ChangeLog

This is a non-comprehensive log of changes to yt over its many releases.

Contributors

The CREDITS file contains the most up-to-date list of everyone who has contributed to the yt source code.

Version 3.5.0

Version 3.5.0 is the first major release of yt since August 2017. It includes 328 pull requests from 41 contributors, including 22 new contributors.

Major Changes

  • yt.analysis_modules has been deprecated in favor of the new yt_astro_analysis package. New features and new astronomy-specific analysis modules will go into yt_astro_analysis and importing from yt.analysis_modules will raise a noisy warning. We will remove yt.analysis_modules in a future release. See PR 1938.
  • Vector fields and derived fields depending on vector fields have been systematically updated to account for a bulk correction field parameter. For example, for the velocity field, all derived fields that depend on velocity will now account for the "bulk_velocity" field parameter. In addition, we have defined "relative_velocity" and "relative_magnetic_field" fields that include the bulk correction. Both of these are vector fields, to access the components, use e.g. "relative_velocity_x". The "particle_position_relative" and "particle_velocity_relative" fields have been deprecated. See PR 1693 and PR 2022.
  • Aliases to spatial fields with the "gas" field type will now be returned in the default unit system for the dataset. As an example the "x" field might resolve to the field tuples ("index", "x") or ("gas", "x"). Accessing the former will return data in code units while the latter will return data in whatever unit system the dataset is configured to use (CGS, by default). This means that to ensure the units of a spatial field will always be consistent, one must access the field as a tuple, explicitly specifying the field type. Accessing a spatial field using a string field name may return data in either code units or the dataset’s default unit system depending on the history of field accesses prior to accessing that field. In the future accessing fields using an ambiguous field name will raise an error. See PR 1799 and PR 1850.
  • The max_level and min_level attributes of yt data objects now correctly update the state of the underlying data objects when set. In addition we have added an example to the cookbook that shows how to downsample AMR data using this functionality. See PR 1737.
  • It is now possible to customize the formatting of labels for ion species fields. Rather than using the default spectroscopic notation, one can call ds.set_field_label_format("ionization_label", "plus_minus") to use the more traditional notation where ionization state is indicated with + and - symbols. See PR 1867.

Improvements to the RAMSES frontend

We would particularly like to recognize Corentin Cadiou for his tireless work over the past year on improving support for RAMSES and octree AMR data in yt.

  • Added support for reading RAMSES sink particles. See PR 1548.
  • Add support for the new self-describing Ramses particle output format. See PR 1616.
  • It is now possible to restrict the domain of a loaded Ramses dataset by passing a bbox keyword argument to yt.load(). If passed this corresponds to the coordinates of the top-left and bottom-right hand corner of the subvolume to load. Data outside the bounding box will be ignored. This is useful for loading very large Ramses datasets where yt currently has poor scaling. See PR 1637.
  • The Ramses "particle_birth_time" field now contains the time when star particles form in a simulation in CGS units, formerly these times were only accessible via the incorrectly named "particle_age" field in conformal units. Correspondingly the "particle_age" field has been deprecated. The conformal birth time is not available via the "conformal_birth_time” field. See PR 1649.
  • Substantial performance improvement for reading RAMSES AMR data. See PR 1671.
  • The RAMSES frontend will now produce less voluminous logging feedback when loading the dataset or reading data. This is particularly noticeable for very large datasets with many CPU files. See PR 1738.
  • Avoid repeated parsing of RAMSES particle and RT descriptors. See PR 1739.
  • Added support for reading the RAMSES gravitational potential field. See PR 1751.
  • Add support for RAMSES datasets that use the groupsize feature. See PR 1769.
  • Dramatically improve the overall performance of the RAMSES frontend. See PR 1771.

Additional Improvements

  • Added support for particle data in the Enzo-P frontend. See PR 1490.
  • Added an equivalence keyword argument to YTArray.in_units() and YTArray.to(). This makes it possible to specify an equivalence when converting data to a new unit. Also added YTArray.to_value() which allows convering to a new unit, then stripping off the units to return a plain numpy array. See PR 1563.
  • Rather than crashing, yt will now assume default values for cosmology parameters in Gadget HDF5 data if it cannot find the relevant header information. See PR 1578.
  • Improve detection for OpenMP support at compile-time, including adding support for detecting OpenMP on Windows. See PR 1591, PR 1695 and PR 1696.
  • Add support for 2D cylindrical data for most plot callbacks. See PR 1598.
  • Particles outside the domain are now ignored by load_uniform_grid() and load_amr_grids(). See PR 1602.
  • Fix incorrect units for the Gadget internal energy field in cosmology simulations. See PR 1611.
  • Add support for calculating covering grids in parallel. See PR 1612.
  • The number of particles in a dataset loaded by the stream frontend (e.g. via load_uniform_grid) no longer needs to be explicitly provided via the number_of_particles keyword argument, using the number_of_particles keyword will now generate a deprecation warning. See PR 1620.
  • Add support for non-cartesian GAMER data. See PR 1622.
  • If a particle filter depends on another particle filter, both particle filters will be registered for a dataset if the dependent particle filter is registered with a dataset. See PR 1624.
  • The save() method of the various yt plot objets now optionally can accept a tuple of strings instead of a string. If a tuple is supplied, the elments are joined with os.sep to form a path. See PR 1630.
  • The quiver callback now accepts a plot_args keyword argument that allows passing keyword arguments to matplotlib to allow for customization of the quiver plot. See PR 1636.
  • Updates and improvements for the OpenPMD frontend. See PR 1645.
  • The mapserver now works correctly under Python3 and has new features like a colormap selector and plotting multiple fields via layers. See PR 1654 and PR 1668.
  • Substantial performance improvement for calculating the gravitational potential in the clump finder. See PR 1684.
  • Added new methods to ProfilePlot: set_xlabel(), set_ylabel(), annotate_title(), and annotate_text(). See PR 1700 and PR 1705.
  • Speedup for parallel halo finding operation for the FOF and HOP halo finders. See PR 1724.
  • Add support for halo finding using the rockstar halo finder on Python3. See PR 1740.
  • The ValidateParameter field validator has gained the ability for users to explicitly specify the values of field parameters during field detection. This makes it possible to write fields that access different sets of fields depending on the value of the field parameter. For example, a field might define an 'axis' field parameter that can be either 'x', 'y' or 'z'. One can now explicitly tell the field detection system to access the field using all three values of 'axis'. This improvement avoids errors one would see now where only one value or an invalid value of the field parameter will be tested by yt. See PR 1741.
  • It is now legal to pass a dataset instance as the first argument to ProfilePlot and PhasePlot. This is equivalent to passing ds.all_data().
  • Functions that accept a (length, unit) tuple (e.g. (3, 'km') for 3 kilometers) will not raise an error if length is a YTQuantity instance with units attached. See PR 1749.
  • The annotate_timestamp plot annotation now optionally accepts a time_offset keyword argument that sets the zero point of the time scale. Additionally, the annotate_scale plot annotation now accepts a format keyword argument, allowing custom formatting of the scale annotation. See PR 1755.
  • Add support for magnetic field variables and creation time fields in the GIZMO frontend. See PR 1756 and PR 1914.
  • ParticleProjectionPlot now supports the annotate_particles plot callback. See PR 1765.
  • Optmized the performance of off-axis projections for octree AMR data. See PR 1766.
  • Added support for several radiative transfer fields in the ARTIO frontend. See PR 1804.
  • Performance improvement for Boxlib datasets that don’t use AMR. See PR 1834.
  • It is now possible to set custom profile bin edges. See PR 1837.
  • Dropped support for Python3.4. See PR 1840.
  • Add support for reading RAMSES cooling fields. See PR 1853.
  • Add support for NumPy 1.15. See PR 1854.
  • Ensure that functions defined in the plugins file are available in the yt namespace. See PR 1855.
  • Creating a profiles with log-scaled bins but where the bin edges are negative or zero now raises an error instead of silently generating a corrupt, incorrect answer. See PR 1856.
  • Systematically added validation for inputs to data object initializers. See PR 1871.
  • It is now possible to select only a specific particle type in the particle trajectories analysis module. See PR 1887.
  • Substantially improve the performance of selecting particle fields with a cut_region data object. See PR 1892.
  • The iyt command-line entry-point into IPython now installs yt-specific tab-completions. See PR 1900.
  • Derived quantities have been systematically updated to accept a particle_type keyword argument, allowing easier analysis of only a single particle type. See PR 1902 and PR 1922.
  • The annotate_streamlines() function now accepts a display_threshold keyword argument. This suppresses drawing streamlines over any region of a dataset where the field being displayed is less than the threshold. See PR 1922.
  • Add support for 2D nodal data. See PR 1923.
  • Add support for GAMER outputs that use patch groups. This substantially reduces the memory requirements for loading large GAMER datasets. See PR 1935.
  • Add a data_source keyword argument to the annotate_particles plot callback. See PR 1937.
  • Define species fields in the NMSU Art frontend. See PR 1981.
  • Added a __format__ implementation for YTArray. See PR 1985.
  • Derived fields that use a particle filter now only need to be derived for the particle filter type, not for the particle types used to define the particle filter. See PR 1993.
  • Added support for periodic visualizations using ParticleProjectionPlot. See PR 1996.
  • Added YTArray.argsort(). See PR 2002.
  • Calculate the header size from the header specification in the Gadget frontend to allow reading from Gadget binary datasets with nonstandard headers. See PR 2005 and PR 2036.
  • Save the standard deviation in profile.save_as_dataset(). See PR 2008.
  • Allow the color keyword argument to be passed to matplotlib in the annotate_clumps callback to control the color of the clump annotation. See PR 2019.
  • Raise an exception when profiling fields of unequal shape. See PR 2025.
  • The clump info dictionary is now populated as clumps get created instead of during clump.save_as_dataset(). See PR 2053.
  • Avoid segmentation fault in slice selector by clipping slice integer coordinates. See PR 2055.

