yt 3.4 release notes

The yt community is proud to announce the release of yt 3.4.0. This is a major release and includes a number of new features, minor improvements, and bugfixes.

yt (http://yt-project.org) is an open source, community developed toolkit for the analysis and visualization of volumetric data.

Since our last major release we have moved code hosting to GitHub. If you are interested in contributing to yt, please see our new home at http://github.com/yt-project/yt.

In addition, we have merged 450 pull requests from 44 contributors, including 19 new contributors:

• Alexander Lindsay
• Andrew Myers
• Austin Gilbert
• Avik Laha
• Ben Keller
• Benjamin Thompson
• Bili Dong
• Britton Smith
• Cameron Hummels
• Chang-Goo Kim
• Corentin Cadiou
• David Hannasch
• Enrico Garaldi
• Fabian Koller
• Hilary Egan
• Hsi-Yu Schive
• Hugo Pfister
• Jared Coughlin
• Jill Naiman
• John McCann
• John Regan
• John Wise
• John ZuHone
• Jonah Miller
• Joseph Smidt
• Kacper Kowalik
• Kausik Venkat
• Marianne Corvellec
• Mark Richardson
• Matthew Krafczyk
• Matthew Turk
• Michael Zingale
• Nathan Goldbaum
• Nicholas Earl
• Rafael Ruggiero
• Rasmi Elasmar
• Robert Thompson
• Sam Skillman
• Salvatore Cielo
• Suoqing Ji
• Ting-Wai To
• Weiguang Cui
• Yi-Hao Chen
• Yinghe Lu

The bolded names indicate first-time contributors. We extend our sincere gratitude to everyone who has contributed!

See the changelog below for a summary of new features, changes, and bugfixes.

For more information, including 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 3.4.0 at http://yt-project.org/docs/3.4.0.

Binaries for yt 3.4.0 are available via pip and conda. If you installed via the install script or use conda to manage your python installation, you can update yt via:

$ conda update -c conda-forge yt

And via pip if you manage your python installation with pip:

$ pip install -U yt

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 Slack or IRC channel.

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.

Best, The yt development team https://hackmd.io/EYMxGNgEwRgDgLQFYAsBDKCUAYDswE0QAmATgVLm3AFNcliYRgBmIA==#m...Major Changes and New Features

