New issue 1072: Add support to YTArray for remaining unsupported ufuncs
https://bitbucket.org/yt_analysis/yt/issues/1072/add-support-to-ytarray-f...
Nathan Goldbaum:
Right now YTArray supports most numpy ufuncs, but it looks like there are a few that need to be implemented still.
* bitwise_and
* bitwise_or
* invert
* left_shift
* right_shift
* ldexp
New issue 1071: ART does not auto-detect AGORA files
https://bitbucket.org/yt_analysis/yt/issues/1071/art-does-not-auto-detect...
Kenza Arraki:
ART cannot automatically load the AGORA files. This causes it to fail as it does not know the number of root grid cells.
Data from:
`AGORA-DISK-repository-for-use/Grackle+noSF/ART-I/IC`
```
#!python
In [1]: import yt
In [2]: ds = yt.load('AGORA_Galaxy_LOW.d')
yt : [INFO ] 2015-08-23 11:21:45,490 Using root level of 09
yt : [INFO ] 2015-08-23 11:21:45,677 Max level is 08
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-2-661a3253e356> in <module>()
----> 1 ds = yt.load('AGORA_Galaxy_LOW.d')
...
/global/u1/k/karraki/yt/yt/frontends/art/data_structures.pyc in _set_code_unit_attributes(self)
231 wmu = self.parameters["wmu"]
232 Om0 = self.parameters['Om0']
--> 233 ng = self.parameters['ng']
234 boxh = self.parameters['boxh']
235 aexpn = self.parameters["aexpn"]
KeyError: 'ng'
```
Responsible: karraki
Hi all,
I spent some time this week coming up with a technical solution to our
social problem of doing bugfix releases. This is embodied in a new script,
"pr_backport.py", which I've created a pull request for here to include
with the yt repository.
https://bitbucket.org/yt_analysis/yt/pull-requests/1717/add-pr-backport-s...
Briefly, the script creates a temporary clone of yt_analysis/yt, figures
out which commits on the "yt" branch need to be included on the stable
branch, and then assigns those commits to a pull request, and then
interactively suggests mercurial commands to run in the temporary
repository to backport individual pull requests to the stable branch. This
is all done "manually" by copy/pasting mercurial commands suggested by the
script. I don't think this should be fully automated since merge conflicts
can and likely will be triggered, particularly if the stable and yt
branches begin to substantially diverge.
My hope is that this will make the task of backporting bugfixes, which up
until this point has been associated with such a high cognitive barrier
that no one has wanted to sit down and acutally do it, much easier.
I might be biased since I wrote the script, but using the final version
that I pull requested it took me about 10 minutes or so to go through the
list of pull requests and backport them to create this pull request:
https://bitbucket.org/yt_analysis/yt/pull-requests/1716/backporting-bugfi...
Being able to backport bugfixes like this allows us to possibly make some
changes to our development workflow and suggested best practices.
1. We can now suggest most users stay on the stable branch rather than
switching to the dev branch to get bugfixes. We can also issue bugfix
releases on a much quicker cadence (monthly? biweekly?).
2. Since the "stable" branch is more stable and less buggy and the dev
branch is basically now just for new features, perhaps we can allow more
experimental development on the main yt branch without an onerous
requirement of documentation and review. This will help unblock the
development of major features like support for unstructured mesh data and
the new volume rendering interface.
3. Since there is less pressure to do a feature release just to get
bugfixes out, we might be able to have longer intervals between feature
releases, giving more time
to shake out issues.
I'm more or less just throwing these thoughts out there to get feedback
from the development community. Does the easy availability of bugfix
releases constitute a significant change for our development and release
mindset?
Thanks all for your time and input!
-Nathan
New issue 1070: Cannot access field that needs ghost zones from a covering grid
https://bitbucket.org/yt_analysis/yt/issues/1070/cannot-access-field-that...
Nathan Goldbaum:
The following test script:
```
#!python
import yt
ds = yt.load('GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0100')
ad = ds.all_data()
ml = ad.quantities.min_location('gpot')
center = (ml[2], ml[3], ml[4])
dx = ds.index.get_smallest_dx()
width = 256*dx
LE = center-width.in_units('code_length')/2.
CN = int(width/dx)
Roi = ds.covering_grid(level=ds.index.max_level, left_edge=LE, dims=[CN, CN, CN])
Roi['gas', 'vorticity_x']
```
Fails with the following traceback
```
Traceback (most recent call last):
File "test2.py", line 20, in <module>
Roi['gas', 'vorticity_x']
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 253, in __getitem__
self.get_data(f)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/construction_data_containers.py", line 598, in get_data
fill, gen, part, alias = self._split_fields(fields_to_get)
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/construction_data_containers.py", line 616, in _split_fields
finfo.check_available(self)
File "/Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.py", line 150, in check_available
validator(data)
File "/Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.py", line 293, in __call__
raise NeedsGridType(self.ghost_zones,self.fields)
yt.fields.field_exceptions.NeedsGridType: (1, [('gas', 'velocity_x'), ('gas', 'velocity_y'), ('gas', 'velocity_z')])
```
Thanks to Markus Haider for reporting this on the mailing list.
