Mailman 3 February 2013 - yt-dev

RFC: yt 2.5 changelog
by Matthew Turk 14 Feb '13

14 Feb '13

Hi all, I've opened a pull request here: https://bitbucket.org/yt_analysis/yt-doc/pull-request/74/changelog-update/d… This includes everyone I was able to identify that was a new contributor as well as a changelog of improvements to the code. I did this by going through the pull request log, but I might have missed something. Please make suggestions for new additions or changes via comments in the pull request, either inline or at the top. Thanks, Matt

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Fwd: Announcement of SciPy 2013 Themes
by Matthew Turk 14 Feb '13

14 Feb '13

SciPy is always a really fun conference, and not just for the python aspects. Last year was really great and I came away feeling like I learned a lot -- not just about Python, but about a wide variety of scientific topics. And, I think if a couple of us go, we can probably have a fun Austin-based sprint. ---------- Forwarded message ---------- From: SciPy 2013 <scipy-organizers(a)scipy.org> Date: Wed, Feb 13, 2013 at 6:19 PM Subject: Announcement of SciPy 2013 Themes To: Matthew <matthewturk(a)gmail.com> Email not displaying correctly? View it in your browser.<http://us1.campaign-archive1.com/?u=e91b4574d5d1709a9dc4f7ab7&id=0230006689…> Scientific Computing with Python-Austin, Texas-June 24-29, 2013 *Greetings and News from the SciPy 2013<http://scipy.us1.list-manage.com/track/click?u=e91b4574d5d1709a9dc4f7ab7&id…>Planning Committee: * SciPy 2013 is about four months away, and we’ve been working hard to make this the best one yet. We are very excited to announce the themes of this year’s conference. The main conference themes which will be Machine Learning & Tools for Reproducible Science. Like last year, there will also be 4 mini-symposia, and thanks to your contributions to the poll, the following themes have been selected: - Meteorology, climatology, and atmospheric and oceanic science - Astronomy & astrophysics - Bio-informatics - Medical imaging Thanks to everyone who answered the survey on these themes. The participation was tremendous. Hope to see you in June! Andy Terrel, Co-chair Jonathan Rocher, Co-chair Katy Huff, Program Committee co-chair Matt McCormick, Program Committee co-chair Dharhas Pothina, Tutorial co-chair Francesc Alted, Tutorial co-chair Corran Webster, Sprint co-chair Peter Wang, Sprint co-chair Matthew Turk, BoF co-chair Jarrod Millman, Proceeding co-chair Stéfan van der Walt, Proceeding co-chair Anthony Scopatz, Community contact co-chair Majken Tranby, Community contact co-chair Jeff Daily, Financial Aid co-chair John Wiggins, Financial Aid co-chair Leah Jones, Operations chair Brett Murphy, Sponsor chair Bill Cowan, Financial chair You are receiving this email because you subscribed to the mailing list or registered for the SciPy 2010 or SciPy 2011 conference in Austin, TX. Unsubscribe<http://scipy.us1.list-manage1.com/unsubscribe?u=e91b4574d5d1709a9dc4f7ab7&i…> matthewturk(a)gmail.com from this list | Forward to a friend<http://us1.forward-to-friend.com/forward?u=e91b4574d5d1709a9dc4f7ab7&id=023…>| Update your profile<http://scipy.us1.list-manage.com/profile?u=e91b4574d5d1709a9dc4f7ab7&id=069…> *Our mailing address is:* Enthought, Inc. 515 Congress Ave. Austin, TX 78701 Add us to your address book<http://scipy.us1.list-manage.com/vcard?u=e91b4574d5d1709a9dc4f7ab7&id=069dc…> *Copyright (C) 2013 Enthought, Inc. All rights reserved.*

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[yt_analysis/yt] Missing hierarchy functions (issue #499)
by Sam Skillman 13 Feb '13

13 Feb '13

--- you can reply above this line --- New issue 499: Missing hierarchy functions https://bitbucket.org/yt_analysis/yt/issue/499/missing-hierarchy-functions Sam Skillman: Currently looks like some of the functions hanging off the hierarchy are missing. In 2.x: ``` #!text pf.h.find_field_value_at_point pf.h.find_max_cell_location pf.h.find_particles_by_type pf.h.find_points pf.h.find_slice_grids pf.h.find_max pf.h.find_min pf.h.find_point pf.h.find_ray_grids pf.h.find_sphere_grids ``` In 3.0: ``` #!text pf.h.find_max pf.h.find_max_cell_location pf.h.find_particles_by_type pf.h.find_points ``` -- 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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[yt_analysis/yt] Imports in blenders.py (issue #498)
by Nathan Goldbaum 13 Feb '13

