Sign upLogin

KarrLab/intro_to_wc_modeling

View on GitHub
Star

Showing 93 of 135 total issues

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

    axes[0].set_xticks([0, numpy.pi / 2, numpy.pi, numpy.pi * 3 / 2, numpy.pi * 2])
Severity: Major
Found in intro_to_wc_modeling/concepts_skills/software_engineering/matplotlib_example.py and 1 other location - About 2 hrs to fix
intro_to_wc_modeling/concepts_skills/software_engineering/matplotlib_example.py on lines 44..44

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 53.

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

    axes[1].set_xticks([0, numpy.pi / 2, numpy.pi, numpy.pi * 3 / 2, numpy.pi * 2])
Severity: Major
Found in intro_to_wc_modeling/concepts_skills/software_engineering/matplotlib_example.py and 1 other location - About 2 hrs to fix
intro_to_wc_modeling/concepts_skills/software_engineering/matplotlib_example.py on lines 41..41

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 53.

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

        dx_dt[7] += 1.0 * self.glycolysis_model.v_16(x[0:-1]) - 1.0 * self.v_18(x)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 2 hrs to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 692..692

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 53.

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

        dx_dt[13] += 1.0 * self.glycolysis_model.v_16(x[0:-1]) - 1.0 * self.v_18(x)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 2 hrs to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 691..691

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 53.

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

        return -((self.VmADH*(self.ETOH*x[6] - (x[0]*x[7])/self.KeqADH))/(self.KiADHNAD*self.KmADHETOH*(1 + (self.ETOH*self.KmADHNAD)/(self.KiADHNAD*self.KmADHETOH) + (self.KmADHNADH*x[0])/(self.KiADHNADH*self.KmADHACE) + x[6]/self.KiADHNAD + (self.ETOH*x[6])/(self.KiADHNAD*self.KmADHETOH) + (self.ETOH*x[0]*x[6])/(self.KiADHACE*self.KiADHNAD*self.KmADHETOH) + (self.KmADHNADH*x[0]*x[6])/(self.KiADHNAD*self.KiADHNADH*self.KmADHACE) + x[7]/self.KiADHNADH + (self.ETOH*self.KmADHNAD*x[7])/(self.KiADHNAD*self.KiADHNADH*self.KmADHETOH) + (x[0]*x[7])/(self.KiADHNADH*self.KmADHACE) + (self.ETOH*x[0]*x[7])/(self.KiADHETOH*self.KiADHNADH*self.KmADHACE))))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 2 other locations - About 2 hrs to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 342..342
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 342..342

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 51.

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

        upperBounds = util.nanminimum(upperBounds, self.dryWeight / 3600 * N_AVOGADRO * 1e-3 * self.exchangeRateBounds['upper'])
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 402..402

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 46.

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

        lowerBounds = util.nanmaximum(lowerBounds, self.dryWeight / 3600 * N_AVOGADRO * 1e-3 * self.exchangeRateBounds['lower'])
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 403..403

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 46.

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 part in rxn.participants:
            if part.species.type == 'Protein':
                initCopyNumber = mdl.speciesCounts[part.species.index, part.compartment.index]
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py and 2 other locations - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py on lines 44..46
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py on lines 64..66

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 46.

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 part in rxn.participants:
            if part.species.type == 'RNA':
                initCopyNumber = mdl.speciesCounts[part.species.index, part.compartment.index]
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py and 2 other locations - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py on lines 44..46
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py on lines 54..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 46.

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 part in rxn.participants:
            if part.species.type == 'RNA':
                initCopyNumber = mdl.speciesCounts[part.species.index, part.compartment.index]
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py and 2 other locations - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py on lines 54..56
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py on lines 64..66

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 46.

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

    analysis.plot(
        model=submdl,
        time=time,
        volume=volume,
        speciesCounts=speciesCounts,
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py and 2 other locations - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/simulation.py on lines 181..188
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/simulation.py on lines 191..198

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 43.

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

    analysis.plot(
        model=mdl,
        time=time,
        volume=volume,
        speciesCounts=speciesCounts,
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/simulation.py and 2 other locations - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/simulation.py on lines 181..188
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py on lines 154..161

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 43.

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

    analysis.plot(
        model=submdl,
        time=time,
        volume=volume,
        speciesCounts=speciesCounts,
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py and 1 other location - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/simulation.py on lines 171..178

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 43.

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

    analysis.plot(
        model=mdl,
        time=time,
        volume=volume,
        speciesCounts=speciesCounts,
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/simulation.py and 2 other locations - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/simulation.py on lines 191..198
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py on lines 154..161

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 43.

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

    analysis.plot(
        model=mdl,
        time=time,
        volume=volume,
        speciesCounts=speciesCounts,
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/simulation.py and 1 other location - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py on lines 144..151

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 43.

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

        axes[1].set_ylim([numpy.min(n) - 5, numpy.max(n) + 5])
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 928..928

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 42.

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

        axes[1].set_ylim([numpy.min(n) - 5, numpy.max(n) + 5])
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 866..866

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 42.

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 8 locations. Consider refactoring.
Open

    def dGLCi_dt(self, x):
        return 1.0 * self.v_14(x) - 1.0 * self.v_1(x)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 7 other locations - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 357..358
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 360..361
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 363..364
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 378..379
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 381..382
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 384..385
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 387..388

Duplicated Code

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

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

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

Tuning

This issue has a mass of 40.

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

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

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

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

Refactorings

Further Reading

Similar blocks of code found in 8 locations. Consider refactoring.
Open

    def dF6P_dt(self, x):
        return 1.0 * self.v_2(x) - 1.0 * self.v_5(x)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 7 other locations - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 357..358
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 360..361
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 369..370
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 378..379
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 381..382
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 384..385
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 387..388

Duplicated Code

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

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

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

Tuning

This issue has a mass of 40.

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

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

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

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

Refactorings

Further Reading

Similar blocks of code found in 8 locations. Consider refactoring.
Open

    def dF16BP_dt(self, x):
        return 1.0 * self.v_5(x) - 1.0 * self.v_6(x)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 7 other locations - About 1 hr to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 357..358
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 363..364
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 369..370
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 378..379
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 381..382
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 384..385
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 387..388

Duplicated Code

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

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

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

Tuning

This issue has a mass of 40.

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

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

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

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

Refactorings

Further Reading

Severity
Category
Status
Source
Language