On Thu, Aug 27, 2015 at 2:46 AM, Alexander Heger <alex.heger@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@gmail.com
<mailto:alex.heger@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@space.mit.edu <mailto:jzuhone@space.mit.edu>
<mailto:jzuhone@space.mit.edu

<mailto:jzuhone@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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