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testsuite/AdResS/PIAdResS/test_PIAdResS.py

Summary

Maintainability
F
1 wk
Test Coverage

Function test_PIAdResS has 110 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def test_PIAdResS(self):
        print('param =', self.param)

        constkinmass = self.param['constkinmass']
        PILE = self.param['PILE']
Severity: Major
Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py - About 4 hrs to fix

    Function test_PIAdResS has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.
    Open

        def test_PIAdResS(self):
        print('param =', self.param)

        constkinmass = self.param['constkinmass']
        PILE = self.param['PILE']
    Severity: Minor
    Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py - About 4 hrs to fix

    Cognitive Complexity

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

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

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

    Further reading

    File test_PIAdResS.py has 273 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    #!/usr/bin/env python3
#
#  Copyright (C) 2017,2018
#      Max Planck Institute for Polymer Research
#
    Severity: Minor
    Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py - About 2 hrs to fix

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

              for part in range(num_atoms/3):
            bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+1))
            bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+2))
            bondsHH.append((num_Trotter_beads + 1 + 3*part+1, num_Trotter_beads + 1 + 3*part+2))
      Severity: Major
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 1 day to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 197..200

      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 169.

      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

                  for pid_trotter in range(nTrotter):
                pid = pid_atom*nTrotter+pid_trotter
                allParticles.append([(allParticlesAT[pid])[0],
                                    (allParticlesAT[pid])[1], (allParticlesAT[pid])[2], (allParticlesAT[pid])[3], (allParticlesAT[pid])[4],
                                    (allParticlesAT[pid])[5], (allParticlesAT[pid])[6], (allParticlesAT[pid])[7]])
      Severity: Major
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 1 day to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 165..174

      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 132.

      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

              for pid_trotter in range(num_Trotter_beads):
            allParticlesAT.append([pid_trotter + 1, Real3D(x[pid_trotter], y[pid_trotter], z[pid_trotter]),
                                Real3D(vx[pid_trotter], vy[pid_trotter], vz[pid_trotter]), Real3D(0, 0, 0),
                                pid_trotter%nTrotter + 1, types[pid_trotter], masses[pid_trotter], 1])
      Severity: Major
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 7 hrs to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 139..144

      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 112.

      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

                  allParticles.append([pid_atom+num_Trotter_beads+1, Real3D(cmp[0], cmp[1], cmp[2]), Real3D(cmv[0], cmv[1], cmv[2]), Real3D(0, 0, 0), 0,
                                types[pid_atom*nTrotter], masses[pid_atom*nTrotter], 0])
      Severity: Major
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 6 hrs to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 159..163

      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 108.

      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

              for part in range(num_atoms/3):
            angles.append((num_Trotter_beads + 1 + 3*part+1, num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+2))
      Severity: Major
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 4 hrs to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 215..216

      Duplicated Code

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

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

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

      Tuning

      This issue has a mass of 79.

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

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

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

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

      Refactorings

      Further Reading

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

              integrator = espressopp.integrator.PIAdressIntegrator(system=system, verletlist=vl, timestep=timestep_short, sSteps=multiplier_short_to_medium, mSteps=multiplier_medium_to_long, nTrotter=nTrotter, realKinMass=realkinmass, constKinMass=constkinmass, temperature=temp, gamma=gamma, centroidThermostat=centroidthermostat, CMDparameter=CMDparameter, PILE=PILE, PILElambda=PILElambda, CLmassmultiplier=clmassmultiplier, speedup=speedupFreezeRings, KTI=KTI)
      Severity: Major
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 3 hrs to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 257..257

      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 63.

      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

                  fec = espressopp.integrator.FreeEnergyCompensation(system, center=[Lx/2, Ly/2, Lz/2], ntrotter=nTrotter)
      Severity: Major
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 1 hr to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 260..260

      Duplicated Code

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

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

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

      Tuning

      This issue has a mass of 42.

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

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

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

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

      Refactorings

      Further Reading

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

                  for pid_trotter in range(nTrotter):
                pid = pid_atom*nTrotter+pid_trotter
                tmptuple.append((allParticlesAT[pid])[0])
      Severity: Major
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 1 hr to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 151..153

      Duplicated Code

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

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

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

      Tuning

      This issue has a mass of 39.

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

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

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

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

      Refactorings

      Further Reading

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

              if KTI==False:
            Ecorr = fec.computeCompEnergy() + thdf.computeTDEnergy()
        else:
            Ecorr = 0.0
      Severity: Minor
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 45 mins to fix
      testsuite/AdResS/PIAdResS/test_PIAdResS.py on lines 232..235

      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

              if KTI==False:
            Ecorr = fec.computeCompEnergy() + thdf.computeTDEnergy()
        else:
            Ecorr = 0.0
      Severity: Minor
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 45 mins to fix
      testsuite/AdResS/PIAdResS/test_PIAdResS.py on lines 245..248

      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 4 locations. Consider refactoring.
      Open

              energy_after_thistest = Ek+Eb+EAng+ELj+EPI+Ecorr
      Severity: Major
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 3 other locations - About 45 mins to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 372..372
      examples/adress/piadress_water/AdaptivePIwater.py on lines 388..388
      testsuite/AdResS/PIAdResS/test_PIAdResS.py on lines 236..236

      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 4 locations. Consider refactoring.
      Open

              energy_before_thistest =  Ek+Eb+EAng+ELj+EPI+Ecorr
      Severity: Major
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 3 other locations - About 45 mins to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 372..372
      examples/adress/piadress_water/AdaptivePIwater.py on lines 388..388
      testsuite/AdResS/PIAdResS/test_PIAdResS.py on lines 249..249

      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

              for item in types:
            if item == 1:
                masses.append(15.9994)
            else:
                masses.append(1.008)
      Severity: Minor
      Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 45 mins to fix
      examples/adress/piadress_water/AdaptivePIwater.py on lines 83..87

      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

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