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Function import_calculations_from_file has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

def import_calculations_from_file(filename, skip_incomplete_records=False):
    """
    Construct a list of :obj:`Calculation` objects by reading a YAML file.
    Each YAML document should include ``title``, ``stoichiometry``, and ``energy`` fields, e.g.::
Severity: Minor
Found in vasppy/calculation.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 dr_ij has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

def dr_ij(
    structure: Structure,
    indices_i: Optional[List[int]] = None,
    indices_j: Optional[List[int]] = None,
    self_reference: bool = False,
Severity: Minor
Found in vasppy/utils.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 plot_pdos has 13 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def plot_pdos(
Severity: Major
Found in vasppy/doscar.py - About 1 hr to fix

    Function main has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
    Open

    def main():
    args = parse_command_line_arguments()
    coordinate_types = {
        "d": "Direct",
        "direct": "Direct",
    Severity: Minor
    Found in vasppy/scripts/proc_poscar.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

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

                        for a, b, c in [
                        cell_shift
                        for cell_shift in cell_shift_indices
                        if parity(cell_shift) == odd_even
                    ]:
    Severity: Major
    Found in vasppy/poscar.py and 1 other location - About 1 hr to fix
    vasppy/poscar.py on lines 287..289

    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 43.

    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 read_data has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
    Open

    def read_data(verbose=True):
    dir_list = find_vasp_calculations()
    if not dir_list:
        raise ValueError(
            "Did not find any subdirectories containing vasprun.xml or vasprun.xml.gz files"
    Severity: Minor
    Found in vasppy/scripts/murnfit.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

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

                    for a, b, c in cell_shift_indices:
                    new_coordinate_list.append(
                        [pos_in_origin_cell + np.array([a, b, c] * lattice_shift)][
    Severity: Major
    Found in vasppy/poscar.py and 1 other location - About 1 hr to fix
    vasppy/poscar.py on lines 274..280

    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 43.

    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 chg_dump_log:
        dipoles = lines_to_numpy_array(
            file_data[4 + number_of_atoms * 2 : 4 + number_of_atoms * 3]
    Severity: Major
    Found in vasppy/pimaim.py and 1 other location - About 1 hr to fix
    vasppy/scripts/pimaim_to_poscar.py on lines 53..54

    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 41.

    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

        dipoles = lines_to_numpy_array(
        file_data[4 + number_of_atoms * 2 : 4 + number_of_atoms * 3]
    Severity: Major
    Found in vasppy/scripts/pimaim_to_poscar.py and 1 other location - About 1 hr to fix
    vasppy/pimaim.py on lines 31..33

    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 41.

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

        def print_file_tracking(self):
        if self.meta.track:
            print("file tracking:")
            for f, new_filename in self.meta.track.items():
                print("    {}:".format(f))
    Severity: Minor
    Found in vasppy/summary.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

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

    def lines_to_numpy_array(data):
    return np.array([[float(s) for s in line.split()] for line in data])
    Severity: Major
    Found in vasppy/pimaim.py and 1 other location - About 1 hr to fix
    vasppy/scripts/pimaim_to_poscar.py on lines 30..31

    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

    def lines_to_numpy_array(data):
    return np.array([[float(s) for s in line.split()] for line in data])
    Severity: Major
    Found in vasppy/scripts/pimaim_to_poscar.py and 1 other location - About 1 hr to fix
    vasppy/pimaim.py on lines 9..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

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

        def print_forces(self):
        for theseforces in self.forces:
            output_str = [f"  {force: .6f}" for force in theseforces]
            for force in theseforces:
                if abs(force) > self.convergence:
    Severity: Minor
    Found in vasppy/scripts/checkforce.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 print_plus_u has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
    Open

        def print_plus_u(self):
        if "LDAUU" in self.vasprun.incar:
            lqn = {0: "s", 1: "p", 2: "d", 3: "f"}
            ldauu = self.vasprun.incar["LDAUU"]
            ldauj = self.vasprun.incar["LDAUJ"]
    Severity: Minor
    Found in vasppy/summary.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 2 locations. Consider refactoring.
    Open

        matrix[:, [axes_index[axes[0]], axes_index[axes[1]]]] = matrix[
    Severity: Minor
    Found in vasppy/poscar.py and 1 other location - About 55 mins to fix
    vasppy/poscar.py on lines 25..26

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

        def weighted_band_structure(
        self,
        spins=None,
        ions=None,
        orbitals=None,
    Severity: Minor
    Found in vasppy/procar.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 __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(
    Severity: Major
    Found in vasppy/rdf.py - About 50 mins to fix

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

          def __init__(
      Severity: Major
      Found in vasppy/doscar.py - About 50 mins to fix

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

            def weighted_band_structure(
        Severity: Minor
        Found in vasppy/procar.py - About 45 mins to fix

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

              def __init__(self, title, description, status, notes=None, type=None, track=None):
          Severity: Minor
          Found in vasppy/vaspmeta.py - About 45 mins to fix
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