Fixes from #216

.github/workflows/tests.yml

@@ -28,4 +28,4 @@ jobs:
           python -m pip install -e '.[tests]'
 
       - name: Test
-        run: pytest
+        run: pytest

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
     rev: 22.6.0
     hooks:
     - id: black
-  - repo: https://gitlab.com/pycqa/flake8
+  - repo: https://github.com/pycqa/flake8
     rev: 3.9.2
     hooks:
       - id: flake8

sumo/cli/bandplot.py

@@ -17,10 +17,9 @@
     from importlib.resources import files as ilr_files
 except ImportError:  # Python < 3.9
     from importlib_resources import files as ilr_files
+
 import matplotlib as mpl
-from pymatgen.electronic_structure.bandstructure import (
-    get_reconstructed_band_structure,
-)
+from pymatgen.electronic_structure.bandstructure import get_reconstructed_band_structure
 from pymatgen.electronic_structure.core import Spin
 from pymatgen.io.vasp.outputs import BSVasprun
 
@@ -394,9 +393,7 @@ def bandplot(
                 else:
                     logging.info(f"Found PDOS file {pdos_file}")
             else:
-                logging.info(
-                    f"Cell file {cell_file} does not exist, cannot plot PDOS."
-                )
+                logging.info(f"Cell file {cell_file} does not exist, cannot plot PDOS.")
 
             dos, pdos = read_castep_dos(
                 dos_file,
@@ -620,8 +617,7 @@ def _get_parser():
         "-c",
         "--code",
         default="vasp",
-        help="Electronic structure code (default: vasp)."
-        '"questaal" also supported.',
+        help="Electronic structure code (default: vasp)." '"questaal" also supported.',
     )
     parser.add_argument(
         "-p", "--prefix", metavar="P", help="prefix for the files generated"
@@ -825,9 +821,7 @@ def _get_parser():
     parser.add_argument(
         "--height", type=float, default=None, help="height of the graph"
     )
-    parser.add_argument(
-        "--width", type=float, default=None, help="width of the graph"
-    )
+    parser.add_argument("--width", type=float, default=None, help="width of the graph")
     parser.add_argument(
         "--ymin", type=float, default=-6.0, help="minimum energy on the y-axis"
     )
@@ -886,9 +880,7 @@ def main():
     colours.read(os.path.abspath(config_path))
 
     warnings.filterwarnings("ignore", category=UserWarning, module="matplotlib")
-    warnings.filterwarnings(
-        "ignore", category=UnicodeWarning, module="matplotlib"
-    )
+    warnings.filterwarnings("ignore", category=UnicodeWarning, module="matplotlib")
     warnings.filterwarnings("ignore", category=UserWarning, module="pymatgen")
 
     bandplot(

sumo/cli/dosplot.py

@@ -18,6 +18,7 @@
 
 import matplotlib as mpl
 import numpy as np
+
 try:
     from importlib.resources import files as ilr_files
 except ImportError:  # Python < 3.9
@@ -554,9 +555,7 @@ def _get_parser():
     parser.add_argument(
         "--height", type=float, default=None, help="height of the graph"
     )
-    parser.add_argument(
-        "--width", type=float, default=None, help="width of the graph"
-    )
+    parser.add_argument("--width", type=float, default=None, help="width of the graph")
     parser.add_argument(
         "--xmin", type=float, default=-6.0, help="minimum energy on the x-axis"
     )
@@ -635,9 +634,7 @@ def main():
     colours.read(os.path.abspath(config_path))
 
     warnings.filterwarnings("ignore", category=UserWarning, module="matplotlib")
-    warnings.filterwarnings(
-        "ignore", category=UnicodeWarning, module="matplotlib"
-    )
+    warnings.filterwarnings("ignore", category=UnicodeWarning, module="matplotlib")
     warnings.filterwarnings("ignore", category=UserWarning, module="pymatgen")
 
     if args.zero_energy is not None:

sumo/io/castep.py

@@ -487,7 +487,7 @@ def labels_from_cell(cell_file, phonon=False):
         line = f.readline()  # Skip past block start line
         while blockend.match(line.lower()) is None:
             # Do not parse break lines
-            if 'break' not in line.lower():
+            if "break" not in line.lower():
                 kpt = tuple(map(float, line.split()[:3]))
                 if len(line.split()) > 3:
                     label = line.split()[-1]

sumo/plotting/__init__.py

@@ -4,8 +4,8 @@
 """
 Subpackage providing helper functions for generating publication ready plots.
 """
-from functools import wraps
 import os
+from functools import wraps
 
 import matplotlib.pyplot
 import numpy as np
@@ -43,9 +43,7 @@ def styled_plot(*style_sheets):
 
     def decorator(get_plot):
         @wraps(get_plot)
-        def wrapper(
-            *args, fonts=None, style=None, no_base_style=False, **kwargs
-        ):
+        def wrapper(*args, fonts=None, style=None, no_base_style=False, **kwargs):
             if no_base_style:
                 list_style = []
             else:
@@ -58,9 +56,7 @@ def wrapper(
                     list_style += [style]
 
