[yt-users] [FLASH-USERS] ANN: yt-3.2 released
Nathan Goldbaum
nathan12343 at gmail.com
Thu Aug 27 08:47:11 PDT 2015
On Thu, Aug 27, 2015 at 2:46 AM, Alexander Heger <alex.heger at gmail.com>
wrote:
> 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?
>
We tend to keep breaking changes to an absolute minimum, since we know a
large fraction of our userbase is keeping up with the "yt" branch. We're
trying to be better about backporting fixes to stable and issuing regular
stable releases in the future. In addition, we actually have two "heads" on
our yt branch, one for "experimental" features that aren't ready for the
"mainline" yt branch, so there is even less change of you landing on a
breaking change on the yt branch.
If we ever *do* decide to start merging breaking changes into the dev
branch, we will make it abundantly clear that we are doing so on the
mailing lists.
>
> 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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