Mailman 3 July 2015 - yt-dev

Version selection for Issues
by Kenza Arraki July 28, 2015

July 28, 2015

Hi, Currently the issue tracker allows you to select from the following yt versions: 2.5, 2.6, 2.7, 3.0, and 3.1. Should 3.2 and 3.3-dev be added as well now? -Kenza

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Issue #1050: Not Implemented thrown for 1d enzo3.0 sims (yt_analysis/yt)
by dcollins4096 July 27, 2015

July 27, 2015

New issue 1050: Not Implemented thrown for 1d enzo3.0 sims https://bitbucket.org/yt_analysis/yt/issues/1050/not-implemented-thrown-for… dcollins4096: For 1d simulations with enzo3.0, "Not Implemented" errors are thrown when accessing the data. Attached is a sample dataset that triggers the error. When changing ``` #!python Version = 2.2 ``` to ``` #!python Verions = 2.4 ``` in the parameter file, the error goes away and the data can be analyzed.

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Issue #1049: max_level seems non-functional in ProjectionPlot (yt_analysis/yt)
by dcollins4096 July 27, 2015

July 27, 2015

New issue 1049: max_level seems non-functional in ProjectionPlot https://bitbucket.org/yt_analysis/yt/issues/1049/max_level-seems-non-functi… dcollins4096: Using the max_level argument to ProjectionPlot, ``` #!python yt.ProjectionPlot(ds,2,'grid_level',max_level=0,proj_style='mip') ``` gives the same answer regardless of the value given to max_level. This was initially seen on the Enzo problem AgoraRestart.

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Re: [yt-dev] Issue #1047: Radial Column Density (yt_analysis/yt)
by Bili Dong July 25, 2015

July 25, 2015

Hi all, I’m bringing the update of the discussion here. The current problem is to find a workaround for the code removed for licensing concerns. Could healpy could be an option? Regards Bili

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ANN: yt-3.2 released
by Britton Smith July 24, 2015

