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Similar blocks of code found in 13 locations. Consider refactoring.
Open

            init_reaction.participants.append(metabolites['adp'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=1))
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 12 other locations - About 45 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 439..440
wc_model_gen/eukaryote/transcription.py on lines 442..443
wc_model_gen/eukaryote/transcription.py on lines 445..446
wc_model_gen/eukaryote/transcription.py on lines 448..449
wc_model_gen/eukaryote/transcription.py on lines 451..452
wc_model_gen/eukaryote/translation_translocation.py on lines 358..359
wc_model_gen/eukaryote/translation_translocation.py on lines 360..361
wc_model_gen/eukaryote/translation_translocation.py on lines 362..363
wc_model_gen/eukaryote/translation_translocation.py on lines 369..370
wc_model_gen/eukaryote/translation_translocation.py on lines 371..372
wc_model_gen/eukaryote/translation_translocation.py on lines 375..376
wc_model_gen/eukaryote/translation_translocation.py on lines 377..378

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 35.

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 13 locations. Consider refactoring.
Open

            init_reaction.participants.append(metabolites['amp'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=1))
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 12 other locations - About 45 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 439..440
wc_model_gen/eukaryote/transcription.py on lines 442..443
wc_model_gen/eukaryote/transcription.py on lines 445..446
wc_model_gen/eukaryote/transcription.py on lines 448..449
wc_model_gen/eukaryote/transcription.py on lines 451..452
wc_model_gen/eukaryote/translation_translocation.py on lines 358..359
wc_model_gen/eukaryote/translation_translocation.py on lines 360..361
wc_model_gen/eukaryote/translation_translocation.py on lines 362..363
wc_model_gen/eukaryote/translation_translocation.py on lines 369..370
wc_model_gen/eukaryote/translation_translocation.py on lines 373..374
wc_model_gen/eukaryote/translation_translocation.py on lines 375..376
wc_model_gen/eukaryote/translation_translocation.py on lines 377..378

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 35.

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

                if modifier == self._rxn_species_modifier[reaction.id][0]:
                    modifier_reactants.append(modifier)
Severity: Major
Found in wc_model_gen/eukaryote/protein_degradation.py and 2 other locations - About 45 mins to fix
wc_model_gen/eukaryote/protein_degradation.py on lines 184..186
wc_model_gen/eukaryote/protein_degradation.py on lines 200..201

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 35.

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

                gvar.protein_aa_usage[mrna_kb.protein.id] = {i:0 for i in list(amino_acid_id_conversion.keys())}
Severity: Minor
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 45 mins to fix
wc_model_gen/eukaryote/complexation.py on lines 183..184

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 35.

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

                        el_reaction.participants.append(metabolites['adp'][
                            translation_compartment.id].species_coefficients.get_or_create(
Severity: Minor
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 45 mins to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 429..430

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 35.

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 13 locations. Consider refactoring.
Open

            init_reaction.participants.append(metabolites['h'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=5))
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 12 other locations - About 45 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 439..440
wc_model_gen/eukaryote/transcription.py on lines 442..443
wc_model_gen/eukaryote/transcription.py on lines 445..446
wc_model_gen/eukaryote/transcription.py on lines 448..449
wc_model_gen/eukaryote/transcription.py on lines 451..452
wc_model_gen/eukaryote/translation_translocation.py on lines 358..359
wc_model_gen/eukaryote/translation_translocation.py on lines 360..361
wc_model_gen/eukaryote/translation_translocation.py on lines 362..363
wc_model_gen/eukaryote/translation_translocation.py on lines 371..372
wc_model_gen/eukaryote/translation_translocation.py on lines 373..374
wc_model_gen/eukaryote/translation_translocation.py on lines 375..376
wc_model_gen/eukaryote/translation_translocation.py on lines 377..378

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 35.

