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wc_sim/submodels/dfba.py

Summary

Maintainability
D
1 day
Test Coverage
A
98%

File dfba.py has 703 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" A submodel that uses Dynamic Flux Balance Analysis (dFBA) to model a set of reactions

:Author: Yin Hoon Chew <yinhoon.chew@mssm.edu>
:Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
:Date: 2020-07-29
Severity: Major
Found in wc_sim/submodels/dfba.py - About 1 day to fix

    Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(self, id, dynamic_model, reactions, species, dynamic_compartments,
    Severity: Major
    Found in wc_sim/submodels/dfba.py - About 1 hr to fix

      Function __init__ has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def __init__(self, id, dynamic_model, reactions, species, dynamic_compartments,
                 local_species_population, dfba_time_step, options=None):
        """ Initialize a dFBA submodel instance

        Args:
      Severity: Minor
      Found in wc_sim/submodels/dfba.py - About 55 mins to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function scale_conv_opt_model has 5 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def scale_conv_opt_model(self, conv_opt_model, copy_model=True,
      Severity: Minor
      Found in wc_sim/submodels/dfba.py - About 35 mins to fix

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