Mailman 3 June 2013 - yt-users

Announcing: yt 2.5.3
by Matthew Turk 06 Jun '13

06 Jun '13

Hi all, We're proud to release yt version 2.5.3. This is a scheduled point release that includes all bug fixes identified and fixed since the release of 2.5.2 on May 1. Additions, changes and bug fixes include: * yt can now export to RADMC3D * Athena frontend now supports Static Mesh Refinement and units ( http://hub.yt-project.org/nb/7l1zua ) * PlotWindows now have a set_font function and a new default font setting * Colorbars less likely to extend off the edge of a PlotWindow * Clumps overplotted on PlotWindows are now correctly contoured * Allsky projections and HEALpix camera now correctly use four channels (RGBA) * Many fixes to light ray and profiles for integrated cosmological analysis * Improvements to OpenMP compilation * Typo in value for km_per_pc (not used elsewhere in the code base) has been fixed * Enable parallel IPython notebook sessions ( http://hub.yt-project.org/nb/qgn19h ) * Change (~1e-6) to particle_density deposition, enabling it to be used by FLASH and other frontends * Addition of is_root function for convenience in parallel analysis sessions * Additions to Orion particle reader * Fix long-standing bug for plotting arrays with range of zero * Fixing TotalMass for case when particles not present * Fixing the density threshold or HOP and pHOP to match the merger tree * Reason can now plot with latest plot window * Adding option to have interpolation based on non-uniform bins in interpolator code * Issues with VelocityMagnitude and aliases with velo have been corrected in the FLASH frontend * Halo radii are calculated correctly for domains that do not start at 0,0,0. * Halo mass function now works for non-Enzo frontends. * Bug fixes for directory creation, typos in docstrings If you are using the stable branch of yt from an installation script, you can upgrade using "yt update" or "yt update --all" to upgrade your full dependency stack. If you are using the development branch, you may already have these fixes. A tarball of this release has been uploaded to the Python Package Index (PyPI). This release includes a total of over 150 changesets, contributed over the course of nearly 40 pull requests by over a dozen individuals. The next scheduled release will be on July 1, and will be version 2.6. We are hoping to include a unification of the Boxlib frontends, compatibility with Python 3 (and embedding inside Blender) and other usual improvements to the yt codebase. Documentation for this release can be found at: http://yt-project.org/docs/dev/ Thanks very much, Matt, on behalf of the yt development team

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Installation Failure
by Joseph Godino 05 Jun '13

05 Jun '13

Hello, I am trying to install yt with enzo on a computer running Springdale Linux 6.4 using the shell script install_script.sh. However, I keep getting the following error - ******************************************** FAILURE REPORT: ******************************************** running install_egg_info Writing /home/jgodino/Software/enzo/yt-x86_64/lib/python2.7/site-packages/mercurial-2.5.4-py2.7.egg-info using https://bitbucket.org/yt_analysis/yt-supplemental/ sending capabilities command abort: Python SSL support not found using https://bitbucket.org/yt_analysis/yt/ sending capabilities command abort: Python SSL support not found abort: repository /home/jgodino/Software/enzo/yt-x86_64/src/yt-hg/ not found! /home/jgodino/Software/enzo/yt-x86_64/bin/python2.7: can't open file '/home/jgodino/Software/enzo/yt-x86_64/src/yt-hg//distribute_setup.py': [Errno 2] No such file or directory Any suggestions on how to solve this. Regards, Joe

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Rendering non-cubical volumes
by Chris Beaumont 05 Jun '13

05 Jun '13

Hi, I'm new to yt and this list, so I apologize if this question has been answered before. I'm trying to render a non-cubical volume (observational data: see an early attempt at https://vimeo.com/67421373). If I supply a scalar "resolution" to Camera.__init__, the output is a square, even though the input data is ~2x wider than it is tall. If I supply a tuple of values, I can manually stretch the image but, as you can tell from the movie, I want to spin around the volume. I don't think that messing with resolution will help me in this case, since the projected aspect ratio of the plot changes at each rotation step. I did find an old thread similar to this ( http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2012-July/00279…), but the recipe there seem specific to axis-aligned slices, and not generic rotations. Is there a natural way to force yt to render pixels with the "right" aspect ratio? Thanks, Chris -- ************************************ Chris Beaumont Graduate Student Institute for Astronomy University of Hawaii at Manoa 2680 Woodlawn Drive Honolulu, HI 96822 www.ifa.hawaii.edu/~beaumont ************************************

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Announcing: yt 3.0 alpha 2
by Matthew Turk 03 Jun '13

