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wc_model_gen/utils.py

Summary

Maintainability
F
1 wk
Test Coverage
A
98%

File utils.py has 567 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Utility methods for generating submodels

:Author: Yin Hoon Chew <yinhoon.chew@mssm.edu>
:Date: 2019-01-23
:Copyright: 2019, Karr Lab
Severity: Major
Found in wc_model_gen/utils.py - About 1 day to fix

    Function test_metabolite_production has a Cognitive Complexity of 45 (exceeds 5 allowed). Consider refactoring.
    Open

    def test_metabolite_production(submodel, reaction_bounds, pseudo_reactions=None, 
    test_producibles=None, test_recyclables=None):
    """ Test that an FBA metabolism submodel can produce each reactant component (producible) 
        and recycle each product component (recyclable) in each reaction in the objective 
        function individually. First, a source (sink) reaction is added for each reactant
    Severity: Minor
    Found in wc_model_gen/utils.py - About 6 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_michaelis_menten_like_rate_law has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.
    Open

    def gen_michaelis_menten_like_rate_law(model, reaction, modifiers=None, modifier_reactants=None, exclude_substrates=None):
    """ Generate a Michaelis-Menten-like rate law. For a multi-substrate reaction,  
        the substrate term is formulated as the multiplication of a Hill equation
        with a coefficient of 1 for each substrate. For multi-steps reaction where
        each step is catalyzed by a different enzyme, the enzyme term is formulated
    Severity: Minor
    Found in wc_model_gen/utils.py - About 3 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_response_functions has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
    Open

    def gen_response_functions(model, beta, reaction_id, reaction_class, compartment, reaction_factors):
        """ Generate a list of response function expression string for each factor or 
            group of factors (F) in the form of:
                       
                        F/(Km + F)
    Severity: Minor
    Found in wc_model_gen/utils.py - About 3 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_mass_action_rate_law has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
    Open

    def gen_mass_action_rate_law(model, reaction, model_k, modifiers=None, modifier_reactants=None):
    """ Generate a mass action rate law.

        Example:
    Severity: Minor
    Found in wc_model_gen/utils.py - About 1 hr 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_response_functions has 6 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def gen_response_functions(model, beta, reaction_id, reaction_class, compartment, reaction_factors):
    Severity: Minor
    Found in wc_model_gen/utils.py - About 45 mins to fix

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

      def gen_michaelis_menten_like_rate_law(model, reaction, modifiers=None, modifier_reactants=None, exclude_substrates=None):
      Severity: Minor
      Found in wc_model_gen/utils.py - About 35 mins to fix

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

        def gen_mass_action_rate_law(model, reaction, model_k, modifiers=None, modifier_reactants=None):
        Severity: Minor
        Found in wc_model_gen/utils.py - About 35 mins to fix

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

          def test_metabolite_production(submodel, reaction_bounds, pseudo_reactions=None,
          Severity: Minor
          Found in wc_model_gen/utils.py - About 35 mins to fix

            Function gen_michaelis_menten_like_propensity_function has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
            Open

            def gen_michaelis_menten_like_propensity_function(model, reaction, substrates_as_modifiers=None, exclude_substrates=None):
    """ Generate a Michaelis-Menten-like propensity function. 
        For species that are considered 'substrates', the substrate term is formulated as the 
        multiplication of a Hill equation with a coefficient of 1 for each 'substrate'. 
        For species that are considered 'modifiers', the modifier term is formulated
            Severity: Minor
            Found in wc_model_gen/utils.py - About 35 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

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                for reactant in reactants:            
        obj_reaction = conv_opt.Variable(name=reactant + '_test_reaction', 
                                type=conv_opt.VariableType.continuous,
                                lower_bound=0.0)
        obj_reactants[reactant] = obj_reaction
            Severity: Major
            Found in wc_model_gen/utils.py and 1 other location - About 1 day to fix
            wc_model_gen/utils.py on lines 135..146

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 147.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                for product in products:            
        obj_reaction = conv_opt.Variable(name=product + '_test_reaction', 
                            type=conv_opt.VariableType.continuous,
                            lower_bound=0.0)
        obj_products[product] = obj_reaction
            Severity: Major
            Found in wc_model_gen/utils.py and 1 other location - About 1 day to fix
            wc_model_gen/utils.py on lines 120..131

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 147.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                for product in products:
        obj_reaction = obj_products[product]
        conv_model.objective_terms = [conv_opt.LinearTerm(obj_reaction, 1.),]
        result = conv_model.solve()
        if result.value == 0.0:
            Severity: Major
            Found in wc_model_gen/utils.py and 1 other location - About 3 hrs to fix
            wc_model_gen/utils.py on lines 168..173

