[yt-users] [FLASH-USERS] ANN: yt-3.2 released
Alexander Heger
alex.heger at gmail.com
Thu Aug 27 00:46:18 PDT 2015
Dear Nathan,
I now switched to the current matplotlibrc files and with that it seems
to work.
Thanks a lot.
As another question: is ok or ill-advised to run with the current yt
development version instead of the latest release?
Best wishes,
Alexander
On 27/08/15 00:26, Nathan Goldbaum wrote:
>
>
> On Wed, Aug 26, 2015 at 4:48 AM, Alexander Heger <alex.heger at gmail.com
> <mailto: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>
> <mailto: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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>
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>
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