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KarrLab/wc_model_gen

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wc_model_gen/prokaryote/initalize_model.py

Summary

Maintainability
C
7 hrs
Test Coverage
A
92%

File initalize_model.py has 318 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Initalize the construction of wc_lang-encoded models from wc_kb-encoded knowledge base.

:Author: Balazs Szigeti <balazs.szigeti@mssm.edu>
:Date: 2018-01-21
:Copyright: 2018, Karr Lab
Severity: Minor
Found in wc_model_gen/prokaryote/initalize_model.py - About 3 hrs to fix

    Function gen_kb_rate_laws has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
    Open

        def gen_kb_rate_laws(self):
        """ Generate rate laws for reactions encoded in KB """
        kb = self.knowledge_base
        model = self.model
    Severity: Minor
    Found in wc_model_gen/prokaryote/initalize_model.py - About 2 hrs 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 gen_species_type has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

        def gen_species_type(self, kb_species_type, extra_compartment_ids=None):
        """ Generate a model species type

        Args:
            kb_species_type (:obj:`wc_kb.SpeciesType`): knowledge base species type
    Severity: Minor
    Found in wc_model_gen/prokaryote/initalize_model.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 run has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

        def run(self):
        self.gen_compartments()

        self.gen_parameters()
        self.clean_and_validate_options()
    Severity: Minor
    Found in wc_model_gen/prokaryote/initalize_model.py - About 45 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 gen_kb_reactions has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

        def gen_kb_reactions(self):
        """ Generate reactions encoded within KB
            TODO: rxn.submodel attribute is removed from KB, so submodel assignement needs to be taken care of here.
                  Since all rxns explicitly encoded in KB are metabolic ones, it is manually set to be metablism atm, but
                  not more sophisticated approach
    Severity: Minor
    Found in wc_model_gen/prokaryote/initalize_model.py - About 25 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

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