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Avoid too many return statements within this function.
Open

            return self.cxxclass.compute_int_vector_python(self)
Severity: Major
Found in src/analysis/Observable.py - About 30 mins to fix

    Avoid too many return statements within this function.
    Open

            return p_type, masses, epsilon, sigma, K, r0, bonds, bonds_type_arr, Kt, t0, angles, angles_type_arr, Kdh, ndh, ph0, dihedrals, dihedrals_type_arr, q, x, y, z, Lx, Ly, Lz, vx, vy, vz
    Severity: Major
    Found in src/tools/lammps.py - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

                  return self.cxxclass.compute(self)
      Severity: Major
      Found in src/analysis/Observable.py - About 30 mins to fix

        Avoid too many return statements within this function.
        Open

                return p_type, masses, epsilon, sigma, K, r0, bonds, bonds_type_arr, Kt, t0, angles, angles_type_arr, q, x, y, z, Lx, Ly, Lz
        Severity: Major
        Found in src/tools/lammps.py - About 30 mins to fix

          Avoid too many return statements within this function.
          Open

                  return p_type, masses, epsilon, sigma, K, r0, bonds, bonds_type_arr, Kt, t0, angles, angles_type_arr, Kdh, ndh, ph0, dihedrals, dihedrals_type_arr, q, x, y, z, Lx, Ly, Lz
          Severity: Major
          Found in src/tools/lammps.py - About 30 mins to fix

            Avoid too many return statements within this function.
            Open

                            return positions, bonds, avecostheta
            Severity: Major
            Found in src/tools/topology.py - About 30 mins to fix

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

                      self.assertEqual(vl.totalSize(), N * N * N * 3)
              Severity: Minor
              Found in testsuite/unittest/testVerletList.py and 2 other locations - About 30 mins to fix
              testsuite/unittest/testVerletList.py on lines 103..103
              testsuite/unittest/testVerletList.py on lines 109..109

              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 32.

              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

              defaults, types, atomtypes, masses, charges, atomtypeparameters, bondtypes, bondtypeparams, angletypes, angletypeparams, exclusions, x, y, z, resname, resid, Lx, Ly, Lz= gromacs.read(grofile,topfile)
              Severity: Minor
              Found in testsuite/pi_water/water.py and 1 other location - About 30 mins to fix
              examples/simpleGromacs/simpleGromacs.py on lines 79..79

              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 32.

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

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

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

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

              Refactorings

              Further Reading

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

                  if isController:
        if not args:
            raise UserError('pmi.import_ expects exactly 1 argument on controller!')

        # broadcast the statement
              Severity: Minor
              Found in src/pmi.py and 1 other location - About 30 mins to fix
              src/pmi.py on lines 235..242

              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 32.

              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

                      particle_list = [
            (1, espressopp.Real3D(2.0, 2.0, 2.0), 1.0),
            (2, espressopp.Real3D(3.0, 2.0, 2.0), 1.0),
              Severity: Minor
              Found in testsuite/minimize_energy/testMinimizeEnergy.py and 1 other location - About 30 mins to fix
              testsuite/minimize_energy/testMinimizeEnergy.py on lines 62..64

              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 32.

              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

              defaults, types, atomtypes, masses, charges, atomtypeparameters, bondtypes, bondtypeparams, angletypes, angletypeparams, exclusions, x, y, z, resname, resid, Lx, Ly, Lz =gromacs.read(grofile, topfile)
              Severity: Minor
              Found in examples/simpleGromacs/simpleGromacs.py and 1 other location - About 30 mins to fix
              testsuite/pi_water/water.py on lines 76..76

              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 32.

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

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

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

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

              Refactorings

              Further Reading

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

                  if (hadress):
        print("Error! TI not implemented in VerletListHadressInteractionTemplate yet")
        return
        #interaction=espressopp.interaction.VerletListHadressReactionFieldGeneralized(verletlist, ftpl)
    elif (adress):
              Severity: Minor
              Found in src/tools/gromacs.py and 1 other location - About 30 mins to fix
              src/tools/gromacs.py on lines 1140..1148

              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 32.

              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

                      self.assertEqual(vl.totalSize(), N * N * N * 13)
              Severity: Minor
              Found in testsuite/unittest/testVerletList.py and 2 other locations - About 30 mins to fix
              testsuite/unittest/testVerletList.py on lines 97..97
              testsuite/unittest/testVerletList.py on lines 103..103

              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 32.

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

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

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

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

              Refactorings

              Further Reading

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

                  if (hadress):
        #interaction=espressopp.interaction.VerletListHadressLennardJonesSoftcoreTI(verletlist, ftpl)
        print("Error! TI not implemented in VerletListHadressInteractionTemplate yet")
        return
    elif (adress):
              Severity: Minor
              Found in src/tools/gromacs.py and 1 other location - About 30 mins to fix
              src/tools/gromacs.py on lines 1270..1278

              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 32.

              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

                      particle_list = [
            (1, espressopp.Real3D(2.0, 2.0, 2.0), 1.0),
            (2, espressopp.Real3D(2.1, 2.0, 2.0), 1.0),
              Severity: Minor
              Found in testsuite/minimize_energy/testMinimizeEnergy.py and 1 other location - About 30 mins to fix
              testsuite/minimize_energy/testMinimizeEnergy.py on lines 51..53

              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 32.

              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

                  while not 'atoms' in line:
        line = f.readline()
        if not line: break # break out of while if EOF
              Severity: Minor
              Found in src/tools/gromacs.py and 1 other location - About 30 mins to fix
              src/tools/gromacs.py on lines 613..615

              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 32.

              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

                      self.assertEqual(vl.totalSize(), N * N * N * 9);
              Severity: Minor
              Found in testsuite/unittest/testVerletList.py and 2 other locations - About 30 mins to fix
              testsuite/unittest/testVerletList.py on lines 97..97
              testsuite/unittest/testVerletList.py on lines 109..109

              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 32.

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

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

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

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

              Refactorings

              Further Reading

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

                  if __checkController(exec_):
        if not args:
            raise UserError('pmi.exec_ expects at least one argument(s) on controller!')

        # broadcast the statement
              Severity: Minor
              Found in src/pmi.py and 1 other location - About 30 mins to fix
              src/pmi.py on lines 198..205

              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 32.

              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

                  while not 'moleculetype' in line:
        line = f.readline()
        if not line: break # break out of while if EOF
              Severity: Minor
              Found in src/tools/gromacs.py and 1 other location - About 30 mins to fix
              src/tools/gromacs.py on lines 636..638

              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 32.

              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

              Function particleExists has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
              Open

                  def particleExists(self, pid):
        if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
            if self.cxxclass.lookupRealParticle(self, pid):
                return True
            else:
              Severity: Minor
              Found in src/storage/Storage.py - About 25 mins 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

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