Spyder: Can't import Scipy in latest Spyder version (Anaconda)

[skjerns]

Description of your problem

1. I updated the to the latest spyder version using conda update conda +conda update spyder
   During this process I got the following warning:
   INFO menuinst_win32:__init__(182): Menu: name: 'Anaconda${PY_VER} ${PLATFORM}', prefix: 'C:\Anaconda3', env_name: 'None', mode: 'None', used_mode: 'system'

2. Now any import that calls some sub-module of scipy doesnt work

from scipy import stats

Traceback (most recent call last):

  File "<ipython-input-3-9d55e67ee92d>", line 1, in <module>
    from scipy import stats

  File "C:\Anaconda3\lib\site-packages\scipy\stats\__init__.py", line 348, in <module>
    from .stats import *

  File "C:\Anaconda3\lib\site-packages\scipy\stats\stats.py", line 175, in <module>
    import scipy.special as special

  File "C:\Anaconda3\lib\site-packages\scipy\special\__init__.py", line 648, in <module>
    from ._ellip_harm import ellip_harm, ellip_harm_2, ellip_normal

  File "C:\Anaconda3\lib\site-packages\scipy\special\_ellip_harm.py", line 7, in <module>
    from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm

ImportError: cannot import name '_ellipsoid'

What is the expected output? What do you see instead?
Normal importing.

Please provide any additional information below

• I already tried to reinstall scipy, revert to scipy 0.19.0 (just recently updated to 0.19.1)
• I removed Spyder 3.2.0 and reinstalled 3.1.4 that solved the problem.

Strangely enough the import works with no problem when I call it from the command line, both in a ipython and in python console

Versions and main components

• Spyder Version: 3.2.0
• Python Version: 3.5.2
• Qt Version: 5.6.2
• PyQt Version: 5.6
• Operating system: Windows 10, Anaconda 64bit

Dependencies

IPython >=4.0 : 6.1.0 (OK)
cython >=0.21 : 0.25.2 (OK)
jedi >=0.9.0 : 0.10.2 (OK)
nbconvert >=4.0 : 5.2.1 (OK)
numpy >=1.7 : 1.13.1 (OK)
pandas >=0.13.1 : 0.20.3 (OK)
pycodestyle >=2.3: 2.3.1 (OK)
pyflakes >=0.6.0 : 1.5.0 (OK)
pygments >=2.0 : 2.2.0 (OK)
pylint >=0.25 : 1.7.2 (OK)
qtconsole >=4.2.0: 4.3.0 (OK)
rope >=0.9.4 : 0.9.4-1 (OK)
sphinx >=0.6.6 : 1.6.3 (OK)
sympy >=0.7.3 : 1.1 (OK)

[ccordoba12]

@dalthviz, please try to run from scipy import stats on Windows to see if you have the same result than @skjerns.

[dalthviz]

@ccordoba12 I tried the import but it works for me:

@skjerns could you try to update again Spyder with conda update -f spyder? all the info you can provied us will be greatly appreciated :)

[kvorosh]

I have the same problem.
I installed the latest version of spyder using pip install -U spyder, and executing in spyder (does not matter if in current or dedicated console) scripts like import scipy.stats causes the same error as above:

Traceback (most recent call last):

  File "<ipython-input-1-99c07a9cb063>", line 1, in <module>
    runfile('D:/python-prog/test_script.py', wdir='D:/python-prog')

  File "d:\python36\lib\site-packages\spyder\utils\site\sitecustomize.py", line 688, in runfile
    execfile(filename, namespace)

  File "d:\python36\lib\site-packages\spyder\utils\site\sitecustomize.py", line 101, in execfile
    exec(compile(f.read(), filename, 'exec'), namespace)

  File "D:/python-prog/test_script.py", line 9, in <module>
    import scipy.stats

  File "d:\python36\lib\site-packages\scipy\stats\__init__.py", line 348, in <module>
    from .stats import *

  File "d:\python36\lib\site-packages\scipy\stats\stats.py", line 175, in <module>
    import scipy.special as special

  File "d:\python36\lib\site-packages\scipy\special\__init__.py", line 648, in <module>
    from ._ellip_harm import ellip_harm, ellip_harm_2, ellip_normal

  File "d:\python36\lib\site-packages\scipy\special\_ellip_harm.py", line 7, in <module>
    from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm

ImportError: cannot import name '_ellipsoid'

The same error appears when executing import scipy.stats in spyder's ipython console.
No error appears when executing import scipy.stats in ipython standalone console or when executing a script with this line from the command line.

I tried reinstalling scipy 0.19.1 and spyder 3.2.0, but the error persists.

Versions and main components

• Spyder version 3.2.0
• Python version 3.6.0, 64-bit
• PyQt version 5.9
• Scipy version 0.19.1 (from http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy)
• Operating system: Windows 8.1

Dependencies

IPython >=4.0 : 6.1.0 (OK)
cython >=0.21 : 0.26 (OK)
jedi >=0.9.0 : 0.10.2 (OK)
nbconvert >=4.0 : 5.2.1 (OK)
numpy >=1.7 : 1.13.1 (OK)
pandas >=0.13.1 : 0.20.3 (OK)
pycodestyle >=2.3: 2.3.1 (OK)
pyflakes >=0.6.0 : 1.5.0 (OK)
pygments >=2.0 : 2.2.0 (OK)
pylint >=0.25 : 1.7.2 (OK)
qtconsole >=4.2.0: 4.3.0 (OK)
rope >=0.9.4 : 0.10.5 (OK)
sphinx >=0.6.6 : 1.6.3 (OK)
sympy >=0.7.3 : 1.1.1 (OK)

[ccordoba12]

@dalthviz, please create an empty conda environment and install everything with pip there, including Spyder and PyQt5.

[dalthviz]

@ccordoba12 I created the env but I can import from scipy. Although to install it I used the wheel from http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy and also installed numpy+MKL from http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy

[ccordoba12]

Thanks for the check @dalthviz. I also tried to reproduce this problem on my end, but was unable to.

[kvorosh]

Addendum to my previous reply:
The problem did not appear for me in a virtual environment with only numpy and scipy (both from http://www.lfd.uci.edu/~gohlke/pythonlibs/) and spyder with its dependencies (installed using pip).
Some time later I deleted Python 3.6.0 and installed 3.6.2, after which the problem did not reappear.

[ccordoba12]

3.6.0 had some troubles with compiled dependencies, so that could have been the cause of the problem.