Mailman 3 September 2012 - yt-dev

2nd yt workshop
by Kacper Kowalik 11 Oct '12

11 Oct '12

Hi all, I'd like to ask if there are any plans on organizing 2nd yt workshop? It's this time of the year when I need to apply for grants at my university and I'd very much like to include such event in the application :) Cheers, Kacper

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Grid drawing
by Anthony Scopatz 04 Oct '12

04 Oct '12

Hello yters, Is there already code that can be used to draw or display an AMR grid on the plot itself? Or is this an annotation that I should write ;)? Be Well Anthony

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python 2.7.3?
by Nathan Goldbaum 01 Oct '12

01 Oct '12

Hi all, Is there a reason the install script is still on python 2.7.2? If not, I think we should move to 2.7.3 which fixes several bugs. See: http://www.python.org/download/releases/2.7.3/ I would do this myself but I don't have access to the place where we store the bundled distributions on the yt-project website. Cheers, Nathan

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Fwd: [yt_analysis/yt] annotate_image (issue #430)
by Matthew Turk 30 Sep '12

30 Sep '12

Hi all, We got an anonymous bug today. My guess is this is related to the transpose in write_image. -Matt ---------- Forwarded message ---------- From: Anonymous <issues-reply(a)bitbucket.org> Date: Fri, Sep 28, 2012 at 7:32 AM Subject: [yt_analysis/yt] annotate_image (issue #430) To: matthewturk(a)gmail.com --- you can reply above this line --- New issue 430: annotate_image https://bitbucket.org/yt_analysis/yt/issue/430/annotate_image Anonymous: Text is transposed with annotate_image. -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

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Boxlib changes: RFT
by Matthew Turk 26 Sep '12

26 Sep '12

Hi all (but especially Casey and Tom Robitaille if he's still subscribed :), Andrew Myers found a very nice solution to issue #414: https://bitbucket.org/yt_analysis/yt/issue/414/orion-ghot-zones-not-generat… which he's put in this PR: https://bitbucket.org/yt_analysis/yt/pull-request/275/reading-in-dds-for-ea… I have only limited access to Nyx / Orion data with subgrids, so I can't test this appropriately. I think the changes look good, however, so if I can get from any other boxlib user that they still produce good results, I will accept them. This is also a good time to mention that going forward I hope to consolidate the various boxlib readers. Best, Matt

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Testing Intervention
by Matthew Turk 26 Sep '12

26 Sep '12

Hi all, As some of you have seen (at least Stephen), I filed a ticket this morning about increasing testing coverage. The other night Anthony and I met up in NYC and he had something of an "intervention" about the sufficiency of answer testing for yt; it didn't take too much work on his part to convince me that we should be testing not just against a gold standard, but also performing unit tests. In the past I had eschewed unit testing simply because the task of mocking data was quite tricky, and by adding tests that use smaller bits we could cover unit testable areas with answer testing. But, this isn't really a good strategy. Let's move to having both. The testing infrastructure he recommends is the nearly-omnipresent nose: http://nose.readthedocs.org/en/latest/ The ticket to track this is here: https://bitbucket.org/yt_analysis/yt/issue/426/increase-unit-test-coverage There are a couple sub-items here: 1) NumPy's nose test plugins provide a lot of necessary functionality that we have reimplemented in the answer testing utilities. I'd like to start using the numpy plugins, which include things like conditional test execution, array comparisons, "slow" tests, etc etc. 2) We can evaluate, using conditional test execution, moving to nose for answer testing. But that's not on the agenda now. 3) Writing tests for nose is super easy, and running them is too. Just do: nosetest -w yt/ when in your source directory. 4) I've written a simple sample here: https://bitbucket.org/yt_analysis/yt-3.0/src/da10ffc17f6d/yt/utilities/test… 5) I'll handle writing up some mock data that doesn't require shipping lots of binary files, which can then be used for checking things that absolutely require hierarchies. -- The way to organize tests is easy. Inside each directory with testable items create a new directory called "tests", and in here toss some scripts. You can stick a bunch of functions in those scripts. Anyway, I'm going to start writing more of these (in the main yt repo, and this change will be grafted there as well) and I'll write back once the data mocking is ready. I'd like it if we started encouraging or even mandating simple tests (and/or answer tests) for functionality that gets added, but that's a discussion that should be held separately. The items on the ticket: * kD-tree for nearest neighbor * Geometric selection routines * Profiles * Projections -- underlying quadtree * Data object selection of data containers * Data object selection of points * Orientation class * Pixelization * Color maps * PNG writing Is anyone willing to claim any additional items that they will help write unit tests for? -Matt

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Adding the GAMER code
by Hsi-Yu Schive 26 Sep '12

26 Sep '12

Dear all, Hi. My name is Hsi-Yu Schive. I'm the main developer of the GAMER code, which is a GPU-accelerated AMR code for astrophysical simulations. I'm very interested in adding support of GAMER in yt! I appreciate if anyone has any suggestion about the best way to initialize this work! The AMR implementation of GAMER is very similar to FLASH. The AMR hierarchy is composed of cell blocks, and each of which has a fixed number of cells (e.g., 8^3 cells per block). An octree data structure is adopted to maintain the AMR hierarchy. I'll start with following the suggestions given in the "Adding Support for a New Code" section in the bitbucket yt page and also looking into the Enzo output style. Any suggestion/comment is more than welcome : ) Sincerely, Hsi-Yu