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 63.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                for reactant in reactants:
        obj_reaction = obj_reactants[reactant]
        conv_model.objective_terms = [conv_opt.LinearTerm(obj_reaction, 1.),]
        result = conv_model.solve()
        if result.value == 0.0:
            Severity: Major
            Found in wc_model_gen/utils.py and 1 other location - About 3 hrs to fix
            wc_model_gen/utils.py on lines 176..181

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 63.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                if test_recyclables:
        products = test_recyclables
    else:    
        products = []
        for reaction in submodel.dfba_obj.expression.reactions:
            Severity: Major
            Found in wc_model_gen/utils.py and 1 other location - About 2 hrs to fix
            wc_model_gen/utils.py on lines 77..84

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 60.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                if test_producibles:
        reactants = test_producibles
    else:    
        reactants = []
        for reaction in submodel.dfba_obj.expression.reactions:
            Severity: Major
            Found in wc_model_gen/utils.py and 1 other location - About 2 hrs to fix
            wc_model_gen/utils.py on lines 86..93

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 60.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Identical blocks of code found in 2 locations. Consider refactoring.
            Open

                        model_k_m = model.parameters.get_or_create(id='K_m_{}_{}'.format(reaction.id, species.species_type.id),
                                                type=wc_ontology['WC:K_m'],
                                                units=unit_registry.parse_units('M'))
            Severity: Major
            Found in wc_model_gen/utils.py and 1 other location - About 1 hr to fix
            wc_model_gen/utils.py on lines 363..365

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 46.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Identical blocks of code found in 2 locations. Consider refactoring.
            Open

                        model_k_m = model.parameters.get_or_create(id='K_m_{}_{}'.format(reaction.id, species.species_type.id),
                                                type=wc_ontology['WC:K_m'],
                                                units=unit_registry.parse_units('M'))
            Severity: Major
            Found in wc_model_gen/utils.py and 1 other location - About 1 hr to fix
            wc_model_gen/utils.py on lines 455..457

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 46.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                f = model.parameters.get_or_create(
        id='f_{}_{}'.format(reaction_id, activator.species_type.id),
        type=None,
        units=unit_registry.parse_units(''))
            Severity: Major
            Found in wc_model_gen/utils.py and 2 other locations - About 1 hr to fix
            wc_model_gen/utils.py on lines 217..220
            wc_model_gen/utils.py on lines 262..265

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 38.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                Kr = model.parameters.get_or_create(
            id='Kr_{}_{}'.format(reaction_id, repressor.species_type.id),
            type=None,
            units=unit_registry.parse_units('M'))
            Severity: Major
            Found in wc_model_gen/utils.py and 2 other locations - About 1 hr to fix
            wc_model_gen/utils.py on lines 262..265
            wc_model_gen/utils.py on lines 268..271

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 38.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                Ka = model.parameters.get_or_create(
        id='Ka_{}_{}'.format(reaction_id, activator.species_type.id),
        type=None,
        units=unit_registry.parse_units('M'))
            Severity: Major
            Found in wc_model_gen/utils.py and 2 other locations - About 1 hr to fix
            wc_model_gen/utils.py on lines 217..220
            wc_model_gen/utils.py on lines 268..271

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 38.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 12 locations. Consider refactoring.
            Open

                avogadro = model.parameters.get_or_create(
        id='Avogadro',
        type=None,
        value=scipy.constants.Avogadro,
        units=unit_registry.parse_units('molecule mol^-1'))
            Severity: Major
            Found in wc_model_gen/utils.py and 11 other locations - About 40 mins to fix
            wc_model_gen/eukaryote/complexation.py on lines 363..367
            wc_model_gen/eukaryote/transcription.py on lines 1095..1099
            wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
            wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
            wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
            wc_model_gen/prokaryote/transcription.py on lines 105..109
            wc_model_gen/prokaryote/translation.py on lines 167..171
            wc_model_gen/utils.py on lines 210..214
            wc_model_gen/utils.py on lines 255..259
            wc_model_gen/utils.py on lines 343..347
            wc_model_gen/utils.py on lines 514..518

