Mailman 3 March 2014 - yt-dev

Orientation, coordinate systems
by Matthew Turk April 15, 2014

April 15, 2014

Hi all, I'd like to open up the discussion of "fixing" the yt coordinate systems, as we move nearer and nearer on 3.0. Jeff, Nathan and Britton have brought this up a couple times, that the x/y/z ordering is not consistent with what they expect, and I'd like to figure out if we can fix that now -- it's as good a time as any for bandaid ripping. It may just be a matter of the transposition of buffers and the x_dict and y_dict, or it might be more complex, although I suspect it won't be much more than fixing those two items. -Matt

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Should we remove plot collection before 3.0?
by Matthew Turk April 2, 2014

April 2, 2014

Hi all, I'm inclined to remove plot collection before yt 3.0 is released. PhasePlot and ProfilePlot both work in 2.6, and we've actually seen quite a bit of migration to them. If there's enough support, I'll bring this to a YTEP and we can hash it out there, but before I went to that point I figured I'd look for a handful of +1's here. -Matt

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IPython Notebook Diff Tool
by Stuart Mumford March 30, 2014

March 30, 2014

Hello all, This looks like it could be very useful for anyone who has git or hg repos with IPython notebooks in! https://pypi.python.org/pypi/nbdiff/1.0.2 Stuart

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Fwd: ShiningPanda CI, clap de fin
by Matthew Turk March 29, 2014

March 29, 2014

Hi all, While we did benefit for a long time from ShiningPanda, we have lately been relying on Jenkins hosted by Kacper, and hopefully on Polyphemus in the future. Right now we still use ShiningPanda for building the blog, but that will be easy to fix. Sad to see them go. -Matt ---------- Forwarded message ---------- From: Alexis Tabary <alexis.tabary(a)shiningpanda.com> Date: Sat, Mar 29, 2014 at 8:15 AM Subject: ShiningPanda CI, clap de fin To: Alexis Tabary <alexis.tabary(a)shiningpanda.com>, Olivier Mansion <olivier.mansion(a)shiningpanda.com> Dear all, Today brings some sad news: we are shutting down ShiningPanda CI. Jenkins instances will remain available until April 30th, at which point they will all go offline. This decision became inevitable as we failed to keep ShiningPanda CI relevant in an increasingly competitive environment: our user base has been eroding for a rather long while, so we decided to move forward and simply halt the service. We are incredibly thankful to all the people who have been relying on ShiningPanda for integration and deployment, so we want to ensure as smooth a transition as possible. All users who wish to download Jenkins configuration files, or build history, should contact us. We might also be able to help with migrations to other services, in-house or hosted. Just send us an email. As for us - the team behind ShiningPanda CI - for now we are focusing on requires.io, a web service to keep track of dependencies on pypi. Thank you all for supporting us for so long. Olivier & Alexis -- Alexis Tabary ShiningPanda Founding Partner (+81) 90-6064-3886 Requires.io Monitor your Python dependencies ShiningPanda Consulting Services Build and Release Management

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HiPACC yt workshop wrapup
by Matthew Turk March 29, 2014

March 29, 2014

Hi all, I'm writing with a quick wrapup of the yt workshop we had at UCSC this week, sponsored by UC-HiPACC. All in all, I am extremely pleased with everything that got done. Over the few days, we had a huge number of improvements all over the code base, and I was absolutely delighted by the new contributors and the new improvements. A few highlights: * SPH frontends (Gabriel Altay and Ben Keller) have been vastly improved, including ionization fields and a new system for autodetecting Tipsy frontends (load() now works!) along with domain/endianness detection. * The GPU volume rendering interface (Alex Bogert, John Holdener and Nick Smith) has been well-defined, and will be interoperable with the yt software renderer. * Halo Finder / Analysis (Hilary Egan, Brian Crosby) has been streamlined, the mass function code cleaned up, and the FOF+Rockstar code has been implemented more formally * The NMSU-ART frontend has been cleaned up, double-checked, and particle-type-enabled. (Kenza Arraki) Also, new answer tests! * Software VR has been ripped out and started to be reconstructed (Sam Skillman) with an eye to clarity and simplicity in the interface. * Docs and polish (Nathan Goldbaum) have been worked on a considerable amount -- in fact, the docs now build again for 3.0, and we're getting awfully close to a full set of them that cover the new functionality. * IRATE halo catalogs can now be loaded in and examined (Miguel Rocha), thus furthering the ability of yt to read, write, and analyze halo catalogs as first class datasets. * A new binding-energy check has been started (Andy Elvin) * Boxlib 2D polar has been enabled (Elizabeth Lovegrove) Anyway, it was really fun, productive -- and in many cases, documented! With the docs now building on a regular basis, we'll continue to check things in and update the documentation as new features are added and existing features are polished. Thanks again to Ji-hoon, Miguel, and Nathan for their organization, and thanks to Joel Primack, Sue Grasso and all of UC-HiPACC for their support of the workshop as a whole. -Matt

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Issue #822: volume rendering classes are not imported in yt/__init__.py (yt_analysis/yt)
by Nathan Goldbaum March 28, 2014

March 28, 2014

New issue 822: volume rendering classes are not imported in yt/__init__.py https://bitbucket.org/yt_analysis/yt/issue/822/volume-rendering-classes-are… Nathan Goldbaum: Currently only `off_axis_projection` is imported. We should probably import `ColorTransferFunction`, `TransferFunctionHelper`, and any other names that people used to commonly import from `yt.mods`.

