Gap filler model #1
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§changed idenfity_targets method to raise errors when parameters are None
Added a test file for the Model class, including test methods for initializing the model and identifying seeds and targets. All tests pass successfully
Added a test file for the mentioned function. It passed the tests successfully
It passed successfully the test
It did pass successfully some tests. However, it was not true to: ✺ test_run: accused an error when comparing the return dict values, "'Unproducible targets': <ANY>} != None" ✺ test_evalute_results: tried to build the function, but it was giving many errors; I will try to reformulate the problem
now if there is already a file_name and save_path coincident it adds an extra number to the file_name to avoid overwriting previous files
it passed the test successfuly
…o the GapFIller class
…mpare_reactions_no_added_reactions tests added ✺ test_add_reactions_to_model fails: "Infeasible" error ✺ test_compare_reactions successfully passed the tests ✺ test_compare_reactions_no_added_reactions passed the tests
write_metabolites_to_sbml added to the file
…er organization and clarity
Added type annotations to constructor parameters
Included a step to run unit tests using for the 'biomeneco' module
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To check the results, please unzip the data.zip file that is in the tests folder first. (the data folder was to big to push).
What I changed:
-Add a method (test_e_precursors) to check if bioiso was giving false positives (model class).
-Get all completions instead of just the minimal (up to a maximum of 50 - can be changed in the submission_parameters.json).
-Add additional seeds (add seeds for cofactors associated with target's pathways) - check "identify_additional_seeds"
-Evaluate all completions with fba - description in the "add_reactions_to_model" method.