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Function _fit_circle has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def _fit_circle(hr, hh, nonlinear=True):
        """ fit an arc through the profile h(r) sampled by the class

            :param list hr:        list of arrays with the radial coordinates
            :param list hh:        list of arrays with the elevations
Severity: Minor
Found in pytim/observables/contactangle.py - About 1 hr 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

Function _center has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def _center(group, direction, halfbox_shift=False):
        """
        Centers the liquid slab in the simulation box.

        The algorithm tries to avoid problems with the definition
Severity: Minor
Found in pytim/interface.py - About 1 hr 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

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

def consecutive_filename(universe, basename):
    if basename.endswith('.cube'):
        basename = basename[:-4]
    return utilities.consecutive_filename(universe, basename, 'cube')
Severity: Major
Found in pytim/cube.py and 2 other locations - About 1 hr to fix
pytim/vtk.py on lines 201..204
pytim/wavefront_obj.py on lines 7..10

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

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

    if order == 'zyx':
        z, y, x = np.meshgrid(xyz[0], xyz[1], xyz[2], indexing='ij')
Severity: Major
Found in pytim/utilities_mesh.py and 1 other location - About 1 hr to fix
pytim/utilities_mesh.py on lines 27..30

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

Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(self,
Severity: Major
Found in pytim/simple_interface.py - About 1 hr to fix

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

        except:
            tree = cKDTree(
                np.random.random((self.npoints, 3)) * box, boxsize=_box[:3])
Severity: Major
Found in pytim/observables/free_volume.py and 1 other location - About 1 hr to fix
pytim/observables/free_volume.py on lines 70..72

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 38.

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

        try:  # older scipy versions
            tree = cKDTree(
                np.random.random((self.npoints, 3)) * box, boxsize=_box[:6])
Severity: Major
Found in pytim/observables/free_volume.py and 1 other location - About 1 hr to fix
pytim/observables/free_volume.py on lines 73..75

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 38.

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 __init__ has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self,
                 direction=None,
                 observable=None,
                 interface=None,
                 symmetry='default',
Severity: Minor
Found in pytim/observables/profile.py - About 55 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

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

        return corr / np.sum(np.cumsum(self.timeseries, axis=0), axis=1)[::-1]
Severity: Minor
Found in pytim/observables/correlator.py and 1 other location - About 55 mins to fix
pytim/observables/correlator.py on lines 316..316

Duplicated Code

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

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

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

Tuning

This issue has a mass of 37.

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

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

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

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

Refactorings

Further Reading

Function center_system has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def center_system(symmetry, group, direction, planar_to_origin=False):
        if symmetry == 'planar':
            utilities.centerbox(group.universe, center_direction=direction)
            Interface._center(group, direction, halfbox_shift=True)
            utilities.centerbox(group.universe, center_direction=direction)
Severity: Minor
Found in pytim/interface.py - About 55 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

Function assign_universe has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def assign_universe(self, universe, analysis_group):
        """ Assign the universe and the analysis_group
        """
        self.interface._mode = self._check_universe(universe)
        if self.interface._mode is None:
Severity: Minor
Found in pytim/sanity_check.py - About 55 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

Function patchMDTRAJ has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

def patchMDTRAJ(trajectory, universe):
    """ Patch the mdtraj Trajectory class

        automates the data exchange between MDAnalysis and mdtraj classes
Severity: Minor
Found in pytim/patches.py - About 55 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

Function select_direction has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def select_direction(self, arg):
        _dirs = {'x': 0, 'y': 1, 'z': 2}

        def _inarg(string, inp):
            return np.any([string in e for e in inp])
Severity: Minor
Found in pytim/observables/observable.py - About 55 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

Function compute has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def compute(self, inp, kargs=None):
        """ Compute the local reference frame

            :param AtomGroup inp:  the group of atoms that define the surface
            :returns:              a (len(inp),3,3) set of coordinates defining
Severity: Minor
Found in pytim/observables/local_frame.py - About 55 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

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

        return corr / np.sum(np.cumsum(self.timeseries, axis=0), axis=1)[::-1]
Severity: Minor
Found in pytim/observables/correlator.py and 1 other location - About 55 mins to fix
pytim/observables/correlator.py on lines 336..336

Duplicated Code

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

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

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

Tuning

This issue has a mass of 37.

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

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

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

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

Refactorings

Further Reading

Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(self,
Severity: Major
Found in pytim/observables/profile.py - About 50 mins to fix

Function centerbox has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

def centerbox(universe,
Severity: Major
Found in pytim/utilities.py - About 50 mins to fix

Function _assign_one_side has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def _assign_one_side(self,
Severity: Major
Found in pytim/itim.py - About 50 mins to fix

Function write_file has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

def write_file(filename,
Severity: Major
Found in pytim/cube.py - About 50 mins to fix

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

        upperpos = utilities.generate_periodic_border(
            upper.positions[:, self.xyz], box, delta, method='2d')[0]
Severity: Minor
Found in pytim/surface.py and 1 other location - About 50 mins to fix
pytim/surface.py on lines 153..154

Duplicated Code

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

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

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

Tuning

This issue has a mass of 36.

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

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

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

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

Refactorings

Further Reading

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