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Similar blocks of code found in 4 locations. Consider refactoring.
Open

            for degradosome_kb in cell.observables.get_one(id='degrade_protease_obs').expression.species:
                degradosome_species_type_model = model.species_types.get_one(id=degradosome_kb.species_type.id)
                degradosome_species_model = degradosome_species_type_model.species.get_one(compartment=cytosol)

                reaction.participants.add(degradosome_species_model.species_coefficients.get_or_create(
Severity: Major
Found in wc_model_gen/prokaryote/protein_degradation.py and 3 other locations - About 5 hrs to fix
wc_model_gen/prokaryote/rna_degradation.py on lines 74..80
wc_model_gen/prokaryote/transcription.py on lines 76..81
wc_model_gen/prokaryote/translation.py on lines 140..145

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 96.

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 4 locations. Consider refactoring.
Open

            for rnap_kb in cell.observables.get_one(id='rna_polymerase_obs').expression.species:
                rnap_species_type_model = model.species_types.get_one(id=rnap_kb.species_type.id)
                rnap_model = rnap_species_type_model.species.get_one(compartment=cytosol)

                reaction.participants.add(rnap_model.species_coefficients.get_or_create(coefficient=-1))
Severity: Major
Found in wc_model_gen/prokaryote/transcription.py and 3 other locations - About 5 hrs to fix
wc_model_gen/prokaryote/protein_degradation.py on lines 93..99
wc_model_gen/prokaryote/rna_degradation.py on lines 74..80
wc_model_gen/prokaryote/translation.py on lines 140..145

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 96.

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

Function _import_cytosolic_trna_into_mitochondria has a Cognitive Complexity of 36 (exceeds 5 allowed). Consider refactoring.
Open

    def _import_cytosolic_trna_into_mitochondria(self, cytosolic_trna_ids):
        """ Create reactions and rate laws for importing cytosolic tRNAs into the mitochondria.
            The concentrations of imported tRNAs in the mitochondria are set based on
            the provided fraction and the rates of transport are calibrated accordingly to achieve
            steady-states
Severity: Minor
Found in wc_model_gen/eukaryote/translation_translocation.py - About 5 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

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

            for codon_info in matched_trnas:
                expression_terms.append(codon_info['function'].id)
                objects[wc_lang.Function][codon_info['function'].id] = codon_info['function']                
                for cl, dictionary in objects.items():
                    dictionary.update(codon_info['objects'][cl])
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 5 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 941..945

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 90.

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 average_rate:            
                model_kcat.value = 1.
                eval_rate_law = init_reaction.rate_laws[0].expression._parsed_expression.eval({
                    wc_lang.Species: init_species_counts,
                    wc_lang.Compartment: init_compartment_volumes,
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 5 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1261..1273

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 90.

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

                        for codon_info in matched_trnas:    
                            expression_terms.append(codon_info['function'].id)
                            objects[wc_lang.Function][codon_info['function'].id] = codon_info['function']                        
                            for cl, dictionary in objects.items():
                                dictionary.update(codon_info['objects'][cl])
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 5 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 814..818

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 90.

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 average_rate:            
                model_kcat.value = 1.
                eval_rate_law = el_reaction.rate_laws[0].expression._parsed_expression.eval({
                    wc_lang.Species: el_species_counts,
                    wc_lang.Compartment: init_compartment_volumes,
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 5 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1218..1230

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 90.

