the future of analysis_modules
by Britton Smith
Greetings,
I would like to open a discussion on the idea of moving most of yt’s
analysis modules into an external yt extensions package. For ease of
reading, I will separate this email into what this would mean for the code,
what I see are the pros, cons, logistics, and open questions. I would very
much appreciate comment on this.
What this means
If we did this, most of the contents of yt/analysis_modules would be moved
into a repository named something like yt_astro_analysis. Installing this
would be an option in the install script and would likely also be pip
installable. Imports would change from
from yt.analysis_modules.halo_analysis.api import HaloCatalog
to
from yt.extensions.astro_analysis.halo_analysis.api import HaloCatalog
After creating yt_astro_analysis, there would be a period where the old
analysis_modules would still exist but be deprecated before being removed
at some point down the road.
Pros
-
Almost all of the current analysis modules are specific to
astrophysics. As we continue to make the core functionality of yt less
astro specific, it’s not clear how to make room for non-astro analysis
modules. Putting everything together under analysis_modules will make
navigation and documentation messy and confusing. This would also
significantly slim down the yt codebase.
-
Many of the tools in analysis_modules are very old and are in need of
API-breaking refactor. Some of these, like two_point_functions, did not
make the jump from yt-2 to yt-3 and are no longer usable. Many tools no
longer have a champion, someone interested in using, maintaining, and
updating them as yt’s core functionality develops and changes. Moving
analysis_modules from yt decouples them from yt’s release cycle, allowing
interested parties to make updates and releases on a separate, likely
shorter timescale. Some analysis_modules may even be better suited to be
moved into other extensions that are actively developed, such as the case
of the AbsorptionSpectrum with the Trident project.
-
Similar to the point above, yt releases would not be slowed by the need
to update all of the championless modules. Individual analysis modules can
be tied to specific stable releases of yt and so assured to work there.
Cons
-
This will take a non-zero amount of work. See below for a summary of
the primary tasks.
-
There are some outstanding logistical questions. See below.
-
Not having yt and analysis modules explicitly tied to the same
codebase/releases could result in analysis tools falling behind and out of
date.
-
The disruption and need to alter scripts could irritate and alienate
users.
Proposed progression
This is roughly how this would happen. Here is a table with all existing
analysis modules, their status, and potential future: https://goo.gl/HZykQA
1.
Create yt_astro_analysis repo with all analysis modules that are to be
moved. Add an entry to the extensions page on yt-project.org. Make it
installed by default in the install script, at least at first.
2.
Deprecate all moved modules in yt.
3.
After some time, remove deprecated modules from yt.
Open issues
Here are some logistics and questions that still need to be worked out.
-
Can we set up separate testing for yt_astro_analysis? Would maintaining
this be a pain?
-
How/where would the documentation be hosted?
-
How would we move the analysis modules source code and maintain its
revision history?
Questions to yt-dev
-
Are you +/-1 on this? Any other comments?
-
Changes to the analysis_modules spreadsheet (https://goo.gl/HZykQA)?
-
Interested in helping out with this? If this happens, I propose anyone
interested meets for a hangout to discuss how to proceed.
Thanks for reading!
Britton
2 years, 3 months
Issue #1300: yt.create_profile fails to find the innermost cells (yt_analysis/yt)
by Hsi-Yu Schive
New issue 1300: yt.create_profile fails to find the innermost cells
https://bitbucket.org/yt_analysis/yt/issues/1300/ytcreate_profile-fails-t...
Hsi-Yu Schive:
The following script and dataset fail to find the innermost cells and return zeros in all profile bins. Data are spherical symmetric with a center at (7.13 Mpc, 7.13 Mpc, 7.13 Mpc). The innermost 8 cells have the same peak density about 1.23651e-25 g/cm^3.