             if fonts is not None:
-                list_style += [
-                    {"font.family": "sans-serif", "font.sans-serif": fonts}
-                ]
+                list_style += [{"font.family": "sans-serif", "font.sans-serif": fonts}]
 
             matplotlib.pyplot.style.use(list_style)
             return get_plot(*args, **kwargs)
@@ -273,9 +269,7 @@ def get_interpolated_colors(color1, color2, color3, weights, colorspace="lab"):
         "xyz": XYZColor,
     }
     if colorspace not in list(colorspace_mapping.keys()):
-        raise ValueError(
-            f"colorspace must be one of {colorspace_mapping.keys()}"
-        )
+        raise ValueError(f"colorspace must be one of {colorspace_mapping.keys()}")
 
     colorspace = colorspace_mapping[colorspace]
 
@@ -286,19 +280,13 @@ def get_interpolated_colors(color1, color2, color3, weights, colorspace="lab"):
 
     # now convert to the colorspace basis for interpolation
     basis1 = np.array(
-        convert_color(
-            color1_rgb, colorspace, target_illuminant="d50"
-        ).get_value_tuple()
+        convert_color(color1_rgb, colorspace, target_illuminant="d50").get_value_tuple()
     )
     basis2 = np.array(
-        convert_color(
-            color2_rgb, colorspace, target_illuminant="d50"
-        ).get_value_tuple()
+        convert_color(color2_rgb, colorspace, target_illuminant="d50").get_value_tuple()
     )
     basis3 = np.array(
-        convert_color(
-            color3_rgb, colorspace, target_illuminant="d50"
-        ).get_value_tuple()
+        convert_color(color3_rgb, colorspace, target_illuminant="d50").get_value_tuple()
     )
 
     # ensure weights is a numpy array
@@ -313,8 +301,7 @@ def get_interpolated_colors(color1, color2, color3, weights, colorspace="lab"):
 
     # convert colors to RGB
     rgb_colors = [
-        convert_color(colorspace(*c), sRGBColor).get_value_tuple()
-        for c in colors
+        convert_color(colorspace(*c), sRGBColor).get_value_tuple() for c in colors
     ]
 
     # ensure all rgb values are less than 1 (sometimes issues in interpolation

sumo/plotting/optics_plotter.py

@@ -8,7 +8,6 @@
 import numpy as np
 import scipy.constants as scpc
 from matplotlib import rcParams
-from matplotlib.font_manager import FontProperties, findfont
 from matplotlib.ticker import AutoMinorLocator, FuncFormatter, MaxNLocator
 
 from sumo.plotting import (
@@ -242,7 +241,6 @@ def get_plot(
             ax.set_ylim(ymin, ymax)
 
             if spectrum_key == "absorption":
-                font = findfont(FontProperties(family=["sans-serif"]))
                 ax.yaxis.set_major_formatter(
                     FuncFormatter(curry_power_tick(times_sign=r"\times"))
                 )

sumo/symmetry/brad_crack_kpath.py

@@ -6,7 +6,6 @@
 """
 
 from json import load as load_json
-import os
 
 import numpy as np
 
@@ -66,9 +65,7 @@ def __init__(self, structure, symprec=1e-3, spg=None):
             spg_symbol = self.spg_symbol
             lattice_type = self.lattice_type
 
-        bravais = self._get_bravais_lattice(
-            spg_symbol, lattice_type, a, b, c, unique
-        )
+        bravais = self._get_bravais_lattice(spg_symbol, lattice_type, a, b, c, unique)
         self._kpath = self._get_bradcrack_data(bravais)
 
     @staticmethod

tests/tests_electronic_structure/test_optics.py

@@ -1,26 +1,22 @@
 import json
-import unittest
 import os
+import unittest
 
 try:
     from importlib.resources import files as ilr_files
 except ImportError:  # Python < 3.9
     from importlib_resources import files as ilr_files
+
 import numpy as np
 from numpy.testing import assert_almost_equal
 from pymatgen.io.vasp import Vasprun
 
-from sumo.electronic_structure.optics import (
-    calculate_dielectric_properties,
-    kkr,
-)
+from sumo.electronic_structure.optics import calculate_dielectric_properties, kkr
 
 
 class AbsorptionTestCase(unittest.TestCase):
     def setUp(self):
-        diel_path = os.path.join(
-            ilr_files("tests"), "data", "Ge", "ge_diel.json"
-        )
+        diel_path = os.path.join(ilr_files("tests"), "data", "Ge", "ge_diel.json")
         with open(diel_path) as f:
             self.ge_diel = json.load(f)
 
@@ -35,9 +31,7 @@ def test_absorption(self):
             self.ge_diel,
             {"absorption"},
         )
-        self.assertIsNone(
-            assert_almost_equal(properties["absorption"], self.ge_abs)
-        )
+        self.assertIsNone(assert_almost_equal(properties["absorption"], self.ge_abs))
 
 
 class KramersKronigTestCase(unittest.TestCase):