• yt now supports displaying plots using the interactive matplotlib backends. To enable this functionality call yt.toggle_interactivity(). This is currently supported at an experimental level, please let us know if you come across issues using it. See Bitbucket PR 2294 https://bitbucket.org/yt_analysis/yt/pull-requests/2294.
• The yt configuration file should now be located in a location following the XDG_CONFIG convention (usually ~/.config/yt/ytrc) rather than the old default location (usually ~/.yt/config). You can use yt config migrate at the bash command line to migrate your configuration file to the new location. See Bitbucket PR 2343 https://bitbucket.org/yt_analysis/yt/pull-requests/2343.
• Added yt.LinePlot, a new plotting class for creating 1D plots along lines through a dataset. See Github PR 1509 https://github.com/yt-project/yt/pull/1509 and Github PR 1440 https://github.com/yt-project/yt/pull/1440.
• Added yt.define_unit to easily define new units in yt’s unit system. See Bitbucket PR 2485 https://bitbucket.org/yt_analysis/yt/pull-requests/2485.
• Added yt.plot_2d, a wrapper around SlicePlot for plotting 2D datasets. See Github PR 1476 https://github.com/yt-project/yt/pull/1476.
• We have restored support for boolean data objects. Boolean objects are data objects that are defined in terms of boolean operations on other data objects. See Bitbucket PR 2257 https://bitbucket.org/yt_analysis/yt/pull-requests/2257.
• Datasets now have a fields attribute that allows access to fields via a python object. For example, instead of using a tuple field name like ('gas', 'density'), one can now use ds.fields.gas.density. See Bitbucket PR 2459 https://bitbucket.org/yt_analysis/yt/pull-requests/2459.
• It is now possible to create a wider variety of data objects via ds.r, including rays, fixed resolution rays, points, and images. See Github PR 1518 https://github.com/yt-project/yt/pull/1518 and Github PR 1393 https://github.com/yt-project/yt/pull/1393.
• add_field and ds.add_field must now be called with a sampling_type keyword argument. Possible values are currently cell and particle. We have also deprecated the particle_type keyword argument in favor of sampling_type='cell'. For now a 'cell' sampling_type is assumed if sampling_type is not specified but in the future sampling_type will always need to be specified.
• Added support for the Athena++ code. See Bitbucket PR 2149 https://bitbucket.org/yt_analysis/yt/pull-requests/2149.
• Added support for the Enzo-p code. See Github PR 1447 https://github.com/yt-project/yt/pull/1447, Github PR 1443 https://github.com/yt-project/yt/pull/1443 and Github PR 1439 https://github.com/yt-project/yt/pull/1439.
• Added support for the AMReX code. See Bitbucket PR 2530 https://bitbucket.org/yt_analysis/yt/pull-requests/2530.
• Added support for the openPMD output format. See Bitbucket PR 2376 https://bitbucket.org/yt_analysis/yt/pull-requests/2376.
• Added support for reading face-centered and vertex-centered fields for block AMR codes. See Bitbucket PR 2575 https://bitbucket.org/yt_analysis/yt/pull-requests/2575.
• Added support for loading outputs from the Amiga Halo Finder. See Github PR 1477 https://github.com/yt-project/yt/pull/1477.
• Added support for particle fields for Boxlib data. See Bitbucket PR 2510 https://bitbucket.org/yt_analysis/yt/pull-requests/2510 and Bitbucket PR 2497 https://bitbucket.org/yt_analysis/yt/pull-requests/2497.
• Added support for custom RAMSES particle fields. See Github PR 1470 https://github.com/yt-project/yt/pull/1470.
• Added support for RAMSES-RT data. See Github PR 1456 https://github.com/yt-project/yt/pull/1456 and Github PR 1449 https://github.com/yt-project/yt/pull/1449.
• Added support for Enzo MHDCT fields. See Github PR 1438 https://github.com/yt-project/yt/pull/1438.
• Added support for units and particle fields to the GAMER frontend. See Bitbucket PR 2366 https://bitbucket.org/yt_analysis/yt/pull-requests/2366 and Bitbucket PR 2408 https://bitbucket.org/yt_analysis/yt/pull-requests/2408.
• Added support for type 2 Gadget binary outputs. See Bitbucket PR 2355 https://bitbucket.org/yt_analysis/yt/pull-requests/2355.
• Added the ability to detect and read double precision Gadget data. See Bitbucket PR 2537 https://bitbucket.org/yt_analysis/yt/pull-requests/2537.
• Added the ability to detect and read in big endian Gadget data. See Github PR 1353 https://github.com/yt-project/yt/pull/1353.
• Added support for Nyx datasets that do not contain particles. See Bitbucket PR 2571 https://bitbucket.org/yt_analysis/yt/pull-requests/2571
• A number of untested and unmaintained modules have been deprecated and moved to the yt attic repository https://github.com/yt-project/yt_attic. This includes the functionality for calculating two point functions, the Sunrise exporter, the star analysis module, and the functionality for calculating halo mass functions. If you are interested in working on restoring the functionality in these modules, we welcome contributions. Please contact us on the mailing list or by opening an issue on GitHub if you have questions.