Minor Enhancements and Bugfixes

  • Fix incorrect use of floating point division in the parallel analysis framework. See PR 1538.
  • Fix integration with that matplotlib QT backend for interactive plotting. See PR 1540.
  • Add support for the particle creation time field in the GAMER frontend. See PR 1546.
  • Various minor improvements to the docs. See PR 1542. and PR 1547.
  • Add better error handling for invalid tipsy aux files. See PR 1549.
  • Fix typo in default Gadget header specification. See PR 1550.
  • Use the git version in the get_yt_version function. See PR 1551.
  • Assume dimensionless units for fields from FITS datasets when we can’t infer the units. See PR 1553.
  • Autodetect ramses extra particle fields. See PR 1555.
  • Fix issue with handling unitless halo quantities in HaloCatalog. See PR 1558.
  • Track the halo catalog creation process using a parallel-safe progress bar. See PR 1559.
  • The PPV Cube functionality no longer crashes if there is no temperature field in the dataset. See PR 1562.
  • Fix crash caused by saving the 'x', 'y', or 'z' fields in clump.save_as_dataset(). See PR 1567.
  • Accept both string and tuple field names in ProfilePlot.set_unit() and PhasePlot.set_unit(). See PR 1568.
  • Fix issues with some arbitrary grid attributes not being reloaded properly after being saved with save_as_dataset(). See PR 1569.
  • Fix units issue in the light cone projection operation. See PR 1574.
  • Use astropy.wcsaxes instead of the independent wcsaxes project. See PR 1577.
  • Correct typo in WarpX field definitions. See PR 1583.
  • Avoid crashing when loading an Enzo dataset with a parameter file that has commented out parameters. See PR 1584.
  • Fix a corner case in the clump finding machinery where the reference to the parent clump is invalid after pruning a child clump that has no siblings. See PR 1587.
  • Fix issues with setting up yt fields for the magnetic and velocity field components and associated derived fields in curvilinear coordinate systems. See PR 1588 and PR 1687.
  • Fix incorrect profile values when the profile weight field has values equal to zero. See PR 1590.
  • Fix issues with making matplotlib animations of a ParticleProjectionPlot. See PR 1594.
  • The Scene.annotate_axes() function will now use the correct colors for drawing the axes annotation. See PR 1596.
  • Fix incorrect default plot bounds for a zoomed-in slice plot of a 2D cylindrical dataset. See PR 1597.
  • Fix issue where field accesses on 2D grids would return data with incorrect shapes. See PR 1603.
  • Added a cookbook example for a multipanel phase plot. See PR 1605.
  • Boolean simulation parameters in the Boxlib frontend will now be interpreted correctly. See PR 1618.
  • The ds.particle_type_counts attribute will now be populated correctly for AMReX data.
  • The "rad" unit (added for compatibility with astropy) now has the correct dimensions of angle instead of solid angle. See PR 1628.
  • Fix units issues in several plot callbacks. See PR 1633 and PR 1674.
  • Various fixes for how WarpX fields are interpreted. See PR 1634.
  • Fix incorrect units in the automatically deposited particle fields. See PR 1638.
  • It is now possible to set the axes background color after calling plot.hide_axes(). See PR 1662.
  • Fix a typo in the name of the colors keyword argument passed to matplotlib for the contour callback. See PR 1664.
  • Add support for Enzo Active Particle fields that arrays. See PR 1665.
  • Avoid crash when generating halo catalogs from the rockstar halo finder for small simulation domains. See PR 1679.
  • The clump callback now functions correctly for a reloaded clump dataset. See PR 1683.
  • Fix incorrect calculation for tangential components of vector fields. See PR 1688.
  • Allow halo finders to run in parallel on Python3. See PR 1690.
  • Fix issues with Gadget particle IDs for simulations with large numbers of particles being incorrectly rounded. See PR 1692.
  • ParticlePlot no longer needs to be passed spatial fields in a particular order to ensure that a ParticleProjectionPlot is returned. See PR 1697.
  • Accessing data from a FLASH grid directly now returns float64 data. See PR 1708.
  • Fix periodicity check in YTPoint data object. See PR 1712.
  • Avoid crash on matplotlib 2.2.0 when generating yt plots with symlog colorbars. See PR 1720.
  • Avoid crash when FLASH "unitsystem" parameter is quoted in the HDF5 file. See PR 1722.
  • Avoid issues with creating custom particle filters for OWLS/EAGLE datasets. See PR 1723.
  • Adapt to behavior change in matplotlib that caused plot inset boxes for annotated text to be drawn when none was requested. See PR 1731 and PR 1827.
  • Fix clump finder ignoring field parameters. See PR 1732.
  • Avoid generating NaNs in x-ray emission fields. See PR 1742.
  • Fix compatibility with Sphinx 1.7 when building the docs. See PR 1743.
  • Eliminate usage of deprecated "clobber" keyword argument for various usages of astropy in yt. See PR 1744.
  • Fix incorrect definition of the "d" unit (an alias of "day"). See PR 1746.
  • PhasePlot.set_log() now correctly handles tuple field names as well as string field names. See PR 1787.
  • Fix incorrect axis order in aitoff pixelizer. See PR 1791.
  • Fix crash in when exporting a surface as a ply model. See PR 1792 and PR 1817.
  • Fix crash in scene.save_annotated() in newer numpy versions. See PR 1793.
  • Many tests no longer depend on real datasets. See PR 1801, PR 1805, PR 1809, PR 1883, and PR 1941
  • New tests were added to improve test coverage or the performance of the tests. See PR 1820, PR 1831, PR 1833, PR 1841, PR 1842, PR 1885, PR 1886, PR 1952, PR 1953, PR 1955, and PR 1957.
  • The particle trajectories machinery will raise an error if it is asked to analyze a set of particles with duplicated particle IDs. See PR 1818.
  • Fix incorrect velocity unit int he gadget_fof frontend. See PR 1829.
  • Making an off-axis projection of a cut_region data object with an octree AMR dataset now works correctly. See PR 1858.
  • Replace hard-coded constants in Enzo frontend with calculations to improve agreement with Enzo’s internal constants and improve clarity. See PR 1873.
  • Correct issues with Enzo magnetic units in cosmology simulations. See PR 1876.
  • Use the species names from the dataset rather than hardcoding species names in the WarpX frontend. See PR 1884.
  • Fix issue with masked I/O for unstructured mesh data. See PR 1918.
  • Fix crash when reading DM-only Enzo datasets where some grids have no particles. See PR 1919.
  • Fix crash when loading pure-hydro Nyx dataset. See PR 1950.
  • Avoid crashes when plotting fields that contain NaN. See PR 1951.
  • Avoid crashes when loading NMSU ART data. See PR 1960.
  • Avoid crash when loading WarpX dataset with no particles. See PR 1979.
  • Adapt to API change in glue to fix the to_glue() method on yt data objects. See PR 1991.
  • Fix incorrect width calculation in the annotate_halos() plot callback. See PR 1995.
  • Don’t try to read from files containing zero halos in the gadget_fof frontend. See PR 2001.
  • Fix incorrect calculation in get_ortho_base(). See PR 2013.
  • Avoid issues with the axes background color being inconsistently set. See PR 2018.
  • Fix issue with reading multiple fields at once for octree AMR data sometimes returning data for another field for one of the requested fields. See PR 2020.
  • Fix incorrect domain annotation for Scene.annotate_domain() when using the plane-parallel camera. See PR 2024.
  • Avoid crash when particles are on the domain edges for gadget_fof data. See PR 2034.
  • Avoid stripping code units when processing units through a dataset’s unit system. See PR 2035.
  • Avoid incorrectly rescaling units of metalicity fields. See PR 2038.
  • Fix incorrect units for FLASH "divb" field. See PR 2062.

