Mailman 3 October 2014 - yt-dev

yt 3.1?
by Nathan Goldbaum 05 Nov '14

05 Nov '14

Hi all, There have been a number of cool new features in the pull request queue recently. Some of these have added new features and I think it might be worthwhile to indicate that by bumping the minor version number on the next release. I think it would be a good idea to try to integrate the open PRs as well as any that come in over the next couple of weeks that can be reviewed, call it yt 3.1 and release on or around Dec. 1. This will mean generating a proofread docs build and perhaps a few days of low-hanging issue triaging. I'd nominate John ZuHone to send out the release email to recognize the hard work he's been putting in recently. Just an idea, but I've tried to include specifics as a basis for further discussion. What do you all think? Nathan

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Widgets
by Matthew Turk 31 Oct '14

31 Oct '14

Hey, whatever happened to the ipython notebook widgets? Did they ever get pushed into mainline?

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Issue #931: Make `annotate_title` the standard method for setting the title in PhasePlot objects (yt_analysis/yt)
by Cameron Hummels 29 Oct '14

29 Oct '14

New issue 931: Make `annotate_title` the standard method for setting the title in PhasePlot objects https://bitbucket.org/yt_analysis/yt/issue/931/make-annotate_title-the-stan… Cameron Hummels: Right now, `PhasePlot` and `PlotWindow` classes have separate methods for setting the figure title, `set_title()` and `annotate_title()` respectively. To reduce confusion, it might make sense to combine these to be just one of the two options.

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Issue #930: np.concatenate fails for YTArrays (yt_analysis/yt)
by Douglas Rudd 26 Oct '14

26 Oct '14

New issue 930: np.concatenate fails for YTArrays https://bitbucket.org/yt_analysis/yt/issue/930/npconcatenate-fails-for-ytar… Douglas Rudd: YTArrays cannot be compared using numpy functions like intersect1d because np.concatenate either fails (for dimensional arrays) or for dimensionless arrays it produces a YTArray object where the units attribute is `None` (which then fails in `__eq__`, `__lt__`, etc). This may already be known and may be unfixable (due to the way numpy implements concatenate)... ``` #!python import yt import numpy as np A = yt.YTArray(range(10)) B = yt.YTArray(range(10)) np.intersect1d(A,B) --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-10-90c76c488fa7> in <module>() ----> 1 np.intersect1d(A,B) /usr/local/lib/python2.7/site-packages/numpy/lib/arraysetops.pyc in intersect1d(ar1, ar2, assume_unique) 248 aux = np.concatenate((ar1, ar2)) 249 aux.sort() --> 250 return aux[:-1][aux[1:] == aux[:-1]] 251 252 def setxor1d(ar1, ar2, assume_unique=False): /Users/drudd/Programs/yt/yt/units/yt_array.pyc in __eq__(self, other) 854 return False 855 if isinstance(other, YTArray): --> 856 if not self.units.same_dimensions_as(other.units): 857 raise YTUnitOperationError("equal", self.units, other.units) 858 AttributeError: 'NoneType' object has no attribute 'same_dimensions_as' ```

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Notebook progress bar?
by John ZuHone 24 Oct '14

24 Oct '14

Hey all, I know we nixed the previous notebook progress bar because it was really bogging things down—but it would be handy to have one, and there are some ASCII-only implementations that probably won’t use as much memory. Any thoughts? I’d be happy to look into it myself. Best, John

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Re: [yt-dev] [yt-users] streamlines and volume rendering
by Matthew Turk 21 Oct '14

21 Oct '14

Hi Sam, (Moving over to yt-dev) What do you think the major reasons to hold off on merging are? -Matt On Mon, Oct 20, 2014 at 10:18 PM, Sam Skillman <samskillman(a)gmail.com> wrote: > Hi Kiki, > > Thanks for the compliments on the volume rendering in yt. As of right now > there isn't a simple way to add streamlines in the same figure. However, we > are really close! There is a current work-in-progress [WIP] pull request > https://bitbucket.org/yt_analysis/yt/pull-request/1256/wip-volume-rendering… > where we are adding such a capability. What I'd suggest is to keep your > ears open for new requests for testing the new framework and check back > soon. I hope that by the end of the week we'll have some examples up on the > pull request that would give you enough of a head start to try it out. I > will try to remember to cc you when i send out requests for beta-testers. > > Cheers, > Sam > > > On Mon, Oct 20, 2014 at 6:02 PM, Dionysopoulou K. > <K.Dionysopoulou(a)soton.ac.uk> wrote: >> >> Dear Sir or Madam, >> >> I recently came across the yt libraries for python and was impressed by >> its capabilities and the speed of the volume renderer in particular. The >> library creates superior quality figures and I would like to use it for my >> papers. The problem I have for now is that I would like to have volume >> rendering plus streamlines of a vector field in the same figure and I >> haven’t figured out how one could do that. Is there a way to achieve this in >> yt? >> >> Thanking you in advance. >> >> All the best, >> >> Kiki >> >> Kyriaki Dionysopoulou >> ======================================================= >> Mathematical Sciences >> University of Southampton >> Southampton, SO17 1BJ, UK >> K.Dionysopoulou(a)soton.ac.uk<mailto:K.Dionysopoulou@soton.ac.uk> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >

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"Expert mode"
by Matthew Turk 21 Oct '14

21 Oct '14

Hi all, This blog post was just posted to the #mercurial IRC room and I thought it might be interesting: http://jordi.inversethought.com/blog/customising-mercurial-expert-mode/ -Matt

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Issue #929: ProjectionPlot.set_log fails for radio fits datasets (yt_analysis/yt)
by Kacper Kowalik 21 Oct '14

21 Oct '14

New issue 929: ProjectionPlot.set_log fails for radio fits datasets https://bitbucket.org/yt_analysis/yt/issue/929/projectionplotset_log-fails-… Kacper Kowalik: Following script: ``` #!python import yt from yt.frontends.fits.misc import ds9_region ds = yt.load("radio_fits/grs-50-cube.fits", nan_mask=0.0) region = 'galactic;box(+49:26:35.150,-0:30:04.410,1926.1927",1483.3701",0.0)' box_reg = ds9_region(ds, region) prj = yt.ProjectionPlot(ds, "z", ["temperature"], origin="native", data_source=box_reg, weight_field="ones") # "ones" weights each cell by 1 prj.set_log("temperature", True) ``` fails with rev: 297789d10298, yielding: ``` #!text Traceback (most recent call last): File "bug.py", line 10, in <module> prj.set_log("temperature", True) File ".../yt/visualization/plot_container.py", line 70, in newfunc args[0]._setup_plots() File ".../yt/visualization/plot_window.py", line 898, in _setup_plots mticks = self.plots[f].image.norm( get_symlog_minorticks(flinthresh, vmin.d, vmax.d) ) AttributeError: 'float' object has no attribute 'd' ```

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Issue #928: loglevel not honored when set at runtime in a script (yt_analysis/yt)
by Chris Malone 20 Oct '14

20 Oct '14

New issue 928: loglevel not honored when set at runtime in a script https://bitbucket.org/yt_analysis/yt/issue/928/loglevel-not-honored-when-se… Chris Malone: Running this from yt.config import ytcfg ytcfg['yt', 'loglevel'] = 1 import yt ds = yt.load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150") slc = yt.SlicePlot(ds, 'z', 'density') does not turn off logging as it should. Note, however, that the `~/.yt/config` file is parsed properly. _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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Fwd: Mercurial & SSL & POODLE, Mercurial 2.7 and 2.7.1 and SSL error: sslv3 alert handshake failure
by Matthew Turk 20 Oct '14

20 Oct '14

FYI -- this may explain some issues last week. ---------- Forwarded message ---------- From: Mads Kiilerich <mads(a)kiilerich.com> Date: Mon, Oct 20, 2014 at 2:22 PM Subject: Mercurial & SSL & POODLE, Mercurial 2.7 and 2.7.1 and SSL error: sslv3 alert handshake failure To: "mercurial(a)selenic.com" <mercurial(a)selenic.com> The recent POODLE story has raised the awareness of the problems with old SSL versions. It might make sense to take the opportunity to disable SSLv3 on web servers hosting Mercurial repositories. Note however that there was a client side bug in Mercurial 2.7 and 2.7.1 that made it use SSLv3 without considering more recent versions. Trying to connect to servers without SSLv3 with these Mercurial versions will fail with something like: abort: error: _ssl.c:507: error:14094410:SSL routines:SSL3_READ_BYTES:sslv3 alert handshake failure or if using TortoiseHg: SSL error: sslv3 alert handshake failure The solution is to upgrade Mercurial (or TortoiseHg) to a more recent version. See also http://blogs.atlassian.com/2014/10/ssl-poodle/ . /Mads _______________________________________________ Mercurial mailing list Mercurial(a)selenic.com http://selenic.com/mailman/listinfo/mercurial _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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