Mailman 3 June 2012 - yt-dev

what to do with fork once PR approved?
by Geoffrey So 26 Jun '12

26 Jun '12

Hi yt-devs, I was wondering what to do with my fork after the pull request was accepted. Do you guys usually delete the fork and create a new one if something needed to be changed later, or keep the current fork and pull from the main yt-dev to keep it up to date before making changes? Just feels redundant keeping the old fork around now, but maybe there are advantages I did not consider. From G.S.

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Fwd: [yt_analysis/yt] Reason GUI Refactor: ExtJS4, Server Architecture, 3D rendering and parallelism (pull request #179)
by Matthew Turk 24 Jun '12

24 Jun '12

Hi all, I've just issued a pull request for a major upgrade in Reason functionality. Sam, Britton, Nathan and I have been working on this a bit, and it includes some pretty fun things. Most of them are self-documenting, but some of the architecture is documented in my open PR on yt-doc that describes the new Reason architecture. If you have the time, I'd very much appreciate it if you could test this out. Updating your repository to the state of my yt-extjs4 will do nearly everything you need (all the changes are in Python and JS, no Cython/C, so you don't need to recompile). When you start up "yt serve" it won't be able to find the one remaining zipfile you need of the externally developed javascript, so it'll quit and tell you how to get it. If you have the time, we'd really appreciate your feedback on functionality, style, architecture, suggestions, etc etc. As I noted in the pull request I'm super happy about where this is taking us. Two of the more fun things are the "Dataset Information" widget's mesh statistics view and the "3D Plot" which contains the grid lines and can get isocontours. Thanks, Matt ---------- Forwarded message ---------- From: Matthew Turk <pullrequests-noreply(a)bitbucket.org> Date: Sun, Jun 24, 2012 at 7:29 AM Subject: [yt_analysis/yt] Reason GUI Refactor: ExtJS4, Server Architecture, 3D rendering and parallelism (pull request #179) To: yt(a)enzotools.org A new pull request has been opened by Matthew Turk. MatthewTurk/yt-extjs4 has changes to be pulled into yt_analysis/yt. https://bitbucket.org/yt_analysis/yt/pull-request/179/reason-gui-refactor-e… Title: Reason GUI Refactor: ExtJS4, Server Architecture, 3D rendering and parallelism This PR contains a number of major improvements to Reason: * 3D Scene: isocontours, grid lines, and toggleable display of said items. Currently limited in scope, but promising for the future. All rendered in WebGL with XTK. * The server infrastructure can use a Pyro4 backend to talk to MPI tasks, and all parallel tasks will be executed transparently in parallel * The server infrastructure is completely hot-swappable, as is the execution engine (for future swapping of engines with, for instance, IPython) * Completely refactored javascript, which better fits the MVC pattern used in ExtJS4. This should improve readability, maintainability, and extensibility. * New widgets are easy to add, and the process for doing so is documented. (Easier in python *and* JavaScript.) * Parameter file statistics widget! Now with field source code and mesh statistics * Easier plot window widget creation * Nicer appearance overall * Camera path editing and viewing in WebGL (BETA sequence -- some oddities still plague it) * Better help page * Directly loading binary files when shipping arrays to the browser, instead of array->list->JSON->list->array. * Debugging mode * All externally-developed JS is now shipped in a small zip file that does not need to be uncompressed. Overall I think it's a nice evolutionary step forward in many ways, and very exciting and awesome step forward in others. For instance, we now have a fully 3D scene explorer that requires *no dependencies*. I'm really excited about this. The next step in this (particularly with the MPI-parallel backend) will be exporting both the viewing angle and the camera path to the volume renderer. By using XTK we gain access to a number of very nice features (goxtk.com has examples that are quite impressive.) I'm sure Sam or Nathan have some awesome images to share from the 3D scene. Thanks to Britton Smith, Sam Skillman and Nathan Goldbaum for their gigantic help with this. Britton, Sam and Nathan might also chime in with notes about how to test various features. There are still things to do: * Beta testing by everyone! * Integrate editing of colors, opacity and other attributes on specific objects in the 3D scene. Right now they're all the same! * The camera path still has some odd translations/rotation effects that make it not *quite* ready for prime time * Screencasts/demos/ideas * Develop and ExtJS4-based transfer function widget we can use in the browser * More widgets: clumps, halo finding, cutting plane, 1D profiles, etc etc ... * Suggestions for improvement Please direct any feedback to yt-dev -- looking forward to discussing! Changes to be pulled: -- This is an issue notification from bitbucket.org. You are receiving this either because you are the participating in a pull request, or you are following it.

