Help! Cobra toolbox with CobraPy doesn't work

[Trizali]

Hello,

Using cobra toolbox with CobraPy does not work for me.
I have a tool in matlab, and I need to execute it with Jupyter's Python.

I can connect with Matlab executing:

from pymatbridge import Matlab
mlab = Matlab(executable='/usr/local/MATLAB/R2016b/bin/matlab')
mlab.start()

But I can't convert a model sbml to matlab struct with:
model_to_pymatbridge(model, variable_name="model", matlab=pymatbridge.Matlab)
AttributeError: 'numpy.ndarray' object has no attribute 'todok'

I tried with magics, but I can't connect to Matlab
%load_ext pymatbridge
............................................................MATLAB session timed out after 60 seconds

How does it work? How I can execute a cobra toolbox in Jupyter with Python?

I will be grateful for any help you can provide.
Thank you in advance.

[Midnighter]

Noone has worked on the Matlab interface in a while so thank you for reporting the issue. That also means that we don't have a lot of expertise right now. We'll look into it, of course.

[Trizali]

I finally got connected to Matlab with %load_ext pymatbridge.
I'm following the cobrapy core official document, however model_to_pymatbridge doesn't work.

Any idea?

%load_ext pymatbridge
import cobra.test
m = cobra.test.create_test_model("textbook")

**model_to_pymatbridge**(model, variable_name="model")
**AttributeError: 'numpy.ndarray' object has no attribute 'todok'**

Thank in advance.

[cdiener]

Hi, could you check whether you have scipy installed, since that is required for that functionality. The error suggests that you are missing scipy.

We should probably make that clear when calling the function...

[beacamara]

Hello,
I am trying to work Using cobra toolbox with CobraPy and this bug it is not still fixed. I have checked that the scipy is installed, but still it does not work.

I am using Python 3.6.8 and IPython 7.8.0 --

Any help please?

[Midnighter]

@beacamara please post the output of cobra.show_versions() here.

[beacamara]

System Information

OS Linux
OS-release 4.4.0-148-generic
Python 3.6.8

Package Versions

cobra 0.16.0
depinfo 1.5.1
future 0.17.1
numpy 1.14.0
optlang 1.4.4
pandas 0.22.0
pip 19.2.3
python-libsbml-experimental 5.18.0
ruamel.yaml 0.16.5
setuptools 38.5.1
six 1.11.0
swiglpk 4.65.0
wheel 0.30.0

[cdiener]

Looks like the error was introduced with the new create_stoichiometric_matrix function which now returns a sense array by default. Should be an easy fix but I have no way of testing whether it would work (no Matlab).

[beacamara]

I have an old version of Matlab (R2010b). I there a way a can help to fix it? If you lead me to do it I can try.

[cdiener]

Cool, l'll send a PR with a potential fix and ping you with instructions on how to test it.

[waltersaj101]

@cdiener is this issue fixed? I just ran into the same issue

[cdiener]

Not yet because I do not have access to Matlab and nobody was willing to help out by testing the proposed fix and some example code in #909. I you want to jump in and test the PR and whether pymatbridge still works we would definitely appreciate it.

[waltersaj101]

@cdiener I'd be happy to! Sorry for the delayed response. I can get to this next week sometime and I'll let you know what I figure out!

[cdiener]

That would be great. For now it would be sufficient to run the code from my last comment in #909 and confirm that pymatbridge is still working. That does not require checking out the PR.

[akaviaLab]

This should be closed since pymatbridge has been removed due to lack of maintainers. see #1197 which was merged as of release 0.25