbaum Kacper Kowalik Matthew Krafczyk A summary of changes in this release, along with the number of the pull request implementing the change follows below: Compatibility with matplotlib 2.0 (PR 2467 <https://bitbucket.org/yt_analysis/yt/pull-requests/2467>) Update the description of the yt package (PR 2472 <https://bitbucket.org/yt_analysis/yt/pull-requests/2472>) Compatibility with NumPy 1.12 under python3 (PR 2478 <https://bitbucket.org/yt_analysis/yt/pull-requests/2478>) Correctly detect some non-cosmological Ramses data as such (PR 2491 <https://bitbucket.org/yt_analysis/yt/pull-requests/2491>) Fix issue with periodic mirroring of data in the halos callback (PR 2492 <https://bitbucket.org/yt_analysis/yt/pull-requests/2492>) Ensure field data are contiguous before depositing (PR 2498 <https://bitbucket.org/yt_analysis/yt/pull-requests/2498> and PR 2518 <https://bitbucket.org/yt_analysis/yt/pull-requests/2518>) Adjust internal setup of mutable dataset attributes (PR 2501 <https://bitbucket.org/yt_analysis/yt/pull-requests/2501>) Fix issues creating box data objects (PR 2508 <https://bitbucket.org/yt_analysis/yt/pull-requests/2508>) Register __hg_version__.py with setuptools extension builder (PR 2445 <https://bitbucket.org/yt_analysis/yt/pull-requests/2445>)

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Issue #1319: fields as contiguous arrays for idealized galaxies (yt_analysis/yt)
by Desika Narayanan 07 Feb '17

07 Feb '17

New issue 1319: fields as contiguous arrays for idealized galaxies https://bitbucket.org/yt_analysis/yt/issues/1319/fields-as-contiguous-array… Desika Narayanan: This is related to a previous bugfix: https://bitbucket.org/yt_analysis/yt/pull-requests/2498/ensure-fields-are-c… If I try a related test with an idealized gadget galaxy (a test snapshot can be found here: https://www.dropbox.com/s/q817i6w6wpb42we/snapshot_050.hdf5?dl=0 with the following code: http://paste.yt-project.org/show/7015/ it returns an error similar to PR 2498: ``` jam:scratch desika$ python vel_proj_idealized.py yt : [INFO ] 2017-02-07 11:14:47,621 Omega Lambda is 0.0, so we are turning off Cosmology. yt : [INFO ] 2017-02-07 11:14:47,630 Parameters: current_time = 0.25 yt : [INFO ] 2017-02-07 11:14:47,630 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2017-02-07 11:14:47,631 Parameters: domain_left_edge = [-1000. -1000. -1000.] yt : [INFO ] 2017-02-07 11:14:47,631 Parameters: domain_right_edge = [ 1000. 1000. 1000.] yt : [INFO ] 2017-02-07 11:14:47,632 Parameters: cosmological_simulation = 0 yt : [INFO ] 2017-02-07 11:14:47,634 Allocating for 2.515e+07 particles (index particle type 'all') yt : [INFO ] 2017-02-07 11:14:51,665 Identified 1.540e+06 octs [ 0. 0. 0. ..., 0. 0. 0.] code_velocity Traceback (most recent call last): File "vel_proj_idealized.py", line 23, in <module> vy = arb[ ('deposit', 'PartType0_sum_velocity_y')] File "/Users/desika/yt/yt/data_objects/data_containers.py", line 281, in __getitem__ self.get_data(f) File "/Users/desika/yt/yt/data_objects/construction_data_containers.py", line 635, in get_data if len(gen) > 0: self._generate_fields(gen) File "/Users/desika/yt/yt/data_objects/data_containers.py", line 1353, in _generate_fields fd = self._generate_field(field) File "/Users/desika/yt/yt/data_objects/data_containers.py", line 318, in _generate_field tr = self._generate_fluid_field(field) File "/Users/desika/yt/yt/data_objects/data_containers.py", line 338, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/desika/yt/yt/fields/derived_field.py", line 220, in __call__ dd = self._function(self, data) File "/Users/desika/yt/yt/data_objects/static_output.py", line 1260, in _deposit_field method=method, kernel_name=kernel_name), File "/Users/desika/yt/yt/data_objects/construction_data_containers.py", line 728, in deposit op.process_grid(self, positions, fields) File "yt/geometry/particle_deposit.pyx", line 120, in yt.geometry.particle_deposit.ParticleDepositOperation.process_grid (yt/geometry/particle_deposit.c:5181) ValueError: Buffer and memoryview are not contiguous in the same dimension. ```

