yt 3.4.1 release notes The yt community is proud to announce the release of yt 3.4.1. This is a patch release and includes a number of improvements and bugfixes. Note that one of the bugs fixed in this release silently produced invalid results for the values of certain yt fields. See the release notes below for more details. yt (https://yt-project.org) is an open source, community developed toolkit for the analysis and visualization of volumetric data. Development is hosted on GitHub (https://github.com/yt-project/yt). This release includes contributions from 20 contributors, five of whom contributed for the first time: - *Christoph Behrens* - *Josh Borrow* - Corentin Cadiou - Yi-Hao Chen - Bili Dong - Nathan Goldbaum - Philipp Grete - *Stephanie Ho* - Cameron Hummels - Suoqing Ji - Max Katz - Kacper Kowalik - Andrew Myers - Hugo Pfister - Justin Schive - Britton Smith - *Josh Soref* - Matthew Turk - *Daniel Wilcox* - John ZuHone 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 3.4.1 at http://yt-project.org/docs/3.4.1. Binaries for yt 3.4.1 are available via pip and conda. If you installed via the install script or use conda to manage your python installation, you can update yt via: $ conda update -c conda-forge yt And via pip if you manage your python installation with pip: $ pip install -U yt As always, if you have any questions, concerns, or run into any trouble updating please don’t hesitate to send a message to the mailing list or stop by our Slack or IRC channel. yt is the product of a large community of developers and users and we are extraordinarily grateful for and proud of their contributions. Please forward this announcement on to any interested parties. Best, The yt development team <https://hackmd.io/CYMwhgjGYBzAtAUwGwQEbwCwFYQbIgMabwAMYAnMmoYQOywgDMQA?both#Critical-Bugfixes>Critical Bugfixes - The data returned by fields corresponding to the theta or phi component of a vector field in spherical coordinates or the theta component in cylindrical coordinates, including velocity_spherical_theta, velocity_spherical_phi, and velocity_cylindrical_theta as well as the corresponding magnetic field components have been silently returning incorrect results. If you are doing analysis using those fields we strongly encourage you to update to this latest release to get fixed versions of these fields. See PR 1687 <https://github.com/yt-project/yt/pull/1687>. - Define the code_specific_energy unit and ds.specific_energy_unit attribute. This allows user control over the value of the specific energy unit independent of the velocity unit and fixes an inconsistency in the units of the Gadget internal energy and temperature fields. See PR 1611 <https://github.com/yt-project/yt/pull/1611> and PR 1675 <https://github.com/yt-project/yt/pull/1675>. - Numpy 1.14.0 introduced changes to array printing which caused recursion errors when printing a YTArray instance. This will be fixed upstream in 1.14.1 but we have also restored support for NumPy 1.14.0 in yt by avoiding triggering the error. See PR 1661 <https://github.com/yt-project/yt/pull/1661>. <https://hackmd.io/CYMwhgjGYBzAtAUwGwQEbwCwFYQbIgMabwAMYAnMmoYQOywgDMQA?both#Minor-Improvements-and-Bugfixes>Minor Improvements and Bugfixes - Halo finders can now run in parallel on Python 3. See PR 1538 <https://github.com/yt-project/yt/pull/1538> and pPR 1690]( https://github.com/yt-project/yt/pull/1690). - The QT5 backend can now be used to display yt plots interactively. See PR 1540 <https://github.com/yt-project/yt/pull/1540>. - A number of misspellings across the codebase and documentation have been corrected. See PR 1542 <https://github.com/yt-project/yt/pull/1542> and PR 1575 <https://github.com/yt-project/yt/pull/1575>. - An off-by-one error in the particle_filter_sfr.py cookbook recipe has been fixed. See PR 1547 <https://github.com/yt-project/yt/pull/1547>. - The tipsy frontend will ignore invalid auxiliary files instead of raising an exception. See PR 1549 <https://github.com/yt-project/yt/pull/1549>. - Fixed a typo in the Gadget header specification. See PR 1550 <https://github.com/yt-project/yt/pull/1550>. - Parse units more gracefully in the FITS frontend. See PR 1553 <https://github.com/yt-project/yt/pull/1553>. - Handle units more gracefully when calculating quantities in the halo catalog. See PR 1558 <https://github.com/yt-project/yt/pull/1558>. - Ensure the PPVCube functionality works when a temperature field is not present. See PR 1562 <https://github.com/yt-project/yt/pull/1562>. - Avoid an