[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
>>
>>
>> _______________________________________________
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>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>>
>>
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