Mailman 3 February 2016 - yt-dev

OpenGL VR
by Matthew Turk March 22, 2016

March 22, 2016

Hi folks, Over the last little while, Kacper, Andrew and I have been picking up on some work started by Chuck Rozhon to implement OpenGL-based volume rendering of AMR data. Kacper recorded a demo about a week ago, although it has improved considerably even since then: https://www.youtube.com/watch?v=yiiBDK1OJDo As of right now, it can do these things: * Load up a "data source" (which can be all_data, but doesn't need to be) * Utilize orthographic and perspective cameras * Maximum intensity projection * Integrated projection * Apply colormaps to these two things, using two-pass rendering * Trackball camera with keyboard shortcuts for moving around the domain * Output camera information that is compatible with the software renderer (i.e., it can be used to get a sequence of camera positions) * Save images out * Preliminary support for color transfer function-based VR. At present this only supports isosurfaces that are manually encoded. It will soon take 1D textures from the CTF object. The system has been designed to be very modular, with extensible keyboard and mouse shortcuts. Kacper has even been able to build a very lightweight Qt-based GUI around it (on BB as xarthisius/reason ) without changing much/any of the internal-to-yt code. Also, it works reasonably well even on fairly old graphics cards for reasonably sized data. (And since it'll accept data objects that are cutouts, this means you could pull a sphere or block out of a gigantic dataset and use that.) Anyway, the reason I'm writing is that I'd like to bring it to people's attention sooner rather than later. It'll need some testing, and we're also working to make it in a readily usable state as well. As of right now, before WIP gets removed from the pull request, we're going to add documentation (with notes that it is likely an unstable API) and hopefully a short screencast. But before then, I would like to invite folks to either review the PR or to test it out. https://bitbucket.org/yt_analysis/yt/pull-requests/1598 Note that this requires cyglfw3, which is accessible via pip. I'm pretty excited about this, and the design we have been aiming for with the way it accepts objects and shaders should enable a lot of cool things to be done -- especially with respect to selecting data, presenting it, etc etc. I'd really like to see this be a part of 3.3. -Matt

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PR Triage Hangout (Wednesday)
by Hilary Egan March 8, 2016

March 8, 2016

Hi all, Here's the link to this week's PR triage hangout, at 12pm EST on Wednesday. https://plus.google.com/u/0/events/cpg5tqck8tuufar5nqe5oo790lg -- Hilary Egan Astrophysical and Planetary Science Department University of Colorado Boulder

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Open Astronomy has been accepted for GSOC 2016
by DVD PS March 3, 2016

March 3, 2016

Hello everyone!!! Great tnews!! and I cannot type for teh excitment I have in me!!! This year open astronomy is being the umbrella for all these projects (and maybe more that want to form part) for the Google Summer of Code. https://summerofcode.withgoogle.com/organizations/?sp-search=open%20astrono… Thanks to all the admins for the different organisations that helped with the proposal, the website, mailing lists and of course, the mentors for providing ideas. Yuuuuuhuuuuuuuuuuuuuuuuuuuuuuu!!!! David

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POLL: A New Default Colormap
by Matthew Turk March 1, 2016

March 1, 2016

Hi folks, The current default colormap that yt uses is called "Algae," and it's been with us for a while. Recently some of us on the yt-dev mailing list (which is open to join!) have begun to look at alternate colormaps that have better characteristics, particularly from an accessibility perspective. If you have the time, it would be really, *really* helpful if you could take this anonymous, two question (only one of which is mandatory!) poll about which of the four candidates we've come up with you like the best. http://goo.gl/forms/D4qQqkPIMq Thanks very much! The poll will be open at least a week, and I'll report back the results here sometime after that. -Matt

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The future of yt
by Matthew Turk Feb. 28, 2016

