Mailman 3 June 2013 - yt-dev

yt Strategy Meeting Monday the 22nd
by Matthew Turk Sept. 4, 2013

Sept. 4, 2013

Hi all, I'd like to call a brief, approximately one hour, strategy meeting on Monday, April 22nd at 3PM Eastern. This will cover where yt is at, where we can go, and how things are progressing. Some of this will be dedicated to progress updates (from me and others) as well as soliciting feedback on a number of things. Many other projects -- notably Cactus -- do these on a fixed schedule, so based on the success/failure of this one we can consider having them semi-regularly. The agenda I would like to cover will include: * yt 3.0 status, including near/long term plans for development and support for non-grid codes * Rundown of all YTEPs accepted and outstanding * yt's "presence" on the web * 3.0 paper I will also be soliciting feedback in roundtable style on: * How are we doing? * How is the procedure for code contributions working? * How is the yt "infrastructure" meeting people's needs? (Mailing lists, Bitbucket, etc) * Where are energies being spent that could be better spent elsewhere? If you have either agenda items or discussion items, please reply to this email and suggest them. I think having a large presence at this meeting would be very useful, so if you are able to make it, please try to do so. It'll be held as a google hangout, and I'll send details here when it starts up. If there's a pressing need to reschedule, please write in reply to this email. Thanks, and looking forward to seeing you there, Matt

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NumberDensity in clumps and on FLASH data
by Matthew Turk July 9, 2013

July 9, 2013

Hi all, Mark Richardson wrote to the yt_analysis project with a problem with clumps on FLASH datasets. Here's his email: "Below includes my script and the output (it wouldn't let me attach two files). I get some output in the clump file up until I'd expect to see the Jeans Mass dumped. The output makes me think that it can't calculate this point because Gamma is unknown, or some other essential variable needed to get the number density. I've attempted to change the data_structure.py frontend for Flash to alias Gamma to gamc and game but I still get the 'cannot find Gamma' when loading my dataset." The issue from the traceback is that JeansMassMsun requires MeanMolecularWeight which needs NumberDensity. This can't be generated for his data. I am not an expert on FLASH, but it seems that this should be straightforward to fix, I just don't know how. Anybody from the FLASH or Clump side have any ideas? -Matt

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Oct-diet pull request
by Matthew Turk July 1, 2013

July 1, 2013

Hi all, I've just issued a big pull request that puts octrees (particle and Eulerian) on a major diet. Comments, suggestions and test cases that fail or pass would be welcomed! https://bitbucket.org/yt_analysis/yt-3.0/pull-request/54/octree-diet/diff I've laid out how things are now done, and I'd also be grateful to hear about whether those ideas should be changed/improved/etc. -Matt

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Moab plotting
by Anthony Scopatz June 29, 2013

June 29, 2013

Hello All, At the yt sprint at SciPy 2013, I made a first attempt at building an *.h5m (MOAB) file reader for yt using some data that Elliott Biondo sent me. You can find the notebook here [1]. I think both the PyNE and yt folks would be interested in this. I plan on turning this into a full-fledged yt frontend. Be Well Anthony 1. https://hub.yt-project.org/nb/go5405

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Fwd: [IPython-dev] frontend namespace flattened (major change)
by Matthew Turk June 29, 2013

