Merge pull request #273 from materialsproject/follow-up-#272

Follow up to #272

Author: janosh

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ default_stages: [commit]
 default_install_hook_types: [pre-commit, commit-msg]
 
 # ignore generated doc and dependency lock files
-exclude: ^(docs/.+|.*lock.*)$
+exclude: ^(docs/.+|.*lock.*|.*\.(svg|js|css))$
 
 repos:
   - repo: https://github.com/PyCQA/isort
@@ -23,6 +23,7 @@ repos:
     rev: 4.0.1
     hooks:
       - id: flake8
+        additional_dependencies: [flake8-bugbear]
 
   - repo: https://github.com/asottile/pyupgrade
     rev: v2.34.0
@@ -41,9 +42,7 @@ repos:
       - id: check-case-conflict
       - id: check-symlinks
       - id: check-yaml
-      - id: destroyed-symlinks
       - id: end-of-file-fixer
-        exclude: ^assets/.+\.(svg|html)$
       - id: mixed-line-ending
       - id: trailing-whitespace
 
@@ -54,14 +53,6 @@ repos:
         stages: [commit, commit-msg]
         exclude_types: [csv, svg, html, yaml, jupyter]
 
-  - repo: local
-    hooks:
-      - id: svg-assets
-        name: SVG assets
-        entry: Files under assets/* must end in .(svg|html)
-        language: fail
-        files: ^assets/.*(?<!\.svg)(?<!\.html)$
-
   - repo: https://github.com/myint/autoflake
     rev: v1.4
     hooks:

crystal_toolkit/apps/main.py

@@ -281,12 +281,16 @@
     html.Div(
         [
             dcc.Markdown(
-                f"App created by [Crystal Toolkit Development Team](https://github.com/materialsproject/crystaltoolkit/graphs/contributors).  \n"
-                f"Bug reports and feature requests gratefully accepted, please send them to [@mkhorton](mailto:[email protected]).  \n"
-                f"Powered by [The Materials Project](https://materialsproject.org), "
-                f"[pymatgen v{pmg_version}](http://pymatgen.org) and "
-                f"[Dash by Plotly](https://plot.ly/products/dash/). "
-                f"Deployed on [Spin](http://www.nersc.gov/users/data-analytics/spin/)."
+                f"""
+                App created by [Crystal Toolkit Development Team][contributors].\nBug reports and feature
+                requests gratefully accepted, please send them to [@mkhorton](mailto:[email protected]).\n
+                Powered by [The Materials Project](https://materialsproject.org),
+                [pymatgen v{pmg_version}](http://pymatgen.org) and
+                [Dash by Plotly](https://plot.ly/products/dash/).
+                Deployed on [Spin](http://www.nersc.gov/users/data-analytics/spin/).
+
+                [contributors]: https://github.com/materialsproject/crystaltoolkit/graphs/contributors
+                """
             )
         ],
         className="content has-text-centered",
@@ -513,7 +517,7 @@ def master_update_structure(search_mpid: str | None, upload_data: dict | None):
         # triggered by both on initial load
         load_by = "mpid"
     elif (
-        dash.callback_context.triggered[0]["prop_id"] == search_component.id() + ".data"
+        dash.callback_context.triggered[0]["prop_id"] == f"{search_component.id()}.data"
     ):
         load_by = "mpid"
     else:

crystal_toolkit/components/diffraction.py

@@ -13,8 +13,9 @@
 from crystal_toolkit.core.mpcomponent import MPComponent
 from crystal_toolkit.helpers.layouts import Box, Column, Columns, Loading
 
-# Scherrer equation:
-# Langford, J. Il, and A. J. C. Wilson. "Scherrer after sixty years: a survey and some new results in the determination of crystallite size." Journal of applied crystallography 11.2 (1978): 102-113.
+# Scherrer equation: Langford, J. Il, and A. J. C. Wilson. "Scherrer after sixty years:
+# a survey and some new results in the determination of crystallite size." Journal of
+# applied crystallography 11.2 (1978): 102-113.
 # https://doi.org/10.1107/S0021889878012844
 
