[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ exclude: ^(docs/.+|.*lock.*|jupyterlab-extension/.+|.*\.(svg|js|css))|_version.p
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.13.3
     hooks:
       - id: ruff
         args: [--fix, --ignore, D]
@@ -23,7 +23,7 @@ repos:
   #     - id: mypy
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-case-conflict
       - id: check-symlinks
@@ -33,14 +33,14 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         stages: [pre-commit, commit-msg]
         args: [--ignore-words-list, "nd,te,ois,dscribe", --check-filenames]
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]

README.md

@@ -26,7 +26,6 @@ If you would like a new-contributor issue assigned, get in touch with project ma
 
 [![Tests](https://github.com/materialsproject/crystaltoolkit/actions/workflows/pytest-docs.yml/badge.svg)](https://github.com/materialsproject/crystaltoolkit/actions/workflows/pytest-docs.yml)
 [![Visual Regression Test Status](https://percy.io/static/images/percy-badge.svg)](https://percy.io/6f28436a/crystaltoolkit)
-[![Docker Build Status](https://img.shields.io/docker/cloud/build/materialsproject/crystaltoolkit)](https://hub.docker.com/repository/docker/materialsproject/crystaltoolkit/general)
 [![Release](https://github.com/materialsproject/crystaltoolkit/actions/workflows/release.yml/badge.svg)](https://github.com/materialsproject/crystaltoolkit/actions/workflows/release.yml)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/materialsproject/crystaltoolkit/main.svg)](https://results.pre-commit.ci/latest/github/materialsproject/crystaltoolkit/main)
 [![arXiv link](https://img.shields.io/badge/arXiv-2302.06147-blue)](https://arxiv.org/abs/2302.06147)
@@ -81,7 +80,7 @@ The [Crystal Toolkit Development Team](https://github.com/materialsproject/cryst
 * [Janosh Riebesell](https://github.com/janosh) contributed Phonon band structure component, [3 example apps](https://github.com/materialsproject/crystaltoolkit/blob/main/crystal_toolkit/apps/examples/matbench_dielectric_structure_on_hover.py), tests
 * [Stephen Weitzner](https://github.com/sweitzner) contributed POV-Ray integration (in progress)
 * [Richard Tran](https://github.com/CifLord) for contributing plotly-powered Wulff shapes to pymatgen, which Crystal Toolkit uses
-* [Guy Moore](https://github.com/guymoore13) for contributing magnetic moment visualization
+* Guy Moore for contributing magnetic moment visualization
 * [Steve Zeltmann](https://github.com/sezelt) for contributing electron diffraction
 * [Patrick Huck](https://github.com/tschaume), releases, operations, bugfixes and POC for MP / MPContribs
 
@@ -101,7 +100,7 @@ Thank you to all the authors and maintainers of the libraries Crystal Toolkit
 depends upon, and in particular [pymatgen](http://pymatgen.org) for crystallographic
 analysis and [Dash from Plotly](https://plot.ly/products/dash/) for their web app framework.
 
-Thank you to the [NERSC Spin](https://nersc.gov/systems/spin) service for
+Thank you to the [NERSC Spin](https://docs.nersc.gov/services/spin/) service for
 hosting the app and for their technical support.
 
 ## Contact

crystal_toolkit/apps/examples/mpcontribs/catalysis.py

@@ -436,15 +436,15 @@ def get_search_layout(self, payload=None):
             "Surface Formula": unicodeify(contribution["formula"]),
             "Surface Material ID": dcc.Link(
                 contribution["data"]["mpid"],
-                href=f'/materials/{contribution["data"]["mpid"]}',
+                href=f"/materials/{contribution['data']['mpid']}",
             ),
             "Adsorbate SMILES": adsorbate_smiles,
             "Adsorbate IUPAC Formula": contribution["data"]["adsorbateIUPACFormula"],
             "Adsorption Energy": contribution["data"]["adsorptionEnergy"]["value"],
             "Miller Index": unicodeify_spacegroup(
-                f'({int(contribution["data"]["h"]["value"])} '
-                f'{int(contribution["data"]["k"]["value"])} '
-                f'{int(contribution["data"]["l"]["value"])})'
+                f"({int(contribution['data']['h']['value'])} "
+                f"{int(contribution['data']['k']['value'])} "
+                f"{int(contribution['data']['l']['value'])})"
             ),
             "Surface Shift": contribution["data"]["surfaceShift"]["value"],
         }

crystal_toolkit/apps/examples/tests/test_fermi_surface.py

@@ -2,13 +2,13 @@
 
 from typing import TYPE_CHECKING
 
+from crystal_toolkit.apps.examples.fermi_surface import app
+
 if TYPE_CHECