formatting

macrodensity/__init__.py

@@ -1,15 +1,15 @@
 """
-MacroDensity is a package to read, process and plot electrostatic potential and electron density 
+MacroDensity is a package to read, process and plot electrostatic potential and electron density
 files from electronic structure calculations.
 """
 import math
 
 import numpy as np
 from scipy import interpolate
 
+from macrodensity.averages import *
 from macrodensity.density import *
 from macrodensity.io import *
 from macrodensity.plotting import *
 from macrodensity.tools import *
 from macrodensity.utils import *
-from macrodensity.averages import *

macrodensity/averages.py

@@ -1,12 +1,12 @@
-'''
+"""
 This module contains functions for calculating different types of averages from the dataset.
-'''
+"""
 from __future__ import division, print_function
 
 import numpy as np
 
-from macrodensity.io import read_vasp_density, read_gulp_potential 
-from macrodensity.utils import matrix_2_abc, density_2_grid 
+from macrodensity.io import read_gulp_potential, read_vasp_density
+from macrodensity.utils import density_2_grid, matrix_2_abc
 
 
 def macroscopic_average(
@@ -328,4 +328,4 @@ def planar_average(
             z_plane[:, :] = grid[:, :, z_value]
             average[z_value] = z_plane.mean()
 
-    return average
+    return average

macrodensity/density.py

@@ -1,7 +1,7 @@
 """
-macrodensity.density contains functions to calculate the electron 
-density of a structure, as well as functions to calculate the electrostatic potential 
-and the electrostatic potential gradients of a structure. 
+macrodensity.density contains functions to calculate the electron
+density of a structure, as well as functions to calculate the electrostatic potential
+and the electrostatic potential gradients of a structure.
 """
 
 from __future__ import division, print_function
@@ -75,4 +75,3 @@ def element_vol(vol: float, nx: int, ny: int, nz: int) -> float:
     ele_vol = vol / number_of_elements
 
     return ele_vol
-

macrodensity/plotting.py

@@ -7,31 +7,27 @@
 
 import matplotlib as mpl
 import matplotlib.pyplot as plt
-from matplotlib import cm
-
 import numpy as np
 import pandas as pd
-from scipy.interpolate import interp1d
-
 from ase.io import cube, vasp
+from matplotlib import cm
+from scipy.interpolate import interp1d
 
 from macrodensity.averages import (
     macroscopic_average,
     planar_average,
     travelling_volume_average,
     volume_average,
 )
-from macrodensity.density import (
-    gradient_magnitude,
-)
+from macrodensity.density import gradient_magnitude
 from macrodensity.io import read_gulp_potential, read_vasp_density
 from macrodensity.tools import _find_active_space, create_plotting_mesh
 from macrodensity.utils import (
+    density_2_grid,
     matrix_2_abc,
     numbers_2_grid,
     points_2_plane,
     vector_2_abscissa,
-    density_2_grid
 )
 
 MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
@@ -82,9 +78,9 @@ def energy_band_alignment_diagram(
         edge (None or str, optional): The edge color for the bars.
             If None, there will be no edge color. Default is None.
 
-        fig_format (str, optional): The format used to save the image. 
+        fig_format (str, optional): The format used to save the image.
             Default is "pdf".
-    
+
     Returns:
         Figure: A matplotlib figure object containing the energy band alignment
             diagram.
@@ -697,7 +693,9 @@ def plot_field_at_point(
     # grad_mag=np.linalg.norm( [grad_y,grad_y,grad_z], axis=3)
 
     ## This function in Macrodensity averages Efield ACROSS Z for Slab calculations
-    xx,yy,grd =  md.create_plotting_mesh(NGX,NGY,NGZ,plane_coeff,grad_mag) #AVG over full volume
+    xx, yy, grd = md.create_plotting_mesh(
+        NGX, NGY, NGZ, plane_coeff, grad_mag
+    )  # AVG over full volume
 
     # Here we construct the same xx,yy,grd variables with a SLICE, forming a plane in XY at particular ZSLICE
     xx, yy = np.mgrid[0:NGX, 0:NGY]

macrodensity/tools.py

@@ -1,6 +1,6 @@
 #! /usr/bin/env python
-""" 
-macrodensity.tools contains functions to read and manipulate the electronic 
+"""
+macrodensity.tools contains functions to read and manipulate the electronic
 density data from a material.
 """
 
@@ -11,7 +11,7 @@
 
 from macrodensity.averages import volume_average
 from macrodensity.io import get_band_extrema, read_vasp_density
-from macrodensity.utils import matrix_2_abc, density_2_grid
+from macrodensity.utils import density_2_grid, matrix_2_abc
 
 
 def bulk_interstitial_alignment(

macrodensity/utils.py

@@ -332,6 +332,7 @@ def get_third_coordinate(plane_coeff: np.ndarray, NGX: int, NGY: int) -> list:
 
     return zz
 
+
 def density_2_grid(
     density: np.ndarray,
     nx: int,

tests/unit_tests.py

@@ -4,14 +4,13 @@
 import sys
 import unittest
 from os.path import join as path_join
+
 import matplotlib as mpl
 import matplotlib.pyplot as plt
-import pytest
-
-
 import numpy as np
 import pandas as pd
 import pkg_resources
+import pytest
 
 import macrodensity as md
 
@@ -343,7 +342,7 @@ def test_moving_cube(self):
 
 
 class TestPlottingFunctions(unittest.TestCase):
-    
+
     def test_plot_planar_average(self):
         """Tests the plot_planar_average function"""
         locpot = pkg_resources.resource_filename(
@@ -429,7 +428,7 @@ def test_plot_planar_cube(self):
         self.addCleanup(os.remove, "planar_average.csv")
         self.addCleanup(os.remove, "planar_average.png")
 
-    
+
     @pytest.mark.mpl_image_compare(
         baseline_dir=f"{_file_path}/testIm",
         filename="BandAlignment.png",
@@ -450,10 +449,10 @@ def test_energy_band_alignment_diagram(self):
                 "TiO2": [4.8, 7.8],
             },
             ylims=(-10, 0.0),
-            arrowhead=0.15, 
+            arrowhead=0.15,
             fig_format='png'
         )
-        
+
         if os.path.exists("BandAlignment.png"):
             self.addCleanup(os.remove, "BandAlignment.png")
         return fig