Mailman 3 April 2013 - yt-dev

yt Strategy Meeting Monday the 22nd
by Matthew Turk Sept. 4, 2013

Sept. 4, 2013

Hi all, I'd like to call a brief, approximately one hour, strategy meeting on Monday, April 22nd at 3PM Eastern. This will cover where yt is at, where we can go, and how things are progressing. Some of this will be dedicated to progress updates (from me and others) as well as soliciting feedback on a number of things. Many other projects -- notably Cactus -- do these on a fixed schedule, so based on the success/failure of this one we can consider having them semi-regularly. The agenda I would like to cover will include: * yt 3.0 status, including near/long term plans for development and support for non-grid codes * Rundown of all YTEPs accepted and outstanding * yt's "presence" on the web * 3.0 paper I will also be soliciting feedback in roundtable style on: * How are we doing? * How is the procedure for code contributions working? * How is the yt "infrastructure" meeting people's needs? (Mailing lists, Bitbucket, etc) * Where are energies being spent that could be better spent elsewhere? If you have either agenda items or discussion items, please reply to this email and suggest them. I think having a large presence at this meeting would be very useful, so if you are able to make it, please try to do so. It'll be held as a google hangout, and I'll send details here when it starts up. If there's a pressing need to reschedule, please write in reply to this email. Thanks, and looking forward to seeing you there, Matt

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NumberDensity in clumps and on FLASH data
by Matthew Turk July 10, 2013

July 10, 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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When can we turn off serialization by default?
by Matthew Turk June 18, 2013

June 18, 2013

Hi all, I'd like to turn off serialization by default. This includes: 1) Projections 2) Grid hierarchy 3) Field lists and maybe other things. In general, I think it's a bad idea to just litter directories with new files, and specifically I think it's a bad idea to store 2&3 since they are a huge source of errors for new and existing users. My preference would be to disable all auto-serialization of anything and make that not possible, mandating explicit, manual saves of data instead. However I recognize that is likely unpopular, as even though my simulations have a lot of data on disk, I know that they also take a relatively short time to project. So when can we make it disabled-by-default? 2.6? 3.0? Now? -Matt

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reorganizing YTEPs
by Britton Smith May 17, 2013

May 17, 2013

Hi all, One of the things that came out of the yt strategy meeting last week was a discussion of reorganizing how the YTEPs are listed. Currently, it looks like this: http://ytep.readthedocs.org/en/latest/ There are essentially two problems with this. First, once a YTEP is accepted, it is difficult to tell the status of the actual enhancement that was proposed. Is it being implemented? Is it done? Second, because we are doing revisions in PRs, there is no listing of unaccepted YTEPs. For comparison, here is the enhancement proposal index for python: http://www.python.org/dev/peps/ They have categories for types (standards, information, and process) and status (accepted, rejected, withdrawn, draft, etc.). This may be slightly overkill for us since we are only on YTEP 14 and they have hundreds. I still think some organization would be helpful. I will have a go at that and issue a PR. The question I have for people is with regard to process. In order to have statuses for the unaccepted proposals, they have to exist in some fashion in the main repo. How do we want to do that? Or do we want to do that? One way would be to issue a PR that would include adding it to the index as Draft status and have it be accepted quickly. People can still leave comments on a merged PR and the author can then issue a new one which moves the listing to the accepted status. I'd really like to hear people's thoughts about this. Even if we don't adopt the above strategy, I'd still like to organize the accepted YTEPs as implemented and not implemented so people can get a better idea of where they might get involved. Britton

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Units sprint
by Nathan Goldbaum May 6, 2013

May 6, 2013

Hi all, Casey Stark and I are planning on sprinting on the yt-3.0 units refactor next Thursday and Friday in Berkeley. If anyone is interested in joining (even remotely), let us know so we can keep you in the loop. -Nathan

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[yt_analysis/yt] Hardcoded values are used in several places in the code (issue #557)
by Kacper Kowalik April 30, 2013