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Fwd: [yt_analysis/yt] Adding OffAxisSlice (pull request #178)
by Matthew Turk 23 Jun '12

23 Jun '12

Awesome work, Nathan! I've looked these over and seen the example images and they look good, but maybe Jeff could take a quick look at how the PlotWindow is shaping up. ---------- Forwarded message ---------- From: Nathan Goldbaum <pullrequests-noreply(a)bitbucket.org> Date: Sat, Jun 23, 2012 at 4:39 PM Subject: [yt_analysis/yt] Adding OffAxisSlice (pull request #178) To: matthewturk(a)gmail.com A new pull request has been opened by Nathan Goldbaum. ngoldbaum/yt-ngoldbaum has changes to be pulled into yt_analysis/yt. https://bitbucket.org/yt_analysis/yt/pull-request/178/adding-offaxisslice Title: Adding OffAxisSlice This finishes up the new plotting interface by adding OffAxisSlice. I've also taken the opportunity to add a docstring for get_rotation_matrix() in utilities/math_utils.py and to correct a bug in ObliqueFixedResolutionBuffer that caused the buffer to be inverted. Changes to be pulled: -- This is an issue notification from bitbucket.org. You are receiving this either because you are the participating in a pull request, or you are following it.

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pull request for plot and images
by Geoffrey So 23 Jun '12

23 Jun '12

Again I apologize for being stupid, but here's what I sent earlier to the "no-reply" address about 2 days ago: http://paste.yt-project.org/show/2470/ The script will do a 3D scatter plot of the "Ones" field included by the ellipsoid, and do a x,y projection for ease of inspection. I don't think aspect ratio is working quite right, but not sure how to fix it. The aspect thing seems to work better in interactive mode. Give it a try and see if it's a big concern. At least when I set A=B=C the ellipsoid looks like a sphere, in 3D and projection. How would I send in the png images that the file should produce? The paste only allows text, let me know where to send the images, or I can reply to this email with the images attached. From G.S.

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Accidental push to yt_analysis/yt
by Nathan Goldbaum 23 Jun '12

23 Jun '12

Hey guys, I accidentally pushed the changes I've been working on to the main repo. I would strip them but I'm unable to. Really sorry for the trouble - that was totally my fault! I'll try my best to be more careful in the future. -Nathan

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ellipsoid pull request suggestions from Matt
by Geoffrey So 23 Jun '12

23 Jun '12

Hi Matt, thanks for the suggestions you've made on the pull request, there's just a couple questions and technical terms that I didn't understand. * I'd suggest you put all of the ellipsoidal functions in the base class instead of distributing throughout the subclasses. This avoids code reuse. You can then override them in parallelHF's halos. - What is a base class or subclasses in YT? Where can I avoid the code reuse, and override? * Please move all of the rotation matrix functions into yt/utilities/math_utils.py and add docstrings. These can then be imported in both data_containers.py and the halo functions. - I see inside math_utils.py already has an get_rotation_matrix at the end, which is probably the general case you're referring to earlier when we talked (not sure how to use that with the "self" in the input). I'll just stick in the less general case of RX, RY, RZ unless you think it's redundant. * Instead of printing, I would suggest either raising an exception (which you can define in yt/exceptions.py) or issuing a warning with {{{mylog.warning("Not enough particles to determine ellipsoidal parameters.")}}} - What is better? Should I do a warning message and let the user know I'm returning zeros for the ellipsoid parameters? Or raise an exception, then let the user decide what to do if an exception is raised? - I think I tried to write an exception but didn't quite understand how it works, going to give it another try here Do I replace if na.size(self["particle_position_x"]) < 4: print "not enough particles to form ellipsoid returning zeros" return (0, 0, 0, 0, 0, 0, 0) with something like if na.size(self["particle_position_x"]) < 4: raise YTNotEnoughParticles(na.size(self["particle_position_x"])) and in exceptions.py class YTNotEnoughParticles(YTException): def __init__(self, nparticles): self.nparticles = nparticles def __str__(self): return "There are only %i particles, not enough to form an ellipsoid" % (self.nparticles) From G.S.