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ANN: PyTAPS now on Bitbucket!
by Anthony Scopatz March 28, 2014

March 28, 2014

Hello All, It is my esteemed pleasure to announce that PyTAPS - the Python wrapper to iTAPS, MOAB, CGM, and Lasso is now available on bitbucket [1]. It is my hope that this will serve as a launching point for further improvements to PyTAPS and further collaborations using MOAB. Vijay and I will be working towards and to enable this goal. Personally, I am very excited to see this happen. If you are interested in helping PyTAPS evolve or know someone who is, please let us know! Be Well Anthony 1. https://bitbucket.org/fathomteam/pytaps

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Issue #821: Numpy not found in install_script.sh (yt_analysis/yt)
by Andreas Schreiber March 27, 2014

March 27, 2014

New issue 821: Numpy not found in install_script.sh https://bitbucket.org/yt_analysis/yt/issue/821/numpy-not-found-in-install_s… Andreas Schreiber: Hi Guys, unfortunately executing ``` bash install_script.sh ``` results in an error: ``` Using wget Using sha512sum Downloading xray_emissivity.h5 from yt-project.org Setting YT_DIR=/home/aschreiber/yt-x86_64/src/yt-hg/ Installing distribute Installing pip Installing matplotlib-1.3.0 ******************************************** FAILURE REPORT: ******************************************** Edit setup.cfg to change the build options BUILDING MATPLOTLIB matplotlib: yes [1.3.0] python: yes [2.7.6 (default, Mar 27 2014, 16:56:17) [GCC 4.8.1 20130909 [gcc-4_8-branch revision 202388]]] platform: yes [linux2] REQUIRED DEPENDENCIES AND EXTENSIONS Requires numpy 1.5 or later to build. (Numpy not found) ``` Ive already installed a different python distribution and hence assume an conflict with the already definied PATHs: $PYTHONPATH: /home/aschreiber/pencil-code/python:/home/aschreiber/python: Anyone can help me to fix that? Could I come along with a manual installation of yt? Best regards Andreas

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Issue #820: "all" particle type fields are dimensionless (yt_analysis/yt)
by Britton Smith March 27, 2014

March 27, 2014

New issue 820: "all" particle type fields are dimensionless https://bitbucket.org/yt_analysis/yt/issue/820/all-particle-type-fields-are… Britton Smith: All particles fields that are accessed with "all" are now being returned as dimensionless. For example, with an enzo-3.0 dataset: data["all", "particle_mass"] returns dimensionless, but data["DarkMatter", "particle_mass"] returns the proper units.

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Free CI for bitbucket mercurial repositories
by Nathan Goldbaum March 27, 2014

March 27, 2014

Hi all, Today I found a cool new free service that the readers of this list might be interested in. Take a look at this page: https://magnum-ci.com/ This is a free continuous integration service that supports bitbucket and mercurial repositories. If you're familiar with Travis CI, this is very similar, but they don't require you host your code using git on github. It looks like they're mostly in the business of testing ruby and node webapps, but it's still possible to set up a scientific python stack using anaconda and then test python code. To get a basic yt testing setup working, I used the following configuration: Dependency installation: wget http://09c8d0b2229f813c1b93-c95ac804525aac4b6dba79b00b39d1d3.r79.cf1.rackcd… chmod +x ./Anaconda-1.9.1-Linux-x86_64.sh ./Anaconda-1.9.1-Linux-x86_64.sh -b cd /home/magnum/yt-ngoldbaum PYTHONPATH= PATH=/home/magnum/anaconda/bin:$PATH python setup.py develop Testing suite commands: cd /home/magnum/yt-ngoldbaum PYTHONPATH= PATH=/home/magnum/anaconda/bin:$PATH nosetests Unfortuantely it's not perfect - there are some resource limitations that prevent it from running the full yt unit tests. That said, I've contacted their support and they're interested in seeing if they can configure something on their end to prevent the resource limits from kicking in in this case. In any case, I think this is generically useful - particularly among this group, who tend to use mercurial and bitbucket a lot more often than a random sample of developers. If you want to test a small side project, this might be just what you need. Hope that's helpful, Nathan

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