Mailman 3 May 2014 - yt-dev

Issue #842: Document derived_fields in 3.0 (yt_analysis/yt)
by Cameron Hummels 19 May '14

19 May '14

New issue 842: Document derived_fields in 3.0 https://bitbucket.org/yt_analysis/yt/issue/842/document-derived_fields-in-30 Cameron Hummels: Currently the derived_field docs are out of sync with the unit changes in 3.0. Specifically, using a `convert_function` fails when you use it as specified in: http://yt-project.org/docs/dev-3.0/analyzing/creating_derived_fields.html

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Issue #841: AbsorptionSpectrum import fails (yt_analysis/yt)
by Cameron Hummels 19 May '14

19 May '14

New issue 841: AbsorptionSpectrum import fails https://bitbucket.org/yt_analysis/yt/issue/841/absorptionspectrum-import-fa… Cameron Hummels: This bug appears to be similar to Issue #766, but it is occurring for me on the tip of yt-3.0 (changeset 7a08af110b44) with yt installed from the install_script. When I try to import AbsorptionSpectrum with this line: `from yt.analysis_modules.api import AbsorptionSpectrum` yt fails and raises this error: http://paste.yt-project.org/show/4654/ Perhaps this is related to all of the stuff @jzuhone is doing with the FITS frontend? Maybe it's fixed in his open PR, but I have not yet tested this.

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yt-3 bug in PhasePlot save() call
by Brian O'Shea 17 May '14

17 May '14

Hi yt-ites, Using the current tip of yt-3 (change set 5f2c6b6da9cf), this script: http://paste.yt-project.org/show/4643/ spits out this error: http://paste.yt-project.org/show/4644/ which seems to have a problem in the PhasePlot save() call. This seems to have crept into the codebase in the last week or so. Thanks! --Brian

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Fwd: [WSSSPE] CFP: 2nd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2)
by Matthew Turk 14 May '14

