.. _changelog:
ChangeLog
=========
This is a non-comprehensive log of changes to yt over its many releases.
Contributors
------------
The `CREDITS file <https://github.com/yt-project/yt/blob/main/CREDITS>`_
contains the most up-to-date list of everyone who has contributed to the yt
source code.
yt 4.0
------
Welcome to yt 4.0! This release is the result of several years worth of
developer effort and has been in progress since the mid 3.x series. Please keep
in mind that this release **will** have breaking changes. Please see the yt 4.0
differences page for how you can expect behavior to differ from the 3.x series.
This is a manually curated list of pull requests that went in to yt 4.0,
representing a subset of `the full
list <https://gist.github.com/matthewturk/7a1f21d98aa5188de7645eda082ce4e6>`__.
New Functions
^^^^^^^^^^^^^
- ``yt.load_sample`` (PR
#\ `2417 <https://github.com/yt-project/yt/pull/2417>`__, PR
#\ `2496 <https://github.com/yt-project/yt/pull/2496>`__, PR
#\ `2875 <https://github.com/yt-project/yt/pull/2875>`__, PR
#\ `2877 <https://github.com/yt-project/yt/pull/2877>`__, PR
#\ `2894 <https://github.com/yt-project/yt/pull/2894>`__, PR
#\ `3262 <https://github.com/yt-project/yt/pull/3262>`__, PR
#\ `3263 <https://github.com/yt-project/yt/pull/3263>`__, PR
#\ `3277 <https://github.com/yt-project/yt/pull/3277>`__, PR
#\ `3309 <https://github.com/yt-project/yt/pull/3309>`__, and PR
#\ `3336 <https://github.com/yt-project/yt/pull/3336>`__)
- ``yt.set_log_level`` (PR
#\ `2869 <https://github.com/yt-project/yt/pull/2869>`__ and PR
#\ `3094 <https://github.com/yt-project/yt/pull/3094>`__)
- ``list_annotations`` method for plots (PR
#\ `2562 <https://github.com/yt-project/yt/pull/2562>`__)
API improvements
^^^^^^^^^^^^^^^^
- ``yt.load`` with support for ``os.PathLike`` objects, improved UX
and moved a new ``yt.loaders`` module, along with sibling functions (PR
#\ `2405 <https://github.com/yt-project/yt/pull/2405>`__, PR
#\ `2722 <https://github.com/yt-project/yt/pull/2722>`__, PR
#\ `2695 <https://github.com/yt-project/yt/pull/2695>`__, PR
#\ `2818 <https://github.com/yt-project/yt/pull/2818>`__, and PR
#\ `2831 <https://github.com/yt-project/yt/pull/2831>`__, PR
#\ `2832 <https://github.com/yt-project/yt/pull/2832>`__)
- ``Dataset`` now has a more useful repr (PR
#\ `3217 <https://github.com/yt-project/yt/pull/3217>`__)
- Explicit JPEG export support (PR
#\ `2549 <https://github.com/yt-project/yt/pull/2549>`__)
- ``annotate_clear`` is now ``clear_annotations`` (PR
#\ `2569 <https://github.com/yt-project/yt/pull/2569>`__)
- Throw an error if field access is ambiguous (PR
#\ `2967 <https://github.com/yt-project/yt/pull/2967>`__)
Newly supported data formats
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Arepo
~~~~~
- PR #\ `1807 <https://github.com/yt-project/yt/pull/1807>`__
- PR #\ `2236 <https://github.com/yt-project/yt/pull/2236>`__
- PR #\ `2244 <https://github.com/yt-project/yt/pull/2244>`__
- PR #\ `2344 <https://github.com/yt-project/yt/pull/2344>`__
- PR #\ `2434 <https://github.com/yt-project/yt/pull/2434>`__
- PR #\ `3258 <https://github.com/yt-project/yt/pull/3258>`__
- PR #\ `3265 <https://github.com/yt-project/yt/pull/3265>`__
- PR #\ `3291 <https://github.com/yt-project/yt/pull/3291>`__
Swift
~~~~~
- PR #\ `1962 <https://github.com/yt-project/yt/pull/1962>`__
Improved support and frontend specific bugfixes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
adaptahop
~~~~~~~~~
- PR #\ `2678 <https://github.com/yt-project/yt/pull/2678>`__
AMRVAC
~~~~~~
- PR #\ `2541 <https://github.com/yt-project/yt/pull/2541>`__
- PR #\ `2745 <https://github.com/yt-project/yt/pull/2745>`__
- PR #\ `2746 <https://github.com/yt-project/yt/pull/2746>`__
- PR #\ `3215 <https://github.com/yt-project/yt/pull/3215>`__
ART
~~~
- PR #\ `2688 <https://github.com/yt-project/yt/pull/2688>`__
ARTIO
~~~~~
- PR #\ `2613 <https://github.com/yt-project/yt/pull/2613>`__
Athena++
~~~~~~~~
- PR #\ `2985 <https://github.com/yt-project/yt/pull/2985>`__
Boxlib
~~~~~~
- PR #\ `2807 <https://github.com/yt-project/yt/pull/2807>`__
- PR #\ `2814 <https://github.com/yt-project/yt/pull/2814>`__
- PR #\ `2938 <https://github.com/yt-project/yt/pull/2938>`__ (AMReX)
Enzo-E (formerly Enzo-P)
~~~~~~~~~~~~~~~~~~~~~~~~
- PR #\ `3273 <https://github.com/yt-project/yt/pull/3273>`__
- PR #\ `3274 <https://github.com/yt-project/yt/pull/3274>`__
- PR #\ `3290 <https://github.com/yt-project/yt/pull/3290>`__
- PR #\ `3372 <https://github.com/yt-project/yt/pull/3372>`__
fits
~~~~
- PR #\ `2246 <https://github.com/yt-project/yt/pull/2246>`__
- PR #\ `2345 <https://github.com/yt-project/yt/pull/2345>`__
Gadget
~~~~~~
- PR #\ `2145 <https://github.com/yt-project/yt/pull/2145>`__
- PR #\ `3233 <https://github.com/yt-project/yt/pull/3233>`__
- PR #\ `3258 <https://github.com/yt-project/yt/pull/3258>`__
Gadget FOF Halo
~~~~~~~~~~~~~~~
- PR #\ `2296 <https://github.com/yt-project/yt/pull/2296>`__
GAMER
~~~~~
- PR #\ `3033 <https://github.com/yt-project/yt/pull/3033>`__
Gizmo
~~~~~
- PR #\ `3234 <https://github.com/yt-project/yt/pull/3234>`__
MOAB
~~~~
- PR #\ `2856 <https://github.com/yt-project/yt/pull/2856>`__
Owls
~~~~
- PR #\ `3325 <https://github.com/yt-project/yt/pull/3325>`__
Ramses
~~~~~~
- PR #\ `2679 <https://github.com/yt-project/yt/pull/2679>`__
- PR #\ `2714 <https://github.com/yt-project/yt/pull/2714>`__
- PR #\ `2960 <https://github.com/yt-project/yt/pull/2960>`__
- PR #\ `3017 <https://github.com/yt-project/yt/pull/3017>`__
- PR #\ `3018 <https://github.com/yt-project/yt/pull/3018>`__
Tipsy
~~~~~
- PR #\ `2193 <https://github.com/yt-project/yt/pull/2193>`__
Octree Frontends
~~~~~~~~~~~~~~~~
- Ghost zone access (PR
#\ `2425 <https://github.com/yt-project/yt/pull/2425>`__ and PR
#\ `2958 <https://github.com/yt-project/yt/pull/2958>`__)
- Volume Rendering (PR
#\ `2610 <https://github.com/yt-project/yt/pull/2610>`__)
Configuration file
^^^^^^^^^^^^^^^^^^
- Config files are now in `TOML <https://toml.io/en/>`__ (PR
#\ `2981 <https://github.com/yt-project/yt/pull/2981>`__)
- Allow a local plugin file (PR
#\ `2534 <https://github.com/yt-project/yt/pull/2534>`__)
- Allow per-field local config (PR
#\ `1931 <https://github.com/yt-project/yt/pull/1931>`__)
yt CLI
^^^^^^
- Fix broken command-line options (PR
#\ `3361 <https://github.com/yt-project/yt/pull/3361>`__)
- Drop yt hub command (PR
#\ `3363 <https://github.com/yt-project/yt/pull/3363>`__)
Deprecations
^^^^^^^^^^^^
- Smoothed fields are no longer necessary (PR
#\ `2194 <https://github.com/yt-project/yt/pull/2194>`__)
- Energy and momentum field names are more accurate (PR
#\ `3059 <https://github.com/yt-project/yt/pull/3059>`__)
- Incorrectly-named ``WeightedVariance`` is now
``WeightedStandardDeviation`` and the old name has been deprecated
(PR #\ `3132 <https://github.com/yt-project/yt/pull/3132>`__)
- Colormap auto-registration has been changed and yt 4.1 will not
register ``cmocean`` (PR
#\ `3175 <https://github.com/yt-project/yt/pull/3175>`__ and PR
#\ `3214 <https://github.com/yt-project/yt/pull/3214>`__)
Removals
~~~~~~~~
- ``analysis_modules`` has been
`extracted <https://github.com/yt-project/yt_astro_analysis/>`__ (PR
#\ `2081 <https://github.com/yt-project/yt/pull/2081>`__)
- Interactive volume rendering has been
`extracted <https://github.com/yt-project/yt_idv/>`__ (PR
#\ `2896 <https://github.com/yt-project/yt/pull/2896>`__)
- The bundled version of ``poster`` has been removed (PR
#\ `2783 <https://github.com/yt-project/yt/pull/2783>`__)
- The deprecated ``particle_position_relative`` field has been removed
(PR #\ `2901 <https://github.com/yt-project/yt/pull/2901>`__)
- Deprecated functions have been removed (PR
#\ `3007 <https://github.com/yt-project/yt/pull/3007>`__)
- Vendored packages have been removed (PR
#\ `3008 <https://github.com/yt-project/yt/pull/3008>`__)
- ``yt.pmods`` has been removed (PR
#\ `3061 <https://github.com/yt-project/yt/pull/3061>`__)
- yt now utilizes unyt as an external package (PR
#\ `2219 <https://github.com/yt-project/yt/pull/2219>`__, PR
#\ `2300 <https://github.com/yt-project/yt/pull/2300>`__, and PR
#\ `2303 <https://github.com/yt-project/yt/pull/2303>`__)
Version 3.6.1
-------------
Version 3.6.1 is a bugfix release. It includes the following backport:
- hotfix: support matplotlib 3.3.0.
