Looking at the yt-3.0 docs that are online, it appears that something has
gone wrong in the build process. I see that Kacper has re-enabled the
cookbook build process, but now it seems that every recipe is also
producing a funky density plot from a random AMR pf:
http://yt-project.org/docs/dev-3.0/_images/simple_slice__AMRGridData_Slice_…
It *does* look cool, but I think we should figure out what is producing it.
Here is one of the cookbook pages where it shows up for every recipe:
http://yt-project.org/docs/dev-3.0/cookbook/simple_plots.html
--
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
New issue 863: mach_number field has units "code_length"
https://bitbucket.org/yt_analysis/yt/issue/863/mach_number-field-has-units-…
Cameron Hummels:
I realize that mach_number is unlikely to work with units of "mach" given that it is a dynamical unit, but it should have a dimensionless unit as opposed to "code_length". i don't know how to set dimensionless units.
Hi all,
Anybody up for a hangout/sprint either Friday or next week? Looks to
me like there's almost nothing besides docs and existing outstanding
PRs before we can release 3.0, so it'd be good to have a sprint where
we just went over the docs and PRs and got it in a workable state.
Trello has been fastidiously updated by various people, so if you're
looking for things that need doing:
https://trello.com/b/Y5XV4Hod/yt-3-0
-Matt
Hey everyone,
I've created a pull request which changes the defaults of the
ProjectionPlot and OffAxisProjectionPlot, although I'm looking for feedback
from the community.
Right now, when you create a projection, say for "Density", it labels the
colorbar with "Density" and then gives its projected units (instead of
g/cm^3, it gives g/cm^2). My PR is simply to change the default label to
be "Projected <field>" in this case "Projected Density (g/cm^2)". It will
do this in the case of non-weighted projections. I think this is the
expected behavior and more accurate than the former behavior, but I'm open
to discussion from the rest of the dev community.
In addition, it might be worthwhile to change the defaults on
weighted-projections (e.g. density-weighted temperature projection), to
give it and appropriate label as well, but I'm less convinced of this
change. Perhaps something like "<weight_field>-Weighted <field> (units)" ?
There is also a PR awaiting approval by John Regan that deals with this
behavior which will allow users to easily specify whatever label they want
for the colorbar, but I thought having a sensible default was appropriate
as well.
Anyway, what do people think about these potential changes?
Cameron
--
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
New issue 862: Removal of halo_profiler has broken halo_merger_tree
https://bitbucket.org/yt_analysis/yt/issue/862/removal-of-halo_profiler-has…
Kacper Kowalik:
After pull request #1009 importing `halo_merger_tree` fails with:
```
#!text
>>> import yt.analysis_modules.halo_merger_tree.api
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/tmp/yt/yt/analysis_modules/halo_merger_tree/api.py", line 16, in <module>
from .merger_tree import \
File "/tmp/yt/yt/analysis_modules/halo_merger_tree/merger_tree.py", line 25, in <module>
from yt.analysis_modules.halo_profiler.multi_halo_profiler import \
ImportError: No module named multi_halo_profiler
```
New issue 860: One of the animation recipes in the docs build raises the following error:
https://bitbucket.org/yt_analysis/yt/issue/860/one-of-the-animation-recipes…
Nathan Goldbaum:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-4-e3b9f89be543> in <module>()
12
13 # call the animator. blit=True means only re-draw the parts that have changed.
---> 14 anim = animation.FuncAnimation(fig, animate, frames=44, interval=200, blit=False)
15
16 # call our new function to display the animation
/home/xarth/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/animation.pyc in __init__(self, fig, func, frames, init_func, fargs, save_count, **kwargs)
1008 self._save_seq = []
1009
-> 1010 TimedAnimation.__init__(self, fig, **kwargs)
1011
1012 # Need to reset the saved seq, since right now it will contain data
/home/xarth/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/animation.pyc in __init__(self, fig, interval, repeat_delay, repeat, event_source, *args, **kwargs)
862
863 Animation.__init__(self, fig, event_source=event_source,
--> 864 *args, **kwargs)
865
866 def _step(self, *args):
/home/xarth/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/animation.pyc in __init__(self, fig, event_source, blit)
543
544 # Clear the initial frame
--> 545 self._init_draw()
546
547 # Instead of starting the event source now, we connect to the figure's
/home/xarth/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/animation.pyc in _init_draw(self)
1033 # artists.
