yt 3.4 release notes

# 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: ```bash $ conda update -c conda-forge yt ``` And via `pip` if you manage your python installation with `pip`: ```bash $ 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 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 `pyXSIM` package, 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). 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/1521) and [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).

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