Difficulties setting up Python in STATA16

[Peppe Grasso]

Dear Statalist,

I am having difficulties in setting up Python in Stata16. I have read several threads from this forum (e.g. https://www.statalist.org/forums/for...le-not-working) but still cannot find a solution to my problem.

I am running Stata16 on macOS 10.15.4. My current version of Python is 3.74 which works just fine with IDEs such as Jupyter Notebook and Spyder.

Please find below the output of a few Stata command lines (in the example I am trying to import seaborn.) which I hope will provide you with enough information to help me.

Many thanks in advance

Best,
PG

. python search
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 Python environments found:  
 /usr/bin/python
 /usr/local/bin/python3
 /usr/local/bin/python3.7m
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

. python query
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
    Python Settings
      set python_exec      /opt/anaconda3/bin/python
      set python_userpath  /opt/anaconda3/lib/python3.7/site-packages

    Python system information
      initialized          yes
      version              3.7.4
      architecture         64-bit
      library path         /opt/anaconda3/lib/libpython3.7m.dylib

. python
----------------------------------------------- python (type end to exit) -----------------------------------------------------------------------------------------------------------
>>> import sys
>>> print(sys.path)
['', '/Applications/Stata/ado/base/py', '', '/opt/anaconda3/lib/python37.zip', '/opt/anaconda3/lib/python3.7', '/opt/anaconda3/lib/python3.7/lib-dynload', '/opt/anaconda3/lib/python
> 3.7/site-packages', '/opt/anaconda3/lib/python3.7/site-packages/aeosa', '.', '/Applications/Stata/', '/Applications/Stata/ado/base/', '/Applications/Stata/ado/base/py', '/Applicat
> ions/Stata/ado/site/', '/Applications/Stata/ado/site/py', '/Users/peppegrass/Library/Application Support/Stata/ado/plus/', '/Users/peppegrass/Library/Application Support/Stata/ado
> /plus/py', '/Users/peppegrass/Library/Application Support/Stata/ado/personal/', '/Users/peppegrass/Library/Application Support/Stata/ado/personal/py', '~/ado/', '/opt/anaconda3/li
> b/python3.7/site-packages']
>>> import seaborn as sns
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/anaconda3/lib/python3.7/site-packages/seaborn/__init__.py", line 6, in <module>
    from .rcmod import *
  File "/opt/anaconda3/lib/python3.7/site-packages/seaborn/rcmod.py", line 5, in <module>
    from . import palettes, _orig_rc_params
  File "/opt/anaconda3/lib/python3.7/site-packages/seaborn/palettes.py", line 12, in <module>
    from .utils import desaturate, set_hls_values, get_color_cycle
  File "/opt/anaconda3/lib/python3.7/site-packages/seaborn/utils.py", line 7, in <module>
    from scipy import stats
  File "/opt/anaconda3/lib/python3.7/site-packages/scipy/stats/__init__.py", line 379, in <module>
    from .stats import *
  File "/opt/anaconda3/lib/python3.7/site-packages/scipy/stats/stats.py", line 180, in <module>
    import scipy.special as special
  File "/opt/anaconda3/lib/python3.7/site-packages/scipy/special/__init__.py", line 641, in <module>
    from ._ufuncs import *
ImportError: dlopen(/opt/anaconda3/lib/python3.7/site-packages/scipy/special/_ufuncs.cpython-37m-darwin.so, 2): Symbol not found: _main
  Referenced from: /opt/anaconda3/lib/python3.7/site-packages/scipy/special/_ufuncs.cpython-37m-darwin.so
  Expected in: flat namespace
 in /opt/anaconda3/lib/python3.7/site-packages/scipy/special/_ufuncs.cpython-37m-darwin.so
r(7102);
>>> end
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

.

[Joseph Luchman]

Hi Peppe,

It looks like you have a few different versions of Python on your machine.

Are you sure that the version of -seaborn- being called is "in" the same environment as the version of Python invoked in Stata?

It appears as though it's having trouble with a C library (the _ufuncs.cpython-37m-darwin.so file it's referring to) and in looking over similar issues on StackExchange, a commonality seems to be that there are multiple versions of Python and the version of Python being used cannot load the C library as called.