See `PR 2754 <https://github.com/yt-project/yt/pull/2754>`__.
Version 3.6.0
-------------
Version 3.6.0 our next major release since 3.5.1, which was in February
2019. It includes roughly 180 pull requests contributed from 39 contributors,
22 of which committed for their first time to the project.
We have also updated our project governance and contribution guidelines, which
you can `view here <https://yt-project.github.io/governance/>`_ .
We'd like to thank all of the individuals who contributed to this release. There
are lots of new features and we're excited to share them with the community.
Breaking Changes
^^^^^^^^^^^^^^^^
The following breaking change was introduced. Please be aware that this could
impact your code if you use this feature.
- The angular momentum has been reversed compared to previous versions of yt.
See `PR 2043 <https://github.com/yt-project/yt/pull/2043>`__.
Major Changes and New Features
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- New frontend support for the code AMRVAC. Many thanks to Clément Robert
and Niels Claes who were major contributors to this initiative. Relevant PRs include
- Initial PR to support AMRVAC native data files
`PR 2321 <https://github.com/yt-project/yt/pull/2321>`__.
- added support for dust fields and derived fields
`PR 2387 <https://github.com/yt-project/yt/pull/2387>`__.
- added support for derived fields for hydro runs
`PR 2381 <https://github.com/yt-project/yt/pull/2381>`__.
- API documentation and docstrings for AMRVAC frontend
`PR 2384 <https://github.com/yt-project/yt/pull/2384>`__,
`PR 2380 <https://github.com/yt-project/yt/pull/2380>`__,
`PR 2382 <https://github.com/yt-project/yt/pull/2382>`__.
- testing-related PRs for AMRVAC:
`PR 2379 <https://github.com/yt-project/yt/pull/2379>`__,
`PR 2360 <https://github.com/yt-project/yt/pull/2360>`__.
- add verbosity to logging of geometry or ``geometry_override``
`PR 2421 <https://github.com/yt-project/yt/pull/2421>`__.
- add attribute to ``_code_unit_attributes`` specific to AMRVAC to ensure
consistent renormalisation of AMRVAC datasets. See
`PR 2357 <https://github.com/yt-project/yt/pull/2357>`__.
- parse AMRVAC's parfiles if user-provided
`PR 2369 <https://github.com/yt-project/yt/pull/2369>`__.
- ensure that min_level reflects dataset that has refinement
`PR 2475 <https://github.com/yt-project/yt/pull/2475>`__.
- fix derived unit parsing `PR 2362 <https://github.com/yt-project/yt/pull/2362>`__.
- update energy field to be ``energy_density`` and have units of code
pressure `PR 2376 <https://github.com/yt-project/yt/pull/2376>`__.
- Support for the AdaptaHOP halo finder code
`PR 2385 <https://github.com/yt-project/yt/pull/2385>`__.
- yt now supports geographic transforms and projections of data with
cartopy with support from `PR 1966 <https://github.com/yt-project/yt/pull/1966>`__.
- annotations used to work for only a single point, they now work for multiple points
on a plot, see `PR 2122 <https://github.com/yt-project/yt/pull/2122>`__.
- cosmology calculations now have support for the relativistic energy density of the
universe, see `PR 1714 <https://github.com/yt-project/yt/pull/1714>`__.
This feature is accessible to cosmology datasets and was added to the Enzo frontend.
- the eps writer now allows for arrow rotation. this is accessible with
the ``rotate`` kwarg in the ``arrow`` function.
See `PR 2151 <https://github.com/yt-project/yt/pull/2151>`__.
- allow for dynamic load balancing with parallel loading of timeseries
data using the ``dynamic`` kwarg. `PR 2149 <https://github.com/yt-project/yt/pull/2149>`__.
- show/hide colorbar and show/hide axes are now available for
``ProfilePlot`` s. These functions were also moved from the PlotWindow to the
PlotContainer class. `PR 2169 <https://github.com/yt-project/yt/pull/2169>`__.
- add support for ipywidgets with an ``__ipython_display__`` method on the
FieldTypeContainer. Field variables, source, and the field array can be
viewed with this widget. See PRs `PR 1844 <https://github.com/yt-project/yt/pull/1844>`__
and `PR 1848 <https://github.com/yt-project/yt/pull/1848>`__,
or try ``display(ds.fields)`` in a Jupyter notebook.
- cut regions can now be made with ``exclude_`` and ``include_`` on a number of objects,
including above and below values, inside or outside regions, equal values, or nans.
See `PR 1964 <https://github.com/yt-project/yt/pull/1964>`__ and supporting
documentation fix at `PR 2262 <https://github.com/yt-project/yt/pull/2262>`__.
- previously aliased fluid vector fields in curvilinear geometries were not
converted to curvilinear coordinates, this was addressed in
`PR 2105 <https://github.com/yt-project/yt/pull/2105>`__.
- 2d polar and 3d cylindrical geometries now support annotate_quivers,
streamlines, line integral convolutions, see
`PR 2105 <https://github.com/yt-project/yt/pull/2105>`__.
- add support for exporting data to firefly `PR 2190 <https://github.com/yt-project/yt/pull/2190>`__.
- gradient fields are now supported in curvilinear geometries. See
`PR 2483 <https://github.com/yt-project/yt/pull/2483>`__.
- plotwindow colorbars now utilize mathtext in their labels,
from `PR 2516 <https://github.com/yt-project/yt/pull/2516>`__.
- raise deprecation warning when using ``mylog.warn``. Instead use
``mylog.warning``. See `PR 2285 <https://github.com/yt-project/yt/pull/2285>`__.
- extend support of the ``marker``, ``text``, ``line`` and ``sphere`` annotation
callbacks to polar geometries `PR 2466 <https://github.com/yt-project/yt/pull/2466>`__.
- Support MHD in the GAMER frontend `PR 2306 <https://github.com/yt-project/yt/pull/2306>`__.
- Export data container and profile fields to AstroPy QTables and
pandas DataFrames `PR 2418 <https://github.com/yt-project/yt/pull/2418>`__.
- Add turbo colormap, a colorblind safe version of jet. See
`PR 2339 <https://github.com/yt-project/yt/pull/2339>`__.
- Enable exporting regular grids (i.e., covering grids, arbitrary grids and
smoothed grids) to ``xarray`` `PR 2294 <https://github.com/yt-project/yt/pull/2294>`__.
- add automatic loading of ``namelist.txt``, which contains the parameter file
RAMSES uses to produce output `PR 2347 <https://github.com/yt-project/yt/pull/2347>`__.
- adds support for a nearest neighbor value field, accessible with
the ``add_nearest_neighbor_value_field`` function for particle fields. See
`PR 2301 <https://github.com/yt-project/yt/pull/2301>`__.
- speed up mesh deposition (uses caching) `PR 2136 <https://github.com/yt-project/yt/pull/2136>`__.
- speed up ghost zone generation. `PR 2403 <https://github.com/yt-project/yt/pull/2403>`__.
- ensure that a series dataset has kwargs passed down to data objects `PR 2366 <https://github.com/yt-project/yt/pull/2366>`__.
