SyntaxError when running with Python 2

Question

I have a Python script called "controlled_biomass_exp.py" that generates some data and plots it. Its over 100 lines long so I don't want to dump it all here.

I can run it from Ipython in the terminal once and it works fine. If I repeat the command to run the script again with:

In [3]: run controlled_biomass_exp.py

I get:

File "< ipython-input-3-3ec3d096e779>", line 1

run controlled_biomass_exp.py
                     ^
SyntaxError: invalid syntax

(The carrot is pointing at the last letter of the filename, "p".)

I get the same problem if I run any other python script after running this one. If I quit Ipython in the terminal and restart it the problem "re-sets". I can run other scripts fine, until I run the broken one once. I haven't encountered a problem like this before. Any help directing me where to look for solutions much appreciated.

I'm not familiar with iPython but does your script contain a run function? One that overrides the original. — Rik Verbeek
– Rik Verbeek, Commented Nov 18, 2014 at 12:18
Hi Daniel, in that case, maybe you could post the code so we can check for problems there. — Rik Verbeek
– Rik Verbeek, Commented Nov 18, 2014 at 13:19
Have you tried to use python instead of run ? open terminal and enter python controlled_biomass_exp.py. Of course you have to be in directory where this file located — micgeronimo
– micgeronimo, Commented Nov 18, 2014 at 13:33
Thanks Rik, micgeronimo. I can see now you were both pointing me in the right direction. — Daniel Power
– Daniel Power, Commented Nov 21, 2014 at 8:55

cel · Accepted Answer · 2014-11-18 15:18:11Z

3

It appears that your script controlled_biomass_exp.py overwrites run in your current namespace.

This toy example will produce a similar problem:

# file: test.py
run = "hello world!"
print(run)

Calling run in IPython is just a shortcut for %run which is a built-in magic function. Once you overwrite run (e.g. as shown in my toy example) you cannot use the shortcut anymore.

However, %run controlled_biomass_exp.py should still work for you.

answered Nov 18, 2014 at 15:18

cel

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1 Comment

Daniel Power Over a year ago

Thanks cel. This was exactly the problem. I knew it would be something daft. I had a loop of "runs" with a variable "run". Once I changed the name of this, everything is awesome!

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