New issue 1069: Data objects used to create a profile in a for loop get garbage collected
https://bitbucket.org/yt_analysis/yt/issues/1069/data-objects-used-to-cre...
Nathan Goldbaum:
Illustrated by a test script Mateusz Ruszkowski reported on the mailing list:
```
#!python
import yt
profiles = []
labels = []
for i in range(0,2,1):
print i
ds = yt.load("Sedov_3D/sedov_hdf5_chk_%04i" % i)
my_data = ds.sphere(ds.domain_center, 1.0)
sim_time = ds.current_time
profiles.append(yt.create_profile(my_data, "radius", fields=["density"], weight_field="cell_volume", n_bins=32))
labels.append("t= %.0f" % sim_time)
plot = yt.ProfilePlot.from_profiles(profiles, labels=labels)
plot.set_xlim([0.1, 1.0])
plot.save()
```
This uses the Sedov3D test dataset on yt-project.org/data.
New issue 1068: Cannot use ipython notebook with anaconda once yt is installed
https://bitbucket.org/yt_analysis/yt/issues/1068/cannot-use-ipython-noteb...
ggoodwin52:
I installed the most updated version of anaconda for linux-64bit and was able to open ipython, ipython notebook, spyder, etc. without any issue. Then, I installed yt using the "conda install yt" command. The install was successful, but now when I try and start ipython notebook or spyder to use yt I get an error message.
The following script from my terminal shows successful starting of the ipython notebook via anaconda, closing the ipython notebook, installing yt, and then trying to re-open the ipython notebook and getting an error.
```
#!bash
[ggoodwin@Omoikane ~]$ ipython notebook
[I 13:36:38.296 NotebookApp] Using MathJax from CDN: https://cdn.mathjax.org/mathjax/latest/MathJax.js
[I 13:36:38.376 NotebookApp] The port 8888 is already in use, trying another random port.
[I 13:36:38.376 NotebookApp] The port 8889 is already in use, trying another random port.
[I 13:36:38.377 NotebookApp] The port 8890 is already in use, trying another random port.
[I 13:36:38.385 NotebookApp] Serving notebooks from local directory: /home/ggoodwin
[I 13:36:38.385 NotebookApp] 0 active kernels
[I 13:36:38.386 NotebookApp] The IPython Notebook is running at: http://localhost:8891/
[I 13:36:38.386 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
^C[I 13:36:40.027 NotebookApp] interrupted
Serving notebooks from local directory: /home/ggoodwin
0 active kernels
The IPython Notebook is running at: http://localhost:8891/
Shutdown this notebook server (y/[n])? y
[C 13:36:41.525 NotebookApp] Shutdown confirmed
[I 13:36:41.525 NotebookApp] Shutting down kernels
[ggoodwin@Omoikane ~]$ conda install yt
Fetching package metadata: ....
Solving package specifications: .
Package plan for installation in environment /home/ggoodwin/anaconda:
The following packages will be downloaded:
package | build
---------------------------|-----------------
openblas-0.2.14 | 0 6.6 MB
conda-env-2.4.2 | py27_0 24 KB
decorator-4.0.2 | py27_0 11 KB
ipython_genutils-0.1.0 | py27_0 32 KB
numpy-1.9.2 | py27_1 5.7 MB
path.py-7.6 | py27_0 41 KB
pexpect-3.3 | py27_0 60 KB
pickleshare-0.5 | py27_0 8 KB
setuptools-18.1 | py27_0 341 KB
simplegeneric-0.8.1 | py27_0 6 KB
traitlets-4.0.0 | py27_0 88 KB
wheel-0.24.0 | py27_0 75 KB
conda-3.16.0 | py27_0 172 KB
ipython-4.0.0 | py27_0 915 KB
pip-7.1.0 | py27_1 1.4 MB
yt-3.2 | np19py27_0 8.0 MB
------------------------------------------------------------
Total: 23.3 MB
The following NEW packages will be INSTALLED:
ipython_genutils: 0.1.0-py27_0
openblas: 0.2.14-0
path.py: 7.6-py27_0
pexpect: 3.3-py27_0
pickleshare: 0.5-py27_0
simplegeneric: 0.8.1-py27_0
traitlets: 4.0.0-py27_0
wheel: 0.24.0-py27_0
yt: 3.2-np19py27_0
The following packages will be UPDATED:
conda: 3.14.1-py27_0 --> 3.16.0-py27_0
conda-env: 2.2.3-py27_0 --> 2.4.2-py27_0
decorator: 3.4.2-py27_0 --> 4.0.2-py27_0
ipython: 3.2.0-py27_0 --> 4.0.0-py27_0
numpy: 1.9.2-py27_0 --> 1.9.2-py27_1
pip: 7.0.3-py27_0 --> 7.1.0-py27_1
setuptools: 17.1.1-py27_0 --> 18.1-py27_0
Proceed ([y]/n)? y
Fetching packages ...
