File procar.py has 558 lines of code (exceeds 250 allowed). Consider refactoring.

Open

from functools import reduce
from copy import deepcopy
from typing import Optional
import warnings
import math

Function main has a Cognitive Complexity of 49 (exceeds 5 allowed). Consider refactoring.

Open

def main():
    supported_flags = Summary.supported_flags
    to_print = [
        "title",
        "status",

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Function plot_pdos has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.

Open

    def plot_pdos(
        self,
        ax: Optional[Axes] = None,
        to_plot: Optional[Dict[str, List[str]]] = None,
        colors: Optional[Iterable] = None,

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File doscar.py has 329 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import numpy as np
import pandas as pd  # type: ignore
import matplotlib.pyplot as plt  # type: ignore
from matplotlib.axes import Axes  # type: ignore
from matplotlib.figure import Figure  # type: ignore

Summary has 31 functions (exceeds 20 allowed). Consider refactoring.

Open

class Summary:
    """
    TODO Document Summary class
    """

File summary.py has 324 lines of code (exceeds 250 allowed). Consider refactoring.

Open

# Summary class and helper methods
# Used for summarising VASP calculations as YAML

from pymatgen.io.vasp.outputs import Vasprun  # type: ignore
from pymatgen.analysis.transition_state import NEBAnalysis  # type: ignore

Function output_coordinates_only has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.

Open

    def output_coordinates_only(self, coordinate_type="Direct", opts=None):
        prefix = []
        suffix = []
        for i in range(self.coordinates.shape[0]):
            prefix_string = ""

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Poscar has 28 functions (exceeds 20 allowed). Consider refactoring.

Open

class Poscar:
    lines_offset = 9

    def __init__(self):
        self.title = "Title"

Function pdos_select has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

    def pdos_select(
        self,
        atoms: Optional[Union[int, List[int]]] = None,
        spin: Optional[str] = None,
        l: Optional[str] = None,

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File poscar.py has 284 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import numpy as np
import sys
import re
import copy
from vasppy import cell

Procar has 24 functions (exceeds 20 allowed). Consider refactoring.

Open

class Procar:
    """
    Object for working with PROCAR data.

    Attributes:

Function replicate has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def replicate(self, h, k, l, group=False):
        lattice_scaling = np.array([h, k, l], dtype=float)
        lattice_shift = np.reciprocal(lattice_scaling)
        new_poscar = Poscar()
        new_poscar.title = self.title

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Function get_forces_data has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

def get_forces_data(outcar_filename="OUTCAR", convergence=None, warn=False):
    """Parse an OUTCAR file and return forces data, includig various summary statistics.

    args:
        outcar_filename (optional, `str`): OUTCAR filename. Default is "OUTCAR".

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Function potcar_spec has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

def potcar_spec(filename, return_hashes=False):
    """
    Returns a dictionary specifying the pseudopotentials contained in a POTCAR file.

    Args:

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Function import_calculations_from_file has a Cognitive Complexity of 16 (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.::

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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,

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Function plot_pdos has 13 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def plot_pdos(

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",

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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"

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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))

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