Version 3.4

Version 3.4 is the first major release of yt since July 2016. It includes 450 pull requests from 44 contributors including 18 new contributors.

  • 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.
  • 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.
  • Added yt.LinePlot, a new plotting class for creating 1D plots along lines through a dataset. See Github PR 1509 and Github PR 1440.
  • Added yt.define_unit to easily define new units in yt’s unit system. See Bitbucket PR 2485.
  • Added yt.plot_2d, a wrapper around SlicePlot for plotting 2D datasets. See Github PR 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.
  • 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.
  • 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 and Github PR 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.
  • Added support for the Enzo-p code. See Github PR 1447, Github PR 1443 and Github PR 1439.
  • Added support for the AMReX code. See Bitbucket PR 2530.
  • Added support for the openPMD output format. See Bitbucket PR 2376.
  • Added support for reading face-centered and vertex-centered fields for block AMR codes. See Bitbucket PR 2575.
  • Added support for loading outputs from the Amiga Halo Finder. See Github PR 1477.
  • Added support for particle fields for Boxlib data. See Bitbucket PR 2510 and Bitbucket PR 2497.
  • Added support for custom RAMSES particle fields. See Github PR 1470.
  • Added support for RAMSES-RT data. See Github PR 1456 and Github PR 1449.
  • Added support for Enzo MHDCT fields. See Github PR 1438.
  • Added support for units and particle fields to the GAMER frontend. See Bitbucket PR 2366 and Bitbucket PR 2408.
  • Added support for type 2 Gadget binary outputs. See Bitbucket PR 2355.
  • Added the ability to detect and read double precision Gadget data. See Bitbucket PR 2537.
  • Added the ability to detect and read in big endian Gadget data. See Github PR 1353.
  • Added support for Nyx datasets that do not contain particles. See Bitbucket PR 2571
  • A number of untested and unmaintained modules have been deprecated and moved to the yt attic repository. 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.
  • The photon_simulator analysis module has been deprecated in favor of the pyXSIM package, available separately from yt. See Bitbucket PR 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.
  • 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.
  • 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.
  • PlotWindow plots can now optionally use a right-handed coordinate system. See Bitbucket PR 2318.
  • The isocontour API has been overhauled to make use of units. See Bitbucket PR 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.
  • Added a data_source keyword argument to OffAxisProjectionPlot. See Bitbucket PR 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 and Bitbucket PR 2471.
  • Added a yt upload command-line helper to upload files to the yt curldrop at the bash command line. See Github PR 1471.
  • If it’s installed, colormaps from the cmocean package will be made available as yt colormaps. See Bitbucket PR 2439.
  • It is now possible to visualize unstructured mesh fields defined on multiple mesh blocks. See Bitbucket PR 2487.
  • Add support for second-order interpolation when slicing tetrahedral unstructured meshes. See Bitbucket PR 2550.
  • Add support for volume rendering second-order tetrahedral meshes. See Bitbucket PR 2401.
  • Add support for QUAD9 mesh elements. See Bitbucket PR 2549.
  • Add support for second-order triangle mesh elements. See Bitbucket PR 2378.
  • Added support for dynamical dark energy parameterizations to the Cosmology object. See Bitbucket PR 2572.
  • ParticleProfile can now handle log-scaled bins and data with negative values. See Bitbucket PR 2564 and Github PR 1510.
  • Cut region data objects can now be saved as reloadable datasets using save_as_dataset. See Bitbucket PR 2541.
  • Clump objects can now be saved as reloadable datasets using save_as_dataset. See Bitbucket PR 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.
  • 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.
  • The PointSource volume rendering source now optionally accepts a radius keyword argument to draw spatially extended points. See Bitbucket PR 2404.
  • It is now possible to save volume rendering images in eps, ps, and pdf format. See Github PR 1504.

Minor Enhancements and Bugfixes

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

Version 3.3

Version 3.3 is the first major release of yt since July 2015. It includes more than 3000 commits from 41 contributors, including 12 new contributors.

Major enhancements

  • Raw and processed data from selections, projections, profiles and so forth can now be saved in a ytdata format and loaded back in by yt. See Saving Reloadable Data.
  • Totally re-worked volume rendering API. The old API is still available for users who prefer it, however. See 3D Visualization and Volume Rendering.
  • Support for unstructured mesh visualization. See Unstructured Mesh Slices and Unstructured Mesh Rendering.
  • Interactive Data Visualization for AMR and unstructured mesh datasets. See Interactive Data Visualization.
  • Several new colormaps, including a new default, ‘arbre’. The other new colormaps are named ‘octarine’, ‘kelp’, and ‘dusk’. All these new colormaps were generated using the viscm package and should do a better job of representing the data for colorblind viewers and when printed out in grayscale. See Colormaps for more detail.
  • New frontends for the ExodusII, GAMER, and Gizmo data formats.
  • The unit system associated with a dataset is now customizable, defaulting to CGS. See Unit Systems.
  • Enhancements and usability improvements for analysis modules, especially the absorption_spectrum, photon_simulator, and light_ray modules. See Synthetic Observation.
  • Data objects can now be created via an alternative Numpy-like API. See Slicing Syntax for Selecting Data.
  • A line integral convolution plot modification. See Overplot Line Integral Convolution.
  • Many speed optimizations, including to the volume rendering, units, tests, covering grids, the absorption spectrum and photon simulator analysis modules, and ghost zone generation.
  • Packaging and release-related improvements: better install and setup scripts, automated PR backporting.
  • Readability improvements to the codebase, including linting, removing dead code, and refactoring much of the Cython.
  • Improvements to the CI infrastructure, including more extensible answer tests and automated testing for Python 3 and Windows.
  • Numerous documentation improvements, including formatting tweaks, bugfixes, and many new cookbook recipes.
  • Support for geographic (lat/lon) coordinates.
  • Several improvements for SPH codes, including alternative smoothing kernels, an add_smoothed_particle_field function, and particle type-aware octree construction for Gadget data.
  • Roundtrip conversions between Pint and yt units.
  • Added halo data containers for gadget_fof frontend.
  • Enabled support for spherical datasets in the BoxLib frontend.
  • Many new tests have been added.
  • Better hashing for Selector objects.

