Merge pull request #227 from SMTG-Bham/fixes

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

setup.py

@@ -38,7 +38,7 @@
         "h5py",
         "pymatgen>=2020.10.20",
         "phonopy>=2.1.3",
-        "matplotlib",
+        "matplotlib>=3.2.0",
         "seekpath",
         "castepxbin<1.0",
         "colormath",

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"
@@ -762,24 +758,20 @@ def _get_parser():
         "--orbitals",
         type=_el_orb,
         metavar="O",
-        help=(
-            "orbitals to split into lm-decomposed "
-            'contributions (e.g. "Ru.d")'
-        ),
+        help="orbitals to split into lm-decomposed contributions (e.g. 'Ru.d')",
     )
     parser.add_argument(
         "--atoms",
         type=_atoms,
         metavar="A",
-        help=('atoms to include (e.g. "O.1.2.3,Ru.1.2.3")'),
+        help='atoms to include (e.g. "O.1.2.3,Ru.1.2.3")',
     )
     parser.add_argument(
         "--spin",
         type=str,
         default=None,
         help=(
-            "select only one spin channel for a "
-            "spin-polarised calculation "
+            "select only one spin channel for a spin-polarised calculation "
             "(options: up, 1; down, -1)"
         ),
     )
@@ -829,9 +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"
     )
@@ -883,18 +873,14 @@ def main():
     logging.getLogger("").addHandler(console)
 
     if args.config is None:
-        config_path = os.path.join(
-            ilr_files("sumo.plotting"), "orbital_colours.conf"
-        )
+        config_path = ilr_files("sumo.plotting") / "orbital_colours.conf"
     else:
         config_path = args.config
     colours = configparser.ConfigParser()
     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
@@ -441,9 +442,7 @@ def _get_parser():
         "--code",
         default="vasp",
         metavar="C",
-        help=(
-            'Input file format: "vasp" (vasprun.xml) or ' '"questaal" (opt.ext)'
-        ),
+        help='Input file format: "vasp" (vasprun.xml) or "questaal" (opt.ext)',
     )
     parser.add_argument(
         "-p", "--prefix", metavar="P", help="prefix for the files generated"
@@ -463,25 +462,21 @@ def _get_parser():
         "--orbitals",
         type=_el_orb,
         metavar="O",
-        help=(
-            "orbitals to split into lm-decomposed "
-            'contributions (e.g. "Ru.d")'
-        ),
+        help="orbitals to split into lm-decomposed contributions (e.g. 'Ru.d')",
     )
     parser.add_argument(
         "-a",
         "--atoms",
         type=_atoms,
         metavar="A",
-        help=('atoms to include (e.g. "O.1.2.3,Ru.1.2.3")'),
+        help='atoms to include (e.g. "O.1.2.3,Ru.1.2.3")',
     )
     parser.add_argument(
         "--spin",
         type=str,
         default=None,
         help=(
-            "select one spin channel only for a "
-            "spin-polarised calculation "
+            "select one spin channel only for a spin-polarised calculation "
             "(options: up, 1; down, -1)"
         ),
     )
@@ -560,9 +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"
     )
@@ -634,18 +627,14 @@ def main():
     logging.getLogger("").addHandler(console)
 
     if args.config is None:
-        config_path = os.path.join(
-            ilr_files("sumo.plotting"), "orbital_colours.conf"
-        )
+        config_path = ilr_files("sumo.plotting") / "orbital_colours.conf"
     else:
         config_path = args.config
     colours = configparser.ConfigParser()
     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
@@ -19,15 +19,11 @@
 
 colour_cache = {}
 
-sumo_base_style = os.path.join(ilr_files("sumo.plotting"), "sumo_base.mplstyle")
-sumo_dos_style = os.path.join(ilr_files("sumo.plotting"), "sumo_dos.mplstyle")
-sumo_bs_style = os.path.join(ilr_files("sumo.plotting"), "sumo_bs.mplstyle")
-sumo_phonon_style = os.path.join(
-    ilr_files("sumo.plotting"), "sumo_phonon.mplstyle"
-)
-sumo_optics_style = os.path.join(
-    ilr_files("sumo.plotting"), "sumo_optics.mplstyle"
-)
+sumo_base_style = ilr_files("sumo.plotting") / "sumo_base.mplstyle"
+sumo_dos_style = ilr_files("sumo.plotting") / "sumo_dos.mplstyle"
+sumo_bs_style = ilr_files("sumo.plotting") / "sumo_bs.mplstyle"
+sumo_phonon_style = ilr_files("sumo.plotting") / "sumo_phonon.mplstyle"
+sumo_optics_style = ilr_files("sumo.plotting") / "sumo_optics.mplstyle"
 
 
 def styled_plot(*style_sheets):
@@ -47,9 +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:
@@ -62,9 +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)
@@ -277,9 +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]
 
@@ -290,19 +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
@@ -317,8 +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
@@ -85,7 +82,7 @@ def _get_bradcrack_data(bravais):
                'path': [['\Gamma', 'X', ..., 'P'], ['H', 'N', ...]]}
 
         """
-        json_file = os.path.join(ilr_files("sumo.symmetry"), "bradcrack.json")
+        json_file = ilr_files("sumo.symmetry") / "bradcrack.json"
         with open(json_file) as f:
             bradcrack_data = load_json(f)
             return bradcrack_data[bravais]

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):