Sign upLogin

KarrLab/wc_sim

View on GitHub
Star

Showing 34 of 141 total issues

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

            if rate_law_type.name == 'constant':
                param = model.parameters.create(id='k_cat_{}_1_for'.format(submodel_num),
                                                value=1., units=unit_registry.parse_units('s^-1'))
                expression_str = param.id
            elif rate_law_type.name == 'reactant_pop':
Severity: Major
Found in wc_sim/testing/make_models.py and 1 other location - About 1 day to fix
wc_sim/testing/make_models.py on lines 213..230

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 216.

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 rate_law_type.name == 'constant':
                    param = model.parameters.create(id='k_cat_{}_1_bck'.format(submodel_num),
                                                    value=1., units=unit_registry.parse_units('s^-1'))
                    expression_str = param.id
                elif rate_law_type.name == 'reactant_pop':
Severity: Major
Found in wc_sim/testing/make_models.py and 1 other location - About 1 day to fix
wc_sim/testing/make_models.py on lines 178..195

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 216.

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

def get_debug_logs_config(extra=None):
    """ Get debug logs configuration

    Args:
        extra (:obj:`dict`, optional): additional configuration to override
Severity: Major
Found in examples/config/core.py and 1 other location - About 4 hrs to fix
wc_sim/config/core.py on lines 36..51

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 79.

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

def get_debug_logs_config(extra=None):
    """ Get debug logs configuration

    Args:
        extra (:obj:`dict`, optional): additional configuration to override
Severity: Major
Found in wc_sim/config/core.py and 1 other location - About 4 hrs to fix
examples/config/core.py on lines 28..43

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 79.

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

    axes1[1][1].plot(time / 3600, h2o_c / (cell_100_ag * 6.71e-17 / 511) / 6.022e23 * 1e0)
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 1 other location - About 2 hrs to fix
examples/translation_metabolism_hybrid_model/run.py on lines 74..74

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 58.

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

    axes1[0][1].plot(time / 3600, ala_c / (cell_100_ag * 6.71e-17 / 511) / 6.022e23 * 1e3)
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 1 other location - About 2 hrs to fix
examples/translation_metabolism_hybrid_model/run.py on lines 89..89

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 58.

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 5 locations. Consider refactoring.
Open

    axes1[0][0].set_xlim((time[0] / 3600, time[-1] / 3600))
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 4 other locations - About 1 hr to fix
examples/translation_metabolism_hybrid_model/run.py on lines 75..75
examples/translation_metabolism_hybrid_model/run.py on lines 83..83
examples/translation_metabolism_hybrid_model/run.py on lines 90..90
examples/translation_metabolism_hybrid_model/run.py on lines 101..101

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 48.

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 5 locations. Consider refactoring.
Open

    axes1[1][1].set_xlim((time[0] / 3600, time[-1] / 3600))
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 4 other locations - About 1 hr to fix
examples/translation_metabolism_hybrid_model/run.py on lines 68..68
examples/translation_metabolism_hybrid_model/run.py on lines 75..75
examples/translation_metabolism_hybrid_model/run.py on lines 83..83
examples/translation_metabolism_hybrid_model/run.py on lines 101..101

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 48.

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 5 locations. Consider refactoring.
Open

    axes1[2][1].set_xlim((time[0] / 3600, time[-1] / 3600))
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 4 other locations - About 1 hr to fix
examples/translation_metabolism_hybrid_model/run.py on lines 68..68
examples/translation_metabolism_hybrid_model/run.py on lines 75..75
examples/translation_metabolism_hybrid_model/run.py on lines 83..83
examples/translation_metabolism_hybrid_model/run.py on lines 90..90

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 48.

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 5 locations. Consider refactoring.
Open

    axes1[0][1].set_xlim((time[0] / 3600, time[-1] / 3600))
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 4 other locations - About 1 hr to fix
examples/translation_metabolism_hybrid_model/run.py on lines 68..68
examples/translation_metabolism_hybrid_model/run.py on lines 83..83
examples/translation_metabolism_hybrid_model/run.py on lines 90..90
examples/translation_metabolism_hybrid_model/run.py on lines 101..101

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 48.