Minor enhancements and bugfixes

  • Fixed many bugs related to Python 3 compatibility
  • Fixed bugs related to compatibility issues with newer versions of numpy
  • Added the ability to export data objects to a Pandas dataframe
  • Added support for the fabs ufunc to YTArray
  • Fixed two licensing issues
  • Fixed a number of bugs related to Windows compatibility.
  • We now avoid hard-to-decipher tracebacks when loading empty files or directories
  • Fixed a bug related to ART star particle creation time field
  • Fixed a bug caused by using the wrong int type for indexing in particle deposit
  • Fixed a NameError bug in comparing temperature units with offsets
  • Fixed an API bug in YTArray casting during coercion from YTQuantity
  • Added loadtxt and savetxt convenience functions for YTArray
  • Fixed an issue caused by not sort species names with Enzo
  • Fixed a units bug for RAMSES when boxlen > 1.
  • Fixed process_chunk function for non-cartesian geometry.
  • Added scale_factor attribute to cosmological simulation datasets
  • Fixed a bug where “center” vectors are used instead of “normal” vectors in get_sph_phi(), etc.
  • Fixed issues involving invalid FRBs when uses called _setup_plots in their scripts
  • Added a text_args keyword to annotate_scale() callback
  • Added a print_stats function for RAMSES
  • Fixed a number of bugs in the Photon Simulator
  • Added support for particle fields to the [Min,Max]Location derived quantities
  • Fixed some units bugs for Gadget cosmology simulations
  • Fixed a bug with Gadget/GIZMO StarFormationRate units
  • Fixed an issue in TimeSeriesData where all the filenames were getting passed to load on each processor.
  • Fixed a units bug in the Tipsy frontend
  • Ensured that ARTIOIndex.get_smallest_dx() returns a quantity with units
  • Ensured that plots are valid after invalidating the figure
  • Fixed a bug regarding code unit labels
  • Fixed a bug with reading Tipsy Aux files
  • Added an effective redshift field to the Light Ray analysis module for use in AbsorptionSpectrum
  • Fixed a bug with the redshift calculation in LightRay analysis module
  • Fixed a bug in the Orion frontend when you had more than 10 on-disk particle fields in the file
  • Detect more types of ART files
  • Update derived_field_list in add_volume_weighted_smoothed_field
  • Fixed casting issues for 1D and 2D Enzo simulations
  • Avoid type indirection when setting up data object entry points
  • Fixed issues with SIMPUT files
  • Fixed loading athena data in python3 with provided parameters
  • Tipsy cosmology unit fixes
  • Fixed bad unit labels for compound units
  • Making the xlim and ylim of the PhasePlot plot axes controllable
  • Adding grid_arrays to grid_container
  • An Athena and a GDF bugfix
  • A small bugfix and some small enhancements for sunyaev_zeldovich
  • Defer to coordinate handlers for width
  • Make array_like_field return same units as get_data
  • Fixing bug in ray “dts” and “t” fields
  • Check against string_types not str
  • Closed a loophole that allowed improper LightRay use
  • Enabling AbsorptionSpectrum to deposit unresolved spectral lines
  • Fixed an ART byte/string/array issue
  • Changing AbsorptionSpectrum attribute lambda_bins to be lambda_field for consistency
  • No longer require user to save to disk when generating an AbsorptionSpectrum
  • ParticlePlot FRBs can now use save_as_dataset and save attributes properly
  • Added checks to assure ARTIO creates a metal_density field from existing metal fields.
  • Added mask to LightRay to assure output elements have non-zero density (a problem in some SPH datasets)
  • Added a “fields” attribute to datasets
  • Updated the TransferFunctionHelper to work with new profiles
  • Fixed a bug where the field_units kwarg to load_amr_grids didn’t do anything
  • Changed photon_simulator’s output file structure
  • Fixed a bug related to setting output_units.
  • Implemented ptp operation.
  • Added effects of transverse doppler redshift to LightRay
  • Fixed a casting error for float and int64 multiplication in sdf class
  • Added ability to read and write YTArrays to and from groups within HDF5 files
  • Made ftype of “on-disk” stream fields “stream”
  • Fixed a strings decoding issue in the photon simulator
  • Fixed an incorrect docstring in load_uniform_grid
  • Made PlotWindow show/hide helpers for axes and colorbar return self
  • Made Profile objects store field metadata.
  • Ensured GDF unit names are strings
  • Taught off_axis_projection about its resolution keyword.
  • Reintroduced sanitize_width for polar/cyl coordinates.
  • We now fail early when load_uniform_grid is passed data with an incorrect shape
  • Replaced progress bar with tqdm
  • Fixed redshift scaling of “Overdensity” field in yt-2.x
  • Fixed several bugs in the eps_writer
  • Fixed bug affecting 2D BoxLib simulations.
  • Implemented to_json and from_json for the UnitRegistry object
  • Fixed a number of issues with ds.find_field_values_at_point[s]
  • Fixed a bug where sunrise_exporter was using wrong imports
  • Import HUGE from utilities.physical_ratios
  • Fixed bug in ARTIO table look ups
  • Adding support for longitude and latitude
  • Adding halo data containers for gadget_fof frontend.
  • Can now compare YTArrays without copying them
  • Fixed several bugs related to active particle datasets
  • Angular_momentum_vector now only includes space for particle fields if they exist.
  • Image comparison tests now print a meaningful error message if they fail.
  • Fixed numpy 1.11 compatibility issues.
  • Changed _skip_cache to be True by default.
  • Enable support for spherical datasets in the BoxLib frontend.
  • Fixed a bug in add_deposited_particle_field.
  • Fixed issues with input sanitization in the point data object.
  • Fixed a copy/paste error introduced by refactoring WeightedMenParticleField
  • Fixed many formatting issues in the docs build
  • Now avoid creating particle unions for particle types that have no common fields
  • Patched ParticlePlot to work with filtered particle fields.
  • Fixed a couple corner cases in gadget_fof frontend
  • We now properly normalise all normal vectors in functions that take a normal vector (for e.g. get_sph_theta)
  • Fixed a bug where the transfer function features were not always getting cleared properly.
  • Made the Chombo frontend is_valid method smarter.
  • Added a get_hash() function to yt/funcs.py which returns a hash for a file
  • Added Sievert to the default unit symbol table
  • Corrected an issue with periodic “wiggle” in AbsorptionSpectrum instances
  • Made ds.field_list sorted by default
  • Bug fixes for the Nyx frontend
  • Fixed a bug where the index needed to be created before calling derived quantities
