Mailman 3 March 2016 - yt-dev

Issue #1197: YTPositionArray doesn't work (yt_analysis/yt)
by Matthew Turk 25 Mar '16

25 Mar '16

New issue 1197: YTPositionArray doesn't work https://bitbucket.org/yt_analysis/yt/issues/1197/ytpositionarray-doesnt-work Matthew Turk: I don't think this is explicitly the fault of `YTArray`, but I don't know how to get around it. Right now, creating a `yt.data_objects.octree_subset.YTPositionArray` just returns `YTArray`. I'm not sure how to make sure that it returns the right class, but I suspect something in the `YTArray` code doesn't pass down subclasses. (It used to, I promise!) Here's example code: ``` import yt from yt.data_objects.octree_subset import YTPositionArray ds = yt.load("enzo_tiny_cosmology/DD0043/DD0043") pos = ds.r["particle_position"] ppos = YTPositionArray(pos) ``` At this point, `ppos` should have `to_octree` as a method, but it doesn't. Not sure how to fix this -- @ngoldbaum do you know how I could make sure that the subclass is correctly handled? Responsible: MatthewTurk

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Issue #1196: Update pip and source installation instructions (yt_analysis/yt)
by Nathan Goldbaum 25 Mar '16

25 Mar '16

New issue 1196: Update pip and source installation instructions https://bitbucket.org/yt_analysis/yt/issues/1196/update-pip-and-source-inst… Nathan Goldbaum: Now that we can "pip install yt" and pick up yt's dependencies, we should update the installation instructions to reflect this.

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Progress toward 3.3 release: blocking issues
by Nathan Goldbaum 25 Mar '16

25 Mar '16

Hi all, As many of you may have noticed, Cameron and I followed through on our plan to triage the issue tracker and identify issues that should block the 3.3 release. Apologies for the inbox damage this may have caused today. This was a qualitative process based on our judgement calls, so if you feel we made any mistakes on issues that you get notifications for, please feel free to re-open or edit issues you have opinions about. In the end, there are now 63 issues marked with a version of 3.3. Provisionally, these are the blockers for the 3.3 release. You can see the issues for yourself in this bitbucket search: https://bitbucket.org/yt_analysis/yt/issues?status=open&status=new&version=… They vary in difficulty and we will probably end up deciding to punt on a number of them, but as a rule of thumb, these issues are generally: * bugs * regressions * not new features or feature requests * documentation improvements and * probably solvable in a maximum of a few hours Hopefully now that there are a finite number of things to do before 3.3, rather than an undefined number of things to do, this will help us in identifying things to work on, and aid in making progress on the release. I'd like to request from the community that you take on these issues and try to fix as many of them as we can before 3.3 goes out. I expect that we will likely have another sprint on our slack channel within the next month or so to try to get the bulk of them done, but please feel free to take any of them on and issue a pull request at any time. To ease managing closing the issues, include the phrase "Closes #XXXX" in your pull request title (where XXXX is the issue number), so that when the pull request is merged, the issue will also be closed. Please reply to this thread if you have concerns about the general strategy I've outlined here for releasing 3.3, or anything else related to the issues or the 3.3 release itself. Best, Nathan Goldbaum

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[GSOC students] < 24 hours for submission of projects
by DVD PS 24 Mar '16

24 Mar '16

Hello!! Note that the deadline is in less than 22 hours! You have to submit the application (in pdf format) to the Google summer of code website before March 25th at 19'00 UTC [1]. Google docs or applications on the wiki are not the official submission though required by some of the sub-organisations. I've read in other mailing lists that you can upload the PDF and replace it if needed up until the deadline. Besides having a very good project plan and desciption I would encourage you to pay attention to the presentation too. With that I don't mean only how the text is formatted in the pdf submitted but also the orthography and grammar of the text written, including punctuation, spaces and proper capitalisation of the words. Check that the pdf you upload looks perfect - that will be what we will use to evaluate your application!! I also encourage students to write a first blog post about their experience so far, no need to do that before the deadline, but it will be nice for us to read your experiences so far while checking that the link to your blog works. Good luck to everyone!! David [1] http://www.timeanddate.com/worldclock/fixedtime.html?msg=GSoC+2016+proposal…

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Issue #1195: Add matplotlib to install_requires (yt_analysis/yt)
by Nathan Goldbaum 24 Mar '16

24 Mar '16

New issue 1195: Add matplotlib to install_requires https://bitbucket.org/yt_analysis/yt/issues/1195/add-matplotlib-to-install_… Nathan Goldbaum: Currently we can't include matplotlib in the install_requires in our setup.py due to issues on the testing box. This needs to be fixed before 3.3 is released. Responsible: xarthisius

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Issue #1194: Update docs to show how to specify units on VR `PointSource` and `LineSource` coords (yt_analysis/yt)
by Cameron Hummels 24 Mar '16

24 Mar '16

New issue 1194: Update docs to show how to specify units on VR `PointSource` and `LineSource` coords https://bitbucket.org/yt_analysis/yt/issues/1194/update-docs-to-show-how-to… Cameron Hummels: Code got updated for this, but not docs. Related to Issue #1123.