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 13 locations. Consider refactoring.
Open

            init_reaction.participants.append(metabolites['gtp'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=-2))
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 12 other locations - About 45 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 439..440
wc_model_gen/eukaryote/transcription.py on lines 442..443
wc_model_gen/eukaryote/transcription.py on lines 445..446
wc_model_gen/eukaryote/transcription.py on lines 448..449
wc_model_gen/eukaryote/transcription.py on lines 451..452
wc_model_gen/eukaryote/translation_translocation.py on lines 358..359
wc_model_gen/eukaryote/translation_translocation.py on lines 360..361
wc_model_gen/eukaryote/translation_translocation.py on lines 369..370
wc_model_gen/eukaryote/translation_translocation.py on lines 371..372
wc_model_gen/eukaryote/translation_translocation.py on lines 373..374
wc_model_gen/eukaryote/translation_translocation.py on lines 375..376
wc_model_gen/eukaryote/translation_translocation.py on lines 377..378

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 35.

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

                        el_reaction.participants.append(metabolites['ppi'][
                            translation_compartment.id].species_coefficients.get_or_create(
Severity: Minor
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 45 mins to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 426..427

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 35.

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 13 locations. Consider refactoring.
Open

                init_reaction.participants.append(metabolites['adp'][
                    transcription_compartment.id].species_coefficients.get_or_create(
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 12 other locations - About 45 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 439..440
wc_model_gen/eukaryote/transcription.py on lines 442..443
wc_model_gen/eukaryote/transcription.py on lines 448..449
wc_model_gen/eukaryote/transcription.py on lines 451..452
wc_model_gen/eukaryote/translation_translocation.py on lines 358..359
wc_model_gen/eukaryote/translation_translocation.py on lines 360..361
wc_model_gen/eukaryote/translation_translocation.py on lines 362..363
wc_model_gen/eukaryote/translation_translocation.py on lines 369..370
wc_model_gen/eukaryote/translation_translocation.py on lines 371..372
wc_model_gen/eukaryote/translation_translocation.py on lines 373..374
wc_model_gen/eukaryote/translation_translocation.py on lines 375..376
wc_model_gen/eukaryote/translation_translocation.py on lines 377..378

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 35.

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/complexation.py and 11 other locations - About 40 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 1095..1099
wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
wc_model_gen/prokaryote/transcription.py on lines 105..109
wc_model_gen/prokaryote/translation.py on lines 167..171
wc_model_gen/utils.py on lines 210..214
wc_model_gen/utils.py on lines 255..259
wc_model_gen/utils.py on lines 343..347
wc_model_gen/utils.py on lines 432..436
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/prokaryote/translation.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/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 343..347
wc_model_gen/utils.py on lines 514..518

Duplicated Code

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

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

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

Tuning

This issue has a mass of 34.

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

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

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

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

Refactorings

Further Reading

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

                ntp_count = {k:v+add_seq[k] for k,v in ntp_count.items()}
Severity: Minor
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 40 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 354..354

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 2 locations. Consider refactoring.
Open

                    add_seq = {k:v+add_count[k] for k,v in add_seq.items()}
Severity: Minor
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 40 mins to fix
wc_model_gen/eukaryote/transcription.py on lines 492..492

Duplicated Code

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

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

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

Tuning

This issue has a mass of 34.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 34.

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

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

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

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

Refactorings

Further Reading

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

        Avogadro = model.parameters.get_or_create(
            id='Avogadro',
            type=None,
            value=scipy.constants.Avogadro,
            units=unit_registry.parse_units('molecule mol^-1'))
Severity: Major
Found in wc_model_gen/prokaryote/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/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/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/prokaryote/rna_degradation.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/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/prokaryote/protein_degradation.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/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 255..259
wc_model_gen/utils.py on lines 343..347
wc_model_gen/utils.py on lines 432..436
wc_model_gen/utils.py on lines 514..518

Duplicated Code

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

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

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

Tuning

This issue has a mass of 34.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 34.

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

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

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

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

Refactorings

Further Reading

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