Mailman 3 January 2013 - yt-dev

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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Testing new AMR kD-tree
by Matthew Turk Feb. 7, 2013

Feb. 7, 2013

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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cheat sheet
by Stephen Skory Jan. 30, 2013

Jan. 30, 2013

Hi all, over the last month or so I have been slowly working on a yt cheat sheet. It is not finished, but I feel that it has reached a point where I'd like some help and input from the rest of you. I am trying to strike a balance between being too sparse with information and putting too much in. So for some things I have been pretty comprehensive (like yt command line stuff) or just giving a teaser (like plotting commands) which is mainly there to show what's available, but not how to use it. I know I'm missing things. That's where you come in! If you're really adventurous, feel free to make your own additions and edits. Or, please reply with a note with things you see that need changing or adding and I'll try to do it. The cheat sheet lives in the yt-doc repository: https://bitbucket.org/yt_analysis/yt-doc/src/tip/cheatsheet.tex?at=default I've just issued a PR for my latest changes: https://bitbucket.org/yt_analysis/yt-doc/src/tip/cheatsheet.tex?at=default and here's a PDF showing what it looks like now (surely to change): http://casa.colorado.edu/~stsk4691/cheatsheet.pdf Thank you! -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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[yt_analysis/yt] Entropy asks for "Gamma" which is not well-defined (issue #491)
by Matthew Turk Jan. 29, 2013

Jan. 29, 2013

--- you can reply above this line --- New issue 491: Entropy asks for "Gamma" which is not well-defined https://bitbucket.org/yt_analysis/yt/issue/491/entropy-asks-for-gamma-which… Matthew Turk: "Gamma" is not defined in all frontends, and Entropy requests it. We should more elegantly handle this situation. 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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[yt_analysis/yt] Don't allow fields to be accessed that don't have dependencies (issue #490)
by Matthew Turk Jan. 29, 2013

Jan. 29, 2013

--- you can reply above this line --- New issue 490: Don't allow fields to be accessed that don't have dependencies https://bitbucket.org/yt_analysis/yt/issue/490/dont-allow-fields-to-be-acce… Matthew Turk: In 3.0, fields that can't be identified are happily requested from the data. This shouldn't happen. 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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from yt.funcs import *
by Nathan Goldbaum Jan. 25, 2013

Jan. 25, 2013

Hi all, I'm doing some work implementing YTEP-6 and have noticed a pattern that happens many times in the code. Specifically, many of the files in the yt source tree import everything in yt.funcs at the top. I can see why this would be helpful when writing routines, but I'd argue that this just makes it harder to understand where things are defined. I've pasted a list of all occurrences in the 2.X branch here: https://gist.github.com/4637442 I'm writing the list to check whether yt.funcs is imported this way for a non-obvious reason. If not, I'll file a bug about this so we can try to come back and make the imports explicit. Cheers, Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum(a)ucolick.org http://www.ucolick.org/~goldbaum

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[yt_analysis/yt] Narrative docs and cookbook recipes for OffAxisProjectionPlot (issue #489)
by Nathan Goldbaum Jan. 25, 2013

Jan. 25, 2013

--- you can reply above this line --- New issue 489: Narrative docs and cookbook recipes for OffAxisProjectionPlot https://bitbucket.org/yt_analysis/yt/issue/489/narrative-docs-and-cookbook-… Nathan Goldbaum: We need to add docs and cookbook recipes for OffAxisProjectionPlot. Care should be taken to point out that only some of the callbacks will work. 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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2.5: Documentation work today
by Matthew Turk Jan. 24, 2013

Jan. 24, 2013

Hi all, Last night over the course of several pull requests, Sam, Nathan and Cameron discussed the current state of documentation and the philosophy of moving forward with docs for 2.5. Today I'm going to spend some time starting around 4PM Eastern working on: * Reading over existing documentation and applying spot fixes * Identifying areas that need substantial improvement and filing bugs * Looking for weak spots in docstrings and either addressing them or filing bugs * Creating a landing page that directs to current, development, and old versions of the docs. I'll be in IRC for this time. If you're interested in taking a look at docs, I'd be happy for the company! -Matt

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2.5 release
by Matthew Turk Jan. 23, 2013

Jan. 23, 2013

Hey all, Here's the open ticket list for 2.5: https://bitbucket.org/yt_analysis/yt/issues?status=new&status=open&mileston… My feeling is that we should close these tickets, and release. If there's anything else, please file a new ticket for 2.5. (Including any documentation.) The big things left: * Answer testing for FLASH * Answer testing for Orion * New kD-tree from Sam * Bootcamp in docs -Matt

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[yt_analysis/yt] pf.field_info[].take_log = False errors (issue #488)
by Michael Kuhlen Jan. 21, 2013

Jan. 21, 2013

--- you can reply above this line --- New issue 488: pf.field_info[].take_log = False errors https://bitbucket.org/yt_analysis/yt/issue/488/pffield_info-take_log-false-… Michael Kuhlen: Setting pf.field_info['Density'].take_log = False immediately after loading the parameter file used to work, but now throws a 'No field named Density' key error. If I first define a sphere or region, then it works. -- 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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