  • Made latex_repr a property, computed on-demand
  • Fixed a bug in off-axis slice deposition
  • Fixed a bug with some types of octree block traversal
  • Ensured that mpi operations retain ImageArray type instead of downgrading to YTArray parent class
  • Added a call to _setup_plots in the custom colorbar tickmark example
  • Fixed two minor bugs in save_annotated
  • Added ability to specify that DatasetSeries is not a mixed data type
  • Fixed a memory leak in ARTIO
  • Fixed copy/paste error in to_frb method.
  • Ensured that particle dataset max_level is consistent with the index max_level
  • Fixed an issue where fields were getting added multiple times to field_info.field_list
  • Enhanced annotate_ray and annotate_arrow callbacks
  • Added GDF answer tests
  • Made the YTFieldTypeNotFound exception more informative
  • Added a new function, fake_vr_orientation_test_ds(), for use in testing
  • Ensured that instances of subclasses of YTArray have the correct type
  • Re-enabled max_level for projections, ProjectionPlot, and OffAxisProjectionPlot
  • Fixed a bug in the Orion 2 field definitions
  • Fixed a bug caused by matplotlib not being added to install_requires
  • Edited PhasePlot class to have an annotate_title method
  • Implemented annotate_cell_edges
  • Handled KeyboardInterrupt in volume rendering Cython loop
  • Made old halo finders now accept ptype
  • Updated the latex commands in yt cheatsheet
  • Fixed a circular dependency loop bug in abar field definition for FLASH datasets
  • Added neutral species aliases as described in YTEP 0003
  • Fixed a logging issue: don’t create a StreamHandler unless we will use it
  • Correcting how theta and phi are calculated in _particle_velocity_spherical_radius, _particle_velocity_spherical_theta, _particle_velocity_cylindrical_radius, and _particle_velocity_cylindrical_theta
  • Fixed a bug related to the field dictionary in load_particles
  • Allowed for the special case of supplying width as a tuple of tuples
  • Made yt compile with MSVC on Windows
  • Fixed a bug involving mask for dt in octree
  • Merged the get_yt.sh and install_script.sh into one
  • Added tests for the install script
  • Allowed use axis names instead of dimensions for spherical pixelization
  • Fixed a bug where close() wasn’t being called in HDF5FileHandler
  • Enhanced commandline image upload/delete
  • Added get_brewer_cmap to get brewer colormaps without importing palettable at the top level
  • Fixed a bug where a parallel_root_only function was getting called inside another parallel_root_only function
  • Exit the install script early if python can’t import ‘_ssl’ module
  • Make PlotWindow’s annotate_clear method invalidate the plot
  • Adding int wrapper to avoid deprecation warning from numpy
  • Automatically create vector fields for magnetic_field
  • Allow users to completely specify the filename of a 1D profile
  • Force nose to produce meaningful traceback for cookbook recipes’ tests
  • Fixed x-ray display_name and documentation
  • Try to guess and load particle file for FLASH dataset
  • Sped up top-level yt import
  • Set the field type correctly for fields added as particle fields
  • Added a position location method for octrees
  • Fixed a copy/paste error in uhstack function
  • Made trig functions give correct results when supplied data with dimensions of angle but units that aren’t radian
  • Print out some useful diagnostic information if check_for_openmp() fails
  • Give user-added derived fields a default field type
  • Added support for periodicity in annotate_particles.
  • Added a check for whether returned field has units in volume-weighted smoothed fields
  • Casting array indices as ints in colormaps infrastructure
  • Fixed a bug where the standard particle fields weren’t getting set up correctly for the Orion frontends
  • Enabled LightRay to accept loaded datasets instead of just filenames
  • Allowed for adding or subtracting arrays filled with zeros without checking units.
  • Fixed a bug in selection for semistructured meshes.
  • Removed ‘io’ from enzo particle types for active particle datasets
  • Added support for FLASH particle datasets.
  • Silenced a deprecation warning from IPython
  • Eliminated segfaults in KDTree construction
  • Fixed add_field handling when passed a tuple
  • Ensure field parameters are correct for fields that need ghost zones
  • Made it possible to use DerivedField instances to access data
  • Added ds.particle_type_counts
  • Bug fix and improvement for generating Google Cardboard VR in StereoSphericalLens
  • Made DarkMatterARTDataset more robust in its _is_valid
  • Added Earth radius to units
  • Deposit hydrogen fields to grid in gizmo frontend
  • Switch to index values being int64
  • ValidateParameter ensures parameter values are used during field detection
  • Switched to using cythonize to manage dependencies in the setup script
  • ProfilePlot style changes and refactoring
  • Cancel terms with identical LaTeX representations in a LaTeX representation of a unit
  • Only return early from comparison validation if base values are equal
  • Enabled particle fields for clump objects
  • Added validation checks for data types in callbacks
  • Enabled modification of image axis names in coordinate handlers
  • Only add OWLS/EAGLE ion fields if they are present
  • Ensured that PlotWindow plots continue to look the same under matplotlib 2.0
  • Fixed bug in quiver callbacks for off-axis slice plots
  • Only visit octree children if going to next level
  • Check that CIC always gets at least two cells
  • Fixed compatibility with matplotlib 1.4.3 and earlier
  • Fixed two EnzoSimulation bugs
  • Moved extraction code from YTSearchCmd to its own utility module
  • Changed amr_kdtree functions to be Node class methods
  • Sort block indices in order of ascending levels to match order of grid patches
  • MKS code unit system fixes
  • Disabled bounds checking on pixelize_element_mesh
  • Updated light_ray.py for domain width != 1
  • Implemented a DOAP file generator
  • Fixed bugs for 2D and 1D enzo IO
  • Converted mutable Dataset attributes to be properties that return copies
  • Allowing LightRay segments to extend further than one box length
  • Fixed a divide-by-zero error that occasionally happens in triangle_plane_intersect
  • Make sure we have an index in subclassed derived quantities
  • Added an initial draft of an extensions document
  • Made it possible to pass field tuples to command-line plotting
  • Ensured the positions of coordinate vector lines are in code units
  • Added a minus sign to definition of sz_kinetic field
  • Added grid_levels and grid_indices fields to octrees
  • Added a morton_index derived field
  • Added Exception to AMRKDTree in the case of particle of oct-based data

