Mailman 3 March 2016 - yt-dev

Proposed change to how YTArray handles sums and differences with zero
by Nathan Goldbaum March 31, 2016

March 31, 2016

Hi all, Today a student I am working with ran into an issue illustrated by the following test script: from yt.units import cm arr = [1, 2, 3]*cm sum(arr) Right now this errors out with the following traceback: http://paste.yt-project.org/show/6378/ The reason for this is that the python builtin sum command has an optional `start` argument, which defaults to 0. The error is happening because the first element of the array (1 km) has different units from 0. Sum is probably not the best way to do this, but I think erroring out here is an overly harsh user experience, especially for a user who is new to python and might not be aware of the possible performance implications of using sum on a large array. Incidentally, an analogous script with astropy quantities does work: from astropy.units import cm arr = [1, 2, 3]*cm sum(arr) This is because astropy's quantities let you add zero (and just zero, no other float or integer will work) to an array or quantity with any units. On a philosophical level, the difference between 0 cm and 0 is not particular useful in practice, and operationally allowing 0 to be added or subtracted from YTArray instances without erroring out should not have any concrete implications for real programs, since until now it has raised an error. To be honest, I'm now regretting not thinking carefully about this until now.... Since this is a change to how YTArray, which is fundamental to yt's internals, I wanted to check with the list before proposing a pull request that implements this change. Does anyone have any objections? Thanks! -Nathan

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Pull request triage today at 1:00 PM CDT
by Nathan Goldbaum March 30, 2016

March 30, 2016

Hi all, I know this announcement is going out a little late, but I'd like to lead a pull request triage hangout today. The link to the event is here: https://plus.google.com/b/107728486871834552760/events/c8eq1orqcsdm2p0tkci7… -Nathan

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Issue #1203: Incorrect particle_velocity_cylindrical_theta and particle_velocity_cylindrical_radius when "center" != [0, 0, 0] (yt_analysis/yt)
by Ji-hoon Kim March 30, 2016

March 30, 2016

New issue 1203: Incorrect particle_velocity_cylindrical_theta and particle_velocity_cylindrical_radius when "center" != [0, 0, 0] https://bitbucket.org/yt_analysis/yt/issues/1203/incorrect Ji-hoon Kim: Dear All, The current implementations of "particle_velocity_cylindrical_theta" and "particle_velocity_cylindrical_radius" seem to incorrectly calculate "theta" when "center" is not at [0, 0, 0]. As an example, for a rotating stellar disk, currently the ParticleProjectionPlot() of "particle_velocity_cylindrical_theta" produces the following (incorrect) image: ![Star_500Myr_art-ii_rotational_vel.png](https://bitbucket.org/repo/BXbAb/images/2072696308-Star_500Myr_art-ii_rotational_vel.png) Note that the center in this particular dataset (ARTIO) is not at [0,0,0], but at ~[64, 64, 64] in a [0,0,0] - [128, 128, 128] box (in code_length units). On the other hand, if you move "theta = get_cyl_theta(pos, normal)" a couple of lines down after "center" is subtracted out of "pos": ``` #!python def _particle_velocity_cylindrical_theta(field, data): """The cylindrical theta component of the particle velocities Relative to the coordinate system defined by the *normal* vector, *bulk_velocity* vector and *center* field parameters. """ normal = data.get_field_parameter('normal') center = data.get_field_parameter('center') bv = data.get_field_parameter("bulk_velocity") pos = data.ds.arr([data[ptype, spos % ax] for ax in "xyz"]) vel = data.ds.arr([data[ptype, svel % ax] for ax in "xyz"]) # theta = get_cyl_theta(pos, normal) pos = pos - np.reshape(center, (3, 1)) vel = vel - np.reshape(bv, (3, 1)) theta = get_cyl_theta(pos, normal) ##### <=== HERE! cylt = get_cyl_theta_component(vel, theta, normal) return cylt ``` Then, the same ParticleProjectionPlot() creates the following (correct) image: ![Star_500Myr_art-ii_rotational_vel_new.png](https://bitbucket.org/repo/BXbAb/images/4051851566-Star_500Myr_art-ii_rotational_vel_new.png) It would be great if someone could independently check this error and the proposed solution. Any information or insight will be appreciated. Thank you as always to the yt community! Best regards, Ji-hoon