Documentation Changes
^^^^^^^^^^^^^^^^^^^^^
Our documentation has received some attention in the following PRs:
- include donation/funding links in README `PR 2520 <https://github.com/yt-project/yt/pull/2520>`__.
- Included instructions on how to install yt on the
Intel Distribution `PR 2355 <https://github.com/yt-project/yt/pull/2355>`__.
- include documentation on package vendors `PR 2494 <https://github.com/yt-project/yt/pull/2494>`__.
- update links to yt hub cookbooks `PR 2477 <https://github.com/yt-project/yt/pull/2477>`__.
- include relevant API docs in .gitignore `PR 2467 <https://github.com/yt-project/yt/pull/2467>`__.
- added docstrings for volume renderer cython code. see
`PR 2456 <https://github.com/yt-project/yt/pull/2456>`__ and
for `PR 2449 <https://github.com/yt-project/yt/pull/2449>`__.
- update documentation install recommendations to include newer
python versions `PR 2452 <https://github.com/yt-project/yt/pull/2452>`__.
- update custom CSS on docs to sphinx >=1.6.1. See
`PR 2199 <https://github.com/yt-project/yt/pull/2199>`__.
- enhancing the contribution documentation on git, see
`PR 2420 <https://github.com/yt-project/yt/pull/2420>`__.
- update documentation to correctly reference issues suitable for new
contributors `PR 2346 <https://github.com/yt-project/yt/pull/2346>`__.
- fix URLs and spelling errors in a number of the cookbook notebooks
`PR 2341 <https://github.com/yt-project/yt/pull/2341>`__.
- update release docs to include information about building binaries, tagging,
and various upload locations. See
`PR 2156 <https://github.com/yt-project/yt/pull/2156>`__ and
`PR 2160 <https://github.com/yt-project/yt/pull/2160>`__.
- ensuring the ``load_octree`` API docs are rendered
`PR 2088 <https://github.com/yt-project/yt/pull/2088>`__.
- fixing doc build errors, see: `PR 2077 <https://github.com/yt-project/yt/pull/2077>`__.
- add an instruction to the doc about continuous mesh colormap
`PR 2358 <https://github.com/yt-project/yt/pull/2358>`__.
- Fix minor typo `PR 2327 <https://github.com/yt-project/yt/pull/2327>`__.
- Fix some docs examples `PR 2316 <https://github.com/yt-project/yt/pull/2316>`__.
- fix sphinx formatting `PR 2409 <https://github.com/yt-project/yt/pull/2409>`__.
- Improve doc and fix docstring in deposition
`PR 2453 <https://github.com/yt-project/yt/pull/2453>`__.
- Update documentation to reflect usage of rcfile (no brackets allowed),
including strings. See `PR 2440 <https://github.com/yt-project/yt/pull/2440>`__.
Minor Enhancements and Bugfixes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- update pressure units in artio frontend (they were unitless
previously) `PR 2521 <https://github.com/yt-project/yt/pull/2521>`__.
- ensure that modules supported by ``on_demand_imports`` are imported
with that functionality `PR 2436 <https://github.com/yt-project/yt/pull/2436/files>`__.
- fix issues with groups in python3 in Ramses frontend
`PR 2092 <https://github.com/yt-project/yt/pull/2092>`__.
- add tests to ytdata frontend api `PR 2075 <https://github.com/yt-project/yt/pull/2075>`__.
- update internal field usage from ``particle_{}_relative`` to ``relative_particle_{}``
so particle-based fields don't see deprecation warnings
see `PR 2073 <https://github.com/yt-project/yt/pull/2073>`__.
- update save of ``field_data`` in clump finder, see
`PR 2079 <https://github.com/yt-project/yt/pull/2079>`__.
- ensure map.js is included in the sdist for mapserver. See
`PR 2158 <https://github.com/yt-project/yt/pull/2158>`__.
- add wrapping around ``yt_astro_analysis`` where it is used, in case it
isn't installed `PR 2159 <https://github.com/yt-project/yt/pull/2159>`__.
- the contour finder now uses a maximum data value supplied by the user,
rather than assuming the maximum value in the data container.
Previously this caused issues in the clump finder.
See `PR 2170 <https://github.com/yt-project/yt/pull/2170>`__.
- previously ramses data with non-hilbert ordering crashed.
fixed by `PR 2200 <https://github.com/yt-project/yt/pull/2200>`__.
- fix an issue related to creating a ds9 region with
FITS `PR 2335 <https://github.com/yt-project/yt/pull/2335>`__.
- add a check to see if pluginfilename is specified in
ytrc `PR 2319 <https://github.com/yt-project/yt/pull/2319>`__.
- sort .so input file list so that the yt package builds in a reproducible
way `PR 2206 <https://github.com/yt-project/yt/pull/2206>`__.
- update ``stack`` ufunc usage to include ``axis`` kwarg.
See `PR 2204 <https://github.com/yt-project/yt/pull/2204>`__.
- extend support for field names in RAMSES descriptor file to include all names
that don't include a comma. See `PR 2202 <https://github.com/yt-project/yt/pull/2202>`__.
- ``set_buff_size`` now works for ``OffAxisProjectionPlot``,
see `PR 2239 <https://github.com/yt-project/yt/pull/2239>`__.
- fix chunking for chained cut regions. previously chunking commands would
only look at the most recent cut region conditionals, and not any of the
previous cut regions. See `PR 2234 <https://github.com/yt-project/yt/pull/2234>`__.
- update git command in Castro frontend to
include ``git describe`` `PR 2235 <https://github.com/yt-project/yt/pull/2235>`__.
- in datasets with a single oct correctly guess the shape of the
array `PR 2241 <https://github.com/yt-project/yt/pull/2241>`__.
- update ``get_yt_version`` function to support python 3.
See `PR 2226 <https://github.com/yt-project/yt/pull/2226>`__.
- the ``"stream"`` frontend now correctly returns ``min_level`` for the mesh refinement.
`PR 2519 <https://github.com/yt-project/yt/pull/2519>`__.
- region expressions (``ds.r[]``) can now be used on 2D
datasets `PR 2482 <https://github.com/yt-project/yt/pull/2482>`__.
- background colors in cylindrical coordinate plots are now set
correctly `PR 2517 <https://github.com/yt-project/yt/pull/2517>`__.
- Utilize current matplotlib interface for the ``_png`` module to write
images to disk `PR 2514 <https://github.com/yt-project/yt/pull/2514>`__.
- fix issue with fortran utils where empty records were not
supported `PR 2259 <https://github.com/yt-project/yt/pull/2259>`__.
- add support for python 3.7 in iterator used by dynamic parallel
loading `PR 2265 <https://github.com/yt-project/yt/pull/2265>`__.
- add support to handle boxlib data where ``raw_fields`` contain
ghost zones `PR 2255 <https://github.com/yt-project/yt/pull/2255>`__.
- update quiver fields to use native units, not assuming
cgs `PR 2292 <https://github.com/yt-project/yt/pull/2292>`__.
- fix annotations on semi-structured mesh data with
exodus II `PR 2274 <https://github.com/yt-project/yt/pull/2274>`__.
- extend support for loading exodus II data
`PR 2274 <https://github.com/yt-project/yt/pull/2274>`__.
- add support for yt to load data generated by WarpX code that
includes ``rigid_injected`` species `PR 2289 <https://github.com/yt-project/yt/pull/2289>`__.
- fix issue in GAMER frontend where periodic boundary conditions were not
identified `PR 2287 <https://github.com/yt-project/yt/pull/2287>`__.
- fix issue in ytdata frontend where data size was calculated to have size
``(nparticles, dimensions)``. Now updated to use
``(nparticles, nparticles, dimensions)``.
see `PR 2280 <https://github.com/yt-project/yt/pull/2280>`__.
- extend support for OpenPMD frontend to load data containing no particles
see `PR 2270 <https://github.com/yt-project/yt/pull/2270>`__.
- raise a meaningful error on negative and zero zooming factors,
see `PR 2443 <https://github.com/yt-project/yt/pull/2443>`__.
- ensure Datasets are consistent in their ``min_level`` attribute.
See `PR 2478 <https://github.com/yt-project/yt/pull/2478>`__.
- adding matplotlib to trove classifiers `PR 2473 <https://github.com/yt-project/yt/pull/2473>`__.
- Add support for saving additional formats supported by
matplotlib `PR 2318 <https://github.com/yt-project/yt/pull/2318>`__.
- add support for numpy 1.18.1 and help ensure consistency with unyt
`PR 2448 <https://github.com/yt-project/yt/pull/2448>`__.
- add support for spherical geometries in ``plot_2d``. See
`PR 2371 <https://github.com/yt-project/yt/pull/2371>`__.
- add support for sympy 1.5 `PR 2407 <https://github.com/yt-project/yt/pull/2407>`__.
- backporting unyt PR 102 for clip `PR 2329 <https://github.com/yt-project/yt/pull/2329>`__.