April 30, 2013

New issue 557: Hardcoded values are used in several places in the code https://bitbucket.org/yt_analysis/yt/issue/557/hardcoded-values-are-used-in… Kacper Kowalik: Several physical constants are defined across multiple places in the code. As an example: ``` #!bash $ grep '1\.98' -r analysis_modules/halo_finding/halo_objects.py: #Jc = 1.98892e33/pf['mpchcm']*1e5 analysis_modules/halo_profiler/multi_halo_profiler.py: Msun2g = 1.989e33 utilities/units.py: "Msun": (1.98892e33, mass), utilities/tests/test_units.py: msun_cgs = 1.98892e33 utilities/tests/test_units.py: Msun_cgs = 1.98892e33 utilities/physical_constants.py:mass_sun_cgs = 1.98841586e33 # g frontends/nyx/fields.py: return (1/1.989e33) frontends/nyx/data_structures.py: self.units["particle_mass"] = 1.989e33 frontends/flash/fields.py: return 1.0/1.989e33 frontends/art/data_structures.py: cf["Mass"] = aM0 * 1.98892e33 frontends/castro/fields.py: return 1.0 / 1.989e33 frontends/castro/data_structures.py: self.units['particle_mass'] = 1.989e33 ### TODO: Make a global solar mass def frontends/enzo/fields.py: return data.convert("Density")*((data.convert("cm")**3.0)/1.989e33) frontends/ramses/fields.py: return data.convert("Density")*((data.convert("cm")**3.0)/1.989e33) data_objects/universal_fields.py: (3/(4*3.1415926535897931))**(0.5) / 1.989e33 data_objects/derived_quantities.py: spin = J * E / (M*1.989e33*G) ``` Instead constants should be imported from `yt.physical_constants` everywhere for the sake of consistency. Responsible: xarthisius

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[yt_analysis/yt] Volume Rendering in curvilinear coordinates (issue #556)
by Kacper Kowalik April 29, 2013

April 29, 2013

New issue 556: Volume Rendering in curvilinear coordinates https://bitbucket.org/yt_analysis/yt/issue/556/volume-rendering-in-curvilin… Kacper Kowalik: Initial work for supporting curvilinear coordinates has been done in yt-3.0 branch. Currently working single-ray tracer could be extended into full VR support

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"Project Ideas" milestone
by Matthew Turk April 29, 2013

April 29, 2013

Hi all, Inspired by Kacper in IRC, I've added the "Project Ideas" milestone to the issue tracker. I think this is a good place to collect ideas for "bite sized" things that can be done, or things for new contributors, and so on. During the meeting last week we came up with this as a place to lower the barrier to entry for new contributors. So if you have an idea for something that would be good for a new contributor, assign it to the milestone "Project Ideas". I'm also kind of -1 on removing the non-versioned, non-ProjectIdeas milestones that are in there like "GDF Support" and so on. Also, once I get a few more roundtuits, I'm going to be working on making the website be a bit easier to navigate, consolidating some stuff. I recognize that it's gotten out of control with too many places to go, decide on, etc etc. -Matt

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Google Hangout of Particle Deposit Fields
by Christopher Moody April 25, 2013

April 25, 2013

Hi folks, Over at YTEP-0013<https://bitbucket.org/yt_analysis/ytep/pull-request/15/ytep-0013-first-clas…> we've been having vigorous discussion over particle deposition. Concrete suggestions have given way to more freeform brainstorming (something I'm quite guilty of too) and it's too much to synthesize at once. Matt has suggested, and I agree, that we would be better off hashing this out in a google hangout. If you're interested, please respond on the doodle poll for WThF of next week. Ideally, I would like to see at least the people who've reviewed YTEP-0013 to participate; if these times don't work out for y'all, we can move around the times. I'll prepare some use cases and material that we can go over. http://www.doodle.com/nc8p92zy469t63te Many thanks, chris

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2013-04-23 Strategy Meeting Roundup
by Matthew Turk April 23, 2013

April 23, 2013

Hi all, Here're the notes from the meeting: https://docs.google.com/document/d/1qlcJp5tzx3ha-frQvOU2VEyWhGlYnBO9V-Uq_0T… Other people can chime in, but there are action items at the bottom. I think this was extremely useful. We did discuss that we should try to aim for these roughly every three months or so. I would like to suggest we have the next one around the middle of July, maybe the 18th or so, but I'll be in touch closer to the date to set that up. We also discussed that these should be held "on air" which will record them and then upload them to YouTube, since at this one we had at least four more people that *wanted* to attend than *could* attend. Having them on air also means people can watch without being directly on camera. A few big takeaways: the YTEPs are mostly moving forward nicely, and we're looking at ways of fixing up our online presence somewhat that include spreading out into other media and consolidating a few places as well. Any other feedback would be welcomed. -Matt

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