Fix sumo-phonon-bandplot

.pre-commit-config.yaml

@@ -1,28 +1,28 @@
 exclude: ^tests/data/
 repos:
   - repo: https://github.com/myint/autoflake
-    rev: v1.4
+    rev: v2.2.1
     hooks:
     - id: autoflake
       args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
   - repo: https://github.com/psf/black
-    rev: 22.6.0
+    rev: 23.12.1
     hooks:
     - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 3.9.2
+    rev: 7.0.0
     hooks:
       - id: flake8
         args: [--max-line-length=125, "--extend-ignore=E203,W503,E402,F401"]
         language_version: python3
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)

sumo/electronic_structure/bandstructure.py

@@ -149,7 +149,6 @@ def get_projections(bs, selection, normalise=None):
 
     # store the projections for all elements and orbitals in a useable format
     for spin, element, orbital in it.product(spins, elements, all_orbitals):
-
         # convert data to [nb][nk]
         el_orb_proj = [
             [all_proj[spin][nb][nk][element][orbital] for nk in range(nkpts)]
@@ -164,7 +163,6 @@ def get_projections(bs, selection, normalise=None):
     # now go through the selected orbitals and extract what's needed
     spec_proj = []
     for spec in selection:
-
         if isinstance(spec, str):
             # spec is just an element type, therefore sum all orbitals
             element = spec

sumo/electronic_structure/effective_mass.py

@@ -61,7 +61,6 @@ def get_fitting_data(bs, spin, band_id, kpoint_id, num_sample_points=3):
     # check to see if there are enough points to sample from first
     # check in the forward direction
     if kpoint_id + num_sample_points <= branch_data["end_index"]:
-
         # calculate sampling limits
         start_id = kpoint_id
         end_id = kpoint_id + num_sample_points + 1
@@ -90,7 +89,6 @@ def get_fitting_data(bs, spin, band_id, kpoint_id, num_sample_points=3):
 
     # check in the backward direction
     if kpoint_id - num_sample_points >= branch_data["start_index"]:
-
         # calculate sampling limits
         start_id = kpoint_id - num_sample_points
         end_id = kpoint_id + 1

sumo/io/castep.py

@@ -138,7 +138,6 @@ def to_file(self, filename):
 
     @classmethod
     def from_file(cls, filename):
-
         with zopen(filename, "rt") as f:
             lines = [line.strip() for line in f]
 

sumo/io/questaal.py

@@ -308,7 +308,6 @@ def _get_structure_from_lattice(self):
     def to_file(self, filename):
         """Write QuestaalInit object to init file"""
         with open(filename, "w") as f:
-
             f.write("LATTICE\n")
             for key, value in self.lattice.items():
                 if key == "PLAT":

sumo/plotting/bs_plotter.py

@@ -556,7 +556,6 @@ def get_projected_plot(
 
         # nd is branch index
         for spin, nd in it.product(spins, range(nbranches)):
-
             # mask data to reduce plotting load
             bands = np.array(data["energy"][str(spin)][nd])
             mask = np.where(
@@ -597,7 +596,6 @@ def get_projected_plot(
             weights[weights < 0] = 0
 
             if mode == "rgb":
-
                 # colours aren't used now but needed later for legend
                 colours = [color1, color2, color3]
 

sumo/plotting/phonon_bs_plotter.py

@@ -156,7 +156,7 @@ def _plot_lines(data, ax, color=None, alpha=1, zorder=1):
 
             # nd is branch index, nb is band index, nk is kpoint index
             for nd, nb in itertools.product(
-                range(len(data["distances"])), range(self._nb_bands)
+                range(len(data["distances"])), range(self.n_bands)
             ):
                 f = freqs[nd][nb]
 
@@ -176,7 +176,7 @@ def _plot_lines(data, ax, color=None, alpha=1, zorder=1):
                 # raise Exception(bs.qpoints)
             json_plotter = PhononBSPlotter(bs)
             json_data = json_plotter.bs_plot_data()
-            if json_plotter._nb_bands != self._nb_bands:
+            if json_plotter.n_bands != self.n_bands:
                 raise Exception(
                     f"Number of bands in {bs_json} does not match main plot"
                 )
@@ -246,7 +246,6 @@ def _makeplot(
         if dos is not None:
             self._plot_phonon_dos(dos, ax=fig.axes[1], color=color, dashline=dashline)
         else:
-
             # keep correct aspect ratio; match axis to canvas
             x0, x1 = ax.get_xlim()
             y0, y1 = ax.get_ylim()

sumo/symmetry/seekpath_kpath.py

@@ -78,7 +78,7 @@ def kpath_from_seekpath(cls, seekpath, point_coords):
         # convert from seekpath format e.g. [(l1, l2), (l2, l3), (l4, l5)]
         # to our preferred representation [[l1, l2, l3], [l4, l5]]
         path = [[seekpath[0][0]]]
-        for (k1, k2) in seekpath:
+        for k1, k2 in seekpath:
             if path[-1] and path[-1][-1] == k1:
                 path[-1].append(k2)
             else:

tests/tests_plotting/test_band_plotter.py

@@ -18,7 +18,6 @@ def test_sanitise_label(self):
             ("@X", None),
             ("@HEX", None),
         ):
-
             self.assertEqual(SBSPlotter._sanitise_label(label_in), label_out)
 
     def test_sanitise_label_group(self):
@@ -45,5 +44,4 @@ def test_sanitise_label_group(self):
             (r"X@$\mid$@Y", r"X"),
             (r"@X@$\mid$@Y", None),
         ):
-
             self.assertEqual(SBSPlotter._sanitise_label_group(label_in), label_out)