File model_composition.py has 614 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Model composition tutorial
- Glycolysis model (Teusink et al., 2000)
- Glycerol synthesis model (Cronwright et al., 2002)
GlycolysisModel has 35 functions (exceeds 20 allowed). Consider refactoring. Open
class GlycolysisModel(object):
""" Glycolysis model (Teusink et al., 2000)
Based on the `version from JWS Online <http://jjj.biochem.sun.ac.za/models/teusink/>`_
Function main has 33 lines of code (exceeds 25 allowed). Consider refactoring. Open
def main(out_dir=None):
""" Simulate individual models and combined model, plot results, and save plots
Args:
out_dir (:obj:`str`, optional): path to directory to save resultsIdentical blocks of code found in 2 locations. Consider refactoring. Open
return (self.gR*self.VmPFK*x[3]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)*(1 + x[3]/self.KmPFKF6P + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPFKATP) + (self.gR*x[3]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KmPFKATP*self.KmPFKF6P)))/((2 - 8*self.KeqAK)*self.KmPFKATP*self.KmPFKF6P*((self.L0*(1 + (self.CPFKF26BP*self.F26BP)/self.KPFKF26BP + (self.CPFKF16BP*x[2])/self.KPFKF16BP)**2*(1 + (2*self.CPFKAMP*self.KeqAK*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)**2)/((-1 + 4*self.KeqAK)*self.KPFKAMP*(self.SUMAXP - x[12] + 4*self.KeqAK*x[12] - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)))**2*(1 + (self.CiPFKATP*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KiPFKATP))**2*(1 + (self.CPFKATP*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KmPFKATP))**2)/((1 + self.F26BP/self.KPFKF26BP + x[2]/self.KPFKF16BP)**2*(1 + (2*self.KeqAK*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)**2)/((-1 + 4*self.KeqAK)*self.KPFKAMP*(self.SUMAXP - x[12] + 4*self.KeqAK*x[12] - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)))**2*(1 + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KiPFKATP))**2) + (1 + x[3]/self.KmPFKF6P + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPFKATP) + (self.gR*x[3]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KmPFKATP*self.KmPFKF6P))**2))- Read upRead up
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 465.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
return (self.VmPGK*((self.KeqPGK*x[1]*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(1 - 4*self.KeqAK) - (x[9]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(2 - 8*self.KeqAK)))/(self.KmPGKATP*self.KmPGKP3G*(1 + x[1]/self.KmPGKBPG + x[9]/self.KmPGKP3G)*(1 + (self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((1 - 4*self.KeqAK)*self.KmPGKADP) + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPGKATP)))- Read upRead up
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 437.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
return (self.VmGLK*(-((x[4]*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)) /
((1 - 4*self.KeqAK)*self.KeqGLK)) + (x[5]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(2 - 8*self.KeqAK)))/(self.KmGLKATP*self.KmGLKGLCi*(1 + x[4]/self.KmGLKG6P + x[5]/self.KmGLKGLCi)*(1 + (self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((1 - 4*self.KeqAK)*self.KmGLKADP) + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmGLKATP)))- Read upRead up
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 437.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
return (self.VmPYK*((x[10]*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(1 - 4*self.KeqAK) - ((-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)*x[11])/((2 - 8*self.KeqAK)*self.KeqPYK)))/(self.KmPYKADP*self.KmPYKPEP*(1 + (self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((1 - 4*self.KeqAK)*self.KmPYKADP) + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPYKATP))*(1 + x[10]/self.KmPYKPEP + x[11]/self.KmPYKPYR))- Read upRead up
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 145.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
def v_9(self, x):
# Phosphoglycerate mutase
# P3G <=> P2G
return (self.VmPGM*(-(x[8]/self.KeqPGM) + x[9]))/(self.KmPGMP3G*(1 + x[8]/self.KmPGMP2G + x[9]/self.KmPGMP3G))- Read upRead up
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 102.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
def v_2(self, x):
# Glucose-6-phosphate isomerase
# G6P <=> F6P
return (self.VmPGI*(-(x[3]/self.KeqPGI) + x[4]))/(self.KmPGIG6P*(1 + x[3]/self.KmPGIF6P + x[4]/self.KmPGIG6P))- Read upRead up
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 102.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
def dNADH_dt(self, x):
return 1.0 * self.v_7(x) + 3.0 * self.v_13(x) - 1.0 * self.v_15(x) - 1.0 * self.v_16(x)- Read upRead up
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 76.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
def dNAD_dt(self, x):
return 1.0 * self.v_15(x) + 1.0 * self.v_16(x) - 1.0 * self.v_7(x) - 3.0 * self.v_13(x)- Read upRead up
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 76.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
def dACE_dt(self, x):
return 1.0 * self.v_12(x) - 1.0 * self.v_15(x) - 2.0 * self.v_13(x)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
def dTRIO_dt(self, x):
return 2.0 * self.v_6(x) - 1.0 * self.v_16(x) - 1.0 * self.v_7(x)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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))))- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 8 locations. Consider refactoring. Open
def dP2G_dt(self, x):
return 1.0 * self.v_9(x) - 1.0 * self.v_10(x)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 8 locations. Consider refactoring. Open
def dPYR_dt(self, x):
return 1.0 * self.v_11(x) - 1.0 * self.v_12(x)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 8 locations. Consider refactoring. Open
def dPEP_dt(self, x):
return 1.0 * self.v_10(x) - 1.0 * self.v_11(x)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 8 locations. Consider refactoring. Open
def dP3G_dt(self, x):
return 1.0 * self.v_8(x) - 1.0 * self.v_9(x)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 8 locations. Consider refactoring. Open
def dBPG_dt(self, x):
return 1.0 * self.v_7(x) - 1.0 * self.v_8(x)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 3 locations. Consider refactoring. Open
return (self.VmGLT*(self.GLCo - x[5]/self.KeqGLT))/(self.KmGLTGLCo*(1 + self.GLCo/self.KmGLTGLCo + x[5]/self.KmGLTGLCi + (0.91*self.GLCo*x[5])/(self.KmGLTGLCi*self.KmGLTGLCo)))- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
return (-((self.VmGAPDHr*x[1]*x[7])/(self.KmGAPDHBPG*self.KmGAPDHNADH)) + (self.KeqTPI*self.VmGAPDHf*x[6]*x[13])/((1 + self.KeqTPI)*self.KmGAPDHGAP*self.KmGAPDHNAD))/((1 + x[6]/self.KmGAPDHNAD + x[7]/self.KmGAPDHNADH)*(1 + x[1]/self.KmGAPDHBPG + (self.KeqTPI*x[13])/((1 + self.KeqTPI)*self.KmGAPDHGAP)))- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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))- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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)))- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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)- Read upRead up
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
(self.K1dhap * (1 + self.ADP/self.K1adp + self.ATP / self.K1atp + self.F16BP / self.K1f16bp)- Read upRead up
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 33.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76