 

crystal_toolkit/components/phase_diagram.py

@@ -514,7 +514,8 @@ def _sub_layouts(self):
                         css=[
                             {
                                 "selector": ".dash-cell div.dash-cell-value",
-                                "rule": "display: inline; white-space: inherit; overflow: inherit; text-overflow: inherit;",
+                                "rule": "display: inline; white-space: inherit; overflow: inherit; "
+                                "text-overflow: inherit;",
                             }
                         ],
                         style_cell_conditional=[

crystal_toolkit/components/structure.py

@@ -289,11 +289,13 @@ def generate_callbacks(self, app, cache):
             """
             function (colorScheme, radiusStrategy, drawOptions, displayOptions) {
 
-                const newDisplayOptions = Object.assign({}, displayOptions);
+                const newDisplayOptions = {...displayOptions}
                 newDisplayOptions.color_scheme = colorScheme
                 newDisplayOptions.radius_strategy = radiusStrategy
                 newDisplayOptions.draw_image_atoms = drawOptions.includes('draw_image_atoms')
-                newDisplayOptions.bonded_sites_outside_unit_cell =  drawOptions.includes('bonded_sites_outside_unit_cell')
+                newDisplayOptions.bonded_sites_outside_unit_cell = drawOptions.includes(
+                    'bonded_sites_outside_unit_cell'
+                )
                 newDisplayOptions.hide_incomplete_bonds = drawOptions.includes('hide_incomplete_bonds')
 
                 return newDisplayOptions

crystal_toolkit/components/transformations/grainboundary.py

@@ -91,7 +91,8 @@ def options_layouts(self, state=None, structure=None):
             kwarg_label="expand_times",
             state=state,
             help_str="""The multiple number of times to expand one unit grain into a larger grain. This is
-            useful to avoid self-interaction issues when using the grain boundary as an input to further simulations.""",
+            useful to avoid self-interaction issues when using the grain boundary as an input to further
+            simulations.""",
             is_int=True,
             shape=(),
             min=1,

crystal_toolkit/core/legend.py

@@ -427,7 +427,7 @@ def get_legend(self) -> dict[str, Any]:
 
         # first get all our colors for different species
         for site in self.site_collection:
-            for sp, occu in site.species.items():
+            for sp in site.species:
                 legend[self.get_color(sp, site)].append(label(site, sp))
 
         legend = {k: ", ".join(sorted(list(set(v)))) for k, v in legend.items()}

crystal_toolkit/core/mpcomponent.py

@@ -215,7 +215,7 @@ def __init__(
         MPComponent._all_id_basenames.add(id)
 
         self._id = id
-        self._all_ids = set()
+        self._all_ids: set[str] = set()
         self._stores = {}
         self._initial_data = {}
 
@@ -497,9 +497,9 @@ def matrix_element(idx, value=0):
 
         # arrange the input boxes in two dimensions (rows, columns)
         matrix_div_contents = []
-        for row_idx, columns in sorted(matrix_contents.items()):
+        for columns in sorted(matrix_contents.values()):
             row = []
-            for column_idx, element in sorted(columns.items()):
+            for element in sorted(columns.values()):
                 row.append(element)
             matrix_div_contents.append(html.Div(row))
 

crystal_toolkit/core/scene.py

@@ -240,7 +240,8 @@ class Ellipsoids(Primitive):
     :param scale: This is the scale to apply to the x,y and z axis of the ellipsoid prior to rotation to the target axes
     :param positions: This is a list of lists corresponding to the vector
     positions of the ellipsoids.
-    :param rotate_to: This is a list of vectors that specify the direction the major axis of the ellipsoid should point towards. The major axis is the z-axis: (0,0,1)
+    :param rotate_to: This is a list of vectors that specify the direction the major axis of the ellipsoid should point
+        towards. The major axis is the z-axis: (0,0,1)
     :param color: Ellipsoid color as a hexadecimal string, e.g. #ff0000
     :param phiStart: Start angle in radians if drawing only a section of the
     ellipsoid, defaults to 0
@@ -554,7 +555,7 @@ class Label:
 
     label: str
     labelHover: str | None = None
-    position: list[list[float]] = None
+    position: list[list[float]] | None = None
     type: str = field(default="labels", init=False)  # private field
     visible: bool | None = None
     clickable: bool = False

crystal_toolkit/helpers/asymptote_renderer.py

@@ -4,7 +4,8 @@
 Since ASY does not have the nested tree structure of threejs,
 we just have to traverse the tree and draw each material as we see them.
 
-TODO The code should also appends a set of special points at the end in case the user wants to add more "hand drawn" features to the plot
+TODO The code should also appends a set of special points at the end in case the user wants to add
+more "hand drawn" features to the plot
 
 """
 import logging