[yt-users] [FLASH-USERS] ANN: yt-3.2 released

Alexander Heger alex.heger at gmail.com
Tue Aug 25 04:13:59 PDT 2015


Dear John,

I just tried the new version of yt.  Installation worked!
But going through the demo notebooks, already
"3)_Simple_Visualization" fails on the first plot.  Error trace below.

I ma not really sure why the first error occurs as the font is
installed, but the second error is a bug with trying to decode a
string (you can decode bytes type and encode strings in python3), the
last one seems strange why it would look for a font in the current
directory.

I also note that the notebook is still python 2 - so all the print
statements don't work.  I am happy to share my notebooks with these
fixed if I can get them to run.

-Alexander

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
/home/alex/Python/lib/python3.4/site-packages/matplotlib/dviread.py in
__getitem__(self, texname)
     706         try:
--> 707             result = self._font[texname]
     708         except KeyError:

KeyError: 'cmsy10'

During handling of the above exception, another exception occurred:

AttributeError                            Traceback (most recent call last)
/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in print_pdf(self, filename, **kwargs)
    2484                 bbox_inches_restore=_bbox_inches_restore)
-> 2485             self.figure.draw(renderer)
    2486             renderer.finalize()

/home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in
draw_wrapper(artist, renderer, *args, **kwargs)
      58         before(artist, renderer)
---> 59         draw(artist, renderer, *args, **kwargs)
      60         after(artist, renderer)

/home/alex/Python/lib/python3.4/site-packages/matplotlib/figure.py in
draw(self, renderer)
    1084         for zorder, a, func, args in dsu:
-> 1085             func(*args)
    1086

/home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in
draw_wrapper(artist, renderer, *args, **kwargs)
      58         before(artist, renderer)
---> 59         draw(artist, renderer, *args, **kwargs)
      60         after(artist, renderer)

/home/alex/Python/lib/python3.4/site-packages/matplotlib/axes/_base.py
in draw(self, renderer, inframe)
    2109         for zorder, a in dsu:
-> 2110             a.draw(renderer)
    2111

/home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in
draw_wrapper(artist, renderer, *args, **kwargs)
      58         before(artist, renderer)
---> 59         draw(artist, renderer, *args, **kwargs)
      60         after(artist, renderer)

/home/alex/Python/lib/python3.4/site-packages/matplotlib/axis.py in
draw(self, renderer, *args, **kwargs)
    1118         for tick in ticks_to_draw:
-> 1119             tick.draw(renderer)
    1120

/home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in
draw_wrapper(artist, renderer, *args, **kwargs)
      58         before(artist, renderer)
---> 59         draw(artist, renderer, *args, **kwargs)
      60         after(artist, renderer)

/home/alex/Python/lib/python3.4/site-packages/matplotlib/axis.py in
draw(self, renderer)
     248         if self.label1On:
--> 249             self.label1.draw(renderer)
     250         if self.label2On:

/home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in
draw_wrapper(artist, renderer, *args, **kwargs)
      58         before(artist, renderer)
---> 59         draw(artist, renderer, *args, **kwargs)
      60         after(artist, renderer)

/home/alex/Python/lib/python3.4/site-packages/matplotlib/text.py in
draw(self, renderer)
     637                 renderer.draw_tex(gc, x, y, clean_line,
--> 638                                   self._fontproperties, angle,
mtext=mtext)
     639             else:

/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in draw_tex(self, gc, x, y, s, prop, angle, ismath, mtext)
    1823                 if dvifont.texname not in self.file.dviFontInfo:
-> 1824                     psfont = self.tex_font_mapping(dvifont.texname)
    1825                     self.file.dviFontInfo[dvifont.texname] = Bunch(

/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in tex_font_mapping(self, texfont)
    1530 dviread.PsfontsMap(dviread.find_tex_file('pdftex.map'))
-> 1531         return self.tex_font_map[texfont]
    1532

