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Hello,

I am testing and running the Illustris python scripts in Jupyter Notebooks and I keep getting the error that the module illustris python has no attribute 'groupcat' or 'snapshot'.
I have a feeling it has something to do with the file/directory I am using, here is the first piece of code that results in a system error:

# Run the full directory
illustris_python = os.path.split(illustris_python)[0]
nose_args = [sys.argv[0], illustris_python]
if len(sys.argv) > 1:
    nose_args.extend(sys.argv[1:])
    # print("nose_args = ", nose_args)
    result = nose.run(argv=nose_args)
Usage: ipykernel_launcher.py [options]

ipykernel_launcher.py: error: no such option: -f

I'm not sure what this is due to. And then here is the next code that results in the attribute error"

#basePath = './Illustris-3/output/'
basePath = './output/'
fields = ['GroupPos','GroupVel']
groups = il.groupcat.loadHalos(basePath,135,fields=fields)
AttributeError: module 'illustris_python' has no attribute 'groupcat'

This occurs even after I have defined all of the test group halos and snapshots from the groupcat_test.py and snapshot_test.py scripts. I have double checked that all the Illlustris python scripts are in the correct folder titled illustris_python.

What do I need to do to solve the Attribute Error?

Kind Regards,
Daniel

Some sort of path issue. Did you install via pip, or did you just download the files and put them in a folder?

Hi Dylan,

Thank you for your response. I installed via pip

Exactly as in the README i.e.

git clone git@github.com:illustristng/illustris_python.git
cd illustris_python
pip install .

?

Yes, I installed the exact same code as in the README

What do you see when you type the following:

$ ipython
Python 3.9.7 (default, Sep 16 2021, 13:09:58)
Type 'copyright', 'credits' or 'license' for more information
IPython 8.4.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import illustris_python

In [2]: illustris_python.__path__
Out[2]: ['/home/dnelson/illustris_release/illustris_python/illustris_python']

In [3]: dir(illustris_python)
Out[3]:
['__all__',
 '__builtins__',
 '__cached__',
 '__doc__',
 '__file__',
 '__loader__',
 '__name__',
 '__package__',
 '__path__',
 '__spec__',
 'groupcat',
 'lhalotree',
 'snapshot',
 'sublink',
 'util']

This is what results when I type the following:

ipython
Traceback (most recent call last):
  File "/Users/lab/Ureka/python/bin/ipython", line 4, in <module>
    from IPython import start_ipython
ImportError: No module named IPython
Python 3.9.7 (default, Sep 16 2021, 13:09:58)
Type 'copyright', 'credits' or 'license' for more information
IPython 8.4.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import illustris_python

In [2]: illustris_python.__path__
Out[2]: ['/home/dnelson/illustris_release/illustris_python/illustris_python']

In [3]: dir(illustris_python)
Out[3]:
['__all__',
 '__builtins__',
 '__cached__',
 '__doc__',
 '__file__',
 '__loader__',
 '__name__',
 '__package__',
 '__path__',
 '__spec__',
 'groupcat',
 'lhalotree',
 'snapshot',
 'sublink',
 'util']2 [MilkyWay:~] lab:Python 3.9.7 (default, Sep 16 2021, 13:09:58)
Badly placed ()'s.
3 [MilkyWay:~] lab:Type 'copyright', 'credits' or 'license' for more information 
/usr/bin/Type: line 4: type: copyright,: not found
/usr/bin/Type: line 4: type: credits: not found
/usr/bin/Type: line 4: type: or: not found
/usr/bin/Type: line 4: type: license: not found
for is a shell keyword
more is /usr/bin/more
/usr/bin/Type: line 4: type: information: not found
4 [MilkyWay:~] lab:IPython 8.4.0 -- An enhanced Interactive Python. Type '?' for help.
IPython: Command not found.
5 [MilkyWay:~] lab:
5 [MilkyWay:~] lab:In [1]: import illustris_python
In: No match.
6 [MilkyWay:~] lab:
6 [MilkyWay:~] lab:In [2]: illustris_python.__path__
In: No match.
7 [MilkyWay:~] lab:Out[2]: ['/home/dnelson/illustris_release/illustris_python/illustris_python']
Out[2]:: Too many arguments.
8 [MilkyWay:~] lab:
8 [MilkyWay:~] lab:In [3]: dir(illustris_python)
Badly placed ()'s.
9 [MilkyWay:~] lab:Out[3]:
10 [MilkyWay:~] lab:['__all__',
[__all__,: Command not found.
11 [MilkyWay:~] lab: '__builtins__',
__builtins__,: Command not found.
12 [MilkyWay:~] lab: '__cached__',
__cached__,: Command not found.
13 [MilkyWay:~] lab: '__doc__',
__doc__,: Command not found.
14 [MilkyWay:~] lab: '__file__',
__file__,: Command not found.
15 [MilkyWay:~] lab: '__loader__',
__loader__,: Command not found.
16 [MilkyWay:~] lab: '__name__',
__name__,: Command not found.
17 [MilkyWay:~] lab: '__package__',
__package__,: Command not found.
18 [MilkyWay:~] lab: '__path__',
__path__,: Command not found.
19 [MilkyWay:~] lab: '__spec__',
__spec__,: Command not found.
20 [MilkyWay:~] lab: 'groupcat',
groupcat,: Command not found.
21 [MilkyWay:~] lab: 'lhalotree',
lhalotree,: Command not found.
22 [MilkyWay:~] lab: 'snapshot',
snapshot,: Command not found.
23 [MilkyWay:~] lab: 'sublink',
sublink,: Command not found.
24 [MilkyWay:~] lab: 'util']

I have also double checked that I installed via pip and I get the output saying that illustris_python already exists.

It appears that you python installation is broken, I'm afraid I cannot really help with that.

(1) ImportError: No module named IPython indicates a larger problem.
(2) You have /home/dnelson/ in illustris_python.__path__? This doesn't make any sense to me.
(3) These MilkyWay errors at the end are strange.

I would suggest you contact your sysadmin, or (i) reinstall a fresh python using Anaconda, (ii) set up a clean environment, and (iii) then proceed.

I'm getting the same error as @Daniel Minyety, however when I type the commands @Dylan Nelson I get the following results:

In  [1]: import illustris_python as il

In  [2]: il.__path__
Out [2]: _NamespacePath(['/vera/u/judigoan/illustris_python', '/vera/u/judigoan/illustris_python'])

In  [3]: dir(il)
Out [3]: 
['__doc__',
 '__file__',
 '__loader__',
 '__name__',
 '__package__',
 '__path__',
 '__spec__']

It seems like I'm missing a couple of things from my installation of illustris_python. Any suggesttions?
Thank you!

How did you install it? Perhaps reinstall.