• The particle trajectories functionality has been removed from the analysis modules API and added as a method of the DatasetSeries object. You can now create a ParticleTrajectories object using ts.particle_trajectories() where ts is a time series of datasets.
• The spectral_integrator analysis module is now available via yt.fields.xray_emission_fields. See Bitbucket PR 2465 https://bitbucket.org/yt_analysis/yt/pull-requests/2465.
• The photon_simulator analysis module has been deprecated in favor of the pyXSIMpackage, available separately from yt. See Bitbucket PR 2441 https://bitbucket.org/yt_analysis/yt/pull-requests/2441.
• yt.utilities.fits_image is now available as yt.visualization.fits_image. In addition classes that were in the yt.utilities.fits_image namespace are now available in the main yt namespace.
• The profile.variance attribute has been deprecated in favor of profile.standard_deviation.
• The number_of_particles key no longer needs to be defined when loading data via the stream frontend. See Github PR 1428 https://github.com/yt-project/yt/pull/1428.
• The install script now only supports installing via miniconda. We have removed support for compiling python and yt’s dependencies from source. See Github PR 1459 https://github.com/yt-project/yt/pull/1459.
• Added plot.set_background_color for PlotWindow and PhasePlot plots. This lets users specify a color to fill in the background of a plot instead of the default color, white. See Bitbucket PR 2513 https://bitbucket.org/yt_analysis/yt/pull-requests/2513.
• PlotWindow plots can now optionally use a right-handed coordinate system. See Bitbucket PR 2318 https://bitbucket.org/yt_analysis/yt/pull-requests/2318.
• The isocontour API has been overhauled to make use of units. See Bitbucket PR 2453 https://bitbucket.org/yt_analysis/yt/pull-requests/2453.
• Dataset instances now have a checksum property, which can be accessed via ds.checksum. This provides a unique identifier that is guaranteed to be the same from session to session. See Bitbucket PR 2503 https://bitbucket.org/yt_analysis/yt/pull-requests/2503.
• Added a data_source keyword argument to OffAxisProjectionPlot. See Bitbucket PR 2490 https://bitbucket.org/yt_analysis/yt/pull-requests/2490.
• Added a yt download command-line helper to download test data from http://yt-project.org/data. For more information see yt download --help at the bash command line. See Bitbucket PR 2495 https://bitbucket.org/yt_analysis/yt/pull-requests/2495 and Bitbucket PR 2471 https://bitbucket.org/yt_analysis/yt/pull-requests/2471.
• Added a yt upload command-line helper to upload files to the yt curldrop https://docs.hub.yt/services.html#curldrop at the bash command line. See Github PR 1471 https://github.com/yt-project/yt/pull/1471.
• If it’s installed, colormaps from the cmocean package http://matplotlib.org/cmocean/ will be made available as yt colormaps. See Bitbucket PR 2439 https://bitbucket.org/yt_analysis/yt/pull-requests/2439.
• It is now possible to visualize unstructured mesh fields defined on multiple mesh blocks. See Bitbucket PR 2487 https://bitbucket.org/yt_analysis/yt/pull-requests/2487.
• Add support for second-order interpolation when slicing tetrahedral unstructured meshes. See Bitbucket PR 2550 https://bitbucket.org/yt_analysis/yt/pull-requests/2550.
• Add support for volume rendering second-order tetrahedral meshes. See Bitbucket PR 2401 https://bitbucket.org/yt_analysis/yt/pull-requests/2401.
• Add support for QUAD9 mesh elements. See Bitbucket PR 2549 https://bitbucket.org/yt_analysis/yt/pull-requests/2549.
• Add support for second-order triangle mesh elements. See Bitbucket PR 2378 https://bitbucket.org/yt_analysis/yt/pull-requests/2378.
• Added support for dynamical dark energy parameterizations to the Cosmology object. See Bitbucket PR 2572 https://bitbucket.org/yt_analysis/yt/pull-requests/2572.
• ParticleProfile can now handle log-scaled bins and data with negative values. See Bitbucket PR 2564 https://bitbucket.org/yt_analysis/yt/pull-requests/2564 and Github PR 1510 https://github.com/yt-project/yt/pull/1510.
• Cut region data objects can now be saved as reloadable datasets using save_as_dataset. See Bitbucket PR 2541 https://bitbucket.org/yt_analysis/yt/pull-requests/2541.
• Clump objects can now be saved as reloadable datasets using save_as_dataset. See Bitbucket PR 2326 https://bitbucket.org/yt_analysis/yt/pull-requests/2326.
• It is now possible to specify the field to use for the size of the circles in the annotate_halos plot modifying function. See Bitbucket PR 2493 https://bitbucket.org/yt_analysis/yt/pull-requests/2493.
• The ds.max_level attribute is now a property that is computed on demand. The more verbose ds.index.max_level will continue to work. See Bitbucket PR 2461 https://bitbucket.org/yt_analysis/yt/pull-requests/2461.
• The PointSource volume rendering source now optionally accepts a radius keyword argument to draw spatially extended points. See Bitbucket PR 2404 https://bitbucket.org/yt_analysis/yt/pull-requests/2404.
• It is now possible to save volume rendering images in eps, ps, and pdf format. See Github PR 1504 https://github.com/yt-project/yt/pull/1504.