error when saving spatial fields for a clump data object. See PR 1567 <https://github.com/yt-project/yt/pull/1567>. - ProfilePlot.set_unit and PhasePlot.set_unit will now handle tuple field names correctly. See PR 1568 <https://github.com/yt-project/yt/pull/1568>. - Properly set attributes when reloading ytdata datasets generated from an arbitrary_grid data object. See PR 1569 <https://github.com/yt-project/yt/pull/1569>. - Fix units in light cone projection. See PR 1574 <https://github.com/yt-project/yt/pull/1574>. - Allow loading Gadget datasets when some cosmology parameters are not present in the header. See PR 1578 <https://github.com/yt-project/yt/pull/1578>. - Correct typo in WarpX field definitions. See PR 1583 <https://github.com/yt-project/yt/pull/1583>. - Fix corner case in parsing Enzo parameter files. See PR 1586 <https://github.com/yt-project/yt/pull/1586>. - Ensure clump parents ids are updated correctly when child clumps are pruned. See PR 1587 <https://github.com/yt-project/yt/pull/1587>. - Ensure the bulk_magnetic_field field parameter is always set to a null default value if it is not otherwise explicitly set. See PR 1588 <https://github.com/yt-project/yt/pull/1588>. - Prevent NaNs from polluting profile calculations when the profile weight field has values equal to zero. See PR 1590 <https://github.com/yt-project/yt/pull/1590>. - Ensure _switch_ds() works with ParticleProjectionPlot. See PR 1594 <https://github.com/yt-project/yt/pull/1594>. - Fix the colors of the axes triad generated by the volume rendering annotate_axes helper function. See PR 1596 <https://github.com/yt-project/yt/pull/1596>. - Fix zooming of slices and projections of data with a 2D cylindrical geometry. See PR 1597 <https://github.com/yt-project/yt/pull/1597>. - Ensure field accesses on 2D grid data objects return data with a dummy dimension. See PR 1603 <https://github.com/yt-project/yt/pull/1603>. - Fix broken links in the documentation. See PR 1615 <https://github.com/yt-project/yt/pull/1615> and PR 1627 <https://github.com/yt-project/yt/pull/1627>. - Avoid errors when parsing boolean parameters in the Boxlib frontend. See PR 1619 <https://github.com/yt-project/yt/pull/1619>. - Populate the _particle_type_counts dictionary for AMReX datasets. This means that ds.particle_type_counts will function correctly. See PR 1621 <https://github.com/yt-project/yt/pull/1621>. - Ensure the "rad" (an alias to the "radian" unit defined for compatibility with Astropy) has the correct dimensions of angle instead of solid angle. See PR 1628 <https://github.com/yt-project/yt/pull/1628>. - Fix unit conversion issue in the annotate_quiver plot callback. See PR 1633 <https://github.com/yt-project/yt/pull/1633>. - Fix unit conversion error in deposited particle velocity and age fields. See PR 1638 <https://github.com/yt-project/yt/pull/1638>. - Added deprecation warnings for the LightRay and AbsorptionSpectrum functionality. Development of this functionality has moved to the Trident package. See PR 1644 <https://github.com/yt-project/yt/pull/1644>. - Support new AMReX particle data files with 5 digit IDs. See PR 1653 <https://github.com/yt-project/yt/pull/1653>. - Handle reloading pickle files with very early YTArray data. See PR 1656 <https://github.com/yt-project/yt/pull/1656>. - Fix initializing species charge and mass fields in the AMReX frontend. See PR 1658 <https://github.com/yt-project/yt/pull/1658>. - Keep units for domain edges when saving ytdata datasets from a FixedResolutionBuffer object. See PR 1659 <https://github.com/yt-project/yt/pull/1659>. - Use the correct matplotlib keyword argument name when specifying contour colors. See PR 1664 <https://github.com/yt-project/yt/pull/1664>. - Support Enzo active particle fields that map to arrays. See PR 1665 <https://github.com/yt-project/yt/pull/1665>. - Use a smarter algorithm for clipping particle positions to the domain boundaries in the rockstar halo finder. See PR 1679 <https://github.com/yt-project/yt/pull/1679>. - Make the annotate_clumps plot callback work correctly with reloaded ytdata clump datasets. See PR 1683 <https://github.com/yt-project/yt/pull/1683>. - Calculate velocity vector components without using the velocity_magnitude field. This avoids inconsistencies when the bulk_velocity field parameter is set to a nonzero value. See PR 1688 <https://github.com/yt-project/yt/pull/1688>. - Avoid truncating Gadget particle IDs by casting from uint32 to float32. See PR 1692 <https://github.com/yt-project/yt/pull/1692>.