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ellipsoid fork
by Geoffrey So 20 Jun '12

20 Jun '12

Hi all, Thanks for all the help everyone, I've finally snuck some time in and submitted a pull request to yt and yt-doc, please let me know what I can improve on. Sorry for the long wait, a deadline can do amazing things to someone's motivation! From G.S.

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Fwd: New Journal: Astronomy and Computing
by John ZuHone 20 Jun '12

20 Jun '12

Any of you get notice on this? I usually ignore announcements about new journals, but this one could be interesting. Begin forwarded message: > From: "Elsevier Physics" <elsevierphysics_(a)elsevier.dmsx.net> > Subject: New Journal: Astronomy and Computing > Date: June 19, 2012 4:02:37 AM EDT > To: zuhone(a)flash.uchicago.edu > Reply-To: "Elsevier Physics" <elsevierphysics_-EMID0AA01CR1LUO034POM03T6BN014MFIDC(a)elsevier.dmsx.net> > > > > > > > > > > > > > > > > > Dear Dr. J A Zuhone, > > We are delighted to introduce the launch of the new journal, Astronomy and Computing (ASCOM), a new journal linking the growing area of astronomy with computer sciences and information technology. To find out about the goals of the journal and to be one of the first to submit a paper, click on the links below: > > Note from the Editor > Rationale and vision > The Editorial Team > Submit your paper online > Register your interest > Subscribe to the journal > An introduction from the Editor > > "I am very excited about this new journal. Astronomy is increasingly dependant on computational techniques and technologies. The journal will provide the astronomical computing community with a forum to share knowledge through peer-reviewed papers, and act as a focus point for the increasingly large number of people in that community who apply computation within astronomy rather than undertaking pure astronomical research per se. It will also help foster the interaction between the astronomical and computer science communities, to the benefit of both, as astronomical datasets increase in size and complexity." > > Robert Mann, Editor Astronomy and Computing > > Rationale and vision > > Astronomy and Computing will focus on the broad area between astronomy, computer science and information technology. The journal aims to publish the work of scientists and (software) engineers in all aspects of astronomical computing, including the collection, analysis, reduction, visualisation, preservation and dissemination of data, and the development of astronomical software and simulations. The journal will cover applications for academic computer science techniques to astronomy, as well as novel applications of information technologies within astronomy. > > The journal will be open to a broad range of contributions about the use of computing used in astronomy. It will accept regular scientific articles and review articles, but will also consider manuscripts on new software and data releases of astronomcal surveys, and "reports on practice" which describe the outcomes (positive and negative) of the practical application of informatics techniques within astronomy research and operations. In general, manuscripts should make a valuable contribution to the field and should display an appropriate familiarity with previous work in the area and alternative approaches to the same problem. Providing a sustainable link to data or source code is strongly encouraged. All manuscripts will be subject to peer-review. > > To read the full aims and scope for the journal visit the homepage. > > The Editorial Team > > The journal will be lead by a team of high-profile Editors and a Scientific Advisory Board, together covering the full scientific spectrum of the journal. > > Editors > > Alberto Accomazzi (Harvard/Smithsonian Centre for Astrophysics, USA) > Tamas Budavari (Johns Hopkins University, USA) > Christopher Fluke (Swinburne University of Technology, Australia) > Norman Gray (University of Glasgow, UK) > Robert Mann (University of Edinburgh, UK) > William O'Mullane (European Space Astronomy Centre, Spain) > Andreas Wicenec (University of Western Australia, Australia) > Michael Wise (ASTRON, The Netherlands) > Scientific Advisory Board > > Kirk Borne (George Mason University, USA) > Andrew Connelly (University of Washington, USA) > André Csillaghy (University of Applied Sciences Northwestern Switzerland (FHNW) Switzerland) > Daniel Durand (Herzberg Institute of Astrophysics of the National Research Council, Canada) > Carlos Gabriel (European Space Astronomy Centre, Spain) > Bob Hanish (Space Telescope Science Institute, USA) > Andrew Lawrence (University of Edinburgh, UK) > Masatoshi Ohishi (National Astronomical Observatory of Japan, Japan) > Fabio Pasian (INAF-Osservatorio Astronomico di Trieste) > Arnold Rots (Harvard/Smithsonian Centre for Astrophysics, USA) > Peter Quinn (University of Western Australia) > Ray Plante (University of Illinois at Urbana-Champaign, USA) > More information on the Editors can be found here. > > Submit your paper online > > Visit the online submission page to submit your paper to the journal and track the process of your manuscript. > > Register your interest in the new journal > > Stay up to date with the latest journal news by registering your interest. > > Subscribe to the journal > > ISSN: 2213-1337 > 4 issues per year > > Subscription prices will be available soon, to stay up to date with the latest journal developments register your interest. > > > > > DATA PROTECTION NOTICE > > This email has been sent to zuhone(a)flash.uchicago.edu from Elsevier B.V., Radarweg 29, 1043 NX Amsterdam, The Netherlands, using 22 Times B.V. technology and platform. This is a one-off email sent to you in the belief that it will be of interest. > > We will not add your name and email address to our database unless you request further information. If you wish to ensure that you will not receive a future marketing message from us about these products or services, please send a reply message toexclusionlist(a)elsevier.com. We respect your privacy and do not rent or sell your personal information to any non-affiliated third parties without your consent, except as may be stated in our privacy policy at: Elsevier privacy policy. > > For the 22 Times privacy policy, please visit: 22 Times B.V. privacy policy. > > We obtained your name and email address from ISI Thomson Scientific, 3501 Market street, Philadelphia, PA 19104 USA. If you wish to be removed from the ISI Thomson Scientific mailing lists, please click here ISI Thomson Scientific. > Copyright © 2012 Elsevier B.V. http://www.elsevier.com. registered office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, under number 33156677, VAT number 002967455B65. All rights reserved. > > > >