I'm not overly familiar with macOS file paths but it seems like -python query- yields different results from where -python search- finds Python executables. I would guess that the problem is somewhere in which version of Python is used vs the specs of the -seaborn- package.

- joe

[Peppe Grasso]

Hi Joseph,

Thanks for your answer

I guess you are right...

I would guess that the problem is somewhere in which version of Python is used vs the specs of the -seaborn- package.

...but I do not know how to check this

Are you sure that the version of -seaborn- being called is "in" the same environment as the version of Python invoked in Stata?

Consequently, I cannot figure out whether my current 'python_exec' and 'python_userpath' configuration is right.

[Peppe Grasso]

I could ascertain that the executable python file that I installed as part of the anaconda distribution is located here "/opt/anaconda3/bin/python"; therefore I guess the first configuration (below) should be correct

python set exec "/opt/anaconda3/bin/python", permanently

Moreover, from my mac terminal, after invoking python3, I call

import sys
print(sys.path)

and get

['', '/opt/anaconda3/lib/python37.zip', '/opt/anaconda3/lib/python3.7', '/opt/anaconda3/lib/python3.7/lib-dynload', '/opt/anaconda3/lib/python3.7/site-packages', '/opt/anaconda3/lib/python3.7/site-packages/aeosa']

All of which (excluding '/opt/anaconda3/lib/python37.zip', which gives me an error) I successfully manage to have Stata parse in

python set userpath "/opt/anaconda3/lib/python3.7" "/opt/anaconda3/lib/python3.7/lib-dynload" "/opt/anaconda3/lib/python3.7/site-packages" "/opt/anaconda3/lib/python3.7/site-packages/aeosa" "/opt/anaconda3/lib/python3.7/site-packages/IPython/extensions", permanently

Notwithstanding, I still cannot import seaborn. However, I can import numpy and pandas.

. python
----------------------------------------------- python (type end to exit) -----------------------------------------------------------
>>> import numpy as np
>>> import pandas as pd
>>> import seaborn as sns
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/anaconda3/lib/python3.7/site-packages/seaborn/__init__.py", line 6, in <module>
    from .rcmod import *
  File "/opt/anaconda3/lib/python3.7/site-packages/seaborn/rcmod.py", line 5, in <module>
    from . import palettes, _orig_rc_params
  File "/opt/anaconda3/lib/python3.7/site-packages/seaborn/palettes.py", line 12, in <module>
    from .utils import desaturate, set_hls_values, get_color_cycle
  File "/opt/anaconda3/lib/python3.7/site-packages/seaborn/utils.py", line 7, in <module>
    from scipy import stats
  File "/opt/anaconda3/lib/python3.7/site-packages/scipy/stats/__init__.py", line 379, in <module>
    from .stats import *
  File "/opt/anaconda3/lib/python3.7/site-packages/scipy/stats/stats.py", line 180, in <module>
    import scipy.special as special
  File "/opt/anaconda3/lib/python3.7/site-packages/scipy/special/__init__.py", line 641, in <module>
    from ._ufuncs import *
ImportError: dlopen(/opt/anaconda3/lib/python3.7/site-packages/scipy/special/_ufuncs.cpython-37m-darwin.so, 2): Symbol not found: _ma
> in
  Referenced from: /opt/anaconda3/lib/python3.7/site-packages/scipy/special/_ufuncs.cpython-37m-darwin.so
  Expected in: flat namespace
 in /opt/anaconda3/lib/python3.7/site-packages/scipy/special/_ufuncs.cpython-37m-darwin.so
r(7102);
>>> end
-------------------------------------------------------------------------------------------------------------------------------------

.

If I look for the three of them (numpy, pandas, seaborn) in Stata using -ls- in the directory which I had originally indicated

 
 /opt/anaconda3/lib/python3.7/site-packages

I find them all. Then why can I not import seaborn? To be more precise this is not unique to seaborn. sklearn for instance is also found in the directory above, but fails to be imported.
Any ideas would be greatly appreciated. Thanks!