14 May '14

---------- Forwarded message ---------- From: Daniel S. Katz <dsk(a)uchicago.edu> Date: Tue, May 13, 2014 at 1:52 PM Subject: [WSSSPE] CFP: 2nd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2) To: "Working on Sustainable Software for Science: Practice and Experience" <wssspe(a)lists.researchcomputing.org.uk> 2nd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2) http://wssspe.researchcomputing.org.uk/wssspe2/ (to be held in conjunction with SC14, Sunday, 16 November 2014, New Orleans, LA, USA) Progress in scientific research is dependent on the quality and accessibility of software at all levels and it is critical to address challenges related to the development, deployment, and maintenance of reusable software as well as education around software practices. These challenges can be technological, policy based, organizational, and educational, and are of interest to developers (the software community), users (science disciplines), and researchers studying the conduct of science (science of team science, science of organizations, science of science and innovation policy, and social science communities). The WSSSPE1 workshop (http://wssspe.researchcomputing.org.uk/WSSSPE1) engaged the broad scientific community to identify challenges and best practices in areas of interest for sustainable scientific software. At WSSSPE2, we invite the community to propose and discuss specific mechanisms to move towards an imagined future practice of software development and usage in science and engineering. The workshop will include multiple mechanisms for participation, encourage team building around solutions, and identify risky solutions with potentially transformative outcomes. Participation by early career students and postdoctoral researchers is strongly encouraged. We invite short (4-page) actionable papers that will lead to improvements for sustainable software science. These papers could be a call to action, or could provide position or experience reports on sustainable software activities. The papers will be used by the organizing committee to design sessions that will be highly interactive and targeted towards facilitating action. Submitted papers should be archived by a third-party service that provides DOIs. We encourage submitters to license their papers under a Creative Commons license that encourages sharing and remixing, as we will combine ideas (with attribution) into the outcomes of the workshop. The organizers will invite one or more submitters of provocative papers to start the workshop by presenting highlights of their papers in a keynote presentation to initiate active discussion that will continue throughout the day. Areas of interest for WSSSPE2, include, but are not limited to: • defining software sustainability in the context of science and engineering software • how to evaluate software sustainability • improving the development process that leads to new software • methods to develop sustainable software from the outset • effective approaches to reusable software created as a by-product of research • impact of computer science research on the development of scientific software • recommendations for the support and maintenance of existing software • software engineering best practices • governance, business, and sustainability models • the role of community software repositories, their operation and sustainability • reproducibility, transparency needs that may be unique to science • successful open source software implementations • incentives for using and contributing to open source software • transitioning users into contributing developers • building large and engaged user communities • developing strong advocates • measurement of usage and impact • encouraging industry’s role in sustainability • engagement of industry with volunteer communities • incentives for industry • incentives for community to contribute to industry-driven projects • recommending policy changes • software credit, attribution, incentive, and reward • issues related to multiple organizations and multiple countries, such as intellectual property, licensing, etc. • mechanisms and venues for publishing software, and the role of publishers • improving education and training • best practices for providing graduate students and postdoctoral researchers in domain communities with sufficient training in software development • novel uses of sustainable software in education (K-20) • case studies from students on issues around software development in the undergraduate or graduate curricula • careers and profession • successful examples of career paths for developers • institutional changes to support sustainable software such as promotion and tenure metrics, job categories, etc. Submissions: Submissions of up to four pages should be formatted to be easily readable and submitted to an open access repository that provides unique identifiers (e.g., DOIs) that can be cited, for example http://arXiv.org or http://figshare.com. Once you have received an identifier for your self-published paper from a repository, submit it to WSSSPE2 by creating a new submission at https://www.easychair.org/conferences/?conf=wssspe2, and entering: • author information for all authors • title • abstract (with the identifier as the first line of the abstract, for example, http://dx.doi.org/10.6084/m9.figshare.791606 or http://arxiv.org/abs/1404.7414 or alternative) • at least three keywords • tick the abstract only box Do not submit the paper itself through EasyChair; the identifier in the abstract that points to the paper is sufficient. Deadline for Submission: 14 July 2014 (any time of day, no extensions) Travel Support Funds are available to support participation in WSSSPE2 by 1) US-based students, early-career researchers, and members of underrepresented groups; and 2) participants who would not otherwise attend the SC14 conference. Priority will be given to those who have submitted papers and can make a compelling case for how their participation will strengthen the overall workshop and/or positively impact their future research or educational activities. Submissions for travel support will be accepted from September 1st to September 15th 2014 following instructions posted on the workshop web site. Financial support to enable this has been generously provided by 1) the National Science Foundation and 2) the Gordon and Betty Moore Foundation. Important Dates: July 14, 2014 Paper submission deadline September 1, 2014 Author notification September 15, 2014 Funding request submission deadline September 22, 2014 Funding decision notification November 16, 2014 WSSSPE2 Workshop Organizers: • Daniel S. Katz, d.katz(a)ieee.org, National Science Foundation, USA • Gabrielle Allen, gdallen(a)illinois.edu, University of Illinois Urbana-Champaign, USA • Neil Chue Hong, N.ChueHong(a)software.ac.uk, Software Sustainability Institute, University of Edinburgh, UK • Karen Cranston, karen.cranston(a)nescent.org, National Evolutionary Synthesis Center (NESCent), USA • Manish Parashar, parashar(a)rutgers.edu, Rutgers University, USA • David Proctor, djproctor(a)gmail.com, National Science Foundation, USA • Matthew Turk, matthewturk(a)gmail.com, Columbia University, USA • Colin C. Venters, colin.venters(a)googlemail.com, University of Huddersfield, UK • Nancy Wilkins-Diehr, wilkinsn(a)sdsc.edu, San Diego Supercomputer Center, University of California, San Diego, USA Program Committee: • Aron Ahmadia, U.S. Army Engineer Research and Development Center, USA • Liz Allen, Wellcome Trust, UK • Lorena A. Barba, The George Washington University, USA • C. Titus Brown, Michigan State University, USA • Coral Calero, Universidad Castilla La Mancha, Spain • Jeffrey Carver, University of Alabama, USA • Ewa Deelman, University of Southern California, USA • Gabriel A. Devenyi, McMaster University, Canada • Charlie E. Dibsdale, O-Sys, Rolls Royce PLC, UK • Alberto Di Meglio, CERN, Switzerland • Anshu Dubey, Lawrence Berkeley National Laboratory, USA • David Gavaghan, University of Oxford, UK • Paul Ginsparg, Cornell University, USA • Josh Greenberg, Alfred P. Sloan Foundation, USA • Sarah Harris, University of Leeds, UK • James Herbsleb, Carnegie Mellon University, USA • James Howison, University of Texas at Austin, USA • Caroline Jay, University of Manchester, UK • Matthew B. Jones, National Center for Ecological Analysis and Synthesis (NCEAS), University of California, Santa Barbara, USA • Jong-Suk Ruth Lee, National Institute of Supercomputing and Networking, KISTI (Korea Institute of Science and Technology Information), Korea • James Lin, Shanghai Jiao Tong University, China • Frank Löffler, Louisiana State University, USA • Chris A. Mattmann, NASA JPL & University of Southern California, USA • Robert H. McDonald, Indiana University, USA • Lois Curfman McInnes, Argonne National Laboratory, USA • Chris Mentzel, Gordon and Betty Moore Foundation, USA • Kenneth M. Merz, Jr., Michigan State University, USA • Marek T. Michalewicz, A*STAR Computational Resource Centre, Singapore • Peter E. Murray, LYRASIS, USA • Kenjo Nakajima, University of Tokyo, Japan • Cameron Neylon, PLOS, UK • Aleksandra Pawlik, Software Sustainability Institute, Manchester University, UK • Birgit Penzenstadler, University of California, Irvine, USA • Marian Petre, The Open University, UK • Mark D. Plumbley, Queen Mary University of London, UK • Andreas Prlic, University of California, San Diego, USA • Victoria Stodden, Columbia University, USA • Kaitlin Thaney, Mozilla Science Lab, USA • Greg Watson, IBM, USA • Theresa Windus, Iowa State University and Ames Laboratory, USA -- Daniel S. Katz University of Chicago (773) 834-7186 (voice) (773) 834-6818 (fax) d.katz(a)ieee.org or dsk(a)uchicago.edu http://www.ci.uchicago.edu/~dsk/ _______________________________________________ WSSSPE mailing list WSSSPE(a)lists.researchcomputing.org.uk http://lists.researchcomputing.org.uk/listinfo.cgi/wssspe-researchcomputing…

