New issue 651: EnzoSimulationTimeSeries fails when par file line has more than one "=" sign.
When a line in an enzo parameter file has more than one equal sign, you get the following when trying to load a SimulationTimeSeries:
Traceback (most recent call last):
File "lc.py", line 15, in <module>
File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 158, in __init__
File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 44, in __init__
File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line 131, in simulation
File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 81, in __init__
File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/data_objects/time_series.py", line 343, in __init__
File "/Users/britton/Documents/work/yt/yt-x86_64/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 273, in _parse_parameter_file
param, vals = (i.strip() for i in line.split("="))
ValueError: too many values to unpack
New issue 650: load helper should fallback to test_data_dir
This is related to [PR99](https://bitbucket.org/yt_analysis/yt-doc/pull-request/99/adding-color…. I've initially wanted to as @chummels to modify his `cmap_images.py` script as follows:
@@ -1,8 +1,9 @@
from yt.mods import *
import matplotlib.cm as cm
# Load the dataset.
-pf = load("IsolatedGalaxy/galaxy0030/galaxy0030")
+pf = load(os.path.join(ytcfg.get("yt", "test_data_dir"),
# Create projections using each colormap available.
Then I thought that if we could make `load` fallback to that path if `args` doesn't exists, that would come handy for docstrings tests.
New issue 649: PlotWindow should have toggles for the annotated axes and colorbar
Something like this:
p = ProjectionPlot(pf, 2, 'Density')
for a PlotCollection-like experience. Or,
p = ProjectionPlot(pf, 2, ['Density', 'Temperature'])
to remove the colorbar but leave the annotated axes.
I'd like to call a brief, approximately one hour, strategy meeting on
Monday, April 22nd at 3PM Eastern. This will cover where yt is at,
where we can go, and how things are progressing. Some of this will be
dedicated to progress updates (from me and others) as well as
soliciting feedback on a number of things. Many other projects --
notably Cactus -- do these on a fixed schedule, so based on the
success/failure of this one we can consider having them
The agenda I would like to cover will include:
* yt 3.0 status, including near/long term plans for development and
support for non-grid codes
* Rundown of all YTEPs accepted and outstanding
* yt's "presence" on the web
* 3.0 paper
I will also be soliciting feedback in roundtable style on:
* How are we doing?
* How is the procedure for code contributions working?
* How is the yt "infrastructure" meeting people's needs? (Mailing
lists, Bitbucket, etc)
* Where are energies being spent that could be better spent elsewhere?
If you have either agenda items or discussion items, please reply to
this email and suggest them.
I think having a large presence at this meeting would be very useful,
so if you are able to make it, please try to do so. It'll be held as
a google hangout, and I'll send details here when it starts up. If
there's a pressing need to reschedule, please write in reply to this
Thanks, and looking forward to seeing you there,
New issue 647: Volume Rendering + Log Fields + Zeros
Currently if you have a volume rendering of a field that is done in log-space and there are zeros/negative values in the raw field data, the resulting NaNs contaminate the image, causing most if not all of the rendering to be empty (zeros).
New issue 646: Trailing Spaces in FLASH datasets carried over to output file names in SlicePlot
All variables in FLASH are internally represented by a 4 character string, if a variable has less characters, it has trailing spaces, for instance, carbon is "c12 ". When you perform a SlicePlot on one of these variables, the output file is annoyingly named "mysimulation_c12 .png". This is only an issue for element names when using either the 13 or 19 element burn network.
New issue 645: Setup script should complain or error out when using intel compilers
As noted on the list, when yt is compiled with icc, there are mysterious hangs during some operations. We should be able to detect that and either error out or print a warning rather than silently generate a broken installation.
After talking with Matt at some length about the yt documentation, we
thought it might be a good idea to have a documentation sprint in a few
months when we've moved over to yt 3.0 as the focus of our development.
The docs in general are good, but there are some gaps here and there with
some functionality not present in the documentation. I'm not proposing an
entire (or even partial) rewrite of the docs, as I think that would be
counterproductive. I'm simply thinking we could fill in the holes to make
sure all of the cool stuff in yt is written up so people know how to use it.
Now, I know doc writing is not often fun, but I think this could be really
beneficial to our user base, and actually cut down on the amount of time we
have to respond to new users on the mailing list and irc (as well as making
it easier for people to use yt).
What I'm asking from you is if you encounter something that you don't think
is well documented in the formal docs (not simply the docstrings), could
you take a moment to create a bitbucket issue about it? You don't even
have to fix it then, just note it, so we know where to work when we do the
sprint in a few months.
Anyone else have any other ideas about this?
University of Arizona
New issue 644: PR 87 causes test failure in test_offaxisprojection
Revision 3aba7ca1ff0b causes
ERROR: Failure: ValueError (The truth value of an array with more than one element is ambiguous. Use a.any() or a.all())
Traceback (most recent call last):
File "/usr/lib64/python2.7/site-packages/nose/loader.py", line 231, in generate
for test in g():
File "/home/xarth/codes/yt-3.0/yt/visualization/tests/test_offaxisprojection.py", line 86, in test_write_projection
write_projection(image, fn, **wp_kwargs)
File "/home/xarth/codes/yt-3.0/yt/visualization/image_writer.py", line 417, in write_projection
cbar = fig.colorbar(cax)
File "/usr/lib64/python2.7/site-packages/matplotlib/figure.py", line 1394, in colorbar
cb = cbar.colorbar_factory(cax, mappable, **kw)
File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 1173, in colorbar_factory
cb = Colorbar(cax, mappable, **kwargs)
File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 854, in __init__
ColorbarBase.__init__(self, ax, **kw)
File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 298, in __init__
File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 319, in draw_all
File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 632, in _process_values
b = self.norm.inverse(self._uniform_y(self.cmap.N+1))
File "/usr/lib64/python2.7/site-packages/matplotlib/colors.py", line 982, in inverse
return vmin * ma.power((vmax / vmin), val)
File "/usr/lib64/python2.7/site-packages/numpy/ma/core.py", line 3648, in __mul__
return multiply(self, other)
File "/usr/lib64/python2.7/site-packages/numpy/ma/core.py", line 941, in __call__
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()