Mailman 3 September 2013 - yt-dev

Current status of Conda?
by Matthew Turk 27 Sep '13

27 Sep '13

Hi all, The get_yt.sh script is now in the repository. If a few people could test it, that would be super helpful. But I think Kacper has also been doing some really cool work on getting buildbots set up for binary builds. Kacper, is there a way to test that out? Or is it premature? Thanks all, Matt

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Issue #669: Creating a custom made total potential field from Enzo datasets (yt_analysis/yt)
by Anonymous 27 Sep '13

27 Sep '13

New issue 669: Creating a custom made total potential field from Enzo datasets https://bitbucket.org/yt_analysis/yt/issue/669/creating-a-custom-made-total… Anonymous: When creating a custom made field for the total potential (the potential of gas and particles) a basic field creation gave some issues while trying to plot the equipotential line through the SlicePlot contour option. The details of the issues are in the post: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-September/… The problem has been solved but the reasons why it showed up are still not clear. The script used to generate the plot has been attached. The sample Enzo datasets given in the website did not have the gravitational potential as output, so here is the download link for one of my outputs: https://www.dropbox.com/sh/zc5bm6dif33uqyh/VeZ4F4ha5O Was big file so I had to split it into three, to reassemble them: cat myfiles_split.tgz_* | tar xz Thanks for the help, Roberto Responsible: MatthewTurk

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Website redesign feedback
by Matthew Turk 27 Sep '13

27 Sep '13

Hi all, The last week or so, I've been working on a redesign of the website. I've gotten some really good feedback from Nathan, Britton and a few others, and I think it's ready to be opened up for more general comments. The redesign pull request is here: https://bitbucket.org/yt_analysis/website/pull-request/11/draft-redesign-us… and the redesign itself can be viewed here: http://yt-project.org/index2.html There were a couple goals here: * Make information much easier to get at * Reduce the text and increase the size of the text on the front page * Make the website *way* easier for people to edit * Make the website *way* less javascript heavy * Indicate much more strongly that we're part of the scientific Python ecosystem * Emphasize that yt is analysis-focused with visualization built on that, rather than the other way around There are a few visual glitches still (the headings underline when you mouse over them, and I'm trying to make the text lighter) but I think it's ready for feedback. I'd appreciate any comments, either here or on the pull request. And, if we decide this is *not* the direction to go, that's fine too! Britton and I have gone back and forth on how to fix up the gallery and integrate the hub and the blog more deeply. That's a much longer project, but we see the three all coming together nicely in the future. As it stands, the Gallery will likely include a few images linked to scientific papers, link to a few things on the hub (notebooks, projects, etc), and is currently handled via version control. Britton's working on expanding it, but if you can read this, you should also add some stuff to it! Ultimately what I think would work best would be to solicit contributions directly, solicit contributions to the hub, and then flag some things for display in the gallery. It would be nice to include basically all types of contributions here -- notebooks, scripts, figures, papers -- and I'm coming to really think the gallery is essential. Incidentally, this week as Anthony and I have been working on getting support for PyNE interoperability with yt, I've had occasion to view their docs and found them to be really nice. The gallery system they have is quite nice and very similar to where we're going with the yt docs and the cookbook, but just a *little* bit further than we've gone: http://pynesim.org/ http://pynesim.org/gallery/index.html If we decide this website is the way to go, I'll spend some time trying to make our docs play look a bit nicer with it, although likely not with black background. Thanks for any feedback, Matt

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Issue #668: Explain how to set custom tick marks for PlotWindow plots. (yt_analysis/yt)
by Nathan Goldbaum 26 Sep '13

26 Sep '13

New issue 668: Explain how to set custom tick marks for PlotWindow plots. https://bitbucket.org/yt_analysis/yt/issue/668/explain-how-to-set-custom-ti… Nathan Goldbaum: See e.g. http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-September/…

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Issue #667: Object deprecation (yt_analysis/yt)
by Matthew Turk 25 Sep '13

25 Sep '13

New issue 667: Object deprecation https://bitbucket.org/yt_analysis/yt/issue/667/object-deprecation Matthew Turk: The following objects have been deprecated and removed in yt 3.0: * InclinedBox * FixedResCuttingPlane Responsible: MatthewTurk

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Issue #666: Grids callback is broken in 3.0 (yt_analysis/yt)
by Nathan Goldbaum 25 Sep '13

