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

        Avogadro = model.parameters.get_or_create(
            id='Avogadro',
            type=None,
            value=scipy.constants.Avogadro,
            units=unit_registry.parse_units('molecule mol^-1'))
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 11 other locations - About 40 mins to fix
wc_model_gen/eukaryote/complexation.py on lines 363..367
wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
wc_model_gen/prokaryote/transcription.py on lines 105..109
wc_model_gen/prokaryote/translation.py on lines 167..171
wc_model_gen/utils.py on lines 210..214
wc_model_gen/utils.py on lines 255..259
wc_model_gen/utils.py on lines 343..347
wc_model_gen/utils.py on lines 432..436
wc_model_gen/utils.py on lines 514..518

Duplicated Code

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

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

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

Tuning

This issue has a mass of 34.

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

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

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

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

Refactorings

Further Reading

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

        Avogadro = model.parameters.get_or_create(
            id='Avogadro',
            type=None,
            value=scipy.constants.Avogadro,
            units=unit_registry.parse_units('molecule mol^-1'))
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 11 other locations - About 40 mins to fix
wc_model_gen/eukaryote/complexation.py on lines 363..367
wc_model_gen/eukaryote/transcription.py on lines 1095..1099
wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
wc_model_gen/prokaryote/transcription.py on lines 105..109
wc_model_gen/prokaryote/translation.py on lines 167..171
wc_model_gen/utils.py on lines 210..214
wc_model_gen/utils.py on lines 255..259
wc_model_gen/utils.py on lines 343..347
wc_model_gen/utils.py on lines 432..436
wc_model_gen/utils.py on lines 514..518

Duplicated Code

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

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

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

Tuning

This issue has a mass of 34.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 34.

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

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

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

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

Refactorings

Further Reading

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

        max_bool = model.parameters.get_or_create(
            id='max_bool_substance',
            type=None,
            value=1,
            units=unit_registry.parse_units('molecule'),
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 35 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 652..656
wc_model_gen/eukaryote/transcription.py on lines 660..664
wc_model_gen/eukaryote/translation_translocation.py on lines 575..579

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

                reaction.participants.append(metabolites['gmp'].species_coefficients.get_or_create(
                    coefficient=ntp_count['G']))
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 35 mins to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1500..1501
wc_model_gen/eukaryote/translation_translocation.py on lines 1502..1503
wc_model_gen/eukaryote/translation_translocation.py on lines 1506..1507

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

            polr_obs_exp, error = wc_lang.ObservableExpression.deserialize(
                ' + '.join(all_subtotal_obs.keys()),
                {wc_lang.Observable: all_subtotal_obs})
Severity: Minor
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 35 mins to fix
wc_model_gen/eukaryote/protein_degradation.py on lines 203..205

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

                reaction.participants.append(metabolites['amp'].species_coefficients.get_or_create(
                    coefficient=ntp_count['A']))
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 35 mins to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1502..1503
wc_model_gen/eukaryote/translation_translocation.py on lines 1504..1505
wc_model_gen/eukaryote/translation_translocation.py on lines 1506..1507

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

                reaction.participants.append(metabolites['cmp'].species_coefficients.get_or_create(
                    coefficient=ntp_count['C']))
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 35 mins to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1500..1501
wc_model_gen/eukaryote/translation_translocation.py on lines 1504..1505
wc_model_gen/eukaryote/translation_translocation.py on lines 1506..1507

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

        min_bool = model.parameters.get_or_create(
            id='min_bool_substance',
            type=None,
            value=0,
            units=unit_registry.parse_units('molecule'),
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 35 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 652..656
wc_model_gen/eukaryote/transcription.py on lines 660..664
wc_model_gen/eukaryote/translation_translocation.py on lines 567..571

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

                    proteasome_total_exp, error = wc_lang.ObservableExpression.deserialize(
                        ' + '.join(modifier_species.keys()),
                        {wc_lang.Species: modifier_species})
Severity: Minor
Found in wc_model_gen/eukaryote/protein_degradation.py and 1 other location - About 35 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 733..735

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

            polr_bound_species_type.structure = wc_lang.ChemicalStructure(
                    empirical_formula = polr_complex.structure.empirical_formula,
                    molecular_weight = polr_complex.structure.molecular_weight,
                    charge = polr_complex.structure.charge)
Severity: Minor
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 35 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 288..291

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

        min_bool = model.parameters.get_or_create(
            id='min_bool_substance',
            type=None,
            value=0,
            units=unit_registry.parse_units('molecule'),
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 3 other locations - About 35 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 652..656
wc_model_gen/eukaryote/translation_translocation.py on lines 567..571
wc_model_gen/eukaryote/translation_translocation.py on lines 575..579

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

        max_bool = model.parameters.get_or_create(
            id='max_bool_substance',
            type=None,
            value=1,
            units=unit_registry.parse_units('molecule'),
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 3 other locations - About 35 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 660..664
wc_model_gen/eukaryote/translation_translocation.py on lines 567..571
wc_model_gen/eukaryote/translation_translocation.py on lines 575..579

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

                reaction.participants.append(metabolites['ump'].species_coefficients.get_or_create(
                    coefficient=ntp_count['U']))
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 35 mins to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1500..1501
wc_model_gen/eukaryote/translation_translocation.py on lines 1502..1503
wc_model_gen/eukaryote/translation_translocation.py on lines 1504..1505

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

            polr_bound_non_specific_species_type.structure = wc_lang.ChemicalStructure(
                    empirical_formula = polr_complex.structure.empirical_formula,
                    molecular_weight = polr_complex.structure.molecular_weight,
                    charge = polr_complex.structure.charge)
Severity: Minor
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 35 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 403..406

Duplicated Code

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

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

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

Tuning

This issue has a mass of 33.

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

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

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

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

Refactorings

Further Reading

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

        for id in ['utp', 'atp', 'ctp', 'gtp']:
            tpps[id] = model.species_types.get_one(id=id)
Severity: Minor
Found in wc_model_gen/prokaryote/metabolism.py and 2 other locations - About 30 mins to fix
wc_model_gen/prokaryote/metabolism.py on lines 51..52
wc_model_gen/prokaryote/metabolism.py on lines 55..56

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 32.

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 id in ['udp', 'adp', 'cdp', 'gdp']:
            dpps[id] = model.species_types.get_one(id=id)
Severity: Minor
Found in wc_model_gen/prokaryote/metabolism.py and 2 other locations - About 30 mins to fix
wc_model_gen/prokaryote/metabolism.py on lines 51..52
wc_model_gen/prokaryote/metabolism.py on lines 59..60

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 32.

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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