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io chunks in yt-3.0
by Britton Smith 13 May '14

13 May '14

Hey all, I'm working on changing how HaloCatalog objects loop over halos from a model where every processor has to hold the entire halo list to a model in which we loop over "io" chunks. This will make the HaloCatalog scale much better to extremely large catalogs. My understanding was that an "io" chunk was essentially one file on disk. However, when I try to get io chunks from any one of the various halo catalog frontends, there seems to only ever be a single chunk that contains everything, regardless of how many files on disk the data is spread over. Is there a way to change this so that an io chunk represents the data from a single file? Britton

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Fwd: [astropy-dev] Lorentz Center Workshop on "Python in Astronomy"
by Matthew Turk 08 May '14

08 May '14

---------- Forwarded message ---------- From: Thomas Robitaille <thomas.robitaille(a)gmail.com> Date: Thu, May 8, 2014 at 7:45 AM Subject: [astropy-dev] Lorentz Center Workshop on "Python in Astronomy" To: astropy-dev <astropy-dev(a)googlegroups.com>, astropy <astropy(a)scipy.org> Hi everyone, Back in December last year I forwarded a call for proposals for workshops at the Lorentz center to this list, and a few of us subsequently put in an application to hold a Python Astronomy workshop. We are now very happy to report that a "Python in Astronomy" workshop has been accepted and will take place at the Lorentz center in Leiden on 20-24 April 2015. This workshop aims to bring together researchers, Python developers, users, and educators, and will include presentations, tutorials, unconference sessions, and coding sprints. In addition to sharing information about the state-of-the art of Python Astronomy packages, the workshop will also focus on improving interoperability between astronomical Python packages, providing training for new contributors, and developing a common set of educational materials for Python in Astronomy. The meeting is therefore not only aimed at current developers, but also users and educators. A formal website and announcement will come later this year, but we wanted to share this with you now so that you can keep the dates free if you are interested in participating. In the mean time, you can already sign up to receive future announcements about the workshop at the following page: http://python-in-astronomy.github.io Please feel free to spread the word to others that this is happening and get them to sign up to the announcement list. We are very excited about the opportunity to hold this workshop, and we hope to see many of you there! The organizing committee: Thomas Robitaille Pauline Barmby Eric Jeschke Stuart Mumford Magnus Persson -- You received this message because you are subscribed to the Google Groups "astropy-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to astropy-dev+unsubscribe(a)googlegroups.com. For more options, visit https://groups.google.com/d/optout.