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 34.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 12 locations. Consider refactoring.
            Open

                avogadro = model.parameters.get_or_create(
        id='Avogadro',
        type=None,
        value=scipy.constants.Avogadro,
        units=unit_registry.parse_units('molecule mol^-1'))
            Severity: Major
            Found in wc_model_gen/utils.py and 11 other locations - About 40 mins to fix
            wc_model_gen/eukaryote/complexation.py on lines 363..367
            wc_model_gen/eukaryote/transcription.py on lines 1095..1099
            wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
            wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
            wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
            wc_model_gen/prokaryote/transcription.py on lines 105..109
            wc_model_gen/prokaryote/translation.py on lines 167..171
            wc_model_gen/utils.py on lines 210..214
            wc_model_gen/utils.py on lines 255..259
            wc_model_gen/utils.py on lines 432..436
            wc_model_gen/utils.py on lines 514..518

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 34.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 12 locations. Consider refactoring.
            Open

                    Avogadro = model.parameters.get_or_create(
            id='Avogadro',
            type=None,
            value=scipy.constants.Avogadro,
            units=unit_registry.parse_units('molecule mol^-1'))
            Severity: Major
            Found in wc_model_gen/utils.py and 11 other locations - About 40 mins to fix
            wc_model_gen/eukaryote/complexation.py on lines 363..367
            wc_model_gen/eukaryote/transcription.py on lines 1095..1099
            wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
            wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
            wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
            wc_model_gen/prokaryote/transcription.py on lines 105..109
            wc_model_gen/prokaryote/translation.py on lines 167..171
            wc_model_gen/utils.py on lines 210..214
            wc_model_gen/utils.py on lines 255..259
            wc_model_gen/utils.py on lines 343..347
            wc_model_gen/utils.py on lines 432..436

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 34.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 12 locations. Consider refactoring.
            Open

                avogadro = model.parameters.get_or_create(
        id='Avogadro',
        type=None,
        value=scipy.constants.Avogadro,
        units=unit_registry.parse_units('molecule mol^-1'))
            Severity: Major
            Found in wc_model_gen/utils.py and 11 other locations - About 40 mins to fix
            wc_model_gen/eukaryote/complexation.py on lines 363..367
            wc_model_gen/eukaryote/transcription.py on lines 1095..1099
            wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
            wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
            wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
            wc_model_gen/prokaryote/transcription.py on lines 105..109
            wc_model_gen/prokaryote/translation.py on lines 167..171
            wc_model_gen/utils.py on lines 255..259
            wc_model_gen/utils.py on lines 343..347
            wc_model_gen/utils.py on lines 432..436
            wc_model_gen/utils.py on lines 514..518

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 34.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 12 locations. Consider refactoring.
            Open

                avogadro = model.parameters.get_or_create(
        id='Avogadro',
        type=None,
        value=scipy.constants.Avogadro,
        units=unit_registry.parse_units('molecule mol^-1'))
            Severity: Major
            Found in wc_model_gen/utils.py and 11 other locations - About 40 mins to fix
            wc_model_gen/eukaryote/complexation.py on lines 363..367
            wc_model_gen/eukaryote/transcription.py on lines 1095..1099
            wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
            wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
            wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
            wc_model_gen/prokaryote/transcription.py on lines 105..109
            wc_model_gen/prokaryote/translation.py on lines 167..171
            wc_model_gen/utils.py on lines 210..214
            wc_model_gen/utils.py on lines 343..347
            wc_model_gen/utils.py on lines 432..436
            wc_model_gen/utils.py on lines 514..518

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 34.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                        expression_terms.append('({} / ({} + {} * {} * {}))'.format(species.gen_id(),
                                                                        species.gen_id(),
                                                                        model_k_m.id, avogadro.id,
                                                                        volume.id))
            Severity: Minor
            Found in wc_model_gen/utils.py and 2 other locations - About 35 mins to fix
            wc_model_gen/utils.py on lines 371..374
            wc_model_gen/utils.py on lines 550..555

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 33.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                            factor_exp.append('({} / ({} + {} * {} * {}))'.format(
                    factor_species.gen_id(),
                    factor_species.gen_id(),
                    model_k_m.id, 
                    Avogadro.id,
            Severity: Minor
            Found in wc_model_gen/utils.py and 2 other locations - About 35 mins to fix
            wc_model_gen/utils.py on lines 371..374
            wc_model_gen/utils.py on lines 463..466

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 33.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                        expression_terms.append('({} / ({} + {} * {} * {}))'.format(species.gen_id(),
                                                                        species.gen_id(),
                                                                        model_k_m.id, avogadro.id,
                                                                        volume.id))
            Severity: Minor
            Found in wc_model_gen/utils.py and 2 other locations - About 35 mins to fix
            wc_model_gen/utils.py on lines 463..466
            wc_model_gen/utils.py on lines 550..555

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 33.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

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