/home/alex/Python/lib/python3.4/site-packages/matplotlib/dviread.py in
__getitem__(self, texname)
     708         except KeyError:
--> 709             result = self._font[texname.decode('ascii')]
     710         fn, enc = result.filename, result.encoding

AttributeError: 'str' object has no attribute 'decode'

During handling of the above exception, another exception occurred:

FileNotFoundError                         Traceback (most recent call last)
/home/alex/Python/lib/python3.4/site-packages/IPython/core/formatters.py
in __call__(self, obj)
     339             method = _safe_get_formatter_method(obj, 
self.print_method)
     340             if method is not None:
--> 341                 return method()
     342             return None
     343         else:

/home/alex/Python/lib/python3.4/site-packages/yt/visualization/plot_container.py
in newfunc(*args, **kwargs)
      75             if hasattr(args[0], 'run_callbacks'):
      76                 args[0].run_callbacks()
---> 77         rv = f(*args, **kwargs)
      78         return rv
      79     return newfunc

/home/alex/Python/lib/python3.4/site-packages/yt/visualization/plot_container.py
in _repr_html_(self)
     642         ret = ''
     643         for field in self.plots:
--> 644             img =
base64.b64encode(self.plots[field]._repr_png_()).decode()
     645             ret += r'<img 
style="max-width:100%%;max-height:100%%;" ' \
     646 r'src="data:image/png;base64,{0}"><br>'.format(img)

/home/alex/Python/lib/python3.4/site-packages/yt/visualization/base_plot_types.py
in _repr_png_(self)
     165         canvas = FigureCanvasAgg(self.figure)
     166         f = BytesIO()
--> 167         canvas.print_figure(f)
     168         f.seek(0)
     169         return f.read()

/home/alex/Python/lib/python3.4/site-packages/matplotlib/backend_bases.py
in print_figure(self, filename, dpi, facecolor, edgecolor,
orientation, format, **kwargs)
    2209                 orientation=orientation,
    2210                 bbox_inches_restore=_bbox_inches_restore,
-> 2211                 **kwargs)
    2212         finally:
    2213             if bbox_inches and restore_bbox:

/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in print_pdf(self, filename, **kwargs)
    2489                 file.endStream()
    2490             else:            # we opened the file above; now
finish it off
-> 2491                 file.close()
    2492
    2493

/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in close(self)
     523         self.endStream()
     524         # Write out the various deferred objects
--> 525         self.writeFonts()
     526         self.writeObject(self.alphaStateObject,
     527                          dict([(val[0], val[1])

/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in writeFonts(self)
     623                 # a normal TrueType font
     624                 matplotlib.verbose.report('Writing TrueType
font', 'debug')
--> 625                 realpath, stat_key = get_realpath_and_stat(filename)
     626                 chars = self.used_characters.get(stat_key)
     627                 if chars is not None and len(chars[1]):

/home/alex/Python/lib/python3.4/site-packages/matplotlib/cbook.py in
__call__(self, path)
    1020                 stat_key = realpath
    1021             else:
-> 1022                 stat = os.stat(realpath)
    1023                 stat_key = (stat.st_ino, stat.st_dev)
    1024             result = realpath, stat_key

FileNotFoundError: [Errno 2] No such file or directory:
'/home/alex/yt/doc/source/quickstart/cmsy10'

<yt.visualization.plot_window.ProjectionPlot at 0x7fb8225470b8>

On 25 July 2015 at 05:48, John ZuHone <jzuhone at space.mit.edu> wrote:
> We are proud to announce the release of yt 3.2!
>
> yt (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 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
> 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 ):
>
> 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
> $ 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/):
>
> # 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/)
> WinPython (http://winpython.sourceforge.net/)
>
>
> Mac OS X x86_64:
>
> Enthought Canopy Python (https://www.enthought.com/products/canopy/)
> Homebrew Python (http://brew.sh/)
> Python.org Python
> Mac OS X’s system Python
> MacPorts Python (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).
>
> 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 and the documentation
> for yt-3.2 at 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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