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Everybody using yt-3.0, turn around
by Matthew Turk 07 May '14

07 May '14

Hi all, Just wanted to drop a note to let you know that we've switched the coordinate system in yt-3.0's mainline to be right-handed. https://bitbucket.org/yt_analysis/yt/pull-request/864/switch-to-right-hande… This should only affect projections and slices along the y axis. According to my understanding of the terms and vocabulary of heraldic coats-of-arms, this makes yt 33% less "sinister." -Matt

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_determine_fields
by Britton Smith 05 May '14

05 May '14

Hi all, I've been discussing with Hilary the best way to allow ProfilePlot to work with profile data loaded from disk. It seems it would be easy enough to make a Profile object from loaded data, but the holdup is that there are a number of calls to data_source._determine_fields for simple things like checking if a field is log or linear. I had a look at this function, which hangs off of YTDataContainer, and noticed that it doesn't seem to really need the data container itself. I'm thinking that this function could be moved to instead hang off of the Dataset object without a problem. If so, then ProfilePlot could much more easily be extended to work with data from disk, since you could also supply None for the data_source. Does anyone see a problem with doing this? Britton

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Strange behavior on SlicePlots with Chombo data in yt-3.0
by Andrew Myers 03 May '14

03 May '14

Hi Folks, I'm seeing a strange issue with Chombo data in yt-3.0. This is before any recent changes I made refactoring the frontend. Attached are two images of the same slice through the same dataset, one with yt-3.0 and one with yt-2.6. The image looks fine in yt-2.6, but there are clearly artifacts at the level boundaries for yt-3.0. What's strange is that, if I loop over all the grids and dump out the density, I get *exactly* the same answers for 3.0 and 2.6. It's almost like there is some kind of additive blending thing going on for the 3.0 slice plots, though. I'm a bit at a loss for where to look for this. Has anyone seen something like this before? Thanks, Andrew

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Issue #840: yt.analysis_modules.level_sets.api.find_clumps raises NotImplementedError (yt_analysis/yt)
by Stuart Mumford 02 May '14

02 May '14

New issue 840: yt.analysis_modules.level_sets.api.find_clumps raises NotImplementedError https://bitbucket.org/yt_analysis/yt/issue/840/ytanalysis_moduleslevel_sets… Stuart Mumford: running `find_clumps.py` from the cook book raises the following error: ``` #!python Finding clumps: min: 1.000000e-28, max: 1.000000e-23, step: 2.000000 Traceback (most recent call last): File "/home/stuart/BitBucket/yt/doc/source/cookbook/find_clumps.py", line 40, in <module> find_clumps(master_clump, c_min, c_max, step) File "/home/stuart/BitBucket/yt/yt/analysis_modules/level_sets/clump_handling.py", line 171, in find_clumps clump.find_children(min_val) File "/home/stuart/BitBucket/yt/yt/analysis_modules/level_sets/clump_handling.py", line 110, in find_children nj, cids = identify_contours(self.data, self.field, min_val, max_val) File "/home/stuart/BitBucket/yt/yt/analysis_modules/level_sets/contour_finder.py", line 36, in identify_contours for (g, node, (sl, dims, gi)) in data_source.tiles.slice_traverse(): File "/home/stuart/BitBucket/yt/yt/utilities/amr_kdtree/amr_kdtree.py", line 189, in slice_traverse raise NotImplementedError NotImplementedError ```

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