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

Nathan Goldbaum nathan12343 at gmail.com
Wed Aug 26 07:26:14 PDT 2015


On Wed, Aug 26, 2015 at 4:48 AM, Alexander Heger <alex.heger at gmail.com>
wrote:

> Dear Nathan,
>
> Thanks for the report about this, we should make the quickstart
>> notebooks work under both python 2 and python 3.  I've filed an issue to
>> track this here:
>>
>>
>> https://bitbucket.org/yt_analysis/yt/issues/1073/quickstart-notebooks-do-not-work-under
>>
>> Python 3 is still new to yt, so there are rough edges that you're
>> running across. It really helps to get reports back from python3 users,
>> especially new users where things are confusing in yt. So thank you!
>>
>
> I ma happy to help, it is my interest to get it run - I use and teach
> students to use python 3 since there is many cool new features in py3.
>
> I'm not sure what's up with the font issue below. I just tried running
>> the simple visualization notebook under python3 and it worked on my
>> laptop, although that doesn't say much given that we likely installed in
>> very different ways. The fact that it's looking for cmsy10 is a bit
>> strange since yt doesn't use that font internally. Do you perhaps have
>> useTex = True somewhere in your matplotlibrc? Even then I'm confused why
>>
>
> yes, I would use that; matplotlib seems to work otherwise.
>
> it's crashing since I know many people use that setting day-to-day with
>> yt and have no issues. I also just tried running that example notebook
>> using matplotlib's useTex=True setting and it worked.
>>
>
> maybe something is special, I admit that after installation on top of my
> custom-built python 3.4.3 on Fedora 22
>
> cd
> hg clone https://bitbucket.org/yt_analysis/yt
> cd yt
> hg update yt
> pip3 install -r requirements.txt
> pip3 install yt
>
> I upgraded all packages to current version
>
> pip3 freeze --local | grep -v '^\-e' | cut -d = -f 1  | xargs -n1 pip3
> install -U
>
> In either case, it's really a matplotlib issue and there's not much we
>> can do about it on the yt side. In particular, I don't see any code
>> outside matplotlib in any of your tracebacks. Did you install yt using
>> the install script, or by "pip install"ing or "conda install"ing? Which
>> matplotlib version are you running? You can check by doing "import
>> matplotlib; print(matplotlib.__version__)" in the python REPL.
>>
>
> In [1]: mpl.__version__
> Out[1]: '1.4.3'
>
> Maybe I need to check/update my mpl resource file which is not 5 yr old...?
>
> I will try to update mpl to current development version
>
> In [1]: mpl.__version__
> Out[1]: '1.5.dev1'
>
> unfortunately the error remains.  I am a bit worried about the line
>
> --> 697             result = self._font[texname.decode('ascii')]
>
> I will check tomorrow where 'cmsy10' may come from.
>
> Should I also be suing the current development version of yt to make error
> tracking against current version (and getting fixes) easier?
>
> (and is this the correct list for this, or should I be using the yt-devel
> list?)
>

Either list is fine, please also feel free to open an issue, especially if
you can make this error reproducible on another setup.


>
> Best wishes,
> Alexander
>
>
>
>>
>>     -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
>>     <mailto: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
>>
>>
>>     _______________________________________________
>>     yt-users mailing list
>>     yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
>>     http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>>
>>
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