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

        for rna_kb, reaction in zip(rnas_kb, self.submodel.reactions):

            rna_product = model.species_types.get_one(id=rna_kb.id).species.get_one(compartment=cytosol)
            half_life = rna_kb.properties.get_one(property='half_life').get_value()
            mean_concentration = rna_product.distribution_init_concentration.mean
Severity: Major
Found in wc_model_gen/prokaryote/transcription.py and 1 other location - About 2 days to fix
wc_model_gen/prokaryote/translation.py on lines 184..207

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 298.

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 protein_kb, reaction in zip(protein_kb, self.submodel.reactions):

            protein_product = model.species_types.get_one(id=protein_kb.id).species.get_one(compartment=cytosol)
            half_life = protein_kb.properties.get_one(property='half_life').get_value()
            mean_concentration = protein_product.distribution_init_concentration.mean
Severity: Major
Found in wc_model_gen/prokaryote/translation.py and 1 other location - About 2 days to fix
wc_model_gen/prokaryote/transcription.py on lines 122..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 298.

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

        for rnap, factors in elongation_negative_factors.items():
            elongation_negative_factor_functions[rnap] = {}
            compartment = mitochondrion if 'polm' in rnap else nucleus
            n = 1
            for factor in factors:
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 2 days to fix
wc_model_gen/eukaryote/transcription.py on lines 757..784
wc_model_gen/eukaryote/transcription.py on lines 788..815

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 236.

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

        for rnap, factors in elongation_termination_factors.items():
            elongation_termination_factor_functions[rnap] = {}
            compartment = mitochondrion if 'polm' in rnap else nucleus
            n = 1
            for factor in factors:
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 2 days to fix
wc_model_gen/eukaryote/transcription.py on lines 757..784
wc_model_gen/eukaryote/transcription.py on lines 819..846

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 236.

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

        for rnap, factors in init_factors.items():
            init_factor_functions[rnap] = {}
            compartment = mitochondrion if 'polm' in rnap else nucleus
            n = 1
            for factor in factors:
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 2 days to fix
wc_model_gen/eukaryote/transcription.py on lines 788..815
wc_model_gen/eukaryote/transcription.py on lines 819..846

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 236.

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 comp, factors in {cytosol: cytoplasmic_initiation_factors, mitochondrion: mitochondrial_initiation_factors}.items():
            n = 1
            for factor in factors:
                factor_exp, all_species, all_parameters, all_volumes, all_observables = utils.gen_response_functions(
                    model, beta, 'translation_init_{}'.format(comp.id), 'translation_init_{}'.format(comp.id), comp, [factor])
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 715..739

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 212.

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 comp, factors in {cytosol: cytoplasmic_elongation_factors, mitochondrion: mitochondrial_elongation_factors}.items():
            n = 1
            for factor in factors:
                factor_exp, all_species, all_parameters, all_volumes, all_observables = utils.gen_response_functions(
                    model, beta, 'translation_el_{}'.format(comp.id), 'translation_el_{}'.format(comp.id), comp, [factor])
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 687..711

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 212.

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 species in init_reaction.rate_laws[0].expression.species:
                init_species_counts[species.id] = species.distribution_init_concentration.mean
                model_Km = model.parameters.get_one(
                        id='K_m_{}_{}'.format(init_reaction.id, species.species_type.id))
                if model_Km:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 1 day to fix
wc_model_gen/eukaryote/transcription.py on lines 1232..1245
wc_model_gen/eukaryote/translation_translocation.py on lines 1237..1250
wc_model_gen/eukaryote/translation_translocation.py on lines 1294..1307

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 171.

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 species in reaction.rate_laws[0].expression.species:
                init_species_counts[species.id] = species.distribution_init_concentration.mean
                model_Km = model.parameters.get_one(
                        id='K_m_{}_{}'.format(reaction.id, species.species_type.id))
                if model_Km:
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 3 other locations - About 1 day to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1194..1207
wc_model_gen/eukaryote/translation_translocation.py on lines 1237..1250
wc_model_gen/eukaryote/translation_translocation.py on lines 1294..1307

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 171.

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 species in el_reaction.rate_laws[0].expression.species:
                el_species_counts[species.id] = species.distribution_init_concentration.mean
                model_Km = model.parameters.get_one(
                        id='K_m_{}_{}'.format(el_reaction.id, species.species_type.id))
                if model_Km:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 1 day to fix
wc_model_gen/eukaryote/transcription.py on lines 1232..1245
wc_model_gen/eukaryote/translation_translocation.py on lines 1194..1207
wc_model_gen/eukaryote/translation_translocation.py on lines 1294..1307

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 171.

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 species in trans_reaction.rate_laws[0].expression.species:
                    trans_species_counts[species.id] = species.distribution_init_concentration.mean
                    model_Km = model.parameters.get_one(
                            id='K_m_{}_{}'.format(trans_reaction.id, species.species_type.id))
                    if model_Km:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 1 day to fix
wc_model_gen/eukaryote/transcription.py on lines 1232..1245
wc_model_gen/eukaryote/translation_translocation.py on lines 1194..1207
wc_model_gen/eukaryote/translation_translocation.py on lines 1237..1250

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 171.

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

                    if model.parameters.get(id='K_m_{}_{}'.format(reaction.id, species.species_type.id)):
                        model_Km = model.parameters.get_one(
                            id='K_m_{}_{}'.format(reaction.id, species.species_type.id))
                        if species.distribution_init_concentration.mean:
                            model_Km.value = beta * species.distribution_init_concentration.mean \
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/rna_degradation.py on lines 235..246

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 159.

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

                if model.parameters.get(id='K_m_{}_{}'.format(reaction.id, species.species_type.id)):
                    model_Km = model.parameters.get_one(
                        id='K_m_{}_{}'.format(reaction.id, species.species_type.id))
                    if species.distribution_init_concentration.mean:
                        model_Km.value = beta * species.distribution_init_concentration.mean \
Severity: Major
Found in wc_model_gen/eukaryote/rna_degradation.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1542..1553

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 159.

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 'Kr_' in param.id:
                    repressor_species = model.species.get_one(
                        id='{}[{}]'.format(param.id.split('_')[-1], transcription_compartment.id))
                    init_reg_species_count[repressor_species.id] = \
                        repressor_species.distribution_init_concentration.mean
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/transcription.py on lines 1141..1154

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 154.

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

                elif 'Ka_' in param.id:
                    activator_species = model.species.get_one(
                        id='{}[{}]'.format(param.id.split('_')[-1], transcription_compartment.id))
                    init_reg_species_count[activator_species.id] = \
                        activator_species.distribution_init_concentration.mean
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/transcription.py on lines 1126..1139

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 154.

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 = 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

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

        id = options.get('id', 'eukaryote')
Severity: Major
Found in wc_model_gen/eukaryote/core.py and 1 other location - About 1 day to fix
wc_model_gen/prokaryote/core.py on lines 30..44

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 144.

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

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

        id = options.get('id', 'rand_wc_model')
Severity: Major
Found in wc_model_gen/prokaryote/core.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/core.py on lines 44..58

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 144.

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

    def calc_rna_copy_num(self):
        """ Calculates the # of RNA molecules at t=0 """

        volume = self.knowledge_base.cell.parameters.get_one(id='mean_volume').value
        cytosol_kb = self.knowledge_base.cell.compartments.get_one(id='c')
Severity: Major
Found in wc_model_gen/prokaryote/metabolism.py and 1 other location - About 1 day to fix
wc_model_gen/prokaryote/metabolism.py on lines 405..420

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 141.

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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