follow PEP 484 in crystal_toolkit/components/__init__.py

Author: janosh

crystal_toolkit/components/__init__.py

@@ -1,51 +1,69 @@
+# use redundant as-import following PEP 484, see
+# https://github.com/microsoft/pylance-release/issues/856#issuecomment-763793949
+# and https://peps.python.org/pep-0484/#stub-files
+
+from crystal_toolkit.components.bandstructure import (
+    BandstructureAndDosComponent as BandstructureAndDosComponent,
+)
 from crystal_toolkit.components.bandstructure import (
-    BandstructureAndDosComponent,
-    BandstructureAndDosPanelComponent,
+    BandstructureAndDosPanelComponent as BandstructureAndDosPanelComponent,
+)
+from crystal_toolkit.components.diffraction import (
+    TEMDiffractionComponent as TEMDiffractionComponent,
 )
 from crystal_toolkit.components.diffraction import (
-    TEMDiffractionComponent,
-    XRayDiffractionComponent,
+    XRayDiffractionComponent as XRayDiffractionComponent,
 )
-from crystal_toolkit.components.localenv import LocalEnvironmentPanel
 from crystal_toolkit.components.phase_diagram import (
-    PhaseDiagramComponent,
-    PhaseDiagramPanelComponent,
+    PhaseDiagramComponent as PhaseDiagramComponent,
+)
+from crystal_toolkit.components.phase_diagram import (
+    PhaseDiagramPanelComponent as PhaseDiagramPanelComponent,
+)
+from crystal_toolkit.components.pourbaix import (
+    PourbaixDiagramComponent as PourbaixDiagramComponent,
+)
+from crystal_toolkit.components.robocrys import RobocrysComponent as RobocrysComponent
+from crystal_toolkit.components.search import SearchComponent as SearchComponent
+from crystal_toolkit.components.structure import (
+    StructureMoleculeComponent as StructureMoleculeComponent,
 )
-from crystal_toolkit.components.pourbaix import PourbaixDiagramComponent
-from crystal_toolkit.components.robocrys import RobocrysComponent
-from crystal_toolkit.components.search import SearchComponent
-from crystal_toolkit.components.structure import StructureMoleculeComponent
 
-# from crystal_toolkit.components.submit_snl import SubmitSNLPanel
-from crystal_toolkit.components.symmetry import SymmetryPanel
+# from crystal_toolkit.components.submit_snl import SubmitSNLPanel as SubmitSNLPanel
+from crystal_toolkit.components.symmetry import SymmetryPanel as SymmetryPanel
 from crystal_toolkit.components.transformations.autooxistatedecoration import (
-    AutoOxiStateDecorationTransformationComponent,
+    AutoOxiStateDecorationTransformationComponent as AutoOxiStateDecorationTransformationComponent,
+)
+from crystal_toolkit.components.transformations.core import (
+    AllTransformationsComponent as AllTransformationsComponent,
 )
-from crystal_toolkit.components.transformations.core import AllTransformationsComponent
 
 # from crystal_toolkit.components.transformations.cubic import (
-#     CubicSupercellTransformationComponent,
+#     CubicSupercellTransformationComponent as CubicSupercellTransformationComponent,
 # )
 from crystal_toolkit.components.transformations.grainboundary import (
-    GrainBoundaryTransformationComponent,
+    GrainBoundaryTransformationComponent as GrainBoundaryTransformationComponent,
+)
+
+# from crystal_toolkit.components.transformations.rattle import (
+#     MonteCarloRattleTransformationComponent as MonteCarloRattleTransformationComponent,
+# )
+from crystal_toolkit.components.transformations.slab import (
+    SlabTransformationComponent as SlabTransformationComponent,
 )
-from crystal_toolkit.components.transformations.slab import SlabTransformationComponent
 from crystal_toolkit.components.transformations.substitution import (
-    SubstitutionTransformationComponent,
+    SubstitutionTransformationComponent as SubstitutionTransformationComponent,
 )
 from crystal_toolkit.components.transformations.supercell import (
-    SupercellTransformationComponent,
+    SupercellTransformationComponent as SupercellTransformationComponent,
+)
+from crystal_toolkit.components.upload import (
+    StructureMoleculeUploadComponent as StructureMoleculeUploadComponent,
 )
-from crystal_toolkit.components.upload import StructureMoleculeUploadComponent
-from crystal_toolkit.core.mpcomponent import MPComponent
-
-# from crystal_toolkit.components.xas import XASComponent, XASPanelComponent
-
-
-# from crystal_toolkit.components.transformations.rattle import (
-#     MonteCarloRattleTransformationComponent,
-# )
 
