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wc_model_gen/prokaryote/rna_degradation.py

Summary

Maintainability
D
1 day
Test Coverage
A
100%

Function calibrate_submodel has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def calibrate_submodel(self):
        """ Calibrate the submodel using data in the KB """
        model = self.model
        beta = self.options.get('beta')
Severity: Minor
Found in wc_model_gen/prokaryote/rna_degradation.py - About 35 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

    def gen_rate_laws(self):
        """ Generate rate laws for the reactions in the submodel """

        model = self.model
Severity: Major
Found in wc_model_gen/prokaryote/rna_degradation.py and 1 other location - About 6 hrs to fix
wc_model_gen/prokaryote/transcription.py on lines 83..98

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 101.

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 degradosome_kb in cell.observables.get_one(id='degrade_rnase_obs').expression.species:
                degradosome_species_type_model = model.species_types.get_one(id=degradosome_kb.species_type.id)
                degradosome_species_model = degradosome_species_type_model.species.get_one(compartment=cytosol)

                reaction.participants.add(degradosome_species_model.species_coefficients.get_or_create(
Severity: Major
Found in wc_model_gen/prokaryote/rna_degradation.py and 3 other locations - About 5 hrs to fix
wc_model_gen/prokaryote/protein_degradation.py on lines 93..99
wc_model_gen/prokaryote/transcription.py on lines 76..81
wc_model_gen/prokaryote/translation.py on lines 140..145

Duplicated Code

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

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

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

Tuning

This issue has a mass of 96.

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

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

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

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

Refactorings

Further Reading

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

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 39.

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

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

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

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

Refactorings

Further Reading

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

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