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Fwd: [astropy-dev] ANN: Astropy v0.1
by Matthew Turk 19 Jun '12

19 Jun '12

---------- Forwarded message ---------- From: Erik Tollerud <erik.tollerud(a)gmail.com> Date: Tue, Jun 19, 2012 at 2:51 AM Subject: [astropy-dev] ANN: Astropy v0.1 To: astropy-dev(a)googlegroups.com, astropy(a)scipy.org Hello all, On behalf of the Astropy team, I'm excited to announce the first release of the Astropy core package: v0.1! The Astropy core package is intended to provide much of the common functionality and tools needed for performing astronomy and astrophysics with Python. This release should be thought of as a "developer preview" - it has much of the packaging and data handling framework in place, but the actual astronomy functionality and frameworks are still incomplete. Nevertheless, you can already make use of the existing functionality, which is fully tested. Key features include: * Standard cosmological distance calculations (astropy.cosmology) * Data Tables (astropy.table) including a wide variety of ASCII formats common in astronomy (astropy.io.ascii) * FITS File handling - formerly PyFITS (astropy.io.fits) * VOTable parser and writer (astropy.io.vo) * WCS representations - formerly pywcs (astropy.wcs) * Consistent documentation style * Utilities to ease creation of new, independent packages (affiliated packages) * A dedicated logging system The package can be downloaded from http://github.com/downloads/astropy/astropy/astropy-0.1.tar.gz . More information is available at the Astropy site ( http://astropy.org ), the package documentation ( http://docs.astropy.org ), and the github repository ( http://github.com/astropy/astropy ). We also encourage developers writing new packages to begin writing the code against this version. Packages making use of Astropy should feel free to join up as affiliated packages and begin transitioning to the affiliated package template ( https://github.com/astropy/package-template ). In the next version, we hope to implement a working affiliated package installer, so it will be worth your while! For the Astropy developers, Erik Tollerud

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Re: [yt-dev] [yt_analysis/yt] Volume Rendering Refactor (pull request #168)
by Sam Skillman 15 Jun '12

15 Jun '12

yt on top of CIA.vc again! On Fri, Jun 15, 2012 at 4:54 PM, Nathan Goldbaum < pullrequests-noreply(a)bitbucket.org> wrote: > Pull request #168 has been accepted by Nathan Goldbaum. > > Changes in MatthewTurk/yt-refactor have been pulled into yt_analysis/yt. > > > https://bitbucket.org/yt_analysis/yt/pull-request/168/volume-rendering-refa… > -- > This is an issue notification from bitbucket.org. > You are receiving this either because you are the participating > in a pull request, or you are following it. > >

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