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

                trans_reaction.participants.append(model.species_types.get_one(id='h').species.get_one(
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 522..522
wc_model_gen/eukaryote/translation_translocation.py on lines 530..530

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 41.

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

            reaction.participants.append(metabolites['gmp'][
                degradation_compartment.id].species_coefficients.get_or_create(coefficient=ntp_count['G']))
Severity: Major
Found in wc_model_gen/eukaryote/rna_degradation.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/rna_degradation.py on lines 125..126
wc_model_gen/eukaryote/rna_degradation.py on lines 127..128
wc_model_gen/eukaryote/rna_degradation.py on lines 131..132

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 41.

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 5 locations. Consider refactoring.
Open

            param = model.parameters.create(id='k_cat_{}'.format(rxn.id),
                                            type=wc_ontology['WC:k_cat'],
                                            units=unit_registry.parse_units('s^-1'))
Severity: Major
Found in wc_model_gen/prokaryote/metabolism.py and 4 other locations - About 1 hr to fix
wc_model_gen/eukaryote/complexation.py on lines 325..327
wc_model_gen/eukaryote/transcription.py on lines 1050..1053
wc_model_gen/eukaryote/translation_translocation.py on lines 980..983
wc_model_gen/eukaryote/translation_translocation.py on lines 1056..1059

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 41.

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 5 locations. Consider refactoring.
Open

            k_cat_elongation = model.parameters.create(
                id='k_cat_{}'.format(elongation_reaction.id),
                type=onto['WC:k_cat'],
                units=unit_registry.parse_units('molecule^-1 s^-1'),
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 4 other locations - About 1 hr to fix
wc_model_gen/eukaryote/complexation.py on lines 325..327
wc_model_gen/eukaryote/translation_translocation.py on lines 980..983
wc_model_gen/eukaryote/translation_translocation.py on lines 1056..1059
wc_model_gen/prokaryote/metabolism.py on lines 165..167

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 41.

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

            reaction.participants.append(metabolites['ump'][
                degradation_compartment.id].species_coefficients.get_or_create(coefficient=ntp_count['U']))
Severity: Major
Found in wc_model_gen/eukaryote/rna_degradation.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/rna_degradation.py on lines 125..126
wc_model_gen/eukaryote/rna_degradation.py on lines 127..128
wc_model_gen/eukaryote/rna_degradation.py on lines 129..130

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 41.

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

                trans_reaction.participants.append(model.species_types.get_one(id=energy_product).species.get_one(
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 520..520

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 41.

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

                trans_reaction.participants.append(model.species_types.get_one(id=energy_reactant).species.get_one(
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 528..528

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 41.

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 rna_elongation_termination_factors:
            for i in set(rna_elongation_termination_factors.values()):
                if i not in elongation_termination_factors:
                    raise ValueError('{} is not a key in elongation_termination_factors'.format(i))
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 119..122

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 41.

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 rna_init_factors:
            for i in set(rna_init_factors.values()):
                if i not in init_factors:
                    raise ValueError('{} is not a key in init_factors'.format(i))
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 126..129

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 41.

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 5 locations. Consider refactoring.
Open

                k_cat_translocation = model.parameters.create(
                    id='k_cat_{}'.format(reaction.id),
                    type=wc_ontology['WC:k_cat'],
                    units=unit_registry.parse_units('molecule^-1 s^-1'),
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 4 other locations - About 1 hr to fix
wc_model_gen/eukaryote/complexation.py on lines 325..327
wc_model_gen/eukaryote/transcription.py on lines 1050..1053
wc_model_gen/eukaryote/translation_translocation.py on lines 980..983
wc_model_gen/prokaryote/metabolism.py on lines 165..167

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 41.

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 5 locations. Consider refactoring.
Open

                diss_k_cat = model.parameters.create(id='k_cat_{}'.format(reaction.id),
                    type=wc_ontology['WC:k_cat'],
                    units=unit_registry.parse_units('molecule^-1 s^-1'))
Severity: Major
Found in wc_model_gen/eukaryote/complexation.py and 4 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 1050..1053
wc_model_gen/eukaryote/translation_translocation.py on lines 980..983
wc_model_gen/eukaryote/translation_translocation.py on lines 1056..1059
wc_model_gen/prokaryote/metabolism.py on lines 165..167

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 41.

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

        ref_kd = wc_lang.Reference(
            model=model,
            title='Macromolecular crowding as a regulator of gene transcription',
            author='Hiroaki Matsuda, Gregory Garbes Putzel, Vadim Backman, Igal Szleifer',        
            year=2014,
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 195..201
wc_model_gen/eukaryote/transcription.py on lines 609..615

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 40.

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

        ref_polr_distribution = wc_lang.Reference(
            model=model,
            title='In vivo dynamics of RNA polymerase II transcription',
            author='Xavier Darzacq, Yaron Shav-Tal, Valeria de Turris, Yehuda Brody, '
                'Shailesh M Shenoy, Robert D Phair, Robert H Singer',
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 609..615
wc_model_gen/eukaryote/transcription.py on lines 622..627

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 40.

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

        ref_model = wc_lang.Reference(
            model=model,
            title='Transcriptional regulation by the numbers: models',
            author='Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia, '
                'Ulrich Gerland, Terence Hwa, Jane Kondev, Rob Phillips',
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 195..201
wc_model_gen/eukaryote/transcription.py on lines 622..627

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 40.

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 4 locations. Consider refactoring.
Open

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

        beta = options.get('beta', 1.)
Severity: Major
Found in wc_model_gen/prokaryote/protein_degradation.py and 3 other locations - About 1 hr to fix
wc_model_gen/prokaryote/rna_degradation.py on lines 30..35
wc_model_gen/prokaryote/transcription.py on lines 30..35
wc_model_gen/prokaryote/translation.py on lines 29..34

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 39.

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_rxn.participants.add(
                                        h2o.species_coefficients.get_or_create(
                                        coefficient=-(sum(aa_content.values())-1)))
Severity: Major
Found in wc_model_gen/eukaryote/complexation.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/protein_degradation.py on lines 147..149

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 39.

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 4 locations. Consider refactoring.
Open

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

        beta = options.get('beta', 1.)
Severity: Major
Found in wc_model_gen/prokaryote/transcription.py and 3 other locations - About 1 hr to fix
wc_model_gen/prokaryote/protein_degradation.py on lines 31..36
wc_model_gen/prokaryote/rna_degradation.py on lines 30..35
wc_model_gen/prokaryote/translation.py on lines 29..34

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 39.

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 4 locations. Consider refactoring.
Open

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

        beta = options.get('beta', 1.)
Severity: Major
Found in wc_model_gen/prokaryote/rna_degradation.py and 3 other locations - About 1 hr to fix
wc_model_gen/prokaryote/protein_degradation.py on lines 31..36
wc_model_gen/prokaryote/transcription.py on lines 30..35
wc_model_gen/prokaryote/translation.py on lines 29..34

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 39.

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_rxn.participants.add(
                    h2o.species_coefficients.get_or_create(
                    coefficient=-(sum(aa_content.values())-1)))
Severity: Major
Found in wc_model_gen/eukaryote/protein_degradation.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/complexation.py on lines 223..225

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 39.

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 4 locations. Consider refactoring.
Open

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

        beta = options.get('beta', 1.)
Severity: Major
Found in wc_model_gen/prokaryote/translation.py and 3 other locations - About 1 hr to fix
wc_model_gen/prokaryote/protein_degradation.py on lines 31..36
wc_model_gen/prokaryote/rna_degradation.py on lines 30..35
wc_model_gen/prokaryote/transcription.py on lines 30..35

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 39.

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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