- allow code units in fields ``jeans_mass`` and ``dynamical_time``.
See`PR 2454 <https://github.com/yt-project/yt/pull/2454>`__.
- fix for the case where boxlib nghost is different in different
directions `PR 2343 <https://github.com/yt-project/yt/pull/2343>`__.
- bugfix for numpy 1.18 `PR 2419 <https://github.com/yt-project/yt/pull/2419>`__.
- Invoke ``_setup_dx`` in the enzo inline analysis. See
`PR 2460 <https://github.com/yt-project/yt/pull/2460>`__.
- Update annotate_timestamp to work with ``"code"`` unit system. See
`PR 2435 <https://github.com/yt-project/yt/pull/2435>`__.
- use ``dict.get`` to pull attributes that may not exist in ytdata
frontend `PR 2471 <https://github.com/yt-project/yt/pull/2471>`__.
- solved bug related to slicing out ghost cells in
chombo `PR 2388 <https://github.com/yt-project/yt/pull/2388>`__.
- correctly register reversed versions of cmocean
cmaps `PR 2390 <https://github.com/yt-project/yt/pull/2390>`__.
- correctly set plot axes units to ``"code length"`` for datasets
loaded with ``unit_system="code"`` `PR 2354 <https://github.com/yt-project/yt/pull/2354>`__.
- deprecate ``ImagePlotContainer.set_cbar_minorticks``. See
`PR 2444 <https://github.com/yt-project/yt/pull/2444>`__.
- enzo-e frontend bugfix for single block datasets. See
`PR 2424 <https://github.com/yt-project/yt/pull/2424>`__.
- explicitly default to solid lines in contour callback. See
`PR 2330 <https://github.com/yt-project/yt/pull/2330>`__.
- replace all bare ``Except`` statements `PR 2474 <https://github.com/yt-project/yt/pull/2474>`__.
- fix an inconsistency between ``argmax`` and ``argmin`` methods in
YTDataContainer class `PR 2457 <https://github.com/yt-project/yt/pull/2457>`__.
- fixed extra extension added by ``ImageArray.save()``. See
`PR 2364 <https://github.com/yt-project/yt/pull/2364>`__.
- fix incorrect usage of ``is`` comparison with ``==`` comparison throughout the codebase
`PR 2351 <https://github.com/yt-project/yt/pull/2351>`__.
- fix streamlines ``_con_args`` attribute `PR 2470 <https://github.com/yt-project/yt/pull/2470>`__.
- fix python 3.8 warnings `PR 2386 <https://github.com/yt-project/yt/pull/2386>`__.
- fix some invalid escape sequences. `PR 2488 <https://github.com/yt-project/yt/pull/2488>`__.
- fix typo in ``_vorticity_z`` field definition. See
`PR 2398 <https://github.com/yt-project/yt/pull/2398>`__.
- fix an inconsistency in annotate_sphere callback.
See `PR 2464 <https://github.com/yt-project/yt/pull/2464>`__.
- initialize unstructured mesh visualization
background to ``nan`` `PR 2308 <https://github.com/yt-project/yt/pull/2308>`__.
- raise a meaningful error on negative and zero
zooming factors `PR 2443 <https://github.com/yt-project/yt/pull/2443>`__.
- set ``symlog`` scaling to ``log`` if ``vmin > 0``.
See `PR 2485 <https://github.com/yt-project/yt/pull/2485>`__.
- skip blank lines when reading parameters.
See `PR 2406 <https://github.com/yt-project/yt/pull/2406>`__.
- Update magnetic field handling for RAMSES.
See `PR 2377 <https://github.com/yt-project/yt/pull/2377>`__.
- Update ARTIO frontend to support compressed files.
See `PR 2314 <https://github.com/yt-project/yt/pull/2314>`__.
- Use mirror copy of SDF data `PR 2334 <https://github.com/yt-project/yt/pull/2334>`__.
- Use sorted glob in athena to ensure reproducible ordering of
grids `PR 2363 <https://github.com/yt-project/yt/pull/2363>`__.
- fix cartopy failures by ensuring data is in lat/lon when passed to
cartopy `PR 2378 <https://github.com/yt-project/yt/pull/2378>`__.
- enforce unit consistency in plot callbacks, which fixes some unexpected
behaviour in the plot annotations callbacks that use the plot
window width or the data width `PR 2524 <https://github.com/yt-project/yt/pull/2524>`__.
Separate from our list of minor enhancements and bugfixes, we've grouped PRs
related to infrastructure and testing in the next three sub-sub-sub sections.
Testing and Infrastructure
~~~~~~~~~~~~~~~~~~~~~~~~~~
- infrastructure to change our testing from nose to pytest, see
`PR 2401 <https://github.com/yt-project/yt/pull/2401>`__.
- Adding test_requirements and test_minimum requirements files to have
bounds on installed testing versioning `PR 2083 <https://github.com/yt-project/yt/pull/2083>`__.
- Update the test failure report to include all failed tests related
to a single test specification `PR 2084 <https://github.com/yt-project/yt/pull/2084>`__.
- add required dependencies for docs testing on Jenkins. See
`PR 2090 <https://github.com/yt-project/yt/pull/2090>`__.
- suppress pyyaml warning that pops up when running
tests `PR 2182 <https://github.com/yt-project/yt/pull/2182>`__.
- add tests for pre-existing ytdata datasets. See
`PR 2229 <https://github.com/yt-project/yt/pull/2229>`__.
- add a test to check if cosmology calculator and cosmology dataset
share the same unit registry `PR 2230 <https://github.com/yt-project/yt/pull/2230>`__.
- fix kh2d test name `PR 2342 <https://github.com/yt-project/yt/pull/2342>`__.
- disable OSNI projection answer test to remove cartopy errors `PR 2350 <https://github.com/yt-project/yt/pull/2350>`__.
CI related support
~~~~~~~~~~~~~~~~~~
- disable coverage on OSX to speed up travis testing and avoid
timeouts `PR 2076 <https://github.com/yt-project/yt/pull/2076>`__.
- update travis base images on Linux and
MacOSX `PR 2093 <https://github.com/yt-project/yt/pull/2093>`__.
- add ``W504`` and ``W605`` to ignored flake8 errors, see
`PR 2078 <https://github.com/yt-project/yt/pull/2078>`__.,
- update pyyaml version in ``test_requirements.txt`` file to address
github warning `PR 2148 <https://github.com/yt-project/yt/pull/2148/files>`__.,
- fix travis build errors resulting from numpy and cython being
unavailable `PR 2171 <https://github.com/yt-project/yt/pull/2171>`__.
- fix appveyor build failures `PR 2231 <https://github.com/yt-project/yt/pull/2231>`__.
- Add Python 3.7 and Python 3.8 to CI test jobs. See
`PR 2450 <https://github.com/yt-project/yt/pull/2450>`__.
- fix build failure on Windows `PR 2333 <https://github.com/yt-project/yt/pull/2333>`__.
- fix warnings due to travis configuration file. See
`PR 2451 <https://github.com/yt-project/yt/pull/2451>`__.
- install pyyaml on appveyor `PR 2367 <https://github.com/yt-project/yt/pull/2367>`__.
- install sympy 1.4 on appveyor to work around regression in
1.5 `PR 2395 <https://github.com/yt-project/yt/pull/2395>`__.
- update CI recipes to fix recent failures `PR 2489 <https://github.com/yt-project/yt/pull/2489>`__.
Other Infrastructure
~~~~~~~~~~~~~~~~~~~~
- Added a welcomebot to our github page for new contributors, see
`PR 2181 <https://github.com/yt-project/yt/pull/2181>`__.
- Added a pep8 bot to pre-run before tests, see
`PR 2179 <https://github.com/yt-project/yt/pull/2179>`__,
`PR 2184 <https://github.com/yt-project/yt/pull/2184>`__ and
`PR 2185 <https://github.com/yt-project/yt/pull/2185>`__.
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
<https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/1693>`__ and `PR 2022
<https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/1799>`__ and `PR
1850 <https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/1548>`__.
- Add support for the new self-describing Ramses particle output format. See `PR
1616 <https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/1649>`__.
- Substantial performance improvement for reading RAMSES AMR data. See `PR 1671
<https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/1738>`__.
- Avoid repeated parsing of RAMSES particle and RT descriptors. See `PR 1739
<https://github.com/yt-project/yt/pull/1739>`__.
- Added support for reading the RAMSES gravitational potential field. See `PR
1751 <https://github.com/yt-project/yt/pull/1751>`__.
- Add support for RAMSES datasets that use the ``groupsize`` feature. See `PR
1769 <https://github.com/yt-project/yt/pull/1769>`__.
- Dramatically improve the overall performance of the RAMSES frontend. See `PR
1771 <https://github.com/yt-project/yt/pull/1771>`__.
