Mailman 3 January 2014 - yt-dev

Unitrefactor to-do's
by Nathan Goldbaum Jan. 27, 2014

Jan. 27, 2014

Hi all, I'd like to figure out what exactly needs to happen before unitrefactor can get merged in. So far, I have the following: 1. Frontend conversions: * moab * NMSU art * chombo/pluto * GDF 2. Validate unchanged answers relative to the current pre-unitrefactor 3.0 tip 3. Update MPI calls that use the buffer interface to properly handle units. 4. Update ProfileND classes to return data with units Are there any other to-do items I am missing? FWIW, I'm currently … [View More]

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Enzo frontend
by Brian Crosby Jan. 27, 2014

Jan. 27, 2014

Hi yt dev, I’ve been working with the Enzo frontend for running yt inline during simulations, and have come across a strange problem that I can’t seem to sort out. I ported a handful of functions in yt/frontends/enzo/io.py from the IOHandlerPackedHDF5 class to IOHandlerInMemory, and clearly messed something up in the _read_particle_fields function. In particular, converting the mass from Enzo’s internal units (actually a density) with the line data *= g.dds.prod(dtype="f8”) (where g.dds.… [View More]

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Issue #766: Import of particle_trajectories fails in yt-2.6.1 (conda install) (yt_analysis/yt)
by Devin Silvia Jan. 27, 2014

Jan. 27, 2014

New issue 766: Import of particle_trajectories fails in yt-2.6.1 (conda install) https://bitbucket.org/yt_analysis/yt/issue/766/import-of-particle_trajector… Devin Silvia: When attempting: from yt.analysis_modules.api import AbsorptionSpectrum I got an important error (unrelated to the spectrum stuff) on particle_trajectories: http://paste.yt-project.org/show/4246/ Importing directly from absorption_spectrum gets around this, but still alerting the community that particle_trajectories … [View More]

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Simple answer testing now in 3.0
by Matthew Turk Jan. 27, 2014

Jan. 27, 2014

Hi all, Just as a quick note, Britton, Nathan and I came up with a very simple answer testing mechanism. Originally we did this for the unit refactor. Here's the PR, with some explanation: https://bitbucket.org/MatthewTurk/yt/pull-request/36/adding-simple-answer-t… This will be added to the docs soon, but the long and the short is that if you can define a function that returns an array, you can easily check that the answer remains the same by comparing min,max,sum,std,size, and (optionally)… [View More]

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Move docs back into repo?
by Matthew Turk Jan. 26, 2014

Jan. 26, 2014

Hi all, A couple years ago we moved the docs into their own repository. This was for two reasons: 1) We wanted to include more images, which bloated the repository size 2) There was a lot of churn at the time in the docs But, the docs are falling behind with 3.0. And, more to the point, the fact that they live separate from the main repo means that the PRs are evaluated separately, they are updated separately, and if you want to write docs for functionality you have to figure out where … [View More]

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Issue #764: matplotlib.delaunay deprecated in matplotlib 1.4 (yt_analysis/yt)
by Nathan Goldbaum Jan. 25, 2014

Jan. 25, 2014

New issue 764: matplotlib.delaunay deprecated in matplotlib 1.4 https://bitbucket.org/yt_analysis/yt/issue/764/matplotlibdelaunay-deprecate… Nathan Goldbaum: When running with the current matplotlib github master, importing yt produces the following error: ``` /Users/goldbaum/Documents/matplotlib/lib/matplotlib/cbook.py:133: MatplotlibDeprecationWarning: The matplotlib.delaunay module was deprecated in version 1.4. Use matplotlib.tri.Triangulation instead. ``` We use matplotlib.delaunay in … [View More]

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Issue #765: ('gas', 'Dark_Matter_Density') fails to load (yt_analysis/yt)
by Nathan Goldbaum Jan. 25, 2014

Jan. 25, 2014

New issue 765: ('gas', 'Dark_Matter_Density') fails to load https://bitbucket.org/yt_analysis/yt/issue/765/gas-dark_matter_density-fail… Nathan Goldbaum: I ran into this while trying to load all of the fields in `pf.h.field_list`. The following script illustrates the issue: ``` from yt.mods import * pf = load("IsolatedGalaxy/galaxy0030/galaxy0030") print pf.h.field_list[0] pf.h.all_data()[pf.h.field_list[0]] ``` on the current tip of yt-3.0 (b3e969705199), this outputs: ``` ('gas', '… [View More]

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NSF funding for yt
by Matthew Turk Jan. 24, 2014

Jan. 24, 2014

Hi all, I'm writing with some good news -- yt is now funded by the National Science Foundation as a project in its Software Infrastructure for Sustained Innovation (SI2) program at the Scientific Software Elements (SSE) level! The SI2 program is designed to fund software that promotes scientific goals at multiple levels. The first level, SSE, is for a short period for a very small team, with the explicit goal of enabling that team or project to move forward to subsequent funding to promote … [View More]the sustainability of the project over the long term. I have accepted a position as an Associate Research Scientist at Columbia, funded by this grant. What this means is that my time will be spent working on developing yt in a particular set of goals, many of which align very well with the goals of yt 3.0 and beyond; aspects of this will include codifying the development strategy that we've been pursuing, as well as fostering more community interaction. The grant proposal has been made public here: http://dx.doi.org/10.6084/m9.figshare.909413 There are three main components, each of which has a set of yearly goals: * Infrastructure * Year 1: Non-Eulerian * Year 2: Non-Cartesian * Year 3: Unstructured Mesh * Interface * Year 1: Data widgets * Year 2: Data hub * Year 3: Outreach hub * Instrumentation * Year 1: Fluid containers * Year 2: In situ library * Year 3: IO library Over the coming months I'll be posting updates on the progress along these goals, but I believe that the "Year 1" goals have already made a considerably amount of progress. These main components will be driving my work over the next few years, which means emphasis on supporting additional codes, data exploration widgets, and supporting simulation infrastructure. A main aspect of the grant, which is noted at some length in the proposal, is to continue developing community around yt -- through running office hours, bootcamps, fostering contributions and continuing to grow the strong community of users and developers we already have. I am proud of the work we've done, and I hope we will continue to grow and flourish as a community. I will be spearheading this, including setting up weekly office hours on G+ Hangouts and pursuing a more directed educational strategy. If you're interested in this, I'll be sending out an invite soon! I am optimistic that this may be a gateway to continue securing funding to for yt, and I am quite excited by the possibilities. I hope you're all having a good semester, and I'm excited to keep working with you all on this. Best, Matt [View Less]

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Adding new derived fields
by Matthew Turk Jan. 23, 2014

Jan. 23, 2014

Hi all, The method for adding derived fields has somewhat changed in the unitrefactor of 3.0, and we have the opportunity to make it a bit easier to add new fields -- especially after a parameter file has been created, which previously has been a pain. Below is a brief summary. The current way we do this is with: add_field(...) or @derived_field def some_function(... The field system is now plugin based, which means we load plugins for different things and fields are dynamically added. … [View More]

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Fwd: [Science Lab] Launching a second pilot on code review in science
by Matthew Turk Jan. 16, 2014

Jan. 16, 2014

This seems like it could be an interesting match for either yt or Enzo. ---------- Forwarded message ---------- From: Kaitlin Thaney <kaitlin(a)mozillafoundation.org> Date: Thu, Jan 16, 2014 at 11:42 AM Subject: [Science Lab] Launching a second pilot on code review in science To: We are launching a second pilot study of code review in science this February, and want you to take part. The main findings of our first study were: everyone involved thought it could be useful, but a drive-… [View More]

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