July 24, 2015

We are proud to announce the release of yt 3.2! 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 simulations and nuclear engineering simulations. Major enhancements - Particle-Only Plots - a series of new plotting functions for visualizing particle data. See here <http://yt-project.org/docs/dev/visualizing/plots.html#particle-plots> for … [View More]more information. - Late-stage beta support for Python 3 - unit tests and answer tests pass for all the major frontends under python 3.4, and yt should now be mostly if not fully usable. Because many of the yt developers are still on Python 2 at this point, this should be considered a “late stage beta” as there may be remaining issues yet to be identified or worked out. - Now supporting Gadget Friend-of-Friends/Subfind catalogs - see here <http://yt-project.org/docs/dev/examining/loading_data.html#halo-catalog-data> to learn how to load halo catalogs as regular yt datasets. - Custom colormaps can now be easily defined and added - see here <http://yt-project.org/docs/dev/visualizing/colormaps/index.html> to learn how! - Now supporting Fargo3D data - Performance improvements throughout the code base for memory and speed Minor enhancements - Various updates to the following frontends: ART, Athena, Castro, Chombo, Gadget, GDF, Maestro, Pluto, RAMSES, Rockstar, SDF, Tipsy - Numerous documentation updates - Generic hexahedral mesh pixelizer - Adding annotate_ray() callback for plots - AbsorptionSpectrum returned to full functionality and now using faster SciPy Voigt profile - Add a color_field argument to annotate_streamline - Smoothing lengths auto-calculated for Tipsy Datasets - Adding SimulationTimeSeries support for Gadget and OWLS. - Generalizing derived quantity outputs to all be YTArrays or lists of YTArrays as appropriate - Star analysis returned to full functionality - FITS image writing refactor - Adding gradient fields on the fly - Adding support for Gadget Nx4 metallicity fields - Updating value of solar metal mass fraction to be consistent with Cloudy. - Gadget raw binary snapshot handling & non-cosmological simulation units - Adding support for LightRay class to work with Gadget+Tipsy - Add support for subclasses of frontends - Dependencies updated - Serialization for projections using minimal representation - Adding Grid visitors in Cython - Improved semantics for derived field units - Add a yaw() method for the PerspectiveCamera + switch back to LHS - Adding annotate_clear() function to remove previous callbacks from a plot - Added documentation for hexahedral mesh on website - Speed up nearest neighbor evaluation - Add a convenience method to create deposited particle fields - UI and docs updates for 3D streamlines - Ensure particle fields are tested in the field unit tests - Allow a suffix to be specified to save() - Add profiling using airspeed velocity - Various plotting enhancements and bugfixes - Use hglib to update - Various minor updates to halo_analysis toolkit - Docker-based tests for install_script.sh - Adding support for single and non-cosmological datasets to LightRay - Adding the Pascal unit - Add weight_field to PPVCube - FITS reader: allow HDU in auxiliary - Fixing electromagnetic units - Specific Angular Momentum [xyz] computed relative to a normal vector Bugfixes - Adding ability to create union fields from alias fields - Small fix to allow enzo AP datasets to load in parallel when no APs present - Use proper cell dimension in gradient function. - Minor memory optimization for smoothed particle fields - Fix thermal_energy for Enzo HydroMethod==6 - Make sure annotate_particles handles unitful widths properly - Improvements for add_particle_filter and particle_filter - Specify registry in off_axis_projection's image finalization - Apply fix for particle momentum units to the boxlib frontend - Avoid traceback in "yt version" when python-hglib is not installed - Expose no_ghost from export_sketchfab down to _extract_isocontours_from_grid - Fix broken magnetic_unit attribute - Fixing an off-by-one error in the set x/y lim methods for profile plots - Providing better error messages to PlotWindow callbacks - Updating annotate_timestamp to avoid auto-override - Updating callbacks to consistently define coordinate system - Fixing species fields for OWLS and tipsy - Fix extrapolation for vertex-centered data - Fix periodicity check in FRBs - Rewrote project_to_plane() in PerspectiveCamera for draw_domain() - Fix intermittent failure in test_add_deposited_particle_field - Improve minorticks for a symlog plot with one-sided data - Fix smoothed covering grid cell computation - Absorption spectrum generator now 3.0 compliant - Fix off-by-one-or-more in particle smallest dx - Fix dimensionality mismatch error in covering grid - Fix curvature term in cosmology calculator - Fix geographic axes and pixelization - Ensure axes aspect ratios respect the user-selected plot aspect ratio - Avoid clobbering field_map when calling profile.add_fields - Fixing the arbitrary grid deposit code - Fix spherical plotting centering - Make the behavior of to_frb consistent with the docstring - Ensure projected units are initialized when there are no chunks. - Removing "field already exists" warnings from the Owls and Gadget frontends - Various photon simulator bugs - Fixed use of LaTeX math mode - Fix upload_image - Enforce plot width in CSS when displayed in a notebook - Fix cStringIO.StringIO -> cStringIO in png_writer - Add some input sanitizing and error checking to covering_grid initializer - Fix for geographic plotting - Use the correct filename template for single-file OWLS datasets. - Fix Enzo IO performance for 32 bit datasets - Adding a number density field for Enzo MultiSpecies=0 datasets. - Fix RAMSES block ordering - Fix ART star particle masses to correctly reflect current and initial mass - Updating ragged array tests for NumPy 1.9.1 - Force returning lists for HDF5FileHandler Coming Soon! The next major release of yt will be version 3.3, which is slated to include an overhaul of the volume rendering system and support for analyzing and visualizing unstructured mesh data. Standard Installation Methods As with previous releases, you can install yt from source using one of the following methods. 1) From the install script (http://yt-project.org/#getyt ): Note, many of the dependencies have been updated since version 3.1. If you previously installed yt from the install script, it is advised that you re-install yt from scratch. # Installation $ wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh $ bash install_script.sh # Update $ yt update 2) From pip (source or binary wheel, see below for more details): # Installation $ pip install yt # Update $ pip install -U yt 3) From the Anaconda Python Distribution ( https://store.continuum.io/cshop/anaconda/): # Installation $ conda install yt # Update $ conda update yt Note that it might take a day or two for the conda package to be updated. If you are on the “stable” branch, updating will bring you from yt 3.1 to 3.2, incorporating all changes since 3.1, whereas if you are on the “dev” or “yt” branch, only the changes since your last update should be incorporated. Installing Binary Packages via pip New to this release is the ability to install binary packages (“wheels”) using pip on Windows and Mac OS X (64-bit only for both). This has the advantage of not needing to install yt from source using a proper compiler setup, which has caused occasional problems on both of these platforms and prevented us from installing yt easily on other Python distributions. We have so far been able to install and run the binary distribution via pip on the following platforms and Python stacks: Note that it might take a day or two for the pip wheels to be updated. Windows x86_64: - Enthought Canopy Python (https://www.enthought.com/products/canopy/) - WinPython (http://winpython.sourceforge.net/) Mac OS X x86_64: - Enthought Canopy Python (https://www.enthought.com/products/canopy/) - Homebrew Python (http://brew.sh/) - Python.org Python - Mac OS X’s system Python - MacPorts Python (https://www.macports.org/) This is somewhat experimental, so other distributions may work (or not), please submit bug reports or successes to the mailing list or to the Bitbucket issues page (http://bitbucket.org/yt_analysis/yt/issues). All distributions are recommended to be Python v. 2.7, although with yt 3.2 there is late-stage beta support for Python 3.4. The requirements for installing yt via this method are the same as from source: - NumPy - h5py - HDF5 - SymPy - Matplotlib - IPython (not required, but strongly recommended) To install a new version of yt on one of these platforms, simply do $ pip install yt and you should get the binary distribution automatically. Also, if your python installation is system-wide (e.g., the Mac system Python) you might need to run pip with administrator privileges. For more information, including more installation instructions, links to community resources, and information on contributing to yt’s development, please see the yt homepage at http://yt-project.org and the documentation for yt-3.2 at http://yt-project.org/docs/3.2. yt is the product of a large community of developers and users and we are extraordinarily grateful for and proud of their contributions. Please forward this announcement on to any interested parties. As always, if you have any questions, concerns, or run into any trouble updating please don't hesitate to send a message to the mailing list or stop by our IRC channel. All the best, The yt development team [View Less]