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 5 locations. Consider refactoring.
Open

    axes1[1][0].set_xlim((time[0] / 3600, time[-1] / 3600))
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 4 other locations - About 1 hr to fix
examples/translation_metabolism_hybrid_model/run.py on lines 68..68
examples/translation_metabolism_hybrid_model/run.py on lines 75..75
examples/translation_metabolism_hybrid_model/run.py on lines 90..90
examples/translation_metabolism_hybrid_model/run.py on lines 101..101

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 48.

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

    axes1[1][0].plot(time / 3600, h2o_e / vol_e / 6.022e23 * 1e0)
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 1 other location - About 1 hr to fix
examples/translation_metabolism_hybrid_model/run.py on lines 67..67

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

    axes1[0][0].plot(time / 3600, ala_e / vol_e / 6.022e23 * 1e3)
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 1 other location - About 1 hr to fix
examples/translation_metabolism_hybrid_model/run.py on lines 82..82

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

    axes1[1].plot([0, time[-1] / 3600], [avg, avg], label='Avg: {}'.format(exp_avg_prot))
Severity: Major
Found in examples/transcription_translation_hybrid_model/run_with_wc_sim.py and 1 other location - About 1 hr to fix
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 65..65

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 44.

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

    axes1[0].plot([0, time[-1] / 3600], [avg, avg], label='Avg: {}'.format(exp_avg_rna))
Severity: Major
Found in examples/transcription_translation_hybrid_model/run_with_wc_sim.py and 1 other location - About 1 hr to fix
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 75..75

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 44.

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 7 locations. Consider refactoring.
Open

    axes2[0].set_xlim((time[0] / 3600, time[-1] / 3600))
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 6 other locations - About 1 hr to fix
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 66..66
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 76..76
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 84..84
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 92..92
examples/translation_metabolism_hybrid_model/run.py on lines 117..117
examples/translation_metabolism_hybrid_model/run.py on lines 125..125

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 7 locations. Consider refactoring.
Open

    axes2[2].set_xlim((time[0] / 3600, time[-1] / 3600))
Severity: Major
Found in examples/translation_metabolism_hybrid_model/run.py and 6 other locations - About 1 hr to fix
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 66..66
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 76..76
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 84..84
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 92..92
examples/translation_metabolism_hybrid_model/run.py on lines 109..109
examples/translation_metabolism_hybrid_model/run.py on lines 117..117

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 7 locations. Consider refactoring.
Open

    axes2[1].set_xlim((time[0] / 3600, time[-1] / 3600))
Severity: Major
Found in examples/transcription_translation_hybrid_model/run_with_wc_sim.py and 6 other locations - About 1 hr to fix
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 66..66
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 76..76
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 84..84
examples/translation_metabolism_hybrid_model/run.py on lines 109..109
examples/translation_metabolism_hybrid_model/run.py on lines 117..117
examples/translation_metabolism_hybrid_model/run.py on lines 125..125

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 7 locations. Consider refactoring.
Open

    axes2[0].set_xlim((time[0] / 3600, time[-1] / 3600))
Severity: Major
Found in examples/transcription_translation_hybrid_model/run_with_wc_sim.py and 6 other locations - About 1 hr to fix
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 66..66
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 76..76
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 92..92
examples/translation_metabolism_hybrid_model/run.py on lines 109..109
examples/translation_metabolism_hybrid_model/run.py on lines 117..117
examples/translation_metabolism_hybrid_model/run.py on lines 125..125

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 7 locations. Consider refactoring.
Open

    axes1[0].set_xlim((time[0] / 3600, time[-1] / 3600))
Severity: Major
Found in examples/transcription_translation_hybrid_model/run_with_wc_sim.py and 6 other locations - About 1 hr to fix
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 76..76
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 84..84
examples/transcription_translation_hybrid_model/run_with_wc_sim.py on lines 92..92
examples/translation_metabolism_hybrid_model/run.py on lines 109..109
examples/translation_metabolism_hybrid_model/run.py on lines 117..117
examples/translation_metabolism_hybrid_model/run.py on lines 125..125

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

Severity
Category
Status
Source
Language