ImportError: No module named scipy.sparse

Question

I installed Scipy on Ubuntu using the following commands:

sudo apt-get install python-scipy
pip install scipy

but when run import, I get this error:

ImportError: No module named scipy.sparse

I searched and tried the following and reinstalled Scipy:

sudo apt-get purge python-scipy

but still got the same error.

Update: I didn't import scipy in my python file, just imported keras.

Here is the error message:

(my_env)  ..  $ python test.py
Using TensorFlow backend.
Traceback (most recent call last):
  File "test.py", line 10, in <module>
    import keras
  File "/home/ ../my_env/lib/python3.5/site-packages/keras/__init__.py", line 3, in <module>
    from . import utils
  File "/home/ ../my_env/lib/python3.5/site-packages/keras/utils/__init__.py", line 27, in <module>
    from .multi_gpu_utils import multi_gpu_model
  File "/home/ ../my_env/lib/python3.5/site-packages/keras/utils/multi_gpu_utils.py", line 7, in <module>
    from ..layers.merge import concatenate
  File "/home/ ../my_env/lib/python3.5/site-packages/keras/layers/__init__.py", line 4, in <module>
    from ..engine.base_layer import Layer
  File "/home/ ../my_env/lib/python3.5/site-packages/keras/engine/__init__.py", line 8, in <module>
    from .training import Model
  File "/home/ ../my_env/lib/python3.5/site-packages/keras/engine/training.py", line 21, in <module>
    from . import training_arrays
  File "/home/../my_env/lib/python3.5/site-packages/keras/engine/training_arrays.py", line 8, in <module>
    from scipy.sparse import issparse
ImportError: No module named 'scipy.sparse'

https://stackoverflow.com/questions/2213551/installing-scipy-with-pip You need libatlas-base-dev gfortran — Balázs Nagyillés, Mar 07 '19 at 12:34
Show us your import line, the full error traceback and your projects file structure. — Klaus D., Mar 07 '19 at 12:45
You missed the file structure. Is there anything called `scipy` in your folder? — Klaus D., Mar 07 '19 at 13:43

score 5 · Answer 1 · edited Jan 11 '20 at 07:58

5

scipy path mixed up. Uninstall

pip uninstall scipy

Install using conda worked for me

conda install scipy

edited Jan 11 '20 at 07:58

slfan

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answered Jan 11 '20 at 07:35

Kennedy Kairu Kariuki

99
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you can also use `conda install -c conda-forge scipy` – kitokid Mar 19 '21 at 16:02

karel · Answer 2 · 2019-10-14T11:50:00.700

In Ubuntu 18.04 and later you could install Scipy and Keras for Python 3 with sudo apt install python3-scipy python3-keras and you'd be good to go, however you are using Ubuntu 16.04 and you installed Scipy for Python 2 which is not compatible with TensorFlow for Python 3.4, 3.5 and 3.6, so install the default Scipy package for Python 3 instead with this command:

sudo apt install python3-scipy

For further instructions on installing TensorFlow in Ubuntu read this answer. It's worth reading because you are going to have to check for package version compatibility when working with TensorFlow from now on.

The command pip install scipy is not correct either if the purpose of that command was to upgrade Scipy. The correct command to upgrade Scipy would have been pip install --upgrade --user scipy and even so it would have been useless because your scipy that is currently installed is only for Python 2 and your TensorFlow is for Python 3.

`pip install --upgrade --user scipy` solved my problem, thanks. — ah bon, Mar 25 '21 at 02:54

score 0 · Answer 3 · answered Mar 07 '19 at 12:34

0

You are using Python 3, but with pip you install scipy for Python 2.
Use:

pip3 install scipy

or:

sudo apt install python3-scipy

answered Mar 07 '19 at 12:34

Ilko

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score 0 · Answer 4 · answered Mar 07 '19 at 12:37

0

try

pip3 install scipy

and to install pip3

sudo python3 get-pip.py

answered Mar 07 '19 at 12:37

Richard Lenkiewicz

59
4

score 0 · Answer 5 · answered Mar 07 '19 at 13:01

0

Just to make sure on which Python version you've installed Scipy try in the terminal:

which Python

Then try:

pip freeze

to get a list of all the installed packages.

Maybe you have more than one python version and have installed the package to one and trying to execute your code using the other.

answered Mar 07 '19 at 13:01

Ahmed Hawary

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Then I think your Scipy install went wrong. Try to uninstall and install the wheel file this time: https://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy – Ahmed Hawary Mar 07 '19 at 13:17
nothing appeared when execute which python .. but with python -- version .. pythn3.5.2 and from pip freeze scipy==1.2.1 is shown – userInThisWorld Mar 07 '19 at 13:31
Did you try to install it through wheel file? – Ahmed Hawary Mar 07 '19 at 13:40
I also do recommend to try installing Anaconda distribution . It would save plenty of time of installing packages and that type of issues. – Ahmed Hawary Mar 07 '19 at 13:45

score 0 · Answer 6 · edited Dec 11 '20 at 05:11

0

On Ubuntu/Debian:

sudo apt-get install python3-scipy

Note the 3 in python, it worked for me.

edited Dec 11 '20 at 05:11

ndrwnaguib

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answered Dec 10 '20 at 23:06

Tatiana

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score -2 · Answer 7 · answered Mar 07 '19 at 12:32

-2

Install it with pip instead, run:

pip install scipy

That did the trick for me, hope it helps!

EDIT: Forgot you're using python 3.x, run this instead:

pip3 install scipy

answered Mar 07 '19 at 12:32

ILikeJava

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ImportError: No module named scipy.sparse

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