Mailman 3 February 2014 - yt-dev

Orientation, coordinate systems
by Matthew Turk 15 Apr '14

15 Apr '14

Hi all, 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. -Matt

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Rebranding sprint
by Matthew Turk 07 Mar '14

07 Mar '14

Hi all, 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. https://plus.google.com/b/107728486871834552760/events/cn8i862986q8fg4lr9st… 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. -Matt

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2.6.2 on Thursday
by Matthew Turk 01 Mar '14

01 Mar '14

Hi all, 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. -Matt

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Issue #794: nosetests runtime warning (yt_analysis/yt)
by Elliott Biondo 01 Mar '14

01 Mar '14

New issue 794: nosetests runtime warning https://bitbucket.org/yt_analysis/yt/issue/794/nosetests-runtime-warning Elliott Biondo: 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 RuntimeWarning)

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Issue #793: Document the PlotWindow origin keyword (yt_analysis/yt)
by Nathan Goldbaum 28 Feb '14

28 Feb '14

New issue 793: Document the PlotWindow origin keyword https://bitbucket.org/yt_analysis/yt/issue/793/document-the-plotwindow-orig… Nathan Goldbaum: It looks like documentation for the origin keyword is missing. This should be added. Responsible: ngoldbaum

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Issue #792: Native support for HDF5 grid structure (yt_analysis/yt)
by Girish Nivarti 28 Feb '14

28 Feb '14

New issue 792: Native support for HDF5 grid structure https://bitbucket.org/yt_analysis/yt/issue/792/native-support-for-hdf5-grid… Girish Nivarti: 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.

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Issue #791: iyt does not display plot using .show() (yt_analysis/yt)
by Girish Nivarti 28 Feb '14

28 Feb '14

New issue 791: iyt does not display plot using .show() https://bitbucket.org/yt_analysis/yt/issue/791/iyt-does-not-display-plot-us… Girish Nivarti: An HDF5 file was read from iyt using the h5py module and load_uniform_grid. On issuing the .show() command, the following output is displayed, but no graph is displayed. Whereas, as suggested by Mathew Turk, on using .save(), the appropriate png is generated correctly. **In [69]:** slc.show() <yt.visualization.plot_window.SlicePlot at 0x8043510> Also, the iyt.imods import doesn't work... <a href="http://justpaste.it/ektk">http://justpaste.it/ektk</a>

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Issue #790: Installation is missing "manual installation" part (yt_analysis/yt)
by Kacper Kowalik 28 Feb '14

28 Feb '14

New issue 790: Installation is missing "manual installation" part https://bitbucket.org/yt_analysis/yt/issue/790/installation-is-missing-manu… Kacper Kowalik: It would be nice if *Getting and Installing yt* covered manual installation process e.g. when user has dependencies already installed.

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Issue #789: PhasePlot save missing string (yt_analysis/yt)
by gsiisg 27 Feb '14

27 Feb '14

New issue 789: PhasePlot save missing string https://bitbucket.org/yt_analysis/yt/issue/789/phaseplot-save-missing-string gsiisg: If I save the phase plot in another directory with: pplot = PhasePlot(dd, "Density", "Temperature", ["Electron_Fraction"], weight_field=None) pplot.save('frames/') 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 "HD1200_2d-Profile_Density_Temperature_Electron_Fraction.png" correctly. So by specifying the folder it replaces the pf string. ProjectionPlot does not have the same issue. Annoying bug, but not critical.

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SciPy this year
by Matthew Turk 26 Feb '14

26 Feb '14

Hi all, 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 whatnot. https://conference.scipy.org/scipy2014/ 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. -Matt

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yt-dev February 2014