remove id access on dash components passed to callbacks

complete CatalysisApp.modify_df() doc str
can be passed directly in newer dash
also auto-changes from docformatter --in-place --config setup.cfg crystal_toolkit

Author: janosh

crystal_toolkit/apps/examples/diffraction_dynamic.py

@@ -22,7 +22,7 @@
 ctc.register_crystal_toolkit(app=app, layout=my_layout)
 
 
-@app.callback(Output(xrd_component.id(), "data"), Input(load_btn.id, "n_clicks"))
+@app.callback(Output(xrd_component.id(), "data"), Input(load_btn, "n_clicks"))
 def load_structure(n_clicks: int) -> Structure:
     structure = Structure(Lattice.cubic(4.2), ["Na", "K"], [[0, 0, 0], [0.5, 0.5, 0.5]])
     return structure

crystal_toolkit/apps/examples/matbench_dielectric_datatable_xrd.py

@@ -64,11 +64,11 @@
     Output(structure_component.id(), "data"),
     # currently broken due to internal callback in XRayDiffractionComponent
     # Output(xrd_component.id(), "data"),
-    Input(datatable_diel.id, "active_cell"),
+    Input(datatable_diel, "active_cell"),
 )
 def update_structure(active_cell: dict[str, int | str]) -> Structure:
-    """Update StructureMoleculeComponent with pymatgen structure when user clicks on
-    new scatter point.
+    """Update StructureMoleculeComponent with pymatgen structure when user clicks on new scatter
+    point.
     """
     row_idx = active_cell["row"]
     structure = df_diel.structure[row_idx]

crystal_toolkit/apps/examples/matbench_dielectric_structure_on_hover.py

@@ -119,8 +119,8 @@ def update_structure(
     click_data: dict[str, list[dict[str, Any]]],  # needed only as callback trigger
     dropdown_value: str,
 ) -> tuple[Structure, str]:
-    """Update StructureMoleculeComponent with pymatgen structure when user clicks or hovers
-    a scatter point.
+    """Update StructureMoleculeComponent with pymatgen structure when user clicks or hovers a
+    scatter point.
     """
     triggered = dash.callback_context.triggered[0]
     if dropdown_value == "click" and triggered["prop_id"].endswith(".hoverData"):

crystal_toolkit/apps/examples/mpcontribs/catalysis.py

@@ -46,9 +46,14 @@ class CatalysisApp(MPApp):
     @staticmethod
     def modify_df(dataframe: pd.DataFrame) -> list[pd.DataFrame]:
         """
-        Filter DataFrame for binary visualization.
-        :param dataframe:
-        :return:
+        Filter DataFrame for unary+binary materials visualization.
+
+        Args:
+          dataframe (pd.DataFrame): the dataframe that you want to modify
+
+        Returns:
+            list[pd.Dataframe): two dataframes, the input df filtered to unary or binary materials
+                and one with the minimum energy of each material
         """
 
         # Extract the elements and number of them from formula
@@ -79,8 +84,8 @@ def get_plot(
         range_E,
         user_options,
     ) -> go.Figure:
-        """
-        Generate a 2D plot for binary visualization.
+        """Generate a 2D plot for binary visualization.
+
         :param df_all_data:
         :param df_min_E:
         :param target_E:
@@ -100,7 +105,7 @@ def construct_grid(df, labels):
             custom_data = np.zeros((grid_dim, grid_dim), dtype=object)
             add_data = np.zeros((grid_dim, grid_dim), dtype=object)
             lookup_dict = df_min_E.set_index("element_tup").to_dict()
-            el_combos = list(lookup_dict["energy"].keys())
+            el_combos = list(lookup_dict["energy"])
             for i in range(len(labels)):
                 for k in range(len(labels)):
                     if i == k:

crystal_toolkit/apps/examples/transformations_minimal.py

@@ -54,8 +54,7 @@
 
 
 @app.callback(
-    Output("structure_out", "data"),
-    Input(transformation_component.id(), "data"),
+    Output("structure_out", "data"), Input(transformation_component.id(), "data")
 )
 def update_structure(struct):
     return struct

