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Similar blocks of code found in 3 locations. Consider refactoring.
Open

             * self.K1nadh * (1 + self.NAD/self.K1nad + self.NADH / self.K1nadh) *
             (1 + self.DHAP / self.K1dhap + x[0] / self.K1g3p))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 2 other locations - About 55 mins to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 292..292
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 337..337

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 37.

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

        return (self.VmALD*(x[2] - (self.KeqTPI*x[13]**2)/(self.KeqALD*(1 + self.KeqTPI)**2)))/(self.KmALDF16P*(1 + x[2]/self.KmALDF16P + x[13]/((1 + self.KeqTPI)*self.KmALDDHAP) + (self.KeqTPI*x[13])/((1 + self.KeqTPI)*self.KmALDGAP) + (self.KeqTPI*x[2]*x[13])/((1 + self.KeqTPI)*self.KmALDF16P*self.KmALDGAPi) + (self.KeqTPI*x[13]**2)/((1 + self.KeqTPI)**2*self.KmALDDHAP*self.KmALDGAP)))
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 55 mins to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 302..302

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 37.

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

                    dp_dt_part_mat[i, j] += self.gamma_n * (n + 1) * p_part_mat[i, j + 1]
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 50 mins to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 492..492

Duplicated Code

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

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

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

Tuning

This issue has a mass of 36.

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

        m = range(int(numpy.min(m)), int(numpy.max(m)) + 1)
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 50 mins to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 951..951

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 36.

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

                    dp_dt_part_mat[i + 1, j] -= self.gamma_m * (m + 1) * p_part_mat[i + 1, j]
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 50 mins to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 483..483

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 36.

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

        n = range(int(numpy.min(n)), int(numpy.max(n)) + 1)
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 50 mins to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 950..950

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 36.

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

                    dp_dt_part_mat[i, j] += self.gamma_m * (m + 1) * p_part_mat[i + 1, j]
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 50 mins to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 484..484

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 36.

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

                    dp_dt_part_mat[i, j + 1] -= self.gamma_n * (n + 1) * p_part_mat[i, j + 1]
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 50 mins to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 491..491

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 36.

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

        t = numpy.linspace(t_0, t_end, int((t_end - t_0) / t_step) + 1)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 6 other locations - About 45 mins to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 439..439
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 594..594
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 248..248
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 511..511
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 767..767
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 830..830

Duplicated Code

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

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

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

Tuning

This issue has a mass of 35.

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

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

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

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

Refactorings

Further Reading

Similar blocks of code found in 7 locations. Consider refactoring.
Open

        t = numpy.linspace(t_0, t_end, int((t_end - t_0) / t_step) + 1)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 6 other locations - About 45 mins to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 439..439
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 594..594
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 710..710
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 511..511
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 767..767
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 830..830

Duplicated Code

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

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

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

Tuning

This issue has a mass of 35.

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

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

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

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

Refactorings

Further Reading

Similar blocks of code found in 7 locations. Consider refactoring.
Open

        t = numpy.linspace(t_0, t_end, int((t_end - t_0) / t_step) + 1)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 6 other locations - About 45 mins to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 439..439
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 710..710
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 248..248
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 511..511
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 767..767
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 830..830

Duplicated Code

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

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

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

Tuning

This issue has a mass of 35.

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

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

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

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

Refactorings

Further Reading

Similar blocks of code found in 7 locations. Consider refactoring.
Open

        t = numpy.linspace(t_0, t_end, int((t_end - t_0) / t_step) + 1)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 6 other locations - About 45 mins to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 439..439
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 594..594
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 710..710
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 248..248
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 511..511
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 767..767

Duplicated Code

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

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

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

Tuning

This issue has a mass of 35.

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

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

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

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

Refactorings

Further Reading

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

        return vec.reshape((self.m_max - self.m_min + 1, self.n_max - self.n_min + 1))
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 45 mins to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 559..559

Duplicated Code

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

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

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

Tuning

This issue has a mass of 35.

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

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

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

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

Refactorings

Further Reading

Similar blocks of code found in 7 locations. Consider refactoring.
Open

        t_eval = numpy.linspace(t_0, t_end, int((t_end - t_0) / t_step) + 1)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 6 other locations - About 45 mins to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 439..439
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 594..594
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 710..710
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 248..248
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 767..767
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 830..830

Duplicated Code

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

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

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

Tuning

This issue has a mass of 35.

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

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

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

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

Refactorings

Further Reading

Similar blocks of code found in 7 locations. Consider refactoring.
Open

        t = numpy.linspace(t_0, t_end, int((t_end - t_0) / t_step) + 1)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 6 other locations - About 45 mins to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 594..594
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 710..710
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 248..248
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 511..511
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 767..767
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 830..830

Duplicated Code

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

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

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

Tuning

This issue has a mass of 35.

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

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

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

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

Refactorings

Further Reading

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

        part_mat_shape = (self.m_max - self.m_min + 1, self.n_max - self.n_min + 1)
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 45 mins to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 393..393

Duplicated Code

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

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

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

Tuning

This issue has a mass of 35.

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

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

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

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

Refactorings

Further Reading

Similar blocks of code found in 7 locations. Consider refactoring.
Open

        t_hist = numpy.linspace(t_0, t_end, int((t_end - t_0) / t_step) + 1)
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 6 other locations - About 45 mins to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 439..439
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 594..594
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 710..710
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 248..248
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 511..511
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 830..830

Duplicated Code

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

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

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

Tuning

This issue has a mass of 35.

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

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

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

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

Refactorings

Further Reading

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

    def dm_dt(self, m, n):
        """ Calculate the rate of change of mRNA

        Args:
            m (:obj:`float`): mRNA number (molecules)
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 40 mins to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 115..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 34.

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

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

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

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

Refactorings

Further Reading

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

    def dn_dt(self, m, n):
        """ Calculate the rate of change of proteins

        Args:
            m (:obj:`float`): mRNA number (molecules)
Severity: Minor
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 40 mins to fix
intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 103..113

Duplicated Code

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

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

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

Tuning

This issue has a mass of 34.

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

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

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

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

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

        if value_init < 0 or numpy.ceil(value_init) != value_init:
            raise ValueError('`value_init` must be a non-negative integer')  # example of how to format a string
Severity: Major
Found in intro_to_wc_modeling/concepts_skills/software_engineering/unit_testing/core.py and 2 other locations - About 40 mins to fix
intro_to_wc_modeling/concepts_skills/software_engineering/unit_testing/core.py on lines 52..53
intro_to_wc_modeling/concepts_skills/software_engineering/unit_testing/core.py on lines 117..118

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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