I'd like to open up the discussion of "fixing" the yt coordinate
systems, as we move nearer and nearer on 3.0. Jeff, Nathan and
Britton have brought this up a couple times, that the x/y/z ordering
is not consistent with what they expect, and I'd like to figure out if
we can fix that now -- it's as good a time as any for bandaid ripping.
It may just be a matter of the transposition of buffers and the
x_dict and y_dict, or it might be more complex, although I suspect it
won't be much more than fixing those two items.
After talking to Britton, Nathan, and Anthony about this, I think I
need to pull a mulligan on the current rebranding effort and start
afresh in unit refactor.
To that end, I'm going to have a sprint a week from Friday, from
11AM-1PM EST or so, to work on this. I'll set up a google hangout,
and if you want to come by, please do. It's going to be mostly some
big, easily done renames, and then fixing unit tests.
Here's the event page; sorry about the weird theme, I don't understand
why the default for a hangout is wine glasses.
Between now and then, I am traveling until Saturday, then next week
will be devoting myself to fixing the remaining unit-refactor issues
as enumerated on the Trello boards for unit refactor and
documentation. Once rebranding is done, the docs will have to be
lightly updated, but not too badly.
We've had a couple critical bug fixes go in to the mainline 2.x branch
lately, and we're also slightly overdue for a 2.6.2. So I would like
to cut a release on Thursday. If there are any objections, let me
know, otherwise I'll proceed with merging into stable, tagging, and
uploading to pypi. John ZuHone pointed out that with Kacper's fixes
to the packaging and his fixes to various imports and whatnot we ought
to keep to this schedule; I've let it slip a little.
New issue 794: nosetests runtime warning
Whatever nosetests plugin that gets installed with yt spits out a runtime warning whenever nosetests is run, even for other projects. This should perhaps be suppressed somehow.
RuntimeWarning: Unable to load plugin answer-testing = yt.utilities.answer_testing.framework:AnswerTesting: No module named sympy
New issue 792: Native support for HDF5 grid structure
Although yt imports HDF5 data when all fields are stored under the root directory, there seems to be no support for reading data stored under groups. One has to go through the somewhat laborious route of importing data as numpy arrays from h5py.
New issue 789: PhasePlot save missing string
If I save the phase plot in another directory with:
pplot = PhasePlot(dd, "Density", "Temperature", ["Electron_Fraction"],
the file name is "frames/_2d-Profile_Density_Temperature_Electron_Fraction.png"
if I just use
pplot.save() it will include the pf string as
So by specifying the folder it replaces the pf string. ProjectionPlot does not have the same issue. Annoying bug, but not critical.
I'd like to encourage everybody to come to SciPy this year. I think
we should aim to submit a yt 3.0 talk that is jointly given by a few
of us, and submit that to the main track and not the astro track.
Additionally, there will be a WSSSPE workshop
(http://wssspe.researchcomputing.org.uk/) and sponsored sprints, so it
should be a really amazing week where we can present a lot of good
work, discuss important things like scientific software
sustainability, and spend a couple days working with provided food and
I'm going to send out a draft of a talk abstract about 3.0 in the next
few days; I think it would be quite a valuable thing to try to jointly
deliver the talk, with whoever is around, or to have ambassadors
getting data into yt over the course of the week.
On that sort of related topic, after the intensity of his last couple
months, I'm going to be taking a break from travel, and I'm aiming not
to be traveling anywhere (modulo day trips) between the yt workshop
and SciPy, and then again from SciPy until probably November or so.