13 Feb '13

--- you can reply above this line --- New issue 498: Imports in blenders.py https://bitbucket.org/yt_analysis/yt/issue/498/imports-in-blenderspy Nathan Goldbaum: The enhance function, defined inside `yt.visualization.volume_rendering.blenders`, has a `from yt.mods import *` in it. This causes imports elsewhere in yt to break. Here's an example import that doesn't work anymore: ``` #!python >>> from yt.analysis_modules.cosmological_observation.light_cone.light_cone import LightCone ``` Responsible: samskillman -- 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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[yt_analysis/yt] Consistent docstrings (issue #497)
by Nathan Goldbaum 13 Feb '13

13 Feb '13

--- you can reply above this line --- New issue 497: Consistent docstrings https://bitbucket.org/yt_analysis/yt/issue/497/consistent-docstrings Nathan Goldbaum: We need to rethink how we handle docstrings. Right now some classes have docstrings that live at the class level, some that live inside __init__, others don't have docstrings at all. This needs to be rationalized and needs to be done in a way that makes the api docs clearer and with more useful information. I've put myself down but if anyone else wants to contribute, please feel free. Responsible: ngoldbaum -- 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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FLASH data in 2.x versus 3.0
by Matthew Turk 12 Feb '13

12 Feb '13

Hi all, Because of some testing/modification for the pull request that Andrew submitted, I tested some IO speeds for FLASH, which I decided to share here. What it came down to was testing a full dataset read, with slicing, versus constructing the H5S and only reading the 8x8 slab in question. I ran this with 30 iterations on the cluster merger FLASH dataset. Constructing a slice and only reading that in 2.x: 1.212s per slice Reading the full block dataset and discarding all but the slice of interest: 1.283s per slice In 3.0: 0.4856s per slice Mind you, seems like we have a big performance regression for finding the location of the most dense point, but that should be easily fixable. The vast majority of the savings come from pushing the selection of points *inside* the IO function, which lets us retain the H5D handles in between IO calls. -Matt

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[yt_analysis/yt] Update to Mercurial 2.5.1 (issue #496)
by Matthew Turk 11 Feb '13

11 Feb '13

--- you can reply above this line --- New issue 496: Update to Mercurial 2.5.1 https://bitbucket.org/yt_analysis/yt/issue/496/update-to-mercurial-251 Matthew Turk: We should update the install script to include Mercurial 2.5.1, and possibly put the evolve extension in yt-supplemental. Responsible: MatthewTurk -- 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 AMR kD-tree
by Matthew Turk 07 Feb '13

07 Feb '13

Hi all, Sam's got a PR out for a new AMR kD-tree: https://bitbucket.org/yt_analysis/yt/pull-request/383/amrkdtree-rewrite-vol… The idea is to make things more flexible, easier to improve, and eventually maybe even move it into Cython. It also includes some really cool improvements to alpha channel blending and the like. (He had a demo in IRC the other day of a plaid background over which he's volume rendered.) This needs user-testing. He has added tests for nose. I think if we can get three more "approve" clicks, which I hope will be from actually having run the code, we can give it an accept. -Matt

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[yt_analysis/yt] install_script builds lapack without -fPIC (issue #495)
by Kacper Kowalik 06 Feb '13

06 Feb '13

--- you can reply above this line --- New issue 495: install_script builds lapack without -fPIC https://bitbucket.org/yt_analysis/yt/issue/495/install_script-builds-lapack… Kacper Kowalik: As reported on #yt by clovell numpy fails to link with lapack installed using `install_script.sh` with following error: ``` #!bash Installing numpy-1.6.1 (arguments: 'numpy-1.6.1 --fcompiler=gnu95') ******************************************** FAILURE REPORT: ******************************************** gcc: numpy/linalg/lapack_litemodule.c gcc: numpy/linalg/python_xerbla.c /usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/home/chris/Documents/enzo/yt/src/lapack-3.4.2 -L/home/chris/Documents/enzo/yt/src/BLAS -Lbuild/temp.linux-x86_64-2.7 -llapack -lfblas -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so /usr/bin/ld: /home/chris/Documents/enzo/yt/src/lapack-3.4.2/liblapack.a(dgeev.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /home/chris/Documents/enzo/yt/src/lapack-3.4.2/liblapack.a: could not read symbols: Bad value collect2: ld returned 1 exit status ``` -- 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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[yt_analysis/yt] Provide answer testing coverage for all the code frontends. (issue #494)
by Nathan Goldbaum 02 Feb '13

02 Feb '13

--- you can reply above this line --- New issue 494: Provide answer testing coverage for all the code frontends. https://bitbucket.org/yt_analysis/yt/issue/494/provide-answer-testing-cover… Nathan Goldbaum: Currently only the enzo frontends is tested via answer testing. We should use small and medium sized datsets from each code to construct a set of common consistency checks. Maybe we can even consolidate the answer testing and test all the codes simultaneously? -- 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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yt-dev February 2013