https://hackmd.io/EYMxGNgEwRgDgLQFYAsBDKCUAYDswE0QAmATgVLm3AFNcliYRgBmIA==#m...Minor Enhancements and Bugfixes

• Fixed issue selecting and visualizing data at very high AMR levels. See Github PR 1521 https://github.com/yt-project/yt/pulls/1521and Github PR 1433 https://github.com/yt-project/yt/pull/1433.
• Print a more descriptive error message when defining a particle filter fails with missing fields See Github PR 1517 https://github.com/yt-project/yt/pull/1517.
• Removed grid edge rounding from the FLASH frontend. This fixes a number of pernicious visualization artifacts for FLASH data. See Github PR 1493 https://github.com/yt-project/yt/pull/1493.
• Parallel projections no longer error if there are less io chunks than MPI tasks. See Github PR 1488 https://github.com/yt-project/yt/pull/1488.
• A memory leak in the volume renderer has been fixed. See Github PR 1485 https://github.com/yt-project/yt/pull/1485 and Github PR 1435 https://github.com/yt-project/yt/pull/1435.
• The force_override keyword argument now raises an error when used with on-disk fields. See Github PR 1516 https://github.com/yt-project/yt/pull/1516.
• Restore support for making plots from reloaded plots. See Github PR 1514 https://github.com/yt-project/yt/pull/1514
• Don’t ever try to read inputs or probin files for Castro and Maestro. See Github PR 1445 https://github.com/yt-project/yt/pull/1445.
• Fixed issue that caused visualization artifacts when creating an off-axis projection for particle or octree AMR data. See Github PR 1434 https://github.com/yt-project/yt/pull/1434.
• Fix i/o for the Enzo 'Dark_Matter_Density' field. See Github PR 1360 https://github.com/yt-project/yt/pull/1360.
• Create the 'particle_ones' field even if we don’t have a particle mass field. See Github PR 1424 https://github.com/yt-project/yt/pull/1424.
• Fixed issues with minor colorbar ticks with symlog colorbar scaling. See Github PR 1423 https://github.com/yt-project/yt/pull/1423.
• Using the rockstar halo finder is now supported under Python3. See Github PR 1414 https://github.com/yt-project/yt/pull/1414.
• Fixed issues with orientations of volume renderings when compositing multiple sources. See Github PR 1411 https://github.com/yt-project/yt/pull/1411.
• Added a check for valid AMR structure in load_amr_grids. See Github PR 1408 https://github.com/yt-project/yt/pull/1408.
• Fix bug in handling of periodic boundary conditions in the annotate_halos plot modifying function. See Github PR 1351 https://github.com/yt-project/yt/pull/1351.
• Add support for plots with non-unit aspect ratios to the annotate_scale plot modifying function. See Bitbucket PR 2551 https://bitbucket.org/yt_analysis/yt/pull-requests/2551.
• Fixed issue with saving light ray datasets. See Bitbucket PR 2589 https://bitbucket.org/yt_analysis/yt/pull-requests/2589.
• Added support for 2D WarpX data. ee Bitbucket PR 2583 https://bitbucket.org/yt_analysis/yt/pull-requests/2583.
• Ensure the particle_radius field is always accessed with the correct field type. See Bitbucket PR 2562 https://bitbucket.org/yt_analysis/yt/pull-requests/2562.
• It is now possible to use a covering grid to access particle filter fields. See Bitbucket PR 2569 https://bitbucket.org/yt_analysis/yt/pull-requests/2569.
• The x limits of a ProfilePlot will now snap exactly to the limits specified in calls to ProfilePlot.set_xlim. See Bitbucket PR 2546 https://bitbucket.org/yt_analysis/yt/pull-requests/2546.
• Added a cookbook example showing how to make movies using matplotlib’s animation framework. See Bitbucket PR 2544 https://bitbucket.org/yt_analysis/yt/pull-requests/2544.
• Use a parallel-safe wrapper around mkdir when creating new directories. See Bitbucket PR 2570 https://bitbucket.org/yt_analysis/yt/pull-requests/2570.
• Removed yt.utilities.spatial. This was a forked version of scipy.spatial with support for a periodic KD-tree. Scipy now has a periodic KD-tree, so we have removed the forked version from yt. Please use scipy.spatial if you were relying on yt.utilities.spatial. See Bitbucket PR 2576 https://bitbucket.org/yt_analysis/yt/pull-requests/2576.
• Improvements for the HaloCatalog. See Bitbucket PR 2536 https://bitbucket.org/yt_analysis/yt/pull-requests/2536 and Bitbucket PR 2535 https://bitbucket.org/yt_analysis/yt/pull-requests/2535.
• Removed 'log' in colorbar label in annotated volume rendering. See Bitbucket PR 2548 https://bitbucket.org/yt_analysis/yt/pull-requests/2548
• Fixed a crash triggered by depositing particle data onto a covering grid. See Bitbucket PR 2545 https://bitbucket.org/yt_analysis/yt/pull-requests/2545.
• Ensure field type guessing is deterministic on Python3. See Bitbucket PR 2559 https://bitbucket.org/yt_analysis/yt/pull-requests/2559.
• Removed unused yt.utilities.exodusII_reader module. See Bitbucket PR 2533 https://bitbucket.org/yt_analysis/yt/pull-requests/2533.
• The cell_volume field in curvilinear coordinates now uses an exact rather than an approximate definition. See Bitbucket PR 2466 https://bitbucket.org/yt_analysis/yt/pull-requests/2466.