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

Function calibrate_submodel has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.
Open

    def calibrate_submodel(self):
        """ Calibrate the submodel using data in the KB """        
        model = self.model        
        cell = self.knowledge_base.cell
Severity: Minor
Found in wc_model_gen/eukaryote/complexation.py - About 5 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 relax_bounds has a Cognitive Complexity of 32 (exceeds 5 allowed). Consider refactoring.
Open

    def relax_bounds(self, target, lower_bound_adjustable, upper_bound_adjustable):
        """ Relax bounds to achieve set target flux(es) while minimizing the total necessary adjustment
            to the flux bounds
        
        Args:
Severity: Minor
Found in wc_model_gen/eukaryote/metabolism.py - About 4 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

Similar blocks of code found in 4 locations. Consider refactoring.
Open

            for func in reaction.rate_laws[0].expression.functions:
                for species in func.expression.species:
                    init_species_counts[species.id] = species.distribution_init_concentration.mean
                for obs in func.expression.observables:
                    for species in obs.expression.species:
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 3 other locations - About 4 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1209..1214
wc_model_gen/eukaryote/translation_translocation.py on lines 1252..1257
wc_model_gen/eukaryote/translation_translocation.py on lines 1309..1314

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 82.

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 4 locations. Consider refactoring.
Open

            for func in init_reaction.rate_laws[0].expression.functions:
                for species in func.expression.species:
                    init_species_counts[species.id] = species.distribution_init_concentration.mean
                for obs in func.expression.observables:
                    for species in obs.expression.species:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 4 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 1247..1252
wc_model_gen/eukaryote/translation_translocation.py on lines 1252..1257
wc_model_gen/eukaryote/translation_translocation.py on lines 1309..1314

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 82.

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 4 locations. Consider refactoring.
Open

            for func in el_reaction.rate_laws[0].expression.functions:                
                for species in func.expression.species:
                    el_species_counts[species.id] = species.distribution_init_concentration.mean
                for obs in func.expression.observables:
                    for species in obs.expression.species:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 4 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 1247..1252
wc_model_gen/eukaryote/translation_translocation.py on lines 1209..1214
wc_model_gen/eukaryote/translation_translocation.py on lines 1309..1314

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 82.

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 4 locations. Consider refactoring.
Open

                for func in trans_reaction.rate_laws[0].expression.functions:
                    for species in func.expression.species:
                        trans_species_counts[species.id] = species.distribution_init_concentration.mean
                    for obs in func.expression.observables:
                        for species in obs.expression.species:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 4 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 1247..1252
wc_model_gen/eukaryote/translation_translocation.py on lines 1209..1214
wc_model_gen/eukaryote/translation_translocation.py on lines 1252..1257

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 82.

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

Function gen_distribution_init_concentrations has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
Open

    def gen_distribution_init_concentrations(self):
        """ Generate concentrations for the model from knowledge base """
        kb = self.knowledge_base
        model = self.model
        media = self.options['media']
Severity: Minor
Found in wc_model_gen/eukaryote/initialize_model.py - About 4 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 clean_and_validate_options has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.
Open

    def clean_and_validate_options(self):
        """ Apply default options and validate options """
        options = self.options

        transcription_unit = options.get('transcription_unit', {})
Severity: Minor
Found in wc_model_gen/eukaryote/transcription.py - About 4 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_kb_reactions has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.
Open

    def gen_kb_reactions(self):
        """ Generate reactions encoded within KB
        """

        kb = self.knowledge_base
Severity: Minor
Found in wc_model_gen/eukaryote/initialize_model.py - About 4 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

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

                        if serine_coefficient:
                            old_coef = serine_coefficient.coefficient
                            el_reaction.participants.remove(serine_coefficient)
                            el_reaction.participants.add(
                                serine_species.species_coefficients.get_or_create(
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 4 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 436..445

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 75.

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 aa_coefficient:
                            old_coef = aa_coefficient.coefficient
                            el_reaction.participants.remove(aa_coefficient)
                            el_reaction.participants.add(
                                aa_species.species_coefficients.get_or_create(
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 4 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 413..422

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 75.

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

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_kb_rate_laws has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.
Open

    def gen_kb_rate_laws(self):
        """ Generate the rate laws for reactions encoded in the knowledge base """
        kb = self.knowledge_base
        model = self.model
Severity: Minor
Found in wc_model_gen/eukaryote/initialize_model.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

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