ImportError: cannot import name 'LinearNDInterpolator'

I've written a program in Python 3.6.2 that I'm trying to freeze for distribution using cx_Freeze. But I'm getting a strange error when trying to run the resulting executable (my base program uses pyLDAvis.sklearn). The error is reproduced below:

Traceback (most recent call last):

File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\cx_Freeze\initscripts\__startup__.py", line 14, in run
    module.run()
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\cx_Freeze\initscripts\Console.py", line 26, in run
    exec(code, m.__dict__)
  File "MYPROGRAM.py", line 1474, in <module>
    import pyLDAvis.sklearn
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\pyLDAvis\__init__.py", line 44, in <module>
    from ._display import *
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\pyLDAvis\_display.py", line 13, in <module>
    from ._prepare import PreparedData
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\pyLDAvis\_prepare.py", line 15, in <module>
    from scipy.stats import entropy
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\scipy\stats\__init__.py", line 345, in <module>
    from .stats import *
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\scipy\stats\stats.py", line 171, in <module>
    from . import distributions
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\scipy\stats\distributions.py", line 10, in <module>
    from ._distn_infrastructure import (entropy, rv_discrete, rv_continuous,
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\scipy\stats\_distn_infrastructure.py", line 16, in <module>
    from scipy.misc import doccer
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\scipy\misc\__init__.py", line 68, in <module>
    from scipy.interpolate._pade import pade as _pade
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\scipy\interpolate\__init__.py", line 187, in <module>
    from .ndgriddata import *
  File "C:\Users\...\AppData\Local\Programs\Python\Python36\lib\site-packages\scipy\interpolate\ndgriddata.py", line 11, in <module>
    from .interpnd import LinearNDInterpolator, NDInterpolatorBase, \
ImportError: cannot import name 'LinearNDInterpolator'

The executable options for my cx_freeze script are below:

build_exe_options = {
                        "packages": ["os","textwrap","msvcrt","warnings","time","datetime","platform","sklearn","operator","nltk.tokenize","stop_words","pandas","nltk.stem.porter","sklearn.feature_extraction.text","sklearn.decomposition","progressbar","numpy","packaging","asyncio",
                        ], 

                        "includes": ["appdirs","packaging.version","packaging.specifiers","packaging.requirements","pyLDAvis.sklearn","pyLDAvis.urls","scipy.sparse.csgraph._validation"],

                        "excludes" : ["tkinter","sqlite3"],

                        "include_msvcr" : True
                    }

I can't seem to find any combination of scipy.interpolate or scipy.interpolate.interpnd to put in the build options that lets this work -- I consistently get the "can't import name 'LinearNDInterpolator'" error. Reinstalling scipy doesn't help.

Can anyone advise? Am I just doomed to not be able to freeze my code?

Solution

Have you tried to add
```
import scipy.interpolate.interpnd
```
in your base program (not in the setup script)? What happens then?

According to the experiences I have made so far, one needs to add scipy to the packages list in order to let it be included correctly by cx_Freeze. But then one also needs to add scipy.spatial.cKDTree to the excludes list due to this issue. Try thus to use the following options in your setup script:

build_exe_options = {
                "packages": ["os","textwrap","msvcrt","warnings","time","datetime","platform","sklearn","operator","nltk.tokenize","stop_words","pandas","nltk.stem.porter","sklearn.feature_extraction.text","sklearn.decomposition","progressbar","numpy","packaging","asyncio","scipy"
                ], 

                "includes": ["appdirs","packaging.version","packaging.specifiers","packaging.requirements","pyLDAvis.sklearn","pyLDAvis.urls","scipy.sparse.csgraph._validation"],

                "excludes" : ["tkinter","sqlite3","scipy.spatial.cKDTree"],

                "include_msvcr" : True
            }

Additional remark: the build_exe option "include_msvcr": True seems to have no effect with cx_Freeze versions 5.0.2, 5.1.1, and 6.0b1. See this issue, my post there (jpeg13) contains some more details. You might need to add the MSVCR DLLs manually using the build_exe option include_files.