Version 3.2

Major enhancements

  • Particle-Only Plots - a series of new plotting functions for visualizing particle data. See here for 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 to learn how to load halo catalogs as regular yt datasets.
  • Custom colormaps can now be easily defined and added - see here 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
  • Updating ragged array tests for NumPy 1.9.1
  • Force returning lists for HDF5FileHandler

Version 3.1

This is a scheduled feature release. Below are the itemized, aggregate changes since version 3.0.

Major changes:

Minor or bugfix changes:

  • The Ampere unit now accepts SI prefixes. PR 1393.
  • The Gadget InternalEnergy and StarFormationRate fields are now read in with the correct units. PR 1392, PR 1379.
  • Substantial improvements for the PPVCube analysis module and support for FITS dataset. PR 1390, PR 1367, PR 1347, PR 1326, PR 1280, PR 1336.
  • The center of a PlotWindow plot can now be set to the maximum or minimum of any field. PR 1280.
  • Fixes for yt testing infrastructure. PR 1388, PR 1348.
  • Projections are now performed using an explicit path length field for all coordinate systems. PR 1307.
  • An example notebook for simulations using the OWLS data format has been added to the documentation. PR 1386.
  • Fix for the camera.draw_line function. PR 1380.
  • Minor fixes and improvements for yt plots. PR 1376, PR 1374, PR 1288, PR 1290.
  • Significant documentation reorganization and improvement. PR 1375, PR 1359.
  • Fixed a conflict in the CFITSIO library used by the x-ray analysis module. PR 1365.
  • Miscellaneous code cleanup. PR 1371, PR 1361.
  • yt now hooks up to the python logging infrastructure in a more standard fashion, avoiding issues with yt logging showing up with using other libraries. PR 1355, PR 1362, PR 1360.
  • The docstring for the projection data object has been corrected. PR 1366
  • A bug in the calculation of the plot bounds for off-axis slice plots has been fixed. PR 1357.
  • Improvements for the yt-rockstar interface. PR 1352, PR 1317.
  • Fix issues with plot positioning with saving to postscript or encapsulated postscript. PR 1353.
  • It is now possible to supply a default value for get_field_parameter. PR 1343.
  • A bug in the interpretation of the units of RAMSES simulations has been fixed. PR 1335.
  • Plot callbacks are now only executed once before the plot is saved. PR 1328.
  • Performance improvements for smoothed covering grid alias fields. PR 1331.
  • Improvements and bugfixes for the halo analysis framework. PR 1349, PR 1325.
  • Fix issues with the default setting for the center field parameter. PR 1327.
  • Avoid triggering warnings in numpy and matplotlib. PR 1334, PR 1300.
  • Updates for the field list reference. PR 1344, PR 1321, PR 1318.
  • yt can now be run in parallel on a subset of available processors using an MPI subcommunicator. PR 1340
  • Fix for incorrect units when loading an Athena simulation as a time series. PR 1341.
  • Improved support for Enzo 3.0 simulations that have not produced any active particles. PR 1329.
  • Fix for parsing OWLS outputs with periods in the file path. PR 1320.
  • Fix for periodic radius vector calculation. PR 1311.
  • Improvements for the Maestro and Castro frontends. PR 1319.
  • Clump finding is now supported for more generic types of data. PR 1314
  • Fix unit consistency issue when mixing dimensionless unit symbols. PR 1300.
  • Improved memory footprint in the photon_simulator. PR 1304.
  • Large grids in Athena datasets produced by the join_vtk script can now be optionally split, improving parallel performance. PR 1304.
  • Slice plots now accept a data_source keyword argument. PR 1310.
  • Corrected inconsistent octrees in the RAMSES frontend. PR 1302
  • Nearest neighbor distance field added. PR 1138.
  • Improvements for the ORION2 frontend. PR 1303
  • Enzo 3.0 frontend can now read active particle attributes that are arrays of any shape. PR 1248.
  • Answer tests added for halo finders. PR 1253
  • A setup_function has been added to the LightRay initializer. PR 1295.
  • The SPH code frontends have been reorganized into separate frontend directories. PR 1281.
  • Fixes for accessing deposit fields for FLASH data. PR 1294
  • Added tests for ORION datasets containing sink and star particles. PR 1252
  • Fix for field names in the particle generator. PR 1278.
  • Added wrapper functions for numpy array manipulation functions. PR 1287.
  • Added support for packed HDF5 Enzo datasets. PR 1282.

Version 3.0

This release of yt features an entirely rewritten infrastructure for data ingestion, indexing, and representation. While past versions of yt were focused on analysis and visualization of data structured as regular grids, this release features full support for particle (discrete point) data such as N-body and SPH data, irregular hexahedral mesh data, and data organized via octrees. This infrastructure will be extended in future versions for high-fidelity representation of unstructured mesh datasets.

Highlighted changes in yt 3.0:

  • Units now permeate the code base, enabling self-consistent unit transformations of all arrays and quantities returned by yt.
  • Particle data is now supported using a lightweight octree. SPH data can be smoothed onto an adaptively-defined mesh using standard SPH smoothing
  • Support for octree AMR codes
  • Preliminary Support for non-Cartesian data, such as cylindrical, spherical, and geographical
  • Revamped analysis framework for halos and halo catalogs, including direct ingestion and analysis of halo catalogs of several different formats
  • Support for multi-fluid datasets and datasets containing multiple particle types
  • Flexible support for dynamically defining new particle types using filters on existing particle types or by combining different particle types.
  • Vastly improved support for loading generic grid, AMR, hexahedral mesh, and particle without hand-coding a frontend for a particular data format.
  • New frontends for ART, ARTIO, Boxlib, Chombo, FITS, GDF, Subfind, Rockstar, Pluto, RAMSES, SDF, Gadget, OWLS, PyNE, Tipsy, as well as rewritten frontends for Enzo, FLASH, Athena, and generic data.
  • First release to support installation of yt on Windows
  • Extended capabilities for construction of simulated observations, and new facilities for analyzing and visualizing FITS images and cube data
  • Many performance improvements

This release is the first of several; while most functionality from the previous generation of yt has been updated to work with yt 3.0, it does not yet have feature parity in all respects. While the core of yt is stable, we suggest the support for analysis modules and volume rendering be viewed as a late-stage beta, with a series of additional releases (3.1, 3.2, etc) appearing over the course of the next year to improve support in these areas.

For a description of how to bring your 2.x scripts up to date to 3.0, and a summary of common gotchas in this transition, please see What’s New and Different in yt 3.0?.

Version 2.6

This is a scheduled release, bringing to a close the development in the 2.x series. Below are the itemized, aggregate changes since version 2.5.

Major changes:

  • yt is now licensed under the 3-clause BSD license.
  • HEALPix has been removed for the time being, as a result of licensing incompatibility.
  • The addition of a frontend for the Pluto code
  • The addition of an OBJ exporter to enable transparent and multi-surface exports of surfaces to Blender and Sketchfab
  • New absorption spectrum analysis module with documentation
  • Adding ability to draw lines with Grey Opacity in volume rendering
  • Updated physical constants to reflect 2010 CODATA data
  • Dependency updates (including IPython 1.0)
  • Better notebook support for yt plots
  • Considerably (10x+) faster kD-tree building for volume rendering
  • yt can now export to RADMC3D
  • Athena frontend now supports Static Mesh Refinement and units ( http://hub.yt-project.org/nb/7l1zua )
  • Fix long-standing bug for plotting arrays with range of zero
  • Adding option to have interpolation based on non-uniform bins in interpolator code
  • Upgrades to most of the dependencies in the install script
  • ProjectionPlot now accepts a data_source keyword argument

Minor or bugfix changes:

  • Fix for volume rendering on the command line
  • map_to_colormap will no longer return out-of-bounds errors
  • Fixes for dds in covering grid calculations
  • Library searching for build process is now more reliable
  • Unit fix for “VorticityGrowthTimescale” field
  • Pyflakes stylistic fixes
  • Number density added to FLASH
  • Many fixes for Athena frontend
  • Radius and ParticleRadius now work for reduced-dimensionality datasets
  • Source distributions now work again!
  • Athena data now 64 bits everywhere
  • Grids displays on plots are now shaded to reflect the level of refinement
  • show_colormaps() is a new function for displaying all known colormaps
  • PhasePlotter by default now adds a colormap.
  • System build fix for POSIX systems
  • Fixing domain offsets for halo centers-of-mass
  • Removing some Enzo-specific terminology in the Halo Mass Function
  • Addition of coordinate vectors on volume render
  • Pickling fix for extracted regions
  • Addition of some tracer particle annotation functions
  • Better error message for “yt” command
  • Fix for radial vs poloidal fields
  • Piernik 2D data handling fix
  • Fixes for FLASH current redshift
  • 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
  • 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
  • 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
  • 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
  • Speed improvements to ellipsoidal particle detection
  • Updates to FLASH fields
  • CASTRO frontend bug fixes
  • Fisheye camera bug fixes
  • Answer testing now includes plot window answer testing
  • Athena data serialization
  • load_uniform_grid can now decompose dims >= 1024. (#537)
  • Axis unit setting works correctly for unit names (#534)
  • ThermalEnergy is now calculated correctly for Enzo MHD simulations (#535)
  • Radius fields had an asymmetry in periodicity calculation (#531)
  • Boolean regions can now be pickled (#517)

Version 2.5

Many below-the-surface changes happened in yt 2.5 to improve reliability, fidelity of the answers, and streamlined user interface. The major change in this release has been the immense expansion in testing of yt. We now have over 2000 unit tests (run on every commit, thanks to both Kacper Kowalik and Shining Panda) as well as answer testing for FLASH, Enzo, Chombo and Orion data.