June 29, 2013

FYI: Since we import from the notebookapp, we will have to change eventually, but we don't now since that construction is backwards compatible. ---------- Forwarded message ---------- From: Paul Ivanov <pi(a)berkeley.edu> Date: Fri, Jun 28, 2013 at 3:30 PM Subject: [IPython-dev] frontend namespace flattened (major change) To: IPython developers list <ipython-dev(a)scipy.org> Hey everyone, we've just landed PR #3450: https://github.com/ipython/ipython/pull/3450 To quote Fernando: > The basic idea is to move all the code we had in frontend and > put it at the top, as recently discussed, and then to create > a shim module capable of forwarding all `from > IPython.frontend... import...` to their new locations. Here's the rundown of name changes: Old name -> New name IPython.frontend.* -> IPython.* IPython.frontend.html.notebook -> IPython.html With only one exception, you do not have to make any immediate changes to your code in order for it to continue working, but will see deprecation warnings The one exception is described by Min in a comment on the PR which I am inlining here: > The shim is a tiny bit more complicated now, since it's not > just moving IPython.frontend.* to IPython.* anymore, as > IPython.frontend.html.notebook became just IPython.html. A > result of the extra shim is that there is one old import that > doesn't work: > > from IPython.frontend.html import notebook > > but > > from IPython.frontend.html.notebook[.submod] import whatever > > works just fine. One issue that we ran into that you should be sure to remove the frontend/ directory, and clean up all .pyc files that may be lying around. This command should do the trick: rm -fr IPython/frontend; find -name \*.pyc -exec rm {} \; best, -- _ / \ A* \^ - ,./ _.`\\ / \ / ,--.S \/ \ / `"~,_ \ \ __o ? _ \<,_ /:\ --(_)/-(_)----.../ | \ --------------.......J Paul Ivanov http://pirsquared.org _______________________________________________ IPython-dev mailing list IPython-dev(a)scipy.org http://mail.scipy.org/mailman/listinfo/ipython-dev

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Issue #597: Autodetection of hdf5 library doesn't work on Linux (yt_analysis/yt)
by Kacper Kowalik June 22, 2013

June 22, 2013

New issue 597: Autodetection of hdf5 library doesn't work on Linux https://bitbucket.org/yt_analysis/yt/issue/597/autodetection-of-hdf5-librar… Kacper Kowalik: When `HDF5_DIR` is unset and `hdf5.cfg` doesn't exists, setup tries to autodetect hdf5 library by using `ctypes.util.find_library("hdf5")`. On Linux it returns only filename without leading path and thus rest of the code fails. Responsible: xarthisius

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Issue #596: yt command does not produce helpful output (yt_analysis/yt)
by Matthew Turk June 21, 2013

June 21, 2013

New issue 596: yt command does not produce helpful output https://bitbucket.org/yt_analysis/yt/issue/596/yt-command-does-not-produce-… Matthew Turk: Currently, simply running "yt" indicates that something has gone wrong. This is actually not the case, and we should default to having a help output. This may be tricky to implement with argparse but can likely be done. Responsible: MatthewTurk

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Push back 2.6 => YTEP-0008 schedule change PR?
by Matthew Turk June 21, 2013

June 21, 2013

Hi all, I've issued a pull request to change the release schedule of 2.6. https://bitbucket.org/yt_analysis/ytep/pull-request/18/proposed-change-to-r… There are two motivations for this -- the first is that I wanted to get the Boxlib stuff and Cython kD-tree included by 2.6, but I don't think we will have time between now and July 1 to finish, review and test these changes. The other is that in the old release schedule I was set to be the coordinator for 2.6.1 on August 1st, but I am somewhat skeptical I'll be able to do so. So someone else will be set up to be release coordinator for 2.6 and handle pushing it out on August 1st. This would give the entire month of July to finish up Boxlib / Cython kD-tree, but still retain a 2.5.4 (new) release on July 1, to include changes since 2.5.3. Please feel free to click "Approve" on the PR if you are okay with this, and if you're not, either reply here to leave a comment. -Matt

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Issue #595: Quad Projection assumes cubical domains (yt_analysis/yt)
by J.S. Oishi June 18, 2013

June 18, 2013

New issue 595: Quad Projection assumes cubical domains https://bitbucket.org/yt_analysis/yt/issue/595/quad-projection-assumes-cubi… J.S. Oishi: It looks like dx and dy are always set identical to each other. This should be an easy fix, we just need a dxs and a dys in the array creation Responsible: jsoishi

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When can we turn off serialization by default?
by Matthew Turk June 18, 2013

June 18, 2013

Hi all, I'd like to turn off serialization by default. This includes: 1) Projections 2) Grid hierarchy 3) Field lists and maybe other things. In general, I think it's a bad idea to just litter directories with new files, and specifically I think it's a bad idea to store 2&3 since they are a huge source of errors for new and existing users. My preference would be to disable all auto-serialization of anything and make that not possible, mandating explicit, manual saves of data instead. However I recognize that is likely unpopular, as even though my simulations have a lot of data on disk, I know that they also take a relatively short time to project. So when can we make it disabled-by-default? 2.6? 3.0? Now? -Matt

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