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Fwd: [yt_analysis/yt] show() failure due to IPython API changes (issue #428)
by Matthew Turk 25 Sep '12

25 Sep '12

Can somebody address this? I'd like to ensure we can continue keeping up with IPython (especially since a bunch of us are investing in it quite heavily for our own workflows) but I can't add this to my queue this at the moment. I think the best way to do this is probably to add an IPython compat layer to yt/utilities/ that handles higher-level functionality, since we use relatively little of the IPython API. -Matt ---------- Forwarded message ---------- From: Anthony Scopatz <issues-reply(a)bitbucket.org> Date: Tue, Sep 25, 2012 at 3:49 PM Subject: [yt_analysis/yt] show() failure due to IPython API changes (issue #428) To: matthewturk(a)gmail.com --- you can reply above this line --- New issue 428: show() failure due to IPython API changes https://bitbucket.org/yt_analysis/yt/issue/428/show-failure-due-to-ipython-… Anthony Scopatz: Reporting that the Plot.show() method seems to fail on IPython 0.14-dev because of an API change. The send_figure function is no longer where yt thinks it is. {{{python ImportError Traceback (most recent call last) <ipython-input-2-4804b2a8abc5> in <module>() 4 p.annotate_flash_ray_data(pf, 'jet', 10) 5 p.annotate_timestamp(0.2/z, 0.2/z, pf, units="days", size=24) ----> 6 p.show() /home/scopatz/.local/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/visualization/plot_window.pyc in show(self) 788 """ 789 if "__IPYTHON__" in dir(__builtin__): --> 790 self._send_zmq() 791 else: 792 raise YTNotInsideNotebook /home/scopatz/.local/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/visualization/plot_window.pyc in _send_zmq(self) 763 764 def _send_zmq(self): --> 765 from IPython.zmq.pylab.backend_inline import \ 766 send_figure 767 for k, v in sorted(self.plots.iteritems()): ImportError: cannot import name send_figure }}} -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

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Testing new feature: Uploading IPython notebooks to the Hub
by Matthew Turk 18 Sep '12

18 Sep '12

Hi all, (This is preliminary! I would love to hear about problems or other issues you end up having with it!) Nathan, Sam and I were chatting today about IPython notebooks. IPython has a really neat Notebook Viewer at nbviewer.ipython.org which accepts a URL and then renders that in the browser. After we played a bit with the pastebin (unsuccessfully) I added a "notebook" type to the Hub. So if you have a Hub user and your API key is set correctly, you can navigate in your filesystem to an .ipynb file and do: yt upload_notebook that_notebook.ipynb This will not only toss it up on the Hub (where you can download it or pass around the URL) but it also will set up a nice little URL redirector to pass it to the nbviewer. So earlier I uploaded one of Sam's notebooks and yt spit this back out at me: -- Upload successful! To access your raw notebook go here: https://hub.yt-project.org/go/i7u32m To view your notebook go here: https://hub.yt-project.org/nb/i7u32m -- If you click on that second one you can see how it gets rendered. Pretty cool! Anyway, let me know if it works for you or if you run into problems. -Matt

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yt-3.0 PR #6 - underlying cylindrical ray tracer
by Anthony Scopatz 16 Sep '12

16 Sep '12

Hello All, I am writing to let you know that I have (finally) built the underlying function for the cylindrical ray tracer which solves for the time, distance, location, and grid indices of the ray. The reason that I opened a PR rather rather than just pushing is that I would appreciate some feedback. First note that you can play around with this functionality using the following ipython notebook [1], though you will also need 2D R,Z data to point it at. The first question I have is that the rays, unless they begin or end on a cell boundary, do not include the start or stop points. This seems like the correct behavior to me, but is this consistent with the rest of yt? The second, weirder point is as follows. For 2D R,Z data, the cell crossings that are calculated *should* be rotationally invariant. Take p1 and p2 to be two points in r, z, theta s.t.: p1 = (r1, z1, theta1) p2 = (r2, z2, theta2) Then the ray should pass through the same cells if instead we take q1 and q2 as: q1 = (r1, z1, theta1 + dtheta) q2 = (r2, z2, theta2 + dtheta) for any constant dtheta and r1, z1, theta1, r2, z2, and theta2 at the same values in p1 and p2. However, this does not seem to be the case. Play around in the notebook and you'll see what I mean. The shape of the r, z and theta components as a function of t are all the same. That is good news in that the algorithm is working. However, not even the same number of cells are being picked up. This seems wrong. But I can't figure out what is the cause, so I was hoping other sets of eyes could take a gander. Additionally, all solutions that I could think of - such as adding the *'best'* dtheta and then transforming back prior to returning - would break the 3D version of this function. I don't think either of the above are deal breakers, but I would like to hear other people's thoughts. I will work on integrating this with the rest of yt-3.0 next week. Be Well Anthony 1. https://bitbucket.org/MatthewTurk/yt.milestones/raw/7d64152de2e1/cylindrica…

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yt-dev September 2012