The Stream frontend, which can construct datasets in memory, has been improved considerably. It’s now easier than ever to load data from disk. If you know how to get volumetric data into Python, you can use either the load_uniform_grid function or the load_amr_grid function to create an in-memory dataset that yt can analyze.

yt now supports the Athena code.

yt is now focusing on providing first class support for the IPython notebook. In this release, plots can be displayed inline. The Reason HTML5 GUI will be merged with the IPython notebook in a future release.

Install Script Changes:

  • SciPy can now be installed
  • Rockstar can now be installed
  • Dependencies can be updated with “yt update –all”
  • Cython has been upgraded to 0.17.1
  • Python has been upgraded to 2.7.3
  • h5py has been upgraded to 2.1.0
  • hdf5 has been upgraded to 1.8.9
  • matplotlib has been upgraded to 1.2.0
  • IPython has been upgraded to 0.13.1
  • Forthon has been upgraded to 0.8.10
  • nose has been added
  • sympy has been added
  • python-hglib has been added

We’ve also improved support for installing on OSX, Ubuntu and OpenSUSE.

Most Visible Improvements

  • Nearly 200 pull requests and over 1000 changesets have been merged since yt 2.4 was release on August 2nd, 2012.
  • numpy is now imported as np, not na. na will continue to work for the foreseeable future.
  • You can now get a yt cheat sheet <http://yt-project.org/docs/2.5/cheatsheet.pdf>!
  • yt can now load simulation data created by Athena.
  • The Rockstar halo finder can now be installed by the install script
  • SciPy can now be installed by the install script
  • Data can now be written out in two ways:
    • Sidecar files containing expensive derived fields can be written and implicitly loaded from.
    • GDF files, which are portable yt-specific representations of full simulations, can be created from any dataset. Work is underway on a pure C library that can be linked against to load these files into simulations.
  • The “Stream” frontend, for loading raw data in memory, has been greatly expanded and now includes initial conditions generation functionality, particle fields, and simple loading of AMR grids with load_amr_grids.
  • Spherical and Cylindrical fields have been sped up and made to have a uniform interface. These fields can be the building blocks of more advanced fields.
  • Coordinate transformations have been sped up and streamlined. It is now possible to convert any scalar or vector field to a new cartesian, spherical, or cylindrical coordinate system with an arbitrary orientation. This makes it possible to do novel analyses like profiling the toroidal and poloidal velocity as a function of radius in an inclined disk.
  • Many improvements to the EnzoSimulation class, which can now find many different types of data.
  • Image data is now encapsulated in an ImageArray class, which carries with it provenance information about its trajectory through yt.
  • Streamlines now query at every step along the streamline, not just at every cell.
  • Surfaces can now be extracted and examined, as well as uploaded to Sketchfab.com for interactive visualization in a web browser.
  • allsky_projection can now accept a datasource, making it easier to cut out regions to examine.
  • Many, many improvements to PlotWindow. If you’re still using PlotCollection, check out ProjectionPlot, SlicePlot, OffAxisProjectionPlot and OffAxisSlicePlot.
  • PlotWindow can now accept a timeseries instead of a dataset.
  • Many fixes for 1D and 2D data, especially in FLASH datasets.
  • Vast improvements to the particle file handling for FLASH datasets.
  • Particles can now be created ex nihilo with CICSample_3.
  • Rockstar halo finding is now a targeted goal. Support for using Rockstar has improved dramatically.
  • Increased support for tracking halos across time using the FOF halo finder.
  • The command yt notebook has been added to spawn an IPython notebook server, and the yt.imods module can replace yt.mods in the IPython Notebook to enable better integration.
  • Metallicity-dependent X-ray fields have now been added.
  • Grid lines can now be added to volume renderings.
  • Volume rendering backend has been updated to use an alpha channel, fixing parallel opaque volume renderings. This also enables easier blending of multiple images and annotations to the rendering. Users are encouraged to look at the capabilities of the ImageArray for writing out renders, as updated in the cookbook examples. Volume renders can now be saved with an arbitrary background color.
  • Periodicity, or alternately non-periodicity, is now a part of radius calculations.
  • The AMRKDTree has been rewritten. This allows parallelism with other than power-of-2 MPI processes, arbitrary sets of grids, and splitting of unigrids.
  • Fixed Resolution Buffers and volume rendering images now utilize a new ImageArray class that stores information such as data source, field names, and other information in a .info dictionary. See the ImageArray docstrings for more information on how they can be used to save to a bitmap or hdf5 file.

Version 2.4

The 2.4 release was particularly large, encompassing nearly a thousand changesets and a number of new features.

To help you get up to speed, we’ve made an IPython notebook file demonstrating a few of the changes to the scripting API. You can download it here.

Most Visible Improvements

  • Threaded volume renderer, completely refactored from the ground up for speed and parallelism.
  • The Plot Window (see Slices & Projections) is now fully functional! No more PlotCollections, and full, easy access to Matplotlib axes objects.
  • Many improvements to Time Series analysis:
    • EnzoSimulation now integrates with TimeSeries analysis!
    • Auto-parallelization of analysis and parallel iteration
    • Memory usage when iterating over datasets reduced substantially
  • Many improvements to Reason, the yt GUI
    • Addition of “yt reason” as a startup command
    • Keyboard shortcuts in projection & slice mode: z, Z, x, X for zooms, hjkl, HJKL for motion
    • Drag to move in projection & slice mode
    • Contours and vector fields in projection & slice mode
    • Color map selection in projection & slice mode
    • 3D Scene
  • Integration with the all new yt Hub ( http://hub.yt-project.org/ ): upload variable resolution projections, slices, project information, vertices and plot collections right from the yt command line!

Other Changes

  • ProjectionPlot and SlicePlot supplant the functionality of PlotCollection.
  • Camera path creation from keyframes and splines
  • Ellipsoidal data containers and ellipsoidal parameter calculation for halos
  • PyX and ZeroMQ now available in the install script
  • Consolidation of unit handling
  • HDF5 updated to 1.8.7, Mercurial updated to 2.2, IPython updated to 0.12
  • Preview of integration with Rockstar halo finder
  • Improvements to merger tree speed and memory usage
  • Sunrise exporter now compatible with Sunrise 4.0
  • Particle trajectory calculator now available!
  • Speed and parallel scalability improvements in projections, profiles and HOP
  • New Vorticity-related fields
  • Vast improvements to the ART frontend
  • Many improvements to the FLASH frontend, including full parameter reads, speedups, and support for more corner cases of FLASH 2, 2.5 and 3 data.
  • Integration of the Grid Data Format frontend, and a converter for Athena data to this format.
  • Improvements to command line parsing
  • Parallel import improvements on parallel filesystems (from yt.pmods import *)
  • proj_style keyword for projections, for Maximum Intensity Projections (proj_style = "mip")
  • Fisheye rendering for planetarium rendering
  • Profiles now provide *_std fields for standard deviation of values
  • Generalized Orientation class, providing 6DOF motion control
  • parallel_objects iteration now more robust, provides optional barrier. (Also now being used as underlying iteration mechanism in many internal routines.)
  • Dynamic load balancing in parallel_objects iteration.
  • Parallel-aware objects can now be pickled.
  • Many new colormaps included
  • Numerous improvements to the PyX-based eps_writer module
  • FixedResolutionBuffer to FITS export.
  • Generic image to FITS export.
  • Multi-level parallelism for extremely large cameras in volume rendering
  • Light cone and light ray updates to fit with current best practices for parallelism

Version 2.3

(yt 2.3 docs)
  • Multi-level parallelism
  • Real, extensive answer tests
  • Boolean data regions (see Combining Objects: Boolean Data Objects)
  • Isocontours / flux calculations (see 3D Surfaces and Sketchfab)
  • Field reorganization
  • PHOP memory improvements
  • Bug fixes for tests
  • Parallel data loading for RAMSES, along with other speedups and improvements there
  • WebGL interface for isocontours and a pannable map widget added to Reason
  • Performance improvements for volume rendering
  • Adaptive HEALPix support
  • Column density calculations
  • Massive speedup for 1D profiles
  • Lots more, bug fixes etc.
  • Substantial improvements to the documentation, including Using the Manual Plotting Interface and a revamped orientation.

