Error occurs when running import cobra

[Yu Chen]

Hi,

I installed cobra 0.8.1 following the procedure here (https://github.com/opencobra/cobrapy/blob/master/INSTALL.rst), but I got the error "ImportError: No module named test" when I ran either "import cobra" or "import cobra.test". Could someone help to fix this?

I am using Python 2.7.13 and on macOS Sierra 10.12.6.

Thanks in advance!

Yu

[henning.red]

Hi Yu,

Seems the installation did not succeed, can you post the whole output you get when you run `pip install cobra`? Are you using a virtual environment (see http://docs.python-guide.org/en/latest/dev/virtualenvs/)?

Cheers, Henning

[Yu Chen]

Thanks for your reply! Below is the output of "pip install cobra", can you tell me if the installation is fine? I did not use a virtual environment but I will try then.

Requirement already satisfied: cobra in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages

Requirement already satisfied: swiglpk in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: pandas>=0.17.0 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: future in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: numpy>=1.6 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: optlang>=1.2.1 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: tabulate in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: ruamel.yaml<0.15 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: python-dateutil in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from pandas>=0.17.0->cobra)

Requirement already satisfied: pytz>=2011k in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from pandas>=0.17.0->cobra)

Requirement already satisfied: six>=1.9.0 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from optlang>=1.2.1->cobra)

Requirement already satisfied: sympy>=1.0.0 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from optlang>=1.2.1->cobra)

Requirement already satisfied: ruamel.ordereddict in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from ruamel.yaml<0.15->cobra)

Requirement already satisfied: mpmath>=0.19 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from sympy>=1.0.0->optlang>=1.2.1->cobra)

Yu

[Yu Chen]

I tried a virtual environment, i.e. uninstalled the previous cobra package and then installed it inside a virtual folder. Still I got the same error when running "import cobra" in python. And below is the output of "pip install cobra" in the virtual environment.

Requirement already satisfied: cobra in ./VirtualENV/lib/python2.7/site-packages

Requirement already satisfied: swiglpk in ./VirtualENV/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: pandas>=0.17.0 in ./VirtualENV/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: future in ./VirtualENV/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: numpy>=1.6 in ./VirtualENV/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: optlang>=1.2.1 in ./VirtualENV/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: tabulate in ./VirtualENV/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: ruamel.yaml<0.15 in ./VirtualENV/lib/python2.7/site-packages (from cobra)

Requirement already satisfied: python-dateutil in ./VirtualENV/lib/python2.7/site-packages (from pandas>=0.17.0->cobra)

Requirement already satisfied: pytz>=2011k in ./VirtualENV/lib/python2.7/site-packages (from pandas>=0.17.0->cobra)

Requirement already satisfied: six>=1.9.0 in ./VirtualENV/lib/python2.7/site-packages (from optlang>=1.2.1->cobra)

Requirement already satisfied: sympy>=1.0.0 in ./VirtualENV/lib/python2.7/site-packages (from optlang>=1.2.1->cobra)

Requirement already satisfied: ruamel.ordereddict in ./VirtualENV/lib/python2.7/site-packages (from ruamel.yaml<0.15->cobra)

Requirement already satisfied: mpmath>=0.19 in ./VirtualENV/lib/python2.7/site-packages (from sympy>=1.0.0->optlang>=1.2.1->cobra)

Yu

[henning.red]

The installations look good (both with and without the virtual env), then it is just for some reason the wrong search path, you are sure you activated your virtual environment? What is the output of

`which python` ?

And in python, what is the output of 

```

import sys

sys.path

```

?

[Yu Chen]

Yes, I think I activated the virtual environment.

The output of "which python" is:

/Users/cheyu/VirtualENV/bin/python

The output of "import sys" and then "sys.path" is:

['', '/Users/cheyu/VirtualENV/lib/python27.zip', '/Users/cheyu/VirtualENV/lib/python2.7', '/Users/cheyu/VirtualENV/lib/python2.7/plat-darwin', '/Users/cheyu/VirtualENV/lib/python2.7/plat-mac', '/Users/cheyu/VirtualENV/lib/python2.7/plat-mac/lib-scriptpackages', '/Users/cheyu/VirtualENV/lib/python2.7/lib-tk', '/Users/cheyu/VirtualENV/lib/python2.7/lib-old', '/Users/cheyu/VirtualENV/lib/python2.7/lib-dynload', '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7', '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin', '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk', '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac', '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages', '/Users/cheyu/VirtualENV/lib/python2.7/site-packages']

[henning.red]

That's bizarre.. so just to be sure, can you

source activate VirtualEnv/bin/activate

python -c 'import cobra; print(cobra)'

again and then post here the entire input/output, should look something like this

(py36) ➜  proj source cobrapy/py36/bin/activate

(py36) ➜  proj python -c 'import cobra; print(cobra)'

<module 'cobra' from '/Users/henred/proj/cobrapy/py36/lib/python3.6/site-packages/cobra/__init__.py'>

//Henning

[Yu Chen]

Please see input and output below:

xxxx:~ cheyu$ source VirtualENV/bin/activate

(VirtualENV) xxxx:~ cheyu$ python -c "import cobra; print cobra"

Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cobra.py", line 1, in <module>

ImportError: No module named test

Besides, I tried another package installed together with cobra, e.g. pandas, it worked:

(VirtualENV) xxxx:~ cheyu$ python -c "import pandas; print pandas"

<module 'pandas' from '/Users/cheyu/VirtualENV/lib/python2.7/site-packages/pandas/__init__.pyc'>

Then I tried "pip list", I found both cobra and pandas are in the activated virtual environment:

(VirtualENV) xxxx:~ cheyu$ pip list

cobra (0.8.1)

future (0.16.0)

mpmath (0.19)

numpy (1.13.1)

optlang (1.2.1)

pandas (0.20.3)

pip (9.0.1)

python-dateutil (2.6.1)

pytz (2017.2)

ruamel.ordereddict (0.4.13)

ruamel.yaml (0.14.12)

setuptools (36.2.7)

six (1.10.0)

swiglpk (1.4.3)

sympy (1.1.1)

tabulate (0.7.7)

wheel (0.29.0)

[Yu Chen]

I think I have fixed this already.

I just deleted a file named "cobra.pyc" in the folder "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7", and then cobra worked. The file could be moved to that folder by accident. But I don't know why this leads to the error.

[henning.red]

This is a clue:

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cobra.py", line 1, in <module>

Python tries to load cobra from outside your virtual env so something is wrong in the order of sys.path. Removing it from there completely should sort it but not sure why the path problem to begin with... Anyway, great you managed to get around it.

[Yu Chen]

Thanks Henning for your kind help and explanation.

Yu