Feb. 28, 2016

Hi everyone, The last couple weeks I’ve been thinking a lot about the future of yt. What I’d like to propose is that we shift investment in yt as a single, monolithic codebase into yt as a project, or an ecosystem of projects. This came out of the discussion of the extension/affiliated packages, analysis modules, and so on. Britton has for a while been pitching the idea [which I will poorly paraphrase here] that yt can be the framework on top of which killer apps can be built. I think this is great. What’s holding us back in some ways from this is that yt is currently structured as a monolithic code base, with little to no discovery of other packages and apps and whatnot. We tried for a while to change this with The Barn, but it ended up not quite taking off. I think the time is right to try to change the way we think about yt to be more about yt the Project, rather than yt the Codebase; the core codebase is an important component of this, but not the whole of it. Encouraging an ecosystem of packages can have a few very important benefits: * External packages will confer greater individual credit to the folks who develop them. * External packages can be versioned and developed independently; the review process can be different. * yt’s core can be emphasized as a generic package, on top of which astronomy analysis can be built. * Packages can be maintained wherever, including alternate locations such as github. On the other hand, having packages inside the main distribution makes discoverability much, much easier. It also enables everything to be In The Box. And, the continuous integration and testing system is already set up for yt. But, these are all possible to overcome -- we can devise a strategy for adding packages to the CI system (and if they are externally managed, they can also rely on yt as a dependency and use whatever CI system they like!) and we can improve discoverability by refocusing the website to enable this. I've asked Kacper about adding new packages, and it's not as easy as it might seem, so we may need to be careful about how that process occurs; one possibility would be to provide servers and ready-made setups, but have individuals do the heavy lifting. We could even have something in the codebase that describes some packages that are available. External packages could have much looser dependency rules, which means they can be free to take advantage of things like OpenCL, numba, etc, without having to add them to the primary codebase. Synchronizing APIs and versions across extension packages may be difficult in some particular cases, but I suspect in practice will not be an issue, as long as we continue to have a reasonably stable *public* API, and graduate a few things (such as .blocks) into a public API from semi-private. To this end, of really encouraging an ecosystem of packages, I’d like to propose two things, in increasing order of disruptiveness. First: Encourage extension packages. This would mean: * Reorganize website to allow for extension packages to be displayed prominently * Add support for name-space packages in yt * (possible) split out some packages from analysis_modules, including halo finding * Codify process of extension package creation, including how to have CI set up for them and build system. The second, more disruptive proposal: * Split yt into subprojects. This would include spinning out the volume rendering and some or all of the frontends, and probably the testing infrastructure as well. * Split further astro-specific routines into an astro extension, and begin the process of doing this with other domains as well. (As in the long-simmering domain context YTEP.) I’ll invite comments from everyone, but particularly from folks who have either not contributed to an analysis module or extension package because of concerns that would be addressed by this, as well as from core developers this would impact. If the thread gets too unweildy we may also want to table this for the next yt team meeting. Thanks, Matt _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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"Putting the user back into software sustainability"
by Matthew Turk Feb. 25, 2016

Feb. 25, 2016

An interesting talk which might be of interest to folks here by Neil Chue Hong of the UK's Software Sustainability Institute: https://figshare.com/articles/Putting_the_user_back_into_software_sustainab… There are some lessons here we could learn.

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setup.py and cython
by Nathan Goldbaum Feb. 25, 2016