Additional Improvements
^^^^^^^^^^^^^^^^^^^^^^^
- Added support for particle data in the Enzo-E frontend. See `PR 1490
<https://github.com/yt-project/yt/pull/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
converting to a new unit, then stripping off the units to return a plain numpy
array. See `PR 1563 <https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/1578>`__.
- Improve detection for OpenMP support at compile-time, including adding support
for detecting OpenMP on Windows. See `PR 1591
<https://github.com/yt-project/yt/pull/1591>`__, `PR 1695
<https://github.com/yt-project/yt/pull/1695>`__ and `PR 1696
<https://github.com/yt-project/yt/pull/1696>`__.
- Add support for 2D cylindrical data for most plot callbacks. See `PR 1598
<https://github.com/yt-project/yt/pull/1598>`__.
- Particles outside the domain are now ignored by ``load_uniform_grid()`` and
``load_amr_grids()``. See `PR 1602
<https://github.com/yt-project/yt/pull/1602>`__.
- Fix incorrect units for the Gadget internal energy field in cosmology
simulations. See `PR 1611
<https://github.com/yt-project/yt/pull/1611>`__.
- Add support for calculating covering grids in parallel. See `PR 1612
<https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/1620>`__.
- Add support for non-cartesian GAMER data. See `PR 1622
<https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/1624>`__.
- The ``save()`` method of the various yt plot objects now optionally can accept
a tuple of strings instead of a string. If a tuple is supplied, the elements
are joined with ``os.sep`` to form a path. See `PR 1630
<https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/1636>`__.
- Updates and improvements for the OpenPMD frontend. See `PR 1645
<https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/1654>`__ and `PR 1668
<https://github.com/yt-project/yt/pull/1668>`__.
- Substantial performance improvement for calculating the gravitational
potential in the clump finder. See `PR 1684
<https://github.com/yt-project/yt/pull/1684>`__.
- Added new methods to ``ProfilePlot``: ``set_xlabel()``, ``set_ylabel()``,
``annotate_title()``, and ``annotate_text()``. See `PR 1700
<https://github.com/yt-project/yt/pull/1700>`__ and `PR 1705
<https://github.com/yt-project/yt/pull/1705>`__.
- Speedup for parallel halo finding operation for the FOF and HOP halo
finders. See `PR 1724 <https://github.com/yt-project/yt/pull/1724>`__.
- Add support for halo finding using the rockstar halo finder on Python3. See
`PR 1740 <https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/1755>`__.
- Add support for magnetic field variables and creation time fields in the GIZMO
frontend. See `PR 1756 <https://github.com/yt-project/yt/pull/1756>`__ and `PR
1914 <https://github.com/yt-project/yt/pull/1914>`__.
- ``ParticleProjectionPlot`` now supports the ``annotate_particles`` plot
callback. See `PR 1765 <https://github.com/yt-project/yt/pull/1765>`__.
- Optimized the performance of off-axis projections for octree AMR data. See `PR
1766 <https://github.com/yt-project/yt/pull/1766>`__.
- Added support for several radiative transfer fields in the ARTIO frontend. See
`PR 1804 <https://github.com/yt-project/yt/pull/1804>`__.
- Performance improvement for Boxlib datasets that don't use AMR. See `PR 1834
<https://github.com/yt-project/yt/pull/1834>`__.
- It is now possible to set custom profile bin edges. See `PR 1837
<https://github.com/yt-project/yt/pull/1837>`__.
- Dropped support for Python3.4. See `PR 1840
<https://github.com/yt-project/yt/pull/1840>`__.
- Add support for reading RAMSES cooling fields. See `PR 1853
<https://github.com/yt-project/yt/pull/1853>`__.
- Add support for NumPy 1.15. See `PR 1854
<https://github.com/yt-project/yt/pull/1854>`__.
- Ensure that functions defined in the plugins file are available in the yt
namespace. See `PR 1855 <https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/1856>`__.
- Systematically added validation for inputs to data object initializers. See
`PR 1871 <https://github.com/yt-project/yt/pull/1871>`__.
- It is now possible to select only a specific particle type in the particle
trajectories analysis module. See `PR 1887
<https://github.com/yt-project/yt/pull/1887>`__.
- Substantially improve the performance of selecting particle fields with a
``cut_region`` data object. See `PR 1892
<https://github.com/yt-project/yt/pull/1892>`__.
- The ``iyt`` command-line entry-point into IPython now installs yt-specific
tab-completions. See `PR 1900 <https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/1902>`__
and `PR 1922 <https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/1922>`__.
- Add support for 2D nodal data. See `PR 1923
<https://github.com/yt-project/yt/pull/1923>`__.
- Add support for GAMER outputs that use patch groups. This substantially
reduces the memory requirements for loading large GAMER datasets. See `PR 1935
<https://github.com/yt-project/yt/pull/1935>`__.
- Add a ``data_source`` keyword argument to the ``annotate_particles`` plot
callback. See `PR 1937 <https://github.com/yt-project/yt/pull/1937>`__.
- Define species fields in the NMSU Art frontend. See `PR 1981
<https://github.com/yt-project/yt/pull/1981>`__.
- Added a ``__format__`` implementation for ``YTArray``. See `PR 1985
<https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/1993>`__.
- Added support for periodic visualizations using
``ParticleProjectionPlot``. See `PR 1996
<https://github.com/yt-project/yt/pull/1996>`__.
- Added ``YTArray.argsort()``. See `PR 2002
<https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/2005>`__ and `PR 2036
<https://github.com/yt-project/yt/pull/2036>`__.
- Save the standard deviation in ``profile.save_as_dataset()``. See `PR 2008
<https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/2019>`__.
- Raise an exception when profiling fields of unequal shape. See `PR 2025
<https://github.com/yt-project/yt/pull/2025>`__.
- The clump info dictionary is now populated as clumps get created instead of
during ``clump.save_as_dataset()``. See `PR 2053
<https://github.com/yt-project/yt/pull/2053>`__.
- Avoid segmentation fault in slice selector by clipping slice integer
coordinates. See `PR 2055 <https://github.com/yt-project/yt/pull/2055>`__.
Minor Enhancements and Bugfixes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- Fix incorrect use of floating point division in the parallel analysis framework.
See `PR 1538 <https://github.com/yt-project/yt/pull/1538>`__.
- Fix integration with that matplotlib QT backend for interactive plotting.
See `PR 1540 <https://github.com/yt-project/yt/pull/1540>`__.
- Add support for the particle creation time field in the GAMER frontend.
See `PR 1546 <https://github.com/yt-project/yt/pull/1546>`__.
- Various minor improvements to the docs. See `PR 1542
<https://github.com/yt-project/yt/pull/1542>`__. and `PR 1547
<https://github.com/yt-project/yt/pull/1547>`__.
- Add better error handling for invalid tipsy aux files. See `PR 1549
<https://github.com/yt-project/yt/pull/1549>`__.
- Fix typo in default Gadget header specification. See `PR 1550
<https://github.com/yt-project/yt/pull/1550>`__.
- Use the git version in the get_yt_version function. See `PR 1551
<https://github.com/yt-project/yt/pull/1551>`__.
- Assume dimensionless units for fields from FITS datasets when we can't infer
the units. See `PR 1553 <https://github.com/yt-project/yt/pull/1553>`__.
- Autodetect ramses extra particle fields. See `PR 1555
<https://github.com/yt-project/yt/pull/1555>`__.
- Fix issue with handling unitless halo quantities in HaloCatalog. See `PR 1558
<https://github.com/yt-project/yt/pull/1558>`__.
- Track the halo catalog creation process using a parallel-safe progress bar.
See `PR 1559 <https://github.com/yt-project/yt/pull/1559>`__.
- The PPV Cube functionality no longer crashes if there is no temperature field
in the dataset. See `PR 1562
<https://github.com/yt-project/yt/pull/1562>`__.
- Fix crash caused by saving the ``'x'``, ``'y'``, or ``'z'`` fields in
clump.save_as_dataset(). See `PR 1567
<https://github.com/yt-project/yt/pull/1567>`__.
- Accept both string and tuple field names in ``ProfilePlot.set_unit()`` and
``PhasePlot.set_unit()``. See `PR 1568
<https://github.com/yt-project/yt/pull/1568>`__.
- Fix issues with some arbitrary grid attributes not being reloaded properly
after being saved with ``save_as_dataset()``. See `PR 1569
<https://github.com/yt-project/yt/pull/1569>`__.
- Fix units issue in the light cone projection operation. See `PR 1574
<https://github.com/yt-project/yt/pull/1574>`__.
- Use ``astropy.wcsaxes`` instead of the independent ``wcsaxes`` project. See
`PR 1577 <https://github.com/yt-project/yt/pull/1577>`__.
- Correct typo in WarpX field definitions. See `PR 1583
<https://github.com/yt-project/yt/pull/1583>`__.
