[FLASH-USERS] ANN: yt-3.2 released

Fri Jul 24 15:48:54 EDT 2015

We are proud to announce the release of yt 3.2!

yt (http://yt-project.org <http://yt-project.org/>) is an open source, community-developed toolkit for analysis and visualization of volumetric data of all types, with a particular emphasis on astrophysical simulations and nuclear engineering simulations.

Major enhancements
Particle-Only Plots - a series of new plotting functions for visualizing particle data.  See here <http://yt-project.org/docs/dev/visualizing/plots.html#particle-plots> 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 <http://yt-project.org/docs/dev/examining/loading_data.html#halo-catalog-data> to learn how to load halo catalogs as regular yt datasets.
Custom colormaps can now be easily defined and added - see here <http://yt-project.org/docs/dev/visualizing/colormaps/index.html> 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
Fix ART star particle masses to correctly reflect current and initial mass
Updating ragged array tests for NumPy 1.9.1
Force returning lists for HDF5FileHandler

Coming Soon!

The next major release of yt will be version 3.3, which is slated to include an overhaul of the volume rendering system and support for analyzing and visualizing unstructured mesh data.

Standard Installation Methods

As with previous releases, you can install yt from source using one of the following methods.

1) From the install script (http://yt-project.org/#getyt <http://yt-project.org/#getyt> ):

Note, many of the dependencies have been updated since version 3.1.  If you previously installed yt from the install script, it is advised that you re-install yt from scratch.

# Installation

$ wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh <http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh>
$ bash install_script.sh

# Update

$ yt update

2) From pip (source or binary wheel, see below for more details):

# Installation

$ pip install yt

# Update

$ pip install -U yt

3) From the Anaconda Python Distribution (https://store.continuum.io/cshop/anaconda/ <https://store.continuum.io/cshop/anaconda/>):

# Installation

$ conda install yt

# Update

$ conda update yt

Note that it might take a day or two for the conda package to be updated.

If you are on the “stable” branch, updating will bring you from yt 3.1 to 3.2, incorporating all
changes since 3.1, whereas if you are on the “dev” or “yt” branch, only the changes since
your last update should be incorporated.

Installing Binary Packages via pip

New to this release is the ability to install binary packages (“wheels”) using pip on Windows and Mac OS X (64-bit only for both). This has the advantage of not needing to install yt from source using a proper compiler setup, which has caused occasional problems on both of these platforms and prevented us from installing yt easily on other Python distributions.

We have so far been able to install and run the binary distribution via pip on the following platforms and Python stacks:

Note that it might take a day or two for the pip wheels to be updated.

Windows x86_64:

Enthought Canopy Python (https://www.enthought.com/products/canopy/ <https://www.enthought.com/products/canopy/>)
WinPython (http://winpython.sourceforge.net/ <http://winpython.sourceforge.net/>)

Mac OS X x86_64:

Enthought Canopy Python (https://www.enthought.com/products/canopy/ <https://www.enthought.com/products/canopy/>)
Homebrew Python (http://brew.sh/ <http://brew.sh/>)
Python.org <http://python.org/> Python
Mac OS X’s system Python
MacPorts Python (https://www.macports.org/ <https://www.macports.org/>)

This is somewhat experimental, so other distributions may work (or not), please submit bug reports or successes to the mailing list or to the Bitbucket issues page (http://bitbucket.org/yt_analysis/yt/issues <http://bitbucket.org/yt_analysis/yt/issues>).

All distributions are recommended to be Python v. 2.7, although with yt 3.2 there is late-stage beta support for Python 3.4. The requirements for installing yt via this method are the same as from source:

NumPy
h5py
HDF5
SymPy
Matplotlib
IPython (not required, but strongly recommended)

To install a new version of yt on one of these platforms, simply do

$ pip install yt

and you should get the binary distribution automatically. Also, if your python installation is system-wide (e.g., the Mac system Python) you might need to run pip with administrator privileges.

For more information, including more installation instructions, links to community resources, and information on contributing to yt’s development, please see the yt homepage at http://yt-project.org <http://yt-project.org/> and the documentation for yt-3.2 at http://yt-project.org/docs/3.2 <http://yt-project.org/docs/3.2>.

yt is the product of a large community of developers and users and we are extraordinarily grateful for and proud of their contributions. Please forward this announcement on to any interested parties.

As always, if you have any questions, concerns, or run into any trouble updating please don't hesitate to send a message to the mailing list or stop by our IRC channel.

All the best,
The yt development team
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