Mailman 3 June 2013 - yt-dev

Issue #585: plot collection add_projection not working? (yt_analysis/yt)
by kstewart 06 Jun '13

06 Jun '13

New issue 585: plot collection add_projection not working? https://bitbucket.org/yt_analysis/yt/issue/585/plot-collection-add_projecti… kstewart: When I try to run a very basic projection plot with yt 3.0 I get the following error: pc=PlotCollection(pf, center) pc.add_projection("Density", 'x', "Density") /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_collection.py in add_projection(self, field, axis, weight_field, data_source, center, use_colorbar, figure, axes, fig_size, periodic, obj, field_parameters) 781 obj = self.pf.hierarchy.proj(field, axis, weight_field, 782 source = data_source, center=center, --> 783 **field_parameters) 784 p = self._add_plot(PCProjectionPlot(obj, field, 785 use_colorbar=use_colorbar, axes=axes, figure=figure, TypeError: __init__() got an unexpected keyword argument 'source' Not sure what's going on here. Looks like some kind of bug since this same code works perfectly in 2.5 -Kyle Stewart

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YTEP-0001 proposed revision
by Matthew Turk 05 Jun '13

05 Jun '13

Hi all, I just issued a PR with a revision to YTEP-0001 about chunking. The yt 3.0a2 release process demonstrated how bad particle IO is for Enzo (Enzo mandates a spatial field for every particle mass, because masses are really densities), and how bad particle deposition is for FLASH. This PR is a set of proposed changes to the chunking system to get around this and enable better IO with preloading. The current YTEP: https://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0001.html The PR: https://bitbucket.org/yt_analysis/ytep/pull-request/17/proposed-modificatio… Comments on the PR would be greatly appreciated. -Matt

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Issue #584: Dynamic teration over a time series object doesn't work (yt_analysis/yt)
by Nathan Goldbaum 05 Jun '13

05 Jun '13

New issue 584: Dynamic teration over a time series object doesn't work https://bitbucket.org/yt_analysis/yt/issue/584/dynamic-teration-over-a-time… Nathan Goldbaum: It appears that `TimeSeriesData.piter()` is hardcoded not to use dynamic load balancing. See e.g. [here](https://bitbucket.org/yt_analysis/yt/src/7d765411da341fa45519ecb3ab78…. After modifying `piter()` to accept a dynamic keyword and running with dynamic load balancing turned on, I get the following error: http://paste.yt-project.org/show/3559 A workaround is to directly call `parallel_objects` on a list of filenames and load each `pf` inside the `parallel_objects` loop. It would be nice to do this workflow directly using a `TimeSeriesData` object, but it appears that this may be tricky given the way `TimeSeriesData` works. I've marked this as a low priority enhancement for 2.6, please feel free to mark this as wontfix if it's a pain to fix.

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Announcing: yt 2.5.3
by Matthew Turk 04 Jun '13

04 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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Announcing: yt 3.0 alpha 2
by Matthew Turk 04 Jun '13

04 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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Issue #583: Particles do not work correctly for old Orion Datasets (yt_analysis/yt)
by Andrew Myers 01 Jun '13

01 Jun '13

New issue 583: Particles do not work correctly for old Orion Datasets https://bitbucket.org/yt_analysis/yt/issue/583/particles-do-not-work-correc… Andrew Myers: Older Orion datasets used a slightly different format for the sink particles that is not compatible with yt. Responsible: atmyers

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