openblas-0.2.1 100% |################################| Time: 0:00:00 18.01 MB/s
conda-env-2.4. 100% |################################| Time: 0:00:00 212.81 kB/s
decorator-4.0. 100% |################################| Time: 0:00:00 99.67 kB/s
ipython_genuti 100% |################################| Time: 0:00:00 274.77 kB/s
numpy-1.9.2-py 100% |################################| Time: 0:00:00 7.59 MB/s
path.py-7.6-py 100% |################################| Time: 0:00:00 2.65 MB/s
pexpect-3.3-py 100% |################################| Time: 0:00:00 164.63 kB/s
pickleshare-0. 100% |################################| Time: 0:00:00 68.05 kB/s
setuptools-18. 100% |################################| Time: 0:00:00 9.75 MB/s
simplegeneric- 100% |################################| Time: 0:00:00 4.05 MB/s
traitlets-4.0. 100% |################################| Time: 0:00:00 508.57 kB/s
wheel-0.24.0-p 100% |################################| Time: 0:00:00 3.54 MB/s
conda-3.16.0-p 100% |################################| Time: 0:00:00 1.66 MB/s
ipython-4.0.0- 100% |################################| Time: 0:00:00 5.93 MB/s
pip-7.1.0-py27 100% |################################| Time: 0:00:00 5.45 MB/s
yt-3.2-np19py2 100% |################################| Time: 0:00:00 8.83 MB/s
Extracting packages ...
[ COMPLETE ]|###################################################| 100%
Unlinking packages ...
[ COMPLETE ]|###################################################| 100%
Linking packages ...
[ COMPLETE ]|###################################################| 100%
[ggoodwin@Omoikane ~]$ ipython notebook
Traceback (most recent call last):
File "/home/ggoodwin/anaconda/bin/ipython", line 6, in <module>
sys.exit(start_ipython())
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/IPython/__init__.py", line 118, in start_ipython
return launch_new_instance(argv=argv, **kwargs)
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/traitlets/config/application.py", line 591, in launch_instance
app.initialize(argv)
File "<string>", line 2, in initialize
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/traitlets/config/application.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/IPython/terminal/ipapp.py", line 305, in initialize
super(TerminalIPythonApp, self).initialize(argv)
File "<string>", line 2, in initialize
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/traitlets/config/application.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/IPython/core/application.py", line 386, in initialize
self.parse_command_line(argv)
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/IPython/terminal/ipapp.py", line 300, in parse_command_line
return super(TerminalIPythonApp, self).parse_command_line(argv)
File "<string>", line 2, in parse_command_line
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/traitlets/config/application.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/traitlets/config/application.py", line 487, in parse_command_line
return self.initialize_subcommand(subc, subargv)
File "<string>", line 2, in initialize_subcommand
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/traitlets/config/application.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/traitlets/config/application.py", line 418, in initialize_subcommand
subapp = import_item(subapp)
File "/home/ggoodwin/anaconda/lib/python2.7/site-packages/ipython_genutils/importstring.py", line 31, in import_item
module = __import__(package, fromlist=[obj])
ImportError: No module named notebook.notebookapp
[ggoodwin@Omoikane ~]$
```
Hi all,
As part of my ongoing efforts to clean up the codebase, I just opened a
pull request to remove the Theia hardware volume rendering interface from
yt:
https://bitbucket.org/yt_analysis/yt/pull-requests/1703/removing-theia-ha...
I'd only like to see this pull request merged if there's consensus that
this is the way to go. I'd especially like to hear from anyone that is
actually using this code, or if anyone is interested in maintaining it and
adding tests.
-Nathan
New issue 1067: ds.h.find_max fail with cylindrical data
https://bitbucket.org/yt_analysis/yt/issues/1067/dshfind_max-fail-with-cy...
Suoqing Ji:
Test [data](http://yt-project.org/data/WDMerger_hdf5_chk_1000.tar.gz) and script:
```
#!python
import yt
ds = yt.load("WDmerger_hdf5_chk_1000/WDmerger_hdf5_chk_1000.hdf5")
v, c = ds.h.find_max('density')
```
Error message:
```
#!bash
v, c = ds.h.find_max('density')
File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 583, in find_max
source.quantities.max_location(field)
File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 540, in __call__
rv = super(MaxLocation, self).__call__(field)
File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 58, in __call__
sto.result = self.process_chunk(ds, *args, **kwargs)
File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 547, in process_chunk
mx = array_like_field(data, -1, "x")
File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 1271, in array_like_field
field = data._determine_fields(field)[0]
File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 555, in _determine_fields
finfo = self.ds._get_field_info("unknown", fname)
File "/Users/jisuoqing/Workspace/code/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 543, in _get_field_info
raise YTFieldNotFound((ftype, fname), self)
yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'x')' in WDmerger_hdf5_chk_1000/WDmerger_hdf5_chk_1000.hdf5.
```
Although I'm kind of know what causes this error, someone else might have a better and more global idea about this.
Also I'm in no hurry to use this function -- it just appears and I report it here.