[Dataset URL](http://use.yt/upload/ca211222)
Script:
```
#!python
ds = yt.load('./Data_000000')
sp = ds.sphere( 'c', (15, "kpc") )
print 'peak density = ', sp['density'].max()
profile = yt.create_profile( sp, 'radius', 'density', n_bins=5 )
print 'radial bins = ', profile.x.value
print 'density profile = ', profile['density'].value
```
2 years, 3 months
Issue #1299: order of parameters set in VR matters (yt_analysis/yt)
by Michael Zingale
New issue 1299: order of parameters set in VR matters
https://bitbucket.org/yt_analysis/yt/issues/1299/order-of-parameters-set-...
Michael Zingale:
consider the following script:
```
import yt
import numpy as np
from yt.visualization.volume_rendering.api import \
Scene, \
VolumeSource
# fake test dataset
ds = yt.testing.fake_vr_orientation_test_ds(128)
# no log please
ds._get_field_info("density").take_log = False
sc = Scene()
vol = VolumeSource(ds, field=('gas', 'density'))
sc.add_source(vol)
cam = sc.add_camera(ds, lens_type="perspective")
cam.resolution = (1280, 720)
cam.north_vector = np.array([0., 0., 1.])
cam.focus = ds.arr(np.array([1., 0., 0.]), 'code_length')
cam.position = ds.arr(np.array([0., 0., 0.]), 'code_length')
#sc.annotate_domain(ds)
sc.render()
sc.save("test_{:03}.png".format(0), sigma_clip=6.0)
```
this runs as-is.
If you change the order of the properties to:
```
cam.north_vector = np.array([0., 0., 1.])
cam.position = ds.arr(np.array([0., 0., 0.]), 'code_length')
cam.focus = ds.arr(np.array([1., 0., 0.]), 'code_length')
```
it aborts with
```
RuntimeError: Cannot set the camera focus and position to the same value
```
it you change them to
```
cam.focus = ds.arr(np.array([1., 0., 0.]), 'code_length')
cam.position = ds.arr(np.array([0., 0., 0.]), 'code_length')
cam.north_vector = np.array([0., 0., 1.])
```
it aborts with:
```
yt.utilities.exceptions.YTException: normal_vector and north_vector cannot be aligned.
```
these checks should wait until the user is done setting all the properties and the order of setting them should not matter.
2 years, 3 months
Issue #1297: ds.print_stats() fails (yt_analysis/yt)
by yurivict
New issue 1297: ds.print_stats() fails
https://bitbucket.org/yt_analysis/yt/issues/1297/dsprint_stats-fails
yurivict:
The example from http://yt-project.org/doc/quickstart/data_inspection.html fails:
```
import yt
ds = yt.load("IsolatedGalaxy/galaxy0030/galaxy0030")
ds.print_stats()
```
```
$ python2 chapter-inspect.py
yt : [INFO ] 2016-11-17 00:12:48,682 Parameters: current_time = 0.00600002000283
yt : [INFO ] 2016-11-17 00:12:48,682 Parameters: domain_dimensions = [32 32 32]
yt : [INFO ] 2016-11-17 00:12:48,683 Parameters: domain_left_edge = [ 0. 0. 0.]
yt : [INFO ] 2016-11-17 00:12:48,683 Parameters: domain_right_edge = [ 1. 1. 1.]