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Issue #1193: Add a default particle filter for Enzo (yt_analysis/yt)
by Matthew Turk 24 Mar '16

24 Mar '16

New issue 1193: Add a default particle filter for Enzo https://bitbucket.org/yt_analysis/yt/issues/1193/add-a-default-particle-fil… Matthew Turk: Right now (as pointed out by @rthompson ) particle filters for Star particles from "old" Enzo aren't set up. We may want to do this, so that they show up in particle types. For reference: ```#define PARTICLE_TYPE_GAS 0 #define PARTICLE_TYPE_DARK_MATTER 1 #define PARTICLE_TYPE_STAR 2 #define PARTICLE_TYPE_TRACER 3 #define PARTICLE_TYPE_MUST_REFINE 4 #define PARTICLE_TYPE_SINGLE_STAR 5 #define PARTICLE_TYPE_BLACK_HOLE 6 #define PARTICLE_TYPE_CLUSTER 7 #define PARTICLE_TYPE_MBH 8 #define PARTICLE_TYPE_COLOR_STAR 9 #define PARTICLE_TYPE_SIMPLE_SOURCE 10 ``` This would likely come in around the time that default particle unions are set up.

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Issue #1192: Rotating function for datasets (yt_analysis/yt)
by Anonymous 23 Mar '16

23 Mar '16

New issue 1192: Rotating function for datasets http://link.bitbucket.org/wf/click?upn=8USRlNyft-2BCzk2l4Ywl6gDx2lD2xxoS9E7… Anonymous: I would like to request a feature that allows for an arbitrary rotation in 3D around a chosen origin, for all particles in a loaded HDF5 dataset: e.g. ds_rotated = yt.rotate(ds,[x_angle,y_angle,z_angle],origin) (The example above should change the positions and velocities of particles in 'ds' and save in a new dataset called ds_rotated) Thanks, Karen

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PR triage
by Kacper Kowalik 23 Mar '16

23 Mar '16

Hi! Pull requests are piling up. Right now we have 42 waiting for the review (in reality much less, cause there many WIPs, but I wanted to sound more dramatic). Even though we didn't have official PR triage today I'd encourage you to look at them if have a spare time today. Thanks! Kacper

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Issue #1191: covering_grid with RAMSES dataset (yt_analysis/yt)
by Enrico Garaldi 23 Mar '16

23 Mar '16

New issue 1191: covering_grid with RAMSES dataset http://link.bitbucket.org/wf/click?upn=8USRlNyft-2BCzk2l4Ywl6gDx2lD2xxoS9E7… Enrico Garaldi: When using covering_grid with RAMSES datasets the cells refined beyond the level of the grid are left unfilled. This is not the case with e.g. ENZO datasets. You can verify this using: ``` #!python import yt import matplotlib.pyplot as plt ds = yt.load('output_00080/info_00080.txt') cgrid = ds.covering_grid(0, left_edge=ds.domain_left_edge, dims=ds.domain_dimensions) density_field = cgrid["density"] print (density_field == 0.0).any() #should be False but it is True plt.imshow(numpy.log10(density_field[:,:,48].v), interpolation='none') #log10 to highlight the zeros in density_field plt.show() #holes with zero-density corresponding to refined regions ``` resulting in the following: ![cgrid.png](http://link.bitbucket.org/wf/click?upn=8USRlNyft-2BCzk2l4Ywl6gJkmhpCq670QTqJWWjYIuPnNm0cUwoi12sahp1TzmuVyf0s8fYzjWpRcEWx8ACFP4kqIeLBwXTiSEFf-2F1wW53Lc-3D_JlBWjyZTyKwhM1rBKe-2BcAdFPwdECN4PBooLGVSVl7EKJU04db3QpHMYWBfyuXRxv-2F-2FCx4YQVNGRVJg0iEHZIOsXvA6bEH21d1vKb9NSYiUKhfTJROyFt6z1yMXlAfJUBLNLYADd-2BUjCz-2BrsQh3OyJC0VbZGX2nOU5ZzanxK68VOXtalB0FbTa5EUpaB5sTUuZ-2F0qvxCMFieWJ9lmDlauY1WMjiuTE9MpJF5C4Zsbdms-3D Another (related?) issue is that smoothed_covering_grids fails with RAMSES datasets (raising a RuntimeError because tot != 0, line 880 of construction_data_containers.pyc)

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