[yt-dev] Fwd: [yt_analysis/yt] Modernized LightCone and LightRay (pull request #214)

[Matthew Turk]

Britton has just submitted a pull request to bring LightCone and
LightRay up to date with the current parallelism strategy.  He asks a
few questions that others on this list may have thoughts on; I will be
leaving mine in a comment on the PR.

Thanks, Britton!


---------- Forwarded message ----------
From: Britton Smith <pullrequests-noreply at bitbucket.org>
Date: Mon, Jul 23, 2012 at 11:01 PM
Subject: [yt_analysis/yt] Modernized LightCone and LightRay (pull request #214)
To: matthewturk at gmail.com


A new pull request has been opened by Britton Smith.

brittonsmith/yt has changes to be pulled into yt_analysis/yt.

https://bitbucket.org/yt_analysis/yt/pull-request/214/modernized-lightcone-and-lightray

Title: Modernized LightCone and LightRay

Major changes to the infrastructure supporting the LightCone and LightRay:
1) The LightCone and LightRay generators have now been switched over
to the new SimulationTimeSeries so that they can now, in principle be
used with other simulation codes.  This will require other frontends
to add code similar to what's
yt/frontends/enzo/simulation_handling.py.
2) Both the LightCone and the LightRay are now parallelized using the
parallel_objects function, so they can be used much more flexibly with
multi-level parallelism.  This also removes the direct mpi4py imports
from LightRay.
3) LightCone and LightRay, along with there supporting superclass
CosmologySplice, have been moved to
yt/analysis_modules/cosmological_observation.

This code has been heavily tested and retains all pre-existing
functionality, plus a few more things that will be mentioned in the
documentation and cookbook recipes that will be updated shortly.

Before accepting this PR:
1. Are people happy with the new location:
yt/analysis_modules/cosmological_observation?  I believe that all of
this code belongs in a subdirectory together but that was the best
name I could come up with.
2. The old EnzoSimulation (yt/analysis_modules/simulation_handling)
class still exists, but it is no longer a dependency for anything, and
is totally replaced with the new EnzoSimulation in yt/frontends/enzo,
which is totally superior.  Can I remove this now or should it be
deprecated and scheduled for removal at a later date?

Changes to be pulled:

cd09f872c174 by Britton Smith: "Merged."
f7bc036677fd by Britton Smith: "Merged."
a303d6f14a33 by Britton Smith: "Changing cosmology subdirectory to
cosmological_observation
and adding imports t…"
b3c9210bf072 by Britton Smith: "Added LightRay to api file."
b764002ef788 by Britton Smith: "Modernized the light ray generator and
moved it to a new home.
The direct mpi4py…"
41f4117f4613 by Britton Smith: "Moving light ray to the cosmology subheading."
9604d5d6187a by Britton Smith: "Adding setup for cosmology module."
6475d956eec7 by Britton Smith: "Removing light cone generator from setup."
304187324667 by Britton Smith: "Removing old light cone generator."
c9a318592c97 by Britton Smith: "Cleaned up unique light cone generator."
29aa8b84169c by Britton Smith: "Adding keyword to halo mask to specify
the virial overdensity
to be used to calc…"
bdf0cc5fa462 by Britton Smith: "Changing some more variable names."
f7b9c8466b13 by Britton Smith: "Parallelized light cone halo mask with
parallel objects and
simplified code cons…"
042624ea193e by Britton Smith: "Continued cleanup of light cone halo
mask and changed light cone
variable to low…"
68472c735864 by Britton Smith: "Fixed some style conventions in light
cone and began
fixing light cone halo mask…"
92a989d572f3 by Britton Smith: "Switched lightcone generator from
being a subclass of TimeSeriesData
to using pa…"
64e5330fd707 by Britton Smith: "Merged."
c7c2fcaa10b1 by Britton Smith: "Changed EnzoSimulation.get_time_series
to allow further selection with find_outp…"
1125ca16272c by Britton Smith: "Adding files for new light cone into
analysis_modules/cosmology.
There is curren…"
5656cf35de29 by Britton Smith: "Removed enzoisms from cosmology splice."
db5ec44e0121 by Britton Smith: "Changed absorption spectrum generator
to increase the wavelength
window until th…"
1baa32f77c80 by Britton Smith: "Fixed bug in voigt profile generator
that was causing damping wings to
only be a…"
be28c6705909 by Britton Smith: "Adding files for CosmologyTimeSeries."
7acc4cace811 by Britton Smith: "Changed EnzoSimulation.get_time_series
to allow further selection with find_outp…"


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