added adaptor method and one test

[janisshin]

Added a method to emll/util.py for converting Antimony models into a form that is compatible with Cobra.
Also added a test for this method which checks to see whether the stoichiometric matrices match after conversion

[janisshin]

I am not familiar with pytest, so I am not sure if I incorporated pytest correctly.
However, the adaptor and the test should work. Please let me know if there are other things I can do to improve this pull request.

[mcnaughtonadm]

I am not familiar with pytest, so I am not sure if I incorporated pytest correctly. However, the adaptor and the test should work. Please let me know if there are other things I can do to improve this pull request.

Taking a look, I'll test things and report back if something needs to be fixed.

[mcnaughtonadm]

Okay @janisshin, so to finish out the pytest file, we will need to add an actual .ant model as a "tester". This will allow us to actually run the test and see if we get the expected outcome.

Then we can use some pytest functionality to point the test to the example model, this can be done with a pytest.mark.paramaterize decorator. Let's also change the name of the method from compare__stoich_matrices(antimony_path) to test_antimony_to_cobra_conversion(antimony_path). pytest looks for the method to have the prefix test_ or else it will interpret it as a helper function and not add it to the runtime. So making these changes will look something like:

@pytest.mark.parametrize("antimony_path", [
    "path/to/your/antimony/model1.ant",
])

def test_antimony_to_cobra_conversion(antimony_path):
    ...

you can save the model.ant with the other example models under emll/src/emll/test_models.

Once you make these changes, you can run the script with pytest test_antimony_utils.py

[janisshin]

Hi Andrew,
I made your suggested changes.
I tried to test it in my terminal by running pytest test_antimony_utils.py in an environment with pytensor installed, but it gave me an error (image). However, if it works on your end, I imagine that this pull request should be good to close (hopefully!)

[mcnaughtonadm]

Perfect, let me check to see if it runs on my end. If it's something small not working, I can fix it so we don't need to go back and forth again. Then I can review and merge.

Thanks for this addition!

[mcnaughtonadm]

Made one more change to fix some small issues, but test passes now. Merging.