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

            if self.order == 1:
                self.generalized_coordinate = Position(self.coords_in, cartesian=self.cartesian,
                                                       spherical=self.spherical)
Severity: Minor
Found in pytim/observables/distributionfunction.py and 1 other location - About 50 mins to fix
pytim/observables/distributionfunction.py on lines 154..156

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

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

        lowerpos = utilities.generate_periodic_border(
            lower.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 151..152

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

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

            if self.order == 2:
                self.generalized_coordinate = RelativePosition(self.coords_in, cartesian=self.cartesian,
                                                               spherical=self.spherical)
Severity: Minor
Found in pytim/observables/distributionfunction.py and 1 other location - About 50 mins to fix
pytim/observables/distributionfunction.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 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

Function _compute_local_coords has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def _compute_local_coords(self, box):
        local_coords = []
        for i, patch in enumerate(self.patches):
            p = self.tree.data[patch].copy()
            p = self.remove_pbc(p, box)
Severity: Minor
Found in pytim/observables/local_frame.py - About 45 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_cluster_params has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def assign_cluster_params(self,
                              cluster_cut,
                              cluster_threshold_density,
                              extra_cluster_groups):
        elements = 0
Severity: Minor
Found in pytim/sanity_check.py - About 45 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 _fit_ellipse has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def _fit_ellipse(x, y, nonlinear=True, off=0.0, points_density=25, verbose=False):
Severity: Minor
Found in pytim/observables/contactangle.py - About 45 mins to fix

Function _fit_ellipsoid has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def _fit_ellipsoid(x, y, z, nonlinear=True, off=0.0, points_density=25):
        """  fit an ellipsoid through the points (x,y,z)

             :param list  x        : list of arrays with coordinates x
             :param list  y        : list of arrays with coordinates y
Severity: Minor
Found in pytim/observables/contactangle.py - About 45 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 _fit_ellipsoid has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def _fit_ellipsoid(x, y, z, nonlinear=True, off=0.0, points_density=25):
Severity: Minor
Found in pytim/observables/contactangle.py - About 45 mins to fix

Function dont_skip_any_doctests has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

def dont_skip_any_doctests(app, what, name, obj, skip, options):
Severity: Minor
Found in docs/source/conf.py - About 45 mins to fix

Function _remove_COM has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def _remove_COM(self, group, inter, alpha, box):
        def group_size(g, direction):
            p = g.atoms.positions[:, direction]
            return np.abs(np.max(p) - np.min(p))
Severity: Minor
Found in pytim/observables/contactangle.py - About 45 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

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

        self.q_vectors[0] *= 2. * np.pi / box[0]
Severity: Minor
Found in pytim/surface.py and 1 other location - About 45 mins to fix
pytim/surface.py on lines 98..98

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 2 locations. Consider refactoring.
Open

        d2[np.where(d2 < -box / 2.)] += box
Severity: Minor
Found in pytim/surface.py and 1 other location - About 45 mins to fix
pytim/surface.py on lines 278..278

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

Function label_group has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def label_group(self,
                    group,
                    beta=None,
                    layer=None,
                    cluster=None,
Severity: Minor
Found in pytim/interface.py - About 45 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

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

        self.q_vectors[1] *= 2. * np.pi / box[1]
Severity: Minor
Found in pytim/surface.py and 1 other location - About 45 mins to fix
pytim/surface.py on lines 97..97

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

Function _compute_observable has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def _compute_observable(self, ka1, ka2):
        try:
            fg1 = self.observable.compute(self.g1, ka1)
        except:
            fg1 = self.observable.compute(self.g1)
Severity: Minor
Found in pytim/observables/rdf.py - About 45 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 write_atomgroup has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

def write_atomgroup(filename, group, color=None, radius=None):
    """ write in a vtk file the positions of particles

        :param string filename: the filename
        :param AtomGroup group: the group, whose positions are to be written to
Severity: Minor
Found in pytim/vtk.py - About 45 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 correlate has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

def correlate(a1, a2=None, _normalize=True):
    """
      correlate data series using numpy fft. The function calculates \
      correlation or cross-correlation.
Severity: Minor
Found in pytim/utilities.py - About 45 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

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

            for nlayer in range(max_layers):
                self._surfaces[nlayer] = SurfaceFlatInterface(
                    self, options={'layer': nlayer})
Severity: Minor
Found in pytim/gitim.py and 1 other location - About 45 mins to fix
pytim/gitim.py on lines 184..186

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 2 locations. Consider refactoring.
Open

            for nlayer in range(max_layers):
                self._surfaces[nlayer] = SurfaceGenericInterface(
                    self, options={'layer': nlayer})
Severity: Minor
Found in pytim/gitim.py and 1 other location - About 45 mins to fix
pytim/gitim.py on lines 178..180

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

Function _writepdb has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

def _writepdb(interface,
Severity: Minor
Found in pytim/writepdb.py - About 45 mins to fix
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