list all args in get_site_scene() doc str

Author: janosh

crystal_toolkit/_version.py

@@ -1 +1 @@
-__version__ = "2023.02.28.1"
+__version__ = "2023.02.28.1"

crystal_toolkit/components/phonon.py

@@ -281,8 +281,8 @@ def get_ph_bandstructure_traces(bs, freq_range):
         bands = []
         for band_num in range(bs.nb_bands):
             for segment in bs_data["frequency"]:
-                if any([v <= freq_range[1] for v in segment[band_num]]) and any(
-                    [v >= freq_range[0] for v in segment[band_num]]
+                if any(v <= freq_range[1] for v in segment[band_num]) and any(
+                    v >= freq_range[0] for v in segment[band_num]
                 ):
                     bands.append(band_num)
 

crystal_toolkit/renderables/site.py

@@ -46,18 +46,31 @@ def get_site_scene(
     magmom_scale: float = 1.0,
     legend: Legend | None = None,
 ) -> Scene:
-    """Args:
-        connected_sites:
-        connected_sites_not_drawn:
-        hide_incomplete_edges:
-        site_idx:
-        incomplete_edge_length_scale:
-        connected_sites_colors:
-        connected_sites_not_drawn_colors:
-        origin: x,y,z fractional coordinates of the origin
-        explicitly_calculate_polyhedra_hull:
-        legend:
+    """Get a Scene object for a Site.
+
+    Args:
+        connected_sites (list[ConnectedSite], optional): Defaults to None.
+        connected_sites_not_drawn (list[ConnectedSite], optional): Defaults to None.
+        hide_incomplete_edges (bool, optional): Defaults to False.
+        site_idx (int | None, optional): Defaults to 0.
+        incomplete_edge_length_scale (float | None, optional): Defaults to 1.0.
+        connected_sites_colors (list[str] | None, optional): Defaults to None.
+        connected_sites_not_drawn_colors (list[str] | None, optional): Defaults to None.
+        origin (Sequence[float] | None, optional): Defaults to None.
+        draw_polyhedra (bool, optional): Defaults to True.
+        explicitly_calculate_polyhedra_hull (bool, optional): Defaults to False.
+        bond_radius (float, optional): Defaults to 0.1.
+        draw_magmoms (bool, optional): Defaults to True.
+        show_atom_idx (bool, optional): Defaults to False.
+        show_atom_coord (bool, optional): Defaults to True.
+        show_bond_order (bool, optional): Defaults to True.
+        show_bond_length (bool, optional): Defaults to False.
+        visualize_bond_orders (bool, optional): Defaults to False.
+        magmom_scale (float, optional): Defaults to 1.0.
+        legend (Legend | None, optional): Defaults to None.
+
     Returns:
+        Scene: The scene object containing atoms, bonds, polyhedra, magmoms.
     """
     atoms = []
     bonds = []

jupyterlab-extension/crystaltoolkit-extension/_version.py

@@ -1,7 +1,7 @@
 __all__ = ["__version__"]
 
 
-def _fetchVersion():
+def _fetch_version():
     import json
     import os
 
@@ -17,4 +17,4 @@ def _fetchVersion():
     raise FileNotFoundError(f"Could not find package.json under dir {HERE}")
 
 
-__version__ = _fetchVersion()
+__version__ = _fetch_version()

jupyterlab-extension/setup.py

@@ -1,6 +1,4 @@
-"""
-crystaltoolkit-extension setup
-"""
+"""crystaltoolkit-extension setup."""
 import json
 import os
 

pyproject.toml

@@ -56,7 +56,7 @@ exclude = ["docs_rst"]
 
 [tool.setuptools_scm]
 write_to = "crystal_toolkit/_version.py"
-write_to_template = '__version__ = "{version}"'
+write_to_template = '__version__ = "{version}"\n'
 local_scheme = "no-local-version"
 
 [build-system]
@@ -96,14 +96,12 @@ ignore = [
     "SIM115", # Use context handler for opening files
 ]
 pydocstyle.convention = "google"
-isort.known-third-party = ["wandb"]
 
 [tool.ruff.per-file-ignores]
 "**/tests/*" = ["D"]
-"jupyterlab-extension/setup.py" = ["D"]
 "__init__.py" = ["F401"]
 # future annotations incompatible with pydantic BaseModel schemas below py 3.10
-# TODO remove once py 3.10 is the minimum supported version
+# TODO remove once python 3.10 is the minimum supported version
 "crystal_toolkit/settings.py" = ["UP007"]
 # TODO fix all undefined variables in bandstructure.py
 "crystal_toolkit/components/bandstructure.py" = ["F821"]