- Avoid crashing when loading an Enzo dataset with a parameter file that has
commented out parameters. See `PR 1586
<https://github.com/yt-project/yt/pull/1586>`__.
- 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 <https://github.com/yt-project/yt/pull/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 <https://github.com/yt-project/yt/pull/1588>`__ and `PR
1687 <https://github.com/yt-project/yt/pull/1687>`__.
- Fix incorrect profile values when the profile weight field has values equal to
zero. See `PR 1590 <https://github.com/yt-project/yt/pull/1590>`__.
- Fix issues with making matplotlib animations of a
``ParticleProjectionPlot``. See `PR 1594
<https://github.com/yt-project/yt/pull/1594>`__.
- The ``Scene.annotate_axes()`` function will now use the correct colors for
drawing the axes annotation. See `PR 1596
<https://github.com/yt-project/yt/pull/1596>`__.
- Fix incorrect default plot bounds for a zoomed-in slice plot of a 2D
cylindrical dataset. See `PR 1597
<https://github.com/yt-project/yt/pull/1597>`__.
- Fix issue where field accesses on 2D grids would return data with incorrect
shapes. See `PR 1603 <https://github.com/yt-project/yt/pull/1603>`__.
- Added a cookbook example for a multipanel phase plot. See `PR 1605
<https://github.com/yt-project/yt/pull/1605>`__.
- Boolean simulation parameters in the Boxlib frontend will now be interpreted
correctly. See `PR 1619 <https://github.com/yt-project/yt/pull/1619>`__.
- 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
<https://github.com/yt-project/yt/pull/1628>`__.
- Fix units issues in several plot callbacks. See `PR 1633
<https://github.com/yt-project/yt/pull/1633>`__ and `PR 1674
<https://github.com/yt-project/yt/pull/1674>`__.
- Various fixes for how WarpX fields are interpreted. See `PR 1634
<https://github.com/yt-project/yt/pull/1634>`__.
- Fix incorrect units in the automatically deposited particle fields. See `PR
1638 <https://github.com/yt-project/yt/pull/1638>`__.
- It is now possible to set the axes background color after calling
``plot.hide_axes()``. See `PR 1662
<https://github.com/yt-project/yt/pull/1662>`__.
- Fix a typo in the name of the ``colors`` keyword argument passed to matplotlib
for the contour callback. See `PR 1664
<https://github.com/yt-project/yt/pull/1664>`__.
- Add support for Enzo Active Particle fields that arrays. See `PR 1665
<https://github.com/yt-project/yt/pull/1665>`__.
- Avoid crash when generating halo catalogs from the rockstar halo finder for
small simulation domains. See `PR 1679
<https://github.com/yt-project/yt/pull/1679>`__.
- The clump callback now functions correctly for a reloaded clump dataset. See
`PR 1683 <https://github.com/yt-project/yt/pull/1683>`__.
- Fix incorrect calculation for tangential components of vector fields. See `PR
1688 <https://github.com/yt-project/yt/pull/1688>`__.
- Allow halo finders to run in parallel on Python3. See `PR 1690
<https://github.com/yt-project/yt/pull/1690>`__.
- Fix issues with Gadget particle IDs for simulations with large numbers of
particles being incorrectly rounded. See `PR 1692
<https://github.com/yt-project/yt/pull/1692>`__.
- ``ParticlePlot`` no longer needs to be passed spatial fields in a particular
order to ensure that a ``ParticleProjectionPlot`` is returned. See `PR 1697
<https://github.com/yt-project/yt/pull/1697>`__.
- Accessing data from a FLASH grid directly now returns float64 data. See `PR
1708 <https://github.com/yt-project/yt/pull/1708>`__.
- Fix periodicity check in ``YTPoint`` data object. See `PR 1712
<https://github.com/yt-project/yt/pull/1712>`__.
- Avoid crash on matplotlib 2.2.0 when generating yt plots with symlog
colorbars. See `PR 1720 <https://github.com/yt-project/yt/pull/1720>`__.
- Avoid crash when FLASH ``"unitsystem"`` parameter is quoted in the HDF5
file. See `PR 1722 <https://github.com/yt-project/yt/pull/1722>`__.
- Avoid issues with creating custom particle filters for OWLS/EAGLE
datasets. See `PR 1723 <https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/1731>`__ and `PR 1827
<https://github.com/yt-project/yt/pull/1827>`__.
- Fix clump finder ignoring field parameters. See `PR 1732
<https://github.com/yt-project/yt/pull/1732>`__.
- Avoid generating NaNs in x-ray emission fields. See `PR 1742
<https://github.com/yt-project/yt/pull/1742>`__.
- Fix compatibility with Sphinx 1.7 when building the docs. See `PR 1743
<https://github.com/yt-project/yt/pull/1743>`__.
- Eliminate usage of deprecated ``"clobber"`` keyword argument for various
usages of astropy in yt. See `PR 1744
<https://github.com/yt-project/yt/pull/1744>`__.
- Fix incorrect definition of the ``"d"`` unit (an alias of ``"day"``). See `PR
1746 <https://github.com/yt-project/yt/pull/1746>`__.
- ``PhasePlot.set_log()`` now correctly handles tuple field names as well as
string field names. See `PR 1787
<https://github.com/yt-project/yt/pull/1787>`__.
- Fix incorrect axis order in aitoff pixelizer. See `PR 1791
<https://github.com/yt-project/yt/pull/1791>`__.
- Fix crash in when exporting a surface as a ply model. See `PR 1792
<https://github.com/yt-project/yt/pull/1792>`__ and `PR 1817
<https://github.com/yt-project/yt/pull/1817>`__.
- Fix crash in scene.save_annotated() in newer numpy versions. See `PR 1793
<https://github.com/yt-project/yt/pull/1793>`__.
- Many tests no longer depend on real datasets. See `PR 1801
<https://github.com/yt-project/yt/pull/1801>`__, `PR 1805
<https://github.com/yt-project/yt/pull/1805>`__, `PR 1809
<https://github.com/yt-project/yt/pull/1809>`__, `PR 1883
<https://github.com/yt-project/yt/pull/1883>`__, and `PR 1941
<https://github.com/yt-project/yt/pull/1941>`__
- New tests were added to improve test coverage or the performance of the
tests. See `PR 1820 <https://github.com/yt-project/yt/pull/1820>`__, `PR 1831
<https://github.com/yt-project/yt/pull/1831>`__, `PR 1833
<https://github.com/yt-project/yt/pull/1833>`__, `PR 1841
<https://github.com/yt-project/yt/pull/1841>`__, `PR 1842
<https://github.com/yt-project/yt/pull/1842>`__, `PR 1885
<https://github.com/yt-project/yt/pull/1885>`__, `PR 1886
<https://github.com/yt-project/yt/pull/1886>`__, `PR 1952
<https://github.com/yt-project/yt/pull/1952>`__, `PR 1953
<https://github.com/yt-project/yt/pull/1953>`__, `PR 1955
<https://github.com/yt-project/yt/pull/1955>`__, and `PR 1957
<https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/1818>`__.
- Fix incorrect velocity unit int he ``gadget_fof`` frontend. See `PR 1829
<https://github.com/yt-project/yt/pull/1829>`__.
- Making an off-axis projection of a cut_region data object with an octree AMR
dataset now works correctly. See `PR 1858
<https://github.com/yt-project/yt/pull/1858>`__.
- Replace hard-coded constants in Enzo frontend with calculations to improve
agreement with Enzo's internal constants and improve clarity. See `PR 1873
<https://github.com/yt-project/yt/pull/1873>`__.
- Correct issues with Enzo magnetic units in cosmology simulations. See `PR 1876
<https://github.com/yt-project/yt/pull/1876>`__.
- Use the species names from the dataset rather than hardcoding species names in
the WarpX frontend. See `PR 1884
<https://github.com/yt-project/yt/pull/1884>`__.
- Fix issue with masked I/O for unstructured mesh data. See `PR 1918
<https://github.com/yt-project/yt/pull/1918>`__.
- Fix crash when reading DM-only Enzo datasets where some grids have no particles. See `PR 1919 <https://github.com/yt-project/yt/pull/1919>`__.
- Fix crash when loading pure-hydro Nyx dataset. See `PR 1950
<https://github.com/yt-project/yt/pull/1950>`__.
- Avoid crashes when plotting fields that contain NaN. See `PR 1951
<https://github.com/yt-project/yt/pull/1951>`__.
- Avoid crashes when loading NMSU ART data. See `PR 1960
<https://github.com/yt-project/yt/pull/1960>`__.
- Avoid crash when loading WarpX dataset with no particles. See `PR 1979
<https://github.com/yt-project/yt/pull/1979>`__.
- Adapt to API change in glue to fix the ``to_glue()`` method on yt data
objects. See `PR 1991 <https://github.com/yt-project/yt/pull/1991>`__.
- Fix incorrect width calculation in the ``annotate_halos()`` plot callback. See
`PR 1995 <https://github.com/yt-project/yt/pull/1995>`__.