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OpenGL PR ready for review
by Matthew Turk March 29, 2016

March 29, 2016

Hi folks, The OpenGL PR is in need of some review: http://bitbucket.org/yt_analysis/yt/pull-request/1598 Any help would be great! I don't think the diff is going to get any smaller, sadly. -Matt

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Issue #1202: update Volume Rendering with Annotation cookbook recipe to new VR interface (yt_analysis/yt)
by Michael Zingale March 29, 2016

March 29, 2016

New issue 1202: update Volume Rendering with Annotation cookbook recipe to new VR interface https://bitbucket.org/yt_analysis/yt/issues/1202/update-volume-rendering-wi… Michael Zingale: The *Volume Rendering with Annotation* cookbook recipe currently uses the old VR interface. There are 2 issues preventing us from updating this to the new interface: issue #1129 and issue #1182. Once these are resolved, we can update the recipe.

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Unusually commit traffic today
by Nathan Goldbaum March 28, 2016

March 28, 2016

Hi all, Today I prematurely merged the pull request that adds the new default colormap. This was on me for not being careful to make sure the tests were passing before hitting the merge button. Kacper helpfully suggested on Slack that the yt-fido bot should be able to "approve" pull requests when the tests pass. This should help us more easily see that a pull request is passing the tests just by glancing at the header for the pull request. I've opened an issue to track this here: https://bitbucket.org/yt_analysis/yt/issues/1201/fido-bot-should-approve-pr… The tests were broken for an hour or so, but were fixed by merging PR 2090, so hopefully the disruption was minimal. Sorry for the mistake - I will try to be more conscientious about merging pull requests going forward. -Nathan

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Issue #1201: fido bot should approve PRs when the tests pass (yt_analysis/yt)
by Nathan Goldbaum March 28, 2016

March 28, 2016

New issue 1201: fido bot should approve PRs when the tests pass https://bitbucket.org/yt_analysis/yt/issues/1201/fido-bot-should-approve-pr… Nathan Goldbaum: This will make it clearer that the tests are passing at any given moment.

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Issue #1200: Enable CI testing for python3 (yt_analysis/yt)
by Nathan Goldbaum March 28, 2016

March 28, 2016

New issue 1200: Enable CI testing for python3 https://bitbucket.org/yt_analysis/yt/issues/1200/enable-ci-testing-for-pyth… Nathan Goldbaum: We should be running our full test suite under python3 for every pull request.

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Issue #1199: Add documentation on cmaps (yt_analysis/yt)
by Cameron Hummels March 28, 2016

March 28, 2016

New issue 1199: Add documentation on cmaps https://bitbucket.org/yt_analysis/yt/issues/1199/add-documentation-on-cmaps Cameron Hummels: * New default cmap * That new cmaps help address problems with colorblindness and black and white representation * How to set the default locally

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Issue #1198: Add ability to plot cell edges (yt_analysis/yt)
by Matthew Turk March 27, 2016

March 27, 2016

New issue 1198: Add ability to plot cell edges https://bitbucket.org/yt_analysis/yt/issues/1198/add-ability-to-plot-cell-e… Matthew Turk: Right now we can plot grid patch edges with `annotate_grids`, but not the cell edges. This should be straightforward to implement with a flag in the call to the pixelizer. Much like how the line pixelization occurs in the volume renderer, when a pixel is near to the edge of a cell (comparing `pdx` `pdy` `px` and `py`) closer than some epsilon (user specifiable, probably defaulting to something sane and thin) it should toss in a black line. Since the pixelization right now works as returning data values, this would be a separate call that would return RGBA values where the color is either (0.0, 0.0, 0.0, 1.0) or (0.0, 0.0, 0.0, 0.0). Responsible: MatthewTurk

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