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yt ot mayavi converter
by Stuart Mumford July 24, 2015

July 24, 2015

Hello, I have a very simple bit of code that takes 3 yt fields and outputs a mayavi field. I also have a version for a scalar field. See: https://github.com/SWAT-Sheffield/pysac/blob/master/pysac%2Fanalysis%2Ftube… for the implementation. Would this be something worth submitting to yt? If so where should I put it? Stuart

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Issue #1048: reimplement grid_traversal.pyx (yt_analysis/yt)
by Bili Dong July 23, 2015

July 23, 2015

New issue 1048: reimplement grid_traversal.pyx https://bitbucket.org/yt_analysis/yt/issues/1048/reimplement-grid_traversal… Bili Dong: In **grid_traversal.pyx** the following 10 functions will raise a **`NotImplementedError`** no matter what: * `hp_pix2vec_nest` * `arr_pix2vec_nest` * `hp_vec2pix_nest` * `arr_vec2pix_nest` * `hp_pix2ang_nest` * `arr_pix2ang_nest` * `hp_ang2pix_nest` * `arr_ang2pix_nest` * `pixelize_healpix` * `healpix_aitoff_proj` Based on the discussion in [Issue #1047](… [View More]

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3.2 release hangout tomorrow at 12:00pm EDT
by Britton Smith July 23, 2015

July 23, 2015

Hi all, After today's PR review hangout, we are still on track to release version 3.2 tomorrow. We will have a final hangout tomorrow at noon EDT to dot i's, cross t's, hit buttons, etc. Anyone who wants to help out is welcome to come. Additionally, I have compiled a crude list of major enhancements, minor enhancements, and bugfixes. Because it has been over 6 months since our last release, that list is rather long. If you'd like to take a look and make sure I didn't miss anything, go … [View More]

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PR Triage Hangout
by Hilary Egan July 21, 2015

July 21, 2015

Hi all, Here's the link for this week's PR Triage Hangout. I know we are in a PR freeze leading up to the release of 3.2, so if you don't think it's worth having one this week please chime in accordingly. https://plus.google.com/b/107728486871834552760/events/cj76vapnpnpq0ar2n5em… -Hilary

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Issue #1047: Radial Column Density (yt_analysis/yt)
by Bili Dong July 20, 2015

July 20, 2015

New issue 1047: Radial Column Density https://bitbucket.org/yt_analysis/yt/issues/1047/radial-column-density Bili Dong: Is anyone working on porting the [radial column density analysis module](http://yt-project.org/docs/dev/analyzing/analysis_modules/radial_co… from yt-2.x to yt-3.x? This functionality is exactly what I need for my current research. I'd like to do the work if no one else is already working on it.

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