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Issue #1318: Arepo Temperature bug? (yt_analysis/yt)
by Anonymous 06 Feb '17

06 Feb '17

New issue 1318: Arepo Temperature bug? https://bitbucket.org/yt_analysis/yt/issues/1318/arepo-temperature-bug Anonymous: It seems like something recently changed in the frontend that underestimates gas temperatures in Arepo file structures. I recently went back to a simulation to re-evaluate a temperature-based calculation, and found that all the ('gas','temperature') values seem too low by several orders of magnitude. I'm not sure what's going on, but for example when I compare ('PartType0','Temperature') to ('gas','temperature') in a small volume of the simulation (cosmo. simulation centered on the galaxy), you can see that the distribution of temperatures look very different/offset from each other. (Histograms attached). Any help is appreciated. Thanks! -Kyle Stewart

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Prepping for yt 3.3.4
by Nathan Goldbaum 03 Feb '17

03 Feb '17

Hi all, I just issued a pull request that backports several bugfixes to the stable branch: https://bitbucket.org/yt_analysis/yt/pull-requests/2514 This is in preparation to do a release of yt 3.3.4. Even though there are only a few backports this time I'd like to get it out the door since there are some fixes that avoid crashes under the latest version of numpy as well as annoying deprecation warnings under matplotlib 2.0. Please let me know if I've missed any bugfixes that you'd like to see backported. -Nathan

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Issue #1317: Cannot set background color after changing color map (yt_analysis/yt)
by Hsi-Yu Schive 02 Feb '17

02 Feb '17

New issue 1317: Cannot set background color after changing color map https://bitbucket.org/yt_analysis/yt/issues/1317/cannot-set-background-colo… Hsi-Yu Schive: The following scripts fails. ``` #!python import yt ds = yt.load( "enzo/IsolatedGalaxy/galaxy0030/galaxy0030" ) sz = yt.SlicePlot( ds, 'z', 'density', center='c' ) sz.set_cmap( 'density', 'afmhot' ) sz.set_background_color( 'density' ) sz.save() ``` Error messages: ``` #!python File "demo.py", line 5, in <module> sz.set_background_color( 'density' ) File "/projects/ncsa/grav/hyschive/yt/yt.ori/yt/visualization/plot_container.py", line 69, in newfunc rv = f(*args, **kwargs) File "/projects/ncsa/grav/hyschive/yt/yt.ori/yt/visualization/plot_container.py", line 317, in set_background_color cmap = yt_colormaps[cmap] KeyError: 'afmhot' ``` Note that setting background color explicitly works. For example, ``` #!python sz.set_background_color( 'density', color='black' ) ```

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Issue #1316: Unit conversion with equivalency (yt_analysis/yt)
by Hsi-Yu Schive 01 Feb '17

01 Feb '17

New issue 1316: Unit conversion with equivalency https://bitbucket.org/yt_analysis/yt/issues/1316/unit-conversion-with-equiv… Hsi-Yu Schive: The following script fails. ``` #!python import yt ds = yt.load("IsolatedGalaxy/galaxy0030/galaxy0030") slc = yt.SlicePlot(ds, 'z', 'temperature', width=(10,'kpc')) #this line causes a problem slc.set_buff_size(2048) slc.set_unit('temperature', 'keV', equivalency='thermal') slc.save() ``` Error messages: ``` #!python yt.utilities.exceptions.YTUnitConversionError: Unit dimensionalities do not match. Tried to convert between K**2/erg (dim (temperature)**2*(time)**2/((length)**2*(mass))) and K (dim (temperature)). ``` This issue is related to pull request #2424. Note that calling set_buff_size() AFTER set_unit() does not trigger this issue.

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yt-dev February 2017