yt : [INFO ] 2016-11-17 00:12:48,683 Parameters: cosmological_simulation = 0.0
Traceback (most recent call last):
File "chapter-inspect.py", line 6, in <module>
ds.print_stats()
File "/usr/local/lib/python2.7/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 320, in root_only
return func(*args, **kwargs)
File "/usr/local/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 457, in print_stats
self.index.print_stats()
File "/usr/local/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 419, in index
self, dataset_type=self.dataset_type)
File "/usr/local/lib/python2.7/site-packages/yt/frontends/enzo/data_structures.py", line 212, in __init__
GridIndex.__init__(self, ds, dataset_type)
File "/usr/local/lib/python2.7/site-packages/yt/geometry/geometry_handler.py", line 50, in __init__
self._setup_geometry()
File "/usr/local/lib/python2.7/site-packages/yt/geometry/grid_geometry_handler.py", line 51, in _setup_geometry
self._parse_index()
File "/usr/local/lib/python2.7/site-packages/yt/frontends/enzo/data_structures.py", line 272, in _parse_index
pbar = get_pbar("Parsing Hierarchy ", self.num_grids)
File "/usr/local/lib/python2.7/site-packages/yt/funcs.py", line 414, in get_pbar
pbar = TqdmProgressBar(title,maxval)
File "/usr/local/lib/python2.7/site-packages/yt/funcs.py", line 346, in __init__
self._pbar = tqdm(leave=True, total=maxval, desc=title)
File "/usr/local/lib/python2.7/site-packages/yt/extern/tqdm/_tqdm.py", line 297, in __init__
ncols = _environ_cols_wrapper()(file)
TypeError: 'NoneType' object is not callable
```
2 years, 4 months
to the community
by Britton Smith
Hi everyone,
In light of the recent election and some of the negative events that have
happened, we want to reassure you, and at the same time make it clear to
all, that we expect the yt community to continue to be a place of
tolerance, kindness, and respect for everyone. We will certainly not judge
or discriminate against people based on their values, beliefs, political
affiliation or lack thereof, lifestyles, life experiences, race, color,
religion, sex, national origin, ancestry, age, order of protection status,
genetic information, marital status, disability, sexual orientation
including gender identity, unfavorable discharge from the military or
status as a protected veteran. We have a code of conduct, which can be
reviewed at http://yt-project.org/community.html , which covers
interactions on the mailing list, at in person workshops, on Slack or IRC,
and commit messages.
Importantly, we want to make sure you are aware that this tolerance of
viewpoints does *not* extend to tolerance of harassing, rude, or intolerant
statements or behavior. If any of you experience or witness something along
these lines, please let members of the steering committee know. If you
have something you wish to report that you would like to remain
confidential, please email confidential(a)yt-project.org , and we will work
to address this issue.
For more information, this blog post on the Committee for the Status of
Women in Astronomy has suggested actions for when you find yourself to be a
bystander:
http://womeninastronomy.blogspot.com/2016/11/reflection-moment-importance...
, including links to other resources.
Based on our experiences with the yt community as a group and individually,
none of us anticipate this to be a concern. However, we cannot condemn
strongly enough hateful language or actions, and want to take this
opportunity to reassure this community that we will not tolerate it in our
midst.
Thank you,
yt steering committee
2 years, 4 months
Issue #1295: [GDF] writing and loading dataset yields different result (yt_analysis/yt)
by Kacper Kowalik
New issue 1295: [GDF] writing and loading dataset yields different result
https://bitbucket.org/yt_analysis/yt/issues/1295/gdf-writing-and-loading-...
Kacper Kowalik:
As reported by Andrea Negri on the [yt-user ml](http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2016-Nove... following script:
```
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import yt
def main():
dims = np.array([2, 2, 2])
grid_data = [
dict(left_edge = [0.0, 0.0, 0.0],
right_edge = [1.0, 1.0, 1.0],
level = 0,
dimensions = dims),
dict(left_edge = [0.25, 0.25, 0.25],
right_edge = [0.75, 0.75, 0.75],
level = 1,
dimensions = dims),
]
bbox = np.array([[0, 1], [0, 1], [0, 1]])
ds = yt.load_amr_grids(grid_data, dims, bbox=bbox, periodicity=(0,0,0), \
length_unit=1., refine_by=2)
#make a nice slice
slc = yt.SlicePlot(ds, "z", "grid_level")
slc.set_log("grid_level", False)
slc.save('original_slice.png')
yt.utilities.grid_data_format.writer.write_to_gdf(ds, 'test.h5',
clobber=True)
da = yt.load('test.h5')
slc = yt.SlicePlot(da, "z", "grid_level")
slc.set_log("grid_level", False)
slc.save('test.png')
if __name__ == '__main__':
main()
```
yields different results ![original_slice.png] (https://bitbucket.org/repo/BXbAb/images/355574044-original_slice.png)
for the same dataset that was exported and read as a GDF file.
Responsible: xarthisius
2 years, 4 months
