New issue 626: Deprecate neighbour finding methods in halo_objects.HaloList
https://bitbucket.org/yt_analysis/yt/issue/626/deprecate-neighbour-finding-…
Kacper Kowalik:
There are two methods in the basic `HaloList` class: `nearest_neighbors_3D` and `nearest_neighbors_2D` that invoke unknown function `buildKdHyperRectTree`. It looks like they rely on external dependency that's no longer shipped with *yt* or they are rotten code. Could we raise some exception at the beginning of those methods marking them for removal or should they be revived?
Responsible: brittonsmith
New issue 625: Website should have a way to download the install script using curl
https://bitbucket.org/yt_analysis/yt/issue/625/website-should-have-a-way-to…
Nathan Goldbaum:
Since `wget` is not included on OS X, we should either use `curl` instead of `wget` in the 'get yt' section, or suggest an alternate `curl`-based solution if the user doesn't have wget.
Hi all,
I wanted to update everyone on where things stand on my end, now that
I am back online. These are the yt-specific issues I am targeting for
the next few weeks or months:
Short term:
* Reliability and resiliency of yt 3.0. This includes things like
error checking, failure modes, and so on. Currently, there are a
number of ways to simply fail during loading of datasets like RAMSES,
Gadget, etc, and I want to fix that.
* Other showstopping 3.0 stuff (specifically ARTIO stuff and other
Oct/Particle changes)
* Narrative notebooks regarding 3.0 usage
* IO enhancements for patch-based codes
Medium term:
* Substantial effort on unit tests throughout the 3.0 codebase
* SPH smoothing, which includes a) generalizing octrees to enable >2
zones in each direction b) searching for neighbor particles at level >
L and c) generalizing the smoothing functions sufficiently to enable
greater fleixbility for application of kernels and neighbor particle
selection. (n.b., a working preliminary smoothing implementation can
be found in my "smoothing" bookmark, but it has a way to go!)
* Some solicitations of community input, specifically as related to
"code liasons" and addressing issues of branding (i.e., "analysis"
over "viz") and reaching out into specific simulation code communities
(for some of our flagship codes, we're not even mentioned on the code
website!)
* Concluding the BSD relicense
* Diving into the unit handling system from Nathan & Casey
Things I cannot prioritize at the moment, but which I have not forgotten:
* Narrative docs for 3.0 (docstrings will continue to be added)
* Boxlib refactor
* Python 3 support (the only remaining task is to change how our
metaclasses are handled, which I am somewhat reluctant to do; we may
simply want to use a more advanced 2to3-type converted)
* Clump finding in 3.0
* Cactus data
-Matt
Hi all,
I would like to propose that we replace the enzo_tiny_cosmology dataset
that we store for various examples with one that has a few more physics
modules enabled. Hilary Egan has issued PRs to yt and yt-doc for a very
nice set of absorption line fitting tools. The recipe provided works
really well with a small cosmology simulation, but the ones we have up now
are missing some key physics (H/He chemistry and a UV background) that make
the output from the recipe look quite poor.
We have been able to make a very nice looking recipe using the same
enzo_tiny_cosmology parameter file with these additions, which do not add
significantly to the overall size of the dataset. Additionally, none of
the existing recipes that use this data will change. I think there will
also probably be more analysis_modules coming in the future that will
benefit from using a slightly more sophisticated example dataset.
Can we get a +/-1 on replacement?
Britton
Hi,
I'd like to discuss deprecating glob imports in yt-3.0. Initial work has
been done in PR68 [1].
Main rationale is that '*' confuses all python static checkers and
obscures bugs that otherwise would be trivial to find.
I understand that it's onerous and the very reason yt.funcs exists is to
make devs' live more convenient and allow to easily grab everything
that's defined there. However, using said yt.funcs as an example, it's
worth noticing that there are not many modules that grab more than 2-3
methods from it. That allows me to hope that in the end it won't be such
a great PITA...
Cheers,
Kacper
[1] https://bitbucket.org/yt_analysis/yt-3.0/pull-request/68/
New issue 624: PR#54 broke projections in RAMSES in yt-3.0
https://bitbucket.org/yt_analysis/yt/issue/624/pr-54-broke-projections-in-r…
nickolas1:
For revisions post-Octree diet, in projections it appears that alternating rows are shifted in alternating directions, and the shift seems to be equal to the cell size at the smallest refinement level. This is subtle if you have several levels of refinement, but it is obvious once individual cells are resolved in the image.
Attached are two outputs of a low res single-level run using these commands:
pf = load('output_00001/info_00001.txt')
p = ProjectionPlot(pf,2,'Density')
p.save()
using revisions 559bca4 (merging PR#54) and 596e053, a few days prior to that merge. (More recent revisions show the same problem). I've used ProjectionPlot for simplicity, but plotting with a projection using to_frb shows the same thing.
New issue 622: problem with covering_grid for Nyx data sets
https://bitbucket.org/yt_analysis/yt/issue/622/problem-with-covering_grid-f…
Anonymous:
Hi,
this is triggered by a discussion with Nathan. I have troubles with reading in Nyx
data with covering_grid up to a certain level (0 or higher, it doesn't matter). My script is attached (it's actually for the computation of power spectra).
With the current (yesterday's) development version of yt I get the following error:
Searching grids for values 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00
yt : [ERROR ] 2013-08-08 14:39:24,635 Covering problem: 16777216 cells are uncovered
Traceback (most recent call last):
File "/usr/users/wschmid2/scripts/spect_demo.py", line 59, in <module>
velx_hat = na.fft.fftn( cg['xmom']/cg['density'] )/cg['xmom'].size
File "/home/uni05/wschmid2/yt-i686/src/yt-hg/yt/data_objects/data_containers.py", line 332, in __getitem__
self.get_data(key)
File "/home/uni05/wschmid2/yt-i686/src/yt-hg/yt/data_objects/data_containers.py", line 3776, in get_data
raise KeyError(n_bad)
KeyError: 16777216
With an older version of yt (8dce70a9c689 from April), which happened to be installed on one of the machines I am using for data analysis, I don't have this problem (after I made the fix in yt/frontends/nyx/data_structures.py suggested by Nathan) and the script runs through.
The data set loaded by the script isn't too big, so I could share it if you don't have some Nyx data available. Just let me know.
Cheers,
Wolfram
New issue 620: yt 2.5.4 does not install (missing data_objects/tests directory)
https://bitbucket.org/yt_analysis/yt/issue/620/yt-254-does-not-install-miss…
astrofrog:
I tried installing yt 2.5.4 using the tarball from PyPI but I get the following error:
```
Traceback (most recent call last):
File "setup.py", line 280, in <module>
setup_package()
File "setup.py", line 275, in setup_package
'build_src': my_build_src, 'install_data': my_install_data},
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/core.py", line 152, in setup
config = configuration()
File "setup.py", line 231, in configuration
config.add_subpackage('yt', 'yt')
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
caller_level = 2)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
caller_level = caller_level + 1)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "yt/setup.py", line 11, in configuration
config.add_subpackage('data_objects')
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
caller_level = 2)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
caller_level = caller_level + 1)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "yt/data_objects/setup.py", line 12, in configuration
config.add_subpackage("tests")
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
caller_level = 2)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 965, in get_subpackage
caller_level = caller_level+1)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 744, in __init__
raise ValueError("%r is not a directory" % (package_path,))
ValueError: 'yt/data_objects/tests' is not a directory
```