03 Jun '13

Hi everyone, We're proud to announce the second ALPHA release of yt 3.0. yt has recently transitioned to a time-based release plan ( https://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0008.html ) and this is the second scheduled alpha of 3.0. No date for a "final" release has yet been set. The yt 2.5 codebase, and further updates in the 2.x series, will be supported for a considerable amount of time and you do not need to upgrade. = yt 3.0?! = yt 3.0 represents a new direction forward for yt: getting rid of all the underlying assumptions that data needs to be sectioned off into nice little grid patches. This includes supporting Octree codes natively (NMSU-ART and RAMSES), eventual support for SPH codes, and even opaque data structures where the data is extremely large (ARTIO). We're even planning support for natively handling cylindrical and spherical coordinates. More: http://blog.yt-project.org/post/WhatsUpWith30.html However, this *is* an alpha release. Not all of the existing codes have been ported to 3.0. Additionally, this release benefits from the technical and non-technical contributions from many new people. yt is developed in the context of a community of contributors, and with the push toward a new architecture, we aim to expand that community considerably. In particular, this release has considerably benefited from contributions from many new individuals. = Getting It! = To try out yt 3.0, you can now pull from the main yt repository, update to the yt-3.0 branch, and rebuild your extensions. Or, if you would like to create a new, safely sectioned off environment, simply re-run the normal "development" install script after changing the variable BRANCH to "yt-3.0". If you would like to try out yt 3.0 and are having trouble, please write to the yt-users mailing list for assistance. The yt 3.0 install script may also work, which can be obtained by executing these commands: wget http://hg.yt-project.org/yt/raw/yt-3.0/doc/install_script.sh bash install_script.sh = Examples = New functionality can be seen in IPython notebooks available on the yt data Hub. In particular, these notebooks demonstrate many of the functionality that has been added for PKDgrav, Gasoline, Gadget, Enzo, and RAMSES. * Enzo: https://hub.yt-project.org/nb/tzeizy * Gadget: https://hub.yt-project.org/nb/abu5nb * RAMSES: https://hub.yt-project.org/nb/5zw7qn * PKDgrav: https://hub.yt-project.org/nb/mp46a6 * Gasoline: https://hub.yt-project.org/nb/dfncvy (Apologies for the SSL warning on the Hub site.) = Reporting Problems = If you test out yt 3.0 we want to hear if it DID or DID NOT work! Feedback is crucial at this time. yt-users and yt-dev are both good forums for discussion, asking questions, and reporting problems. Lots of things have changed on the backend, but we have attempted to minimize the user-facing changes. To report a bug please go here: https://bitbucket.org/yt_analysis/yt/issues/new Note that you will not receive updates if you are not logged in when you create the bug. = What's Next? = The next alpha release (3.0a3) is scheduled to be released on July 15, 2013, but development can be monitored either at http://bitbucket.org/yt_analysis/yt-3.0 or in the main yt repository under the named branch "yt-3.0". We hope to have ready for inclusion additional improvements to Octree codes, a units implementation for arrays, a field naming scheme overhaul, and further robustness for particle codes. We also are hoping to include the first attempts to apply SPH smoothing kernels to SPH particles. We anticipate that the next alpha release will involve more invasive changes to the array handling and units handling code, and may include a large number of field renaming operations. Aliases to old fields will be provided at that time. Many bug fixes from the mainline of 2.X development have not been merged into the yt-3.0 repository. Bringing these bugfixes in will occur sometime in the next few weeks. If you'd like to participate in yt development, please stop by #yt on irc.freenode.net ( http://yt-project.org/irc.html ) or yt-dev ( http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org ), or submit a pull request on BitBucket. Thanks very much, Matt, on behalf of the yt development team

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Streamplot error in annotate_streamlines callback
by Ji Suoqing 01 Jun '13

01 Jun '13

Hi, Currently I'm using the plot modification callback "annotate_streamlines". However, I got the following error: Traceback (most recent call last): File "magnetic_streamline.py", line 9, in <module> slc.annotate_streamlines('magx','magy',factor=10.0,density=6) File "/aphelion/jisuoqing/sw/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 101, in newfunc args[0]._setup_plots() File "/aphelion/jisuoqing/sw/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 935, in _setup_plots self.run_callbacks(f) File "/aphelion/jisuoqing/sw/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 955, in run_callbacks callback(cbw) File "/aphelion/jisuoqing/sw/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 450, in __call__ plot._axes.streamplot(X,Y, pixX, pixY, density = self.dens, AttributeError: 'Axes' object has no attribute 'streamplot' Now my yt version code is 2ad91aa91e30. In another desktop I remain another version 04fa9a7d799c, in which the annotate_streamlines callback works for the same data file. Thanks a lot! Best wishes, Suoqing

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New location for in-development documentation
by Nathan Goldbaum 01 Jun '13

01 Jun '13

Hi all, As some of you may be aware, we maintain http://yt.readthedocs.org to store a minimal version of the yt documentation that gets updated whenever the documentation repository is updated. This version of the docs is limited - there are no example images and the API docs do not get autogenerated because they are expensive to create. In the past couple of days, Kacper Kowalik has extended yt's automated testing infrastructure to also build and deploy a a fully complete version of the docs with every commit. This new documentation is located at http://yt-project.org/docs/dev. Right now the 'docs' link on yt-project.org points to the 2.5 release documentation. In the near future we will be improving the structure of the website. Part of that work will be to also link to other versions of the docs, including the new dev documentation. For now, if you use the development version of yt, either make a bookmark or remember the link to the dev docs since this version will be the most complete and up to date relative to the in-development version of yt in between major releases. Thanks for your work on this Kacper, I know I'll be using this new resource in the future. Cheers, Nathan

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