1034 if self._init_func is None:
-> 1035 self._draw_frame(next(self.new_frame_seq()))
1036 else:
1037 self._drawn_artists = self._init_func()
/home/xarth/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/animation.pyc in _draw_frame(self, framedata)
1047 # Call the func with framedata and args. If blitting is desired,
1048 # func needs to return a sequence of any artists that were modified.
-> 1049 self._drawn_artists = self._func(framedata, *self._args)
<ipython-input-4-e3b9f89be543> in animate(i)
9 def animate(i):
10 ds = load('Enzo_64/DD%04i/data%04i' % (i,i))
---> 11 prj._switch_ds(ds)
12
13 # call the animator. blit=True means only re-draw the parts that have changed.
/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/visualization/plot_container.pyc in _switch_ds(self, new_ds, data_source)
282 self._data_valid = self._plot_valid = False
283 self._recreate_frb()
--> 284 self._setup_plots()
285
286 def __getitem__(self, item):
/var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/visualization/plot_window.pyc in _setup_plots(self)
844 hinv = False
845 for i, un in enumerate((unit_x, unit_y)):
--> 846 if hasattr(self.ds.coordinates, "default_unit_label"):
847 axax = getattr(self.ds.coordinates, "%s_axis" % ("xy"[i]))[axis_index]
848 un = self.ds.coordinates.default_unit_label[axax]
AttributeError: 'YTQuadTreeProj' object has no attribute 'coordinates'
Responsible: ngoldbaum
Hi all,
A big pull request, pushed by Nathan and accepted by Britton, has
globally changed "pf" (an enzo-ism for "parameter file") to "ds" (for
"dataset") everywhere in the code base. Fortunately, there's a
backcompat layer, but from here on out, long live "ds"!
-Matt
New issue 859: HaloCatalog tries to use non exisiting field
https://bitbucket.org/yt_analysis/yt/issue/859/halocatalog-tries-to-use-non…
Kacper Kowalik:
Following script:
```
#!python
from yt.mods import load
from yt.analysis_modules.halo_analysis.api import HaloCatalog
import tempfile
import os
# Create temporary directory for storing files
tmpdir = tempfile.mkdtemp()
# Load the data set with the full simulation information
data_pf = load('Enzo_64/RD0006/RedshiftOutput0006')
# Load the rockstar data files
halos_pf = load('rockstar_halos/halos_0.0.bin')
# Instantiate a catalog using those two paramter files
hc = HaloCatalog(data_pf=data_pf, halos_pf=halos_pf,
output_dir=os.path.join(tmpdir, 'halo_catalog'))
```
fails with current tip (d44a659ea62c) yielding
```
#!text
Traceback (most recent call last):
File "ala.py", line 17, in <module>
output_dir=os.path.join(tmpdir, 'halo_catalog'))
File "yt/analysis_modules/halo_analysis/halo_catalog.py", line 139, in __init__
self.add_default_quantities()
File "yt/analysis_modules/halo_analysis/halo_catalog.py", line 448, in add_default_quantities
self.add_quantity("virial_radius", field_type=field_type,prepend=True)
File "yt/analysis_modules/halo_analysis/halo_catalog.py", line 218, in add_quantity
raise RuntimeError("HaloCatalog quantity must be a registered function or a field of a known type.")
RuntimeError: HaloCatalog quantity must be a registered function or a field of a known type.
```
Regression was introduced in 39697406e012
*viral_radius* was renamed to *radius* in `yt/frontends/halo_catalogs/rockstar/definitions.py`, however `yt/analysis_modules/halo_analysis/halo_catalog.py:add_default_quantities` still tries to use it.
