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Marcello-Sega/pytim

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Rename function "patchMDTRAJ_ReplacementTables" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def patchMDTRAJ_ReplacementTables():
Severity: Major
Found in pytim/patches.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Method "__init__" has 8 parameters, which is greater than the 7 authorized.
Open

    def __init__(self,
                 universe,
                 group=None,
                 alpha=1.5,
                 symmetry='generic',
Severity: Major
Found in pytim/simple_interface.py by sonar-python

A long parameter list can indicate that a new structure should be created to wrap the numerous parameters or that the function is doing too many things.

Noncompliant Code Example

With a maximum number of 4 parameters:

def do_something(param1, param2, param3, param4, param5):
    ...

Compliant Solution

def do_something(param1, param2, param3, param4):
    ...

Refactor this function to reduce its Cognitive Complexity from 38 to the 15 allowed.
Open

    def _set_default_values(self, generalized_coordinate, max_distance, nbins):
Severity: Critical
Found in pytim/observables/distributionfunction.py by sonar-python

Cognitive Complexity is a measure of how hard the control flow of a function is to understand. Functions with high Cognitive Complexity will be difficult to maintain.

See

Merge this if statement with the enclosing one.
Open

                        if self.interface._frame != self.frame:
Severity: Major
Found in pytim/patches.py by sonar-python

Merging collapsible if statements increases the code's readability.

Noncompliant Code Example

if condition1:
    if condition2:
        # ...

Compliant Solution

if condition1 and condition2:
    # ...

Rename function "patchNumpy" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def patchNumpy():
Severity: Major
Found in pytim/patches.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Rename function "patchTrajectory" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def patchTrajectory(trajectory, interface):
Severity: Major
Found in pytim/patches.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Rename function "polygonalArea" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def polygonalArea(points):
Severity: Major
Found in pytim/utilities_geometry.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Refactor this function to reduce its Cognitive Complexity from 17 to the 15 allowed.
Open

    def compute_sasa(self, group):
Severity: Critical
Found in pytim/sasa.py by sonar-python

Cognitive Complexity is a measure of how hard the control flow of a function is to understand. Functions with high Cognitive Complexity will be difficult to maintain.

See

Refactor this function to reduce its Cognitive Complexity from 42 to the 15 allowed.
Open

    def sample(self, bins=100, params=None, binning='theta', periodic=None, base_cut=0.0):
Severity: Critical
Found in pytim/observables/contactangle.py by sonar-python

Cognitive Complexity is a measure of how hard the control flow of a function is to understand. Functions with high Cognitive Complexity will be difficult to maintain.

See

Rename function "sample_theta_R" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

        def sample_theta_R(self, bins, th_left, th_right, RR_left, RR_right):
Severity: Major
Found in pytim/observables/contactangle.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Remove the code after this "return".
Open

        return self.arc_ellipse(cofX, rmax=rmax, rmin=rmin, bins=bins)
Severity: Major
Found in pytim/observables/contactangle.py by sonar-python

Jump statements (return, break, continue, and raise) move control flow out of the current code block. Typically, any statements in a block that come after a jump are simply wasted keystrokes lying in wait to confuse the unwary.

Noncompliant Code Example

def fun(a):
  i = 10
  return i + a       # Noncompliant
  i += 1             # this is never executed

Compliant Solution

def fun(a):
  i = 10
  return i + a

See

  • MISRA C:2004, 14.1 - There shall be no unreachable code
  • MISRA C++:2008, 0-1-1 - A project shall not contain unreachable code
  • MISRA C++:2008, 0-1-9 - There shall be no dead code
  • MISRA C:2012, 2.1 - A project shall not contain unreachable code
  • MISRA C:2012, 2.2 - There shall be no dead code
  • MITRE, CWE-561 - Dead Code
  • CERT, MSC56-J. - Detect and remove superfluous code and values
  • CERT, MSC12-C. - Detect and remove code that has no effect or is never executed
  • CERT, MSC07-CPP. - Detect and remove dead code

Method "_assign_one_side" has 8 parameters, which is greater than the 7 authorized.
Open

    def _assign_one_side(self,
                         uplow,
                         sorted_atoms,
                         _x,
                         _y,
Severity: Major
Found in pytim/itim.py by sonar-python

A long parameter list can indicate that a new structure should be created to wrap the numerous parameters or that the function is doing too many things.

Noncompliant Code Example

With a maximum number of 4 parameters:

def do_something(param1, param2, param3, param4, param5):
    ...

Compliant Solution

def do_something(param1, param2, param3, param4):
    ...

Rename function "_NN_query" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def _NN_query(kdtree, position, qrange):
Severity: Major
Found in pytim/utilities.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Remove this commented out code.
Open

        # R_=np.sqrt(R_*R_+z_*z_)
Severity: Major
Found in pytim/observables/contactangle.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Rename function "EulerRotation" to match the regular expression ^[a-z_][a-z0-9_]{2,}$.
Open

def EulerRotation(phi, theta, psi):
Severity: Major
Found in pytim/utilities_geometry.py by sonar-python

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all function names match a provided regular expression.

Noncompliant Code Example

With the default provided regular expression: ^[a-z_][a-z0-9_]{2,30}$

def MyFunction(a,b):
    ...

Compliant Solution

def my_function(a,b):
    ...

Refactor this function to reduce its Cognitive Complexity from 20 to the 15 allowed.
Open

    def sample(self, g1=None, g2=None, kargs1=None, kargs2=None):
Severity: Critical
Found in pytim/observables/distributionfunction.py by sonar-python

Cognitive Complexity is a measure of how hard the control flow of a function is to understand. Functions with high Cognitive Complexity will be difficult to maintain.

See

Remove this commented out code.
Open

        # return X_coord,Y_coord,Z_coord,xx[idy],yy[idy]
Severity: Major
Found in pytim/observables/contactangle.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Method "__init__" has 10 parameters, which is greater than the 7 authorized.
Open

    def __init__(self,
                 universe,
                 max_distance='full',
                 nbins=75,
                 start=None,
Severity: Major
Found in pytim/observables/rdf.py by sonar-python

A long parameter list can indicate that a new structure should be created to wrap the numerous parameters or that the function is doing too many things.

Noncompliant Code Example

With a maximum number of 4 parameters:

def do_something(param1, param2, param3, param4, param5):
    ...

Compliant Solution

def do_something(param1, param2, param3, param4):
    ...

Refactor this function to reduce its Cognitive Complexity from 21 to the 15 allowed.
Open

    def _assign_layers(self):
Severity: Critical
Found in pytim/itim.py by sonar-python

Cognitive Complexity is a measure of how hard the control flow of a function is to understand. Functions with high Cognitive Complexity will be difficult to maintain.

See

Remove this commented out code.
Open

#oxygens = u.select_atoms("name OW")
Severity: Major
Found in pytim/examples/example_water.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"
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