- Don't try to read from files containing zero halos in the ``gadget_fof``
frontend. See `PR 2001 <https://github.com/yt-project/yt/pull/2001>`__.
- Fix incorrect calculation in ``get_ortho_base()``. See `PR 2013
<https://github.com/yt-project/yt/pull/2013>`__.
- Avoid issues with the axes background color being inconsistently set. See `PR
2018 <https://github.com/yt-project/yt/pull/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
<https://github.com/yt-project/yt/pull/2020>`__.
- Fix incorrect domain annotation for ``Scene.annotate_domain()`` when using the
plane-parallel camera. See `PR 2024
<https://github.com/yt-project/yt/pull/2024>`__.
- Avoid crash when particles are on the domain edges for ``gadget_fof``
data. See `PR 2034 <https://github.com/yt-project/yt/pull/2034>`__.
- Avoid stripping code units when processing units through a dataset's unit
system. See `PR 2035 <https://github.com/yt-project/yt/pull/2035>`__.
- Avoid incorrectly rescaling units of metalicity fields. See `PR 2038
<https://github.com/yt-project/yt/pull/2038>`__.
- Fix incorrect units for FLASH ``"divb"`` field. See `PR 2062
<https://github.com/yt-project/yt/pull/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 <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-E`` 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 https://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 <https://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>`__.
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
:ref:`saving_data`.
* Totally re-worked volume rendering API. The old API is still available for users
who prefer it, however. See :ref:`volume_rendering`.
* Support for unstructured mesh visualization. See
:ref:`unstructured-mesh-slices` and :ref:`unstructured_mesh_rendering`.
* Interactive Data Visualization for AMR and unstructured mesh datasets. See
:ref:`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
<https://github.com/matplotlib/viscm>`_ and should do a better job of
representing the data for colorblind viewers and when printed out in
grayscale. See :ref:`colormaps` for more detail.
* New frontends for the :ref:`ExodusII <loading-exodusii-data>`,
:ref:`GAMER <loading-gamer-data>`, and :ref:`Gizmo <loading-gizmo-data>` data
formats.
* The unit system associated with a dataset is now customizable, defaulting to
CGS.
* Enhancements and usability improvements for analysis modules, especially the
``absorption_spectrum``, ``photon_simulator``, and ``light_ray`` modules. See
:ref:`synthetic-observations`.
* Data objects can now be created via an alternative Numpy-like API. See
:ref:`quickly-selecting-data`.
* A line integral convolution plot modification. See
:ref:`annotate-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:
^^^^^^^^^^^^^^
* The RADMC-3D export analysis module has been updated. `PR 1358 <https://bitbucket.org/yt_analysis/yt/pull-requests/1358>`_, `PR 1332 <https://bitbucket.org/yt_analysis/yt/pull-requests/1332>`_.
* Performance improvements for grid frontends. `PR 1350 <https://bitbucket.org/yt_analysis/yt/pull-requests/1350>`_. `PR 1382 <https://bitbucket.org/yt_analysis/yt/pull-requests/1382>`_, `PR 1322 <https://bitbucket.org/yt_analysis/yt/pull-requests/1322>`_.
* Added a frontend for Dark Matter-only NMSU Art simulations. `PR 1258 <https://bitbucket.org/yt_analysis/yt/pull-requests/1258>`_.
* The absorption spectrum generator has been updated. `PR 1356 <https://bitbucket.org/yt_analysis/yt/pull-requests/1356>`_.
* The PerspectiveCamera has been updated and a new SphericalCamera has been
added. `PR 1346 <https://bitbucket.org/yt_analysis/yt/pull-requests/1346>`_, `PR 1299 <https://bitbucket.org/yt_analysis/yt/pull-requests/1299>`_.
* The unit system now supports unit equivalencies and has improved support for MKS units. See :ref:`unit_equivalencies`. `PR 1291 <https://bitbucket.org/yt_analysis/yt/pull-requests/1291>`_, `PR 1286 <https://bitbucket.org/yt_analysis/yt/pull-requests/1286>`_.
* Data object selection can now be chained, allowing selecting based on multiple constraints. `PR 1264 <https://bitbucket.org/yt_analysis/yt/pull-requests/1264>`_.
* Added the ability to manually override the simulation unit system. `PR 1236 <https://bitbucket.org/yt_analysis/yt/pull-requests/1236>`_.
* The documentation has been reorganized and has seen substantial improvements. `PR 1383 <https://bitbucket.org/yt_analysis/yt/pull-requests/1383>`_, `PR 1373 <https://bitbucket.org/yt_analysis/yt/pull-requests/1373>`_, `PR 1364 <https://bitbucket.org/yt_analysis/yt/pull-requests/1364>`_, `PR 1351 <https://bitbucket.org/yt_analysis/yt/pull-requests/1351>`_, `PR 1345 <https://bitbucket.org/yt_analysis/yt/pull-requests/1345>`_. `PR 1333 <https://bitbucket.org/yt_analysis/yt/pull-requests/1333>`_, `PR 1342 <https://bitbucket.org/yt_analysis/yt/pull-requests/1342>`_, `PR 1338 <https://bitbucket.org/yt_analysis/yt/pull-requests/1338>`_, `PR 1330 <https://bitbucket.org/yt_analysis/yt/pull-requests/1330>`_, `PR 1326 <https://bitbucket.org/yt_analysis/yt/pull-requests/1326>`_, `PR 1323 <https://bitbucket.org/yt_analysis/yt/pull-requests/1323>`_, `PR 1315 <https://bitbucket.org/yt_analysis/yt/pull-requests/1315>`_, `PR 1305 <https://bitbucket.org/yt_analysis/yt/pull-requests/1305>`_, `PR 1289 <https://bitbucket.org/yt_analysis/yt/pull-requests/1289>`_, `PR 1276 <https://bitbucket.org/yt_analysis/yt/pull-requests/1276>`_.
Minor or bugfix changes:
^^^^^^^^^^^^^^^^^^^^^^^^
* The Ampere unit now accepts SI prefixes. `PR 1393 <https://bitbucket.org/yt_analysis/yt/pull-requests/1393>`_.
* The Gadget InternalEnergy and StarFormationRate fields are now read in with the correct units. `PR 1392 <https://bitbucket.org/yt_analysis/yt/pull-requests/1392>`_, `PR 1379 <https://bitbucket.org/yt_analysis/yt/pull-requests/1379>`_.
* Substantial improvements for the PPVCube analysis module and support for FITS dataset. `PR 1390 <https://bitbucket.org/yt_analysis/yt/pull-requests/1390>`_, `PR 1367 <https://bitbucket.org/yt_analysis/yt/pull-requests/1367>`_, `PR 1347 <https://bitbucket.org/yt_analysis/yt/pull-requests/1347>`_, `PR 1326 <https://bitbucket.org/yt_analysis/yt/pull-requests/1326>`_, `PR 1280 <https://bitbucket.org/yt_analysis/yt/pull-requests/1280>`_, `PR 1336 <https://bitbucket.org/yt_analysis/yt/pull-requests/1336>`_.
* The center of a PlotWindow plot can now be set to the maximum or minimum of any field. `PR 1280 <https://bitbucket.org/yt_analysis/yt/pull-requests/1280>`_.
* Fixes for yt testing infrastructure. `PR 1388 <https://bitbucket.org/yt_analysis/yt/pull-requests/1388>`_, `PR 1348 <https://bitbucket.org/yt_analysis/yt/pull-requests/1348>`_.
* Projections are now performed using an explicit path length field for all
coordinate systems. `PR 1307 <https://bitbucket.org/yt_analysis/yt/pull-requests/1307>`_.
* An example notebook for simulations using the OWLS data format has been added
to the documentation. `PR 1386 <https://bitbucket.org/yt_analysis/yt/pull-requests/1386>`_.
* Fix for the camera.draw_line function. `PR 1380 <https://bitbucket.org/yt_analysis/yt/pull-requests/1380>`_.
* Minor fixes and improvements for yt plots. `PR 1376 <https://bitbucket.org/yt_analysis/yt/pull-requests/1376>`_, `PR 1374 <https://bitbucket.org/yt_analysis/yt/pull-requests/1374>`_, `PR 1288 <https://bitbucket.org/yt_analysis/yt/pull-requests/1288>`_, `PR 1290 <https://bitbucket.org/yt_analysis/yt/pull-requests/1290>`_.
* Significant documentation reorganization and improvement. `PR 1375 <https://bitbucket.org/yt_analysis/yt/pull-requests/1375>`_, `PR 1359 <https://bitbucket.org/yt_analysis/yt/pull-requests/1359>`_.
* Fixed a conflict in the CFITSIO library used by the x-ray analysis module. `PR 1365 <https://bitbucket.org/yt_analysis/yt/pull-requests/1365>`_.
