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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 90.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 90.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 90.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 90.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 82.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 82.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 82.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 82.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 75.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 75.

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

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

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

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

Refactorings

Further Reading

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

                        add_count = gvar.transcript_ntp_usage[add_transcript] = {
                            'A': seq.upper().count('A'),
                            'C': seq.upper().count('C'),
                            'G': seq.upper().count('G'),
                            'U': seq.upper().count('U'),
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 3 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1487..1492

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 70.

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 = gvar.transcript_ntp_usage[trna_id] = {
                        'A': seq.upper().count('A'),
                        'C': seq.upper().count('C'),
                        'G': seq.upper().count('G'),
                        'U': seq.upper().count('U'),
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 3 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 347..352

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 70.

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

            chunked_data = [chunked_data[i * size:(i + 1) * size] for i in range((len(chunked_data) + size - 1) // size )]
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 3 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 720..720

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 65.

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

                expr = [expr[i * group:(i + 1) * group] for i in range((len(expr) + group - 1) // group )]
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 3 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 713..713

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 65.

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 met in metabolic_participants:
            met_species_type = model.species_types.get_one(id=met)
            metabolites[met] = {
                'n': met_species_type.species.get_or_create(compartment=nucleus, model=model),
                'm': met_species_type.species.get_or_create(compartment=mitochondrion, model=model)
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 3 hrs to fix
wc_model_gen/eukaryote/complexation.py on lines 103..107
wc_model_gen/eukaryote/rna_degradation.py on lines 67..71

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 64.

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 met in metabolic_participants:
            met_species_type = model.species_types.get_one(id=met)
            metabolites[met] = {
                'c': met_species_type.species.get_or_create(compartment=cytoplasm, model=model),
                'm': met_species_type.species.get_or_create(compartment=mitochondrion, model=model)
Severity: Major
Found in wc_model_gen/eukaryote/complexation.py and 2 other locations - About 3 hrs to fix
wc_model_gen/eukaryote/rna_degradation.py on lines 67..71
wc_model_gen/eukaryote/transcription.py on lines 175..179

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 64.

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 subunit.species_type.id in gvar.protein_aa_usage:                                        
                                        for aa, aa_id in amino_acid_id_conversion.items():
                                            if gvar.protein_aa_usage[subunit.species_type.id][aa]:
                                                aa_content[aa_id] = gvar.protein_aa_usage[subunit.species_type.id][aa]
Severity: Major
Found in wc_model_gen/eukaryote/complexation.py and 1 other location - About 3 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 281..284

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 64.

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 met in metabolic_participants:
            met_species_type = model.species_types.get_one(id=met)
            metabolites[met] = {
                'c': met_species_type.species.get_or_create(compartment=cytoplasm, model=model),
                'm': met_species_type.species.get_or_create(compartment=mitochondrion, model=model)
Severity: Major
Found in wc_model_gen/eukaryote/rna_degradation.py and 2 other locations - About 3 hrs to fix
wc_model_gen/eukaryote/complexation.py on lines 103..107
wc_model_gen/eukaryote/transcription.py on lines 175..179

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 64.

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 mrna_kb.protein.id in gvar.protein_aa_usage:                                        
                for aa, aa_id in amino_acid_id_conversion.items():
                    if gvar.protein_aa_usage[mrna_kb.protein.id][aa]:
                        aa_content[aa_id] = gvar.protein_aa_usage[mrna_kb.protein.id][aa]
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 3 hrs to fix
wc_model_gen/eukaryote/complexation.py on lines 178..181

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 64.

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

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

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

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

Refactorings

Further Reading

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

    for product in products:
        obj_reaction = obj_products[product]
        conv_model.objective_terms = [conv_opt.LinearTerm(obj_reaction, 1.),]
        result = conv_model.solve()
        if result.value == 0.0:
Severity: Major
Found in wc_model_gen/utils.py and 1 other location - About 3 hrs to fix
wc_model_gen/utils.py on lines 168..173

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 63.

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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