Version 2.2

(yt 2.2 docs)
  • Command-line submission to the yt Hub (http://hub.yt-project.org/)
  • Initial release of the web-based GUI Reason, designed for efficient remote usage over SSH tunnels
  • Absorption line spectrum generator for cosmological simulations (see absorption_spectrum)
  • Interoperability with ParaView for volume rendering, slicing, and so forth
  • Support for the Nyx code
  • An order of magnitude speed improvement in the RAMSES support
  • Quad-tree projections, speeding up the process of projecting by up to an order of magnitude and providing better load balancing
  • “mapserver” for in-browser, Google Maps-style slice and projection visualization (see Mapserver - A Google-Maps-like Interface to your Data)
  • Many bug fixes and performance improvements
  • Halo loader

Version 2.1

(yt 2.1 docs)
  • HEALPix-based volume rendering for 4pi, allsky volume rendering
  • libconfig is now included
  • SQLite3 and Forthon now included by default in the install script
  • Development guide has been lengthened substantially and a development bootstrap script is now included.
  • Installation script now installs Python 2.7 and HDF5 1.8.6
  • iyt now tab-completes field names
  • Halos can now be stored on-disk much more easily between HaloFinding runs.
  • Halos found inline in Enzo can be loaded and merger trees calculated
  • Support for CASTRO particles has been added
  • Chombo support updated and fixed
  • New code contributions
  • Contour finder has been sped up by a factor of a few
  • Constrained two-point functions are now possible, for LOS power spectra
  • Time series analysis (Time Series Analysis) now much easier
  • Stream Lines now a supported 1D data type
  • Stream Lines now able to be calculated and plotted (Streamlines: Tracking the Trajectories of Tracers in your Data)
  • In situ Enzo visualization now much faster
  • “gui” source directory reorganized and cleaned up
  • Cython now a compile-time dependency, reducing the size of source tree updates substantially
  • yt-supplemental repository now checked out by default, containing cookbook, documentation, handy mercurial extensions, and advanced plotting examples and helper scripts.
  • Pasteboards now supported and available
  • Parallel yt efficiency improved by removal of barriers and improvement of collective operations

Version 2.0

  • Major reorganization of the codebase for speed, ease of modification, and maintainability
  • Re-organization of documentation and addition of Orientation Session
  • Support for FLASH code
  • Preliminary support for MAESTRO, CASTRO, ART, and RAMSES (contributions welcome!)
  • Perspective projection for volume rendering
  • Exporting to Sunrise
  • Preliminary particle rendering in volume rendering visualization
  • Drastically improved parallel volume rendering, via kD-tree decomposition
  • Simple merger tree calculation for FOF catalogs
  • New and greatly expanded documentation, with a “source” button

Version 1.7

  • Direct writing of PNGs
  • Multi-band image writing
  • Parallel halo merger tree (see Halo Merger Tree)
  • Parallel structure function generator (see Two Point Functions)
  • Image pan and zoom object and display widget.
  • Parallel volume rendering (see 3D Visualization and Volume Rendering)
  • Multivariate volume rendering, allowing for multiple forms of emission and absorption, including approximate scattering and Planck emissions. (see 3D Visualization and Volume Rendering)
  • Added Camera interface to volume rendering (See 3D Visualization and Volume Rendering)
  • Off-axis projection (See 3D Visualization and Volume Rendering)
  • Stereo (toe-in) volume rendering (See 3D Visualization and Volume Rendering)
  • DualEPS extension for better EPS construction
  • yt now uses Distribute instead of SetupTools
  • Better iyt initialization for GUI support
  • Rewritten, memory conservative and speed-improved contour finding algorithm
  • Speed improvements to volume rendering
  • Preliminary support for the Tiger code
  • Default colormap is now algae
  • Lightweight projection loading with projload
  • Improvements to yt.data_objects.time_series
  • Improvements to yt.extensions.EnzoSimulation (See Analyzing an Entire Simulation)
  • Removed direct_ray_cast
  • Fixed bug causing double data-read in projections
  • Added Cylinder support to ParticleIO
  • Fixes for 1- and 2-D Enzo datasets
  • Preliminary, largely non-functional Gadget support
  • Speed improvements to basic HOP
  • Added physical constants module
  • Beginning to standardize and enforce docstring requirements, changing to autosummary-based API documentation.

Version 1.6.1

  • Critical fixes to ParticleIO
  • Halo mass function fixes for comoving coordinates
  • Fixes to halo finding
  • Fixes to the installation script
  • “yt instinfo” command to report current installation information as well as auto-update some types of installations
  • Optimizations to the volume renderer (2x-26x reported speedups)

Version 1.6

Version 1.6 is a point release, primarily notable for the new parallel halo finder (see Halo Analysis)

  • (New) Parallel HOP ( http://arxiv.org/abs/1001.3411 , Halo Analysis )
  • (Beta) Software ray casting and volume rendering (see 3D Visualization and Volume Rendering)
  • Rewritten, faster and better contouring engine for clump identification
  • Spectral Energy Distribution calculation for stellar populations (see Synthetic Spectrum Generator)
  • Optimized data structures such as the index
  • Star particle analysis routines (see Star Particle Analysis)
  • Halo mass function routines
  • Completely rewritten, massively faster and more memory efficient Particle IO
  • Fixes for plots, including normalized phase plots
  • Better collective communication in parallel routines
  • Consolidation of optimized C routines into amr_utils
  • Many bug fixes and minor optimizations

Version 1.5

Version 1.5 features many new improvements, most prominently that of the addition of parallel computing abilities (see Parallel Computation With yt) and generalization for multiple AMR data formats, specifically both Enzo and Orion.

  • Rewritten documentation
  • Fully parallel slices, projections, cutting planes, profiles, quantities
  • Parallel HOP
  • Friends-of-friends halo finder
  • Object storage and serialization
  • Major performance improvements to the clump finder (factor of five)
  • Generalized domain sizes
  • Generalized field info containers
  • Dark Matter-only simulations
  • 1D and 2D simulations
  • Better IO for HDF5 sets
  • Support for the Orion AMR code
  • Spherical re-gridding
  • Halo profiler
  • Disk image stacker
  • Light cone generator
  • Callback interface improved
  • Several new callbacks
  • New data objects – ortho and non-ortho rays, limited ray-tracing
  • Fixed resolution buffers
  • Spectral integrator for CLOUDY data
  • Substantially better interactive interface
  • Performance improvements everywhere
  • Command-line interface to many common tasks
  • Isolated plot handling, independent of PlotCollections

Version 1.0

  • Initial release!