* Miscellaneous code cleanup. `PR 1371 <https://bitbucket.org/yt_analysis/yt/pull-requests/1371>`_, `PR 1361 <https://bitbucket.org/yt_analysis/yt/pull-requests/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 <https://bitbucket.org/yt_analysis/yt/pull-requests/1355>`_, `PR 1362 <https://bitbucket.org/yt_analysis/yt/pull-requests/1362>`_, `PR 1360 <https://bitbucket.org/yt_analysis/yt/pull-requests/1360>`_.
* The docstring for the projection data object has been corrected. `PR 1366 <https://bitbucket.org/yt_analysis/yt/pull-requests/1366>`_
* A bug in the calculation of the plot bounds for off-axis slice plots has been fixed. `PR 1357 <https://bitbucket.org/yt_analysis/yt/pull-requests/1357>`_.
* Improvements for the yt-rockstar interface. `PR 1352 <https://bitbucket.org/yt_analysis/yt/pull-requests/1352>`_, `PR 1317 <https://bitbucket.org/yt_analysis/yt/pull-requests/1317>`_.
* Fix issues with plot positioning with saving to postscript or encapsulated postscript. `PR 1353 <https://bitbucket.org/yt_analysis/yt/pull-requests/1353>`_.
* It is now possible to supply a default value for get_field_parameter. `PR 1343 <https://bitbucket.org/yt_analysis/yt/pull-requests/1343>`_.
* A bug in the interpretation of the units of RAMSES simulations has been fixed. `PR 1335 <https://bitbucket.org/yt_analysis/yt/pull-requests/1335>`_.
* Plot callbacks are now only executed once before the plot is saved. `PR 1328 <https://bitbucket.org/yt_analysis/yt/pull-requests/1328>`_.
* Performance improvements for smoothed covering grid alias fields. `PR 1331 <https://bitbucket.org/yt_analysis/yt/pull-requests/1331>`_.
* Improvements and bugfixes for the halo analysis framework. `PR 1349 <https://bitbucket.org/yt_analysis/yt/pull-requests/1349>`_, `PR 1325 <https://bitbucket.org/yt_analysis/yt/pull-requests/1325>`_.
* Fix issues with the default setting for the ``center`` field parameter. `PR 1327 <https://bitbucket.org/yt_analysis/yt/pull-requests/1327>`_.
* Avoid triggering warnings in numpy and matplotlib. `PR 1334 <https://bitbucket.org/yt_analysis/yt/pull-requests/1334>`_, `PR 1300 <https://bitbucket.org/yt_analysis/yt/pull-requests/1300>`_.
* Updates for the field list reference. `PR 1344 <https://bitbucket.org/yt_analysis/yt/pull-requests/1344>`_, `PR 1321 <https://bitbucket.org/yt_analysis/yt/pull-requests/1321>`_, `PR 1318 <https://bitbucket.org/yt_analysis/yt/pull-requests/1318>`_.
* yt can now be run in parallel on a subset of available processors using an MPI subcommunicator. `PR 1340 <https://bitbucket.org/yt_analysis/yt/pull-requests/1340>`_
* Fix for incorrect units when loading an Athena simulation as a time series. `PR 1341 <https://bitbucket.org/yt_analysis/yt/pull-requests/1341>`_.
* Improved support for Enzo 3.0 simulations that have not produced any active particles. `PR 1329 <https://bitbucket.org/yt_analysis/yt/pull-requests/1329>`_.
* Fix for parsing OWLS outputs with periods in the file path. `PR 1320 <https://bitbucket.org/yt_analysis/yt/pull-requests/1320>`_.
* Fix for periodic radius vector calculation. `PR 1311 <https://bitbucket.org/yt_analysis/yt/pull-requests/1311>`_.
* Improvements for the Maestro and Castro frontends. `PR 1319 <https://bitbucket.org/yt_analysis/yt/pull-requests/1319>`_.
* Clump finding is now supported for more generic types of data. `PR 1314 <https://bitbucket.org/yt_analysis/yt/pull-requests/1314>`_
* Fix unit consistency issue when mixing dimensionless unit symbols. `PR 1300 <https://bitbucket.org/yt_analysis/yt/pull-requests/1300>`_.
* Improved memory footprint in the photon_simulator. `PR 1304 <https://bitbucket.org/yt_analysis/yt/pull-requests/1304>`_.
* Large grids in Athena datasets produced by the join_vtk script can now be optionally split, improving parallel performance. `PR 1304 <https://bitbucket.org/yt_analysis/yt/pull-requests/1304>`_.
* Slice plots now accept a ``data_source`` keyword argument. `PR 1310 <https://bitbucket.org/yt_analysis/yt/pull-requests/1310>`_.
* Corrected inconsistent octrees in the RAMSES frontend. `PR 1302 <https://bitbucket.org/yt_analysis/yt/pull-requests/1302>`_
* Nearest neighbor distance field added. `PR 1138 <https://bitbucket.org/yt_analysis/yt/pull-requests/1138>`_.
* Improvements for the ORION2 frontend. `PR 1303 <https://bitbucket.org/yt_analysis/yt/pull-requests/1303>`_
* Enzo 3.0 frontend can now read active particle attributes that are arrays of any shape. `PR 1248 <https://bitbucket.org/yt_analysis/yt/pull-requests/1248>`_.
* Answer tests added for halo finders. `PR 1253 <https://bitbucket.org/yt_analysis/yt/pull-requests/1253>`_
* A ``setup_function`` has been added to the LightRay initializer. `PR 1295 <https://bitbucket.org/yt_analysis/yt/pull-requests/1295>`_.
* The SPH code frontends have been reorganized into separate frontend directories. `PR 1281 <https://bitbucket.org/yt_analysis/yt/pull-requests/1281>`_.
* Fixes for accessing deposit fields for FLASH data. `PR 1294 <https://bitbucket.org/yt_analysis/yt/pull-requests/1294>`_
* Added tests for ORION datasets containing sink and star particles. `PR 1252 <https://bitbucket.org/yt_analysis/yt/pull-requests/1252>`_
* Fix for field names in the particle generator. `PR 1278 <https://bitbucket.org/yt_analysis/yt/pull-requests/1278>`_.
* Added wrapper functions for numpy array manipulation functions. `PR 1287 <https://bitbucket.org/yt_analysis/yt/pull-requests/1287>`_.
* Added support for packed HDF5 Enzo datasets. `PR 1282 <https://bitbucket.org/yt_analysis/yt/pull-requests/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
:ref:`yt3differences`.
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 <http://yt-project.org/files/yt24.ipynb>`_.
Most Visible Improvements
^^^^^^^^^^^^^^^^^^^^^^^^^
* Threaded volume renderer, completely refactored from the ground up for
speed and parallelism.
* The Plot Window (see :ref:`simple-inspection`) 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
^^^^^^^^^^^^^
* :class:`~yt.visualization.plot_window.ProjectionPlot` and
:class:`~yt.visualization.plot_window.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) <http://yt-project.org/docs/2.3>`_
* Multi-level parallelism
* Real, extensive answer tests
* Boolean data regions (see :ref:`boolean_data_objects`)
* Isocontours / flux calculations (see :ref:`extracting-isocontour-information`)
* 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
:ref:`manual-plotting` and a revamped orientation.
Version 2.2
-----------
`(yt 2.2 docs) <http://yt-project.org/docs/2.2>`_
* 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
:ref:`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 :ref:`mapserver`)
* Many bug fixes and performance improvements
* Halo loader
Version 2.1
-----------
`(yt 2.1 docs) <http://yt-project.org/docs/2.1>`_
* 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 (:ref:`time-series-analysis`) now much easier
* Stream Lines now a supported 1D data type
* Stream Lines now able to be calculated and plotted (:ref:`streamlines`)
* 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 :ref:`merger_tree`)
* Parallel structure function generator (see :ref:`two_point_functions`)
* Image pan and zoom object and display widget.
* Parallel volume rendering (see :ref:`volume_rendering`)
* Multivariate volume rendering, allowing for multiple forms of emission and
absorption, including approximate scattering and Planck emissions. (see
:ref:`volume_rendering`)
* Added Camera interface to volume rendering (See :ref:`volume_rendering`)
* Off-axis projection (See :ref:`volume_rendering`)
* Stereo (toe-in) volume rendering (See :ref:`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 :class:`yt.extensions.EnzoSimulation` (See
:ref:`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 :ref:`halo-analysis`)
* (New) Parallel HOP ( https://arxiv.org/abs/1001.3411 , :ref:`halo-analysis` )
* (Beta) Software ray casting and volume rendering
(see :ref:`volume_rendering`)
* Rewritten, faster and better contouring engine for clump identification
* Spectral Energy Distribution calculation for stellar populations
(see :ref:`synthetic_spectrum`)
* Optimized data structures such as the index
* Star particle analysis routines
(see :ref:`star_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 :ref:`parallel-computation`) 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!