25 Sep '13

New issue 666: Grids callback is broken in 3.0 https://bitbucket.org/yt_analysis/yt/issue/666/grids-callback-is-broken-in-… Nathan Goldbaum: ``` #!python File "/usr/local/bin/yt", line 9, in <module> load_entry_point('yt==3.0dev', 'console_scripts', 'yt')() File "/Users/goldbaum/Documents/yt-3.0/yt/utilities/command_line.py", line 1701, in run_main args.func(args) File "/Users/goldbaum/Documents/yt-3.0/yt/utilities/command_line.py", line 87, in run self(args) File "/Users/goldbaum/Documents/yt-3.0/yt/utilities/command_line.py", line 1317, in __call__ plt.annotate_grids() File "/Users/goldbaum/Documents/yt-3.0/yt/visualization/plot_window.py", line 98, in newfunc args[0]._setup_plots() File "/Users/goldbaum/Documents/yt-3.0/yt/visualization/plot_window.py", line 963, in _setup_plots self.run_callbacks(f) File "/Users/goldbaum/Documents/yt-3.0/yt/visualization/plot_window.py", line 983, in run_callbacks callback(cbw) File "/Users/goldbaum/Documents/yt-3.0/yt/visualization/plot_modifications.py", line 365, in __call__ GLE = plot.data.grid_left_edge AttributeError: 'YTSlice' object has no attribute 'grid_left_edge' ``` The solution is to grab the grid left edges from the geometry handler.

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Issue #665: The "all" particle type duplicates memory (yt_analysis/yt)
by Matthew Turk 25 Sep '13

25 Sep '13

New issue 665: The "all" particle type duplicates memory https://bitbucket.org/yt_analysis/yt/issue/665/the-all-particle-type-duplic… Matthew Turk: Currently, the "all" particle type duplicates a large amount of memory. We should push this into the IO layer as a conceptual field, and avoid any usages of the `_field_concat` that we can avoid. Responsible: MatthewTurk

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Issue #664: 2D simulation failing in 3.0 (yt_analysis/yt)
by Sam Skillman 23 Sep '13

23 Sep '13

New issue 664: 2D simulation failing in 3.0 https://bitbucket.org/yt_analysis/yt/issue/664/2d-simulation-failing-in-30 Sam Skillman: A simple sliceplot of a 2D enzo simulation fails with mismatched array sizes. ``` #!python ----> 1 sl = SlicePlot(pf, 2, 'Density') /home/skillman/local/src/yt-3.0/yt/visualization/plot_window.pyc in __init__(self, pf, axis, fields, center, width, axes_unit, origin, fontsize, field_parameters) 1287 slc = pf.h.slice(axis, center[axis], 1288 field_parameters = field_parameters, center=center) -> 1289 slc.get_data(fields) 1290 PWViewerMPL.__init__(self, slc, bounds, fields=fields, origin=origin, 1291 fontsize=fontsize) /home/skillman/local/src/yt-3.0/yt/data_objects/data_containers.pyc in get_data(self, fields) 527 # need to be generated. 528 read_fluids, gen_fluids = self.hierarchy._read_fluid_fields( --> 529 fluids, self, self._current_chunk) 530 self.field_data.update(read_fluids) 531 /home/skillman/local/src/yt-3.0/yt/geometry/geometry_handler.pyc in _read_fluid_fields(self, fields, dobj, chunk) 480 selector, 481 fields_to_read, --> 482 chunk_size) 483 for field in fields_to_read: 484 ftype, fname = field /home/skillman/local/src/yt-3.0/yt/frontends/enzo/io.pyc in _read_fluid_selection(self, chunks, selector, fields, size) 294 ftype, fname = field 295 ds = np.atleast_3d(data[g.id].pop(fname)) --> 296 nd = g.select(selector, ds, rv[field], ind) # caches 297 ind += nd 298 data.pop(g.id) /home/skillman/local/src/yt-3.0/yt/data_objects/grid_patch.pyc in select(self, selector, source, dest, offset) 503 count = self.count(selector) 504 if count == 0: return 0 --> 505 dest[offset:offset+count] = source[mask] 506 return count 507 ValueError: operands could not be broadcast together with shapes (36,20,1) (20,36,1) ```

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Issue #663: Notebook uploads no longer have descriptions (yt_analysis/yt)
by Matthew Turk 23 Sep '13

23 Sep '13

New issue 663: Notebook uploads no longer have descriptions https://bitbucket.org/yt_analysis/yt/issue/663/notebook-uploads-no-longer-h… Matthew Turk: It looks like with the most recent notebook format, our method for grabbing the descriptions and/or titles of notebooks for the hub has broken. What used to be in the JSON `metadata` object with the key `name` no longer is.

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Towards a 3.0 release
by Anthony Scopatz 23 Sep '13

23 Sep '13

Hey yt, I realize I am being fairly selfish here, but I think that it would be great if there was a stable yt-3.0 that was *the* yt. My personal opinion is that it is stable enough. I don't expect this to happen tomorrow. But I don't think that the end of the year would be an unreasonable target. Matt seemed amicable to the idea when we talked about it yesterday. Still, I thought I would throw this out there for folks to give feedback on. Be Well Anthony

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yt-dev September 2013