+# from crystal_toolkit.components.xas import XASComponent as XASComponent
+# from crystal_toolkit.components.xas import XASPanelComponent as XASPanelComponent
+from crystal_toolkit.core.mpcomponent import MPComponent as MPComponent
 
 register_app = MPComponent.register_app
 register_cache = MPComponent.register_cache

crystal_toolkit/core/legend.py

@@ -4,7 +4,7 @@
 import warnings
 from collections import defaultdict
 from itertools import chain
-from typing import Any
+from typing import Any, cast
 
 import numpy as np
 from matplotlib.cm import get_cmap
@@ -134,7 +134,7 @@ def __init__(
         self.color_scheme = color_scheme
         self.radius_scheme = radius_scheme
         self.cmap = cmap
-        self.cmap_range = cmap_range
+        self.cmap_range = cast(tuple[float, float], cmap_range)
 
     @staticmethod
     def generate_accessible_color_scheme_on_the_fly(
@@ -162,12 +162,12 @@ def generate_accessible_color_scheme_on_the_fly(
             (0, 0, 0),  # 0, black
             (230, 159, 0),  # 1, orange
             (86, 180, 233),  # 2, sky blue
-            (0, 158, 115),  #  3, bluish green
+            (0, 158, 115),  # 3, bluish green
             (240, 228, 66),  # 4, yellow
             (0, 114, 178),  # 5, blue
             (213, 94, 0),  # 6, vermilion
             (204, 121, 167),  # 7, reddish purple
-            (255, 255, 255),  #  8, white
+            (255, 255, 255),  # 8, white
         ]
 
         # similar to CPK, mapping element to palette index
@@ -300,8 +300,7 @@ def get_color(self, sp: Specie | Element, site: Site | None = None) -> str:
                 cmap = get_cmap(self.cmap)
 
                 # normalize in [0, 1] range, as expected by cmap
-                prop_min = self.cmap_range[0]
-                prop_max = self.cmap_range[1]
+                prop_min, prop_max = self.cmap_range
                 prop_normed = (prop - prop_min) / (prop_max - prop_min)
 
                 color = [int(c * 255) for c in cmap(prop_normed)[0:3]]

crystal_toolkit/core/scene.py

@@ -48,7 +48,7 @@ class Scene:
 
     name: str  # name for the scene, does not have to be unique
     contents: list = field(default_factory=list)
-    origin: list[float] = field(default=(0, 0, 0))
+    origin: tuple[float, float, float] = field(default=(0, 0, 0))
     visible: bool = True
     lattice: list[list[float]] | None = None
     _meta: dict | None = None

crystal_toolkit/renderables/__init__.py

@@ -1,8 +1,8 @@
-from crystal_toolkit.renderables.lattice import Lattice
-from crystal_toolkit.renderables.molecule import Molecule
-from crystal_toolkit.renderables.moleculegraph import MoleculeGraph
-from crystal_toolkit.renderables.phasediagram import PhaseDiagram
-from crystal_toolkit.renderables.site import Site
-from crystal_toolkit.renderables.structure import Structure
-from crystal_toolkit.renderables.structuregraph import StructureGraph
-from crystal_toolkit.renderables.volumetric import VolumetricData
+from crystal_toolkit.renderables.lattice import Lattice as Lattice
+from crystal_toolkit.renderables.molecule import Molecule as Molecule
+from crystal_toolkit.renderables.moleculegraph import MoleculeGraph as MoleculeGraph
+from crystal_toolkit.renderables.phasediagram import PhaseDiagram as PhaseDiagram
+from crystal_toolkit.renderables.site import Site as Site
+from crystal_toolkit.renderables.structure import Structure as Structure
+from crystal_toolkit.renderables.structuregraph import StructureGraph as StructureGraph
+from crystal_toolkit.renderables.volumetric import VolumetricData as VolumetricData

crystal_toolkit/renderables/moleculegraph.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from collections import defaultdict
 
 from pymatgen.analysis.graphs import MoleculeGraph
@@ -18,7 +20,7 @@ def get_molecule_graph_scene(
 
     legend = legend or Legend(self.molecule)
 
-    primitives = defaultdict(list)
+    primitives: dict[str, list] = defaultdict(list)
 
     for idx, site in enumerate(self.molecule):
 

tests/test_chgcar.py

@@ -21,7 +21,7 @@
 
 
 def get_mesh(chgcar, data_tag="total", isolvl=2.0, step_size=3):
-    vertices, faces, normals, values = measure.marching_cubes_lewiner(
+    vertices, faces, _normals, _values = measure.marching_cubes_lewiner(
         chgcar.data[data_tag], level=isolvl, step_size=step_size
     )
     vertices = (