crystal_toolkit/apps/examples/utils.py

@@ -9,8 +9,8 @@
 
 
 def load_and_store_matbench_dataset(dataset_name: str) -> pd.DataFrame:
-    """Load, process and save Matbench datasets to disk to avoid having to re-process
-    on subsequent app runs.
+    """Load, process and save Matbench datasets to disk to avoid having to re-process on subsequent
+    app runs.
     """
     data_path = os.path.join(os.path.dirname(__file__), f"{dataset_name}.json.gz")
 

crystal_toolkit/components/bandstructure.py

@@ -263,7 +263,7 @@ def get_brillouin_zone_scene(bs: BandStructureSymmLine) -> Scene:
             )
             path += [start, end]
             cylinder_pairs += [[start, end]]
-        # path_lines = Lines(positions=path, color="#ff4b5c",)
+        # path_lines = Lines(positions=path, color="#ff4b5c")
         path_lines = Cylinders(
             positionPairs=cylinder_pairs, color="#5EB1BF", radius=0.01
         )
@@ -387,7 +387,7 @@ def get_bandstructure_traces(
             bs_traces += traces_for_segment
 
         for entry_num in range(len(bs_data["ticks"]["label"])):
-            for key in pretty_labels.keys():
+            for key in pretty_labels:
                 if key in bs_data["ticks"]["label"][entry_num]:
                     bs_data["ticks"]["label"][entry_num] = bs_data["ticks"]["label"][
                         entry_num

crystal_toolkit/components/diffraction_tem.py

@@ -203,9 +203,7 @@ def generate_diffraction_pattern(structure, *args):
 
 
 class TEMDiffractionCalculator:
-    """
-    Docstring
-    """
+    """Docstring."""
 
     def __init__(self) -> None:
         # Initialize parameter caches to invalid so that on the first run,
@@ -233,9 +231,7 @@ def get_plot_2d(
         gamma,
         # **kwargs,
     ) -> go:
-        """
-        generate diffraction pattern using py4DSTEM and return as a plotly Figure object
-        """
+        """Generate diffraction pattern using py4DSTEM and return as a plotly Figure object."""
         t0 = time()
         # figure out what needs to be recomputed:
         new_crystal = py4DSTEM.process.diffraction.Crystal.from_pymatgen_structure(

crystal_toolkit/components/fermi_surface.py

@@ -15,8 +15,7 @@
 
 
 class FermiSurfaceComponent(MPComponent):
-    """
-    Component to display FermiSurface objects generated from ifermi.
+    """Component to display FermiSurface objects generated from ifermi.
 
     Args:
         fermi_surface: An ifermi FermiSurface object.
@@ -35,8 +34,7 @@ def __init__(
 
     @staticmethod
     def get_figure(fermi_surface: FermiSurface, **kwargs) -> Figure:
-        """
-        Get a fermi surface figure.
+        """Get a fermi surface figure.
 
         Args:
             fermi_surface: An ifermi FermiSurface object.

crystal_toolkit/components/phonon.py

@@ -262,7 +262,7 @@ def get_brillouin_zone_scene(bs: PhononBandStructureSymmLine) -> Scene:
             )
             path += [start, end]
             cylinder_pairs += [[start, end]]
-        # path_lines = Lines(positions=path, color="#ff4b5c",)
+        # path_lines = Lines(positions=path, color="#ff4b5c")
         path_lines = Cylinders(
             positionPairs=cylinder_pairs, color="#5EB1BF", radius=0.01
         )
@@ -314,7 +314,7 @@ def get_ph_bandstructure_traces(bs, freq_range):
             bs_traces += traces_for_segment
 
         for entry_num in range(len(bs_data["ticks"]["label"])):
-            for key in pretty_labels.keys():
+            for key in pretty_labels:
                 if key in bs_data["ticks"]["label"][entry_num]:
                     bs_data["ticks"]["label"][entry_num] = bs_data["ticks"]["label"][
                         entry_num
@@ -702,8 +702,8 @@ def bs_dos_data(data, dos_select, label_select):
             Input(self.id("ph-bsdos-graph"), "clickData"),
         )
         def highlight_bz_on_hover_bs(hover_data, click_data, label_select):
-            """Highlight the corresponding point/edge of the Brillouin Zone when hovering
-            the band structure plot.
+            """Highlight the corresponding point/edge of the Brillouin Zone when hovering the band
+            structure plot.
             """
 
             # TODO: figure out what to return (CSS?) to highlight BZ edge/point