Google Colab, module not found when running python script

Question

I have a Colab notebook open and have my files cloned from a github repo. I want to run a python script called models.py. In this file, I am using pandas. When I run this line in Colab:

!python3 models.py

I get the following error:

Traceback (most recent call last):
  File "models.py", line 1, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'

However, if I run in a cell on Google Colab:

!pip3 list

I find that pandas is indeed installed:

pandas                   0.25.3

My assumption is that when I run the script, it is not able to see the libraries I have installed but I am unsure how to fix this issue.

If I run:

!which python3

I get:

/usr/local/bin/python3

The python file I am trying to run is under:

/content/my_project/models.py

Should I instead take a different approach to running this file?

restart the kernel

Pygirl
– Pygirl

2020-03-04 20:27:28 +00:00
Commented Mar 4, 2020 at 20:27 — Pygirl
– Pygirl, Commented Mar 4, 2020 at 20:27
Just tried this and still getting same error

kg5425
– kg5425

2020-03-04 20:30:49 +00:00
Commented Mar 4, 2020 at 20:30 — kg5425
– kg5425, Commented Mar 4, 2020 at 20:30
try pip install pandas

Pygirl
– Pygirl

2020-03-04 20:32:01 +00:00
Commented Mar 4, 2020 at 20:32 — Pygirl
– Pygirl, Commented Mar 4, 2020 at 20:32
Tried this and restarted kernel, not working still.

kg5425
– kg5425

2020-03-04 20:35:01 +00:00
Commented Mar 4, 2020 at 20:35 — kg5425
– kg5425, Commented Mar 4, 2020 at 20:35

korakot · Accepted Answer · 2020-03-04 23:49:52Z

6

Instead of

!python3 models.py

You can use

%run models.py

answered Mar 4, 2020 at 23:49

korakot

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Comments

jakevdp · Accepted Answer · 2020-03-04 22:00:32Z

3

In a clean Colab runtime, the location of python 3 is different than what you show in your question:

!which python3
# /usr/bin/python3

It looks like you are installing another Python instance in your VM. To ensure you're using Colab's bundled Python 3 executable, try using

!/usr/bin/python3 models.py

If you actually want to use the new python instance you've installed, you'll have to also install whatever packages you need. For example

!/usr/local/bin/python3 -m pip install pandas

edited Mar 4, 2020 at 22:00

answered Mar 4, 2020 at 21:31

jakevdp

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