Feb. 25, 2016

Hi all, Recently we refactored our setup.py file to no longer use numpy.distutils. One of the major benefits of this change is that we can now use the `setup_requires` and `install_requires` argument of `setup` to automatically install yt's dependencies when someone does "pip install yt" or "python setup.py develop" in the yt repo. Unfortunately, that doesn't quite work right now. In particular, if cython isn't in install_requires, the installation will fail with a somewhat confusing error (http://paste.yt-project.org/show/6266/). I can fix this error (but unfortunately only for "pip install -e . /path/to/yt-repository", not for "python setup.py develop") by including cython in our install_requires, as in my open pull request: https://bitbucket.org/yt_analysis/yt/pull-requests/2003/add-minimum-setupto… On slack, Kacper objected to this approach, since we should only need cython to generate the C source for our extensions for development, not unconditionally. I see where he is coming from, but think that making it so "pip install yt" installs cython isn't so bad, especially given that up until recently our "setup.py" unconditionally imported cython and would simply bail if it wasn't installed. I see a few paths forward here: 1. Accept pull request 2003 and be ok with "pip install yt" installing cython and "python setup.py develop" failing when cython isn't installed or figure out how to fix that. 2. Stop using setuptools' support for building cython extensions and instead rely on cython to do that. This means going back to unconditionally depending on cython in our setup.py. This will also mean we are no longer depending on setuptools>=18.0, which was releaed on June 2015, and many users do not have installed in their python installations. I'd love to hear about alternate approaches, if people have strong opinions either way, of if my understanding of the situation is incorrect. We should come to a consensus about this before releasing yt 3.3. Thanks for your time, Nathan

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Issue #1175: fcoords and tcoords not the same shape for rays from particle datasets (yt_analysis/yt)
by Britton Smith Feb. 25, 2016

Feb. 25, 2016

New issue 1175: fcoords and tcoords not the same shape for rays from particle datasets https://bitbucket.org/yt_analysis/yt/issues/1175/fcoords-and-tcoords-not-th… Britton Smith: This script: http://paste.yt-project.org/show/6268/ gives the following error: ``` #!python File "test2.py", line 12, in <module> print ray["x"] File "/Users/britton/Documents/work/yt/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__ self.get_data(f) File "/Users/britton/Documents/work/yt/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data self._generate_fields(fields_to_generate) File "/Users/britton/Documents/work/yt/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields fd = self._generate_field(field) File "/Users/britton/Documents/work/yt/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field tr = self._generate_fluid_field(field) File "/Users/britton/Documents/work/yt/yt-hg/yt/data_objects/data_containers.py", line 325, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/britton/Documents/work/yt/yt-hg/yt/fields/derived_field.py", line 184, in __call__ dd = self._function(self, data) File "/Users/britton/Documents/work/yt/yt-hg/yt/geometry/coordinates/coordinate_handler.py", line 40, in _coords rv = data.ds.arr(data.fcoords[...,axi].copy(), units) File "/Users/britton/Documents/work/yt/yt-hg/yt/data_objects/data_containers.py", line 1282, in fcoords return self._current_chunk.fcoords File "/Users/britton/Documents/work/yt/yt-hg/yt/geometry/geometry_handler.py", line 271, in cached_func tr = func(self) File "/Users/britton/Documents/work/yt/yt-hg/yt/geometry/geometry_handler.py", line 322, in fcoords ci[ind:ind+c.shape[0], :] = c ValueError: could not broadcast input array from shape (81,3) into shape (40,3) ``` This seems to be because the fcoords and tcoords for the ray are coming back with different shapes.

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Issue #1174: yt install script Centos 6.6 (yt_analysis/yt)
by Gareth Murphy Feb. 24, 2016

Feb. 24, 2016

New issue 1174: yt install script Centos 6.6 https://bitbucket.org/yt_analysis/yt/issues/1174/yt-install-script-centos-66 Gareth Murphy: On Centos 6.6, the yt stable install_script fails with the following error gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN intel64 -c -o adler32.o adler32.c gcc: intel64: No such file or directory Error 1 Adding an unset TARGET_ARCH just before the ZLIB make install makes it go away. Adding this in case anyone has the same problem.

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Issue #1173: Error when using set_unit for 'particle_mass' on filtered particle data (yt_analysis/yt)
by Anonymous Feb. 23, 2016

Feb. 23, 2016

New issue 1173: Error when using set_unit for 'particle_mass' on filtered particle data https://bitbucket.org/yt_analysis/yt/issues/1173/error-when-using-set_unit-… Anonymous:

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