New issue 1159: Logarithmic Scaling for multiple 1d profiles
https://bitbucket.org/yt_analysis/yt/issues/1159/logarithmic-scaling-for-mu…
Miguel de Val-Borro:
Axis scaling manipulation using the set_log() function does not work
for multiple 1d profiles created using yt.create_profile
```
#!python
#!/usr/bin/python
import yt
profiles = []
basename = "Sedov_3d/sedov_hdf5_chk"
for i in [0, 1]:
filename = "{0}_{1:04d}".format(basename, i)
ds = yt.load(filename)
sphere = ds.sphere([0., 0., 0.], (1, 'cm'))
profile = yt.create_profile(sphere, "radius", ["radial_velocity_absolute"],
logs = {"radius": False, "radial_velocity_absolute": False}
)
profiles.append(profile)
plot = yt.ProfilePlot.from_profiles(profiles)
plot.set_log("radial_velocity_absolute", False)
plot.save()
```
The traceback error obtained from this script is shown below:
```
#!python
Traceback (most recent call last):
File "./profiles_test.py", line 17, in <module>
plot.set_log("radial_velocity_absolute", False)
File "/home/mdevalbo/project/yt_analysis/yt/yt/visualization/plot_container.py", line 64, in newfunc
rv = f(*args, **kwargs)
File "/home/mdevalbo/project/yt_analysis/yt/yt/visualization/profile_plotter.py", line 468, in set_log
field, = self.profiles[0].data_source._determine_fields([field])
File "/home/mdevalbo/project/yt_analysis/yt/yt/data_objects/data_containers.py", line 985, in _determine_fields
finfo = self.ds._get_field_info("unknown", fname)
ReferenceError: weakly-referenced object no longer exists
```
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New issue 1158: data file not recognized IsolatedGalaxy
https://bitbucket.org/yt_analysis/yt/issues/1158/data-file-not-recognized-i…
dan mckeown:
Hello yt community, I have successfully reproduced the plot from tutorial 4 using data folder enzo_tiny_cosmology . this data file had no trouble being loaded into yt for plotting. However, IsolatedGalaxy is not recognized even though it is downloaded and unpacked. I went through the same process as enzo_tiny_cosmology but when I attempted to move the IsolatedGalaxy folder into my working directory I always receive the message "error no such file or directory" even though the file is clearly there.
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New issue 1157: AttributeError when building docs with python 3
https://bitbucket.org/yt_analysis/yt/issues/1157/attributeerror-when-buildi…
Miguel de Val-Borro:
This is the error I get when I build the docs with `make html`:
```
#!python
Exception occurred:
File "/mnt/home/miguel/project/hydro/yt_analysis/yt/doc/extensions/notebook_sphinxext.py", line 61, in run
dest_path_eval = string.replace(dest_path, '.ipynb', '_evaluated.ipynb')
AttributeError: module 'string' has no attribute 'replace'
The full traceback has been saved in /tmp/sphinx-err-shczw5mf.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
Makefile:50: recipe for target 'html' failed
```
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New issue 1155: tips for data
https://bitbucket.org/yt_analysis/yt/issues/1155/tips-for-data
dan mckeown:
Hello all, I am new to yt and starting to work with sample datasets. I was wondering if any of you users have tips for where I could best store my data for use in yt. (in other words, what is the most fluid structure for data locations that you find works best. I will certainly experiment on my own but I was just curious for your insights.
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New issue 1153: difficulty importing yt for Canopy Python 2.7.6 in OSX el Capitan
https://bitbucket.org/yt_analysis/yt/issues/1153/difficulty-importing-yt-fo…
dan mckeown:
Hello all, I have been having a little difficulty getting yt to import. I installed it using a script that was written for osx el capitan called the
get_yt.sh script
Now, this script gives instructions for creating a PATH environment variable which isn't working for some reason. No error is given when I create the suggested variable which is:
$ export PATH=/path/to/yt-conda:$PATH
where /path/to is just /Users/myusername.
However, when I try to import yt from canopy or at the command line it doesn't work.
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New issue 1152: File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file)
https://bitbucket.org/yt_analysis/yt/issues/1152/file-h5fpyx-line-70-in-h5p…
Anonymous:
I ran into this error some times (possibly randomly) using yt legacy version.
File "start_SGE.py", line 28, in <module>
File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line
58, in get_snapshots
File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line
43, in get_redshift
File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py",
line 71, in load
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py",
line 218, in __init__
File
"/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py",
line 165, in __init__
File
"/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py",
line 57, in make_fid
File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626)
IOError: unable to open file (File accessability: Unable to open file)
Exception AttributeError: "'NoneType' object has no attribute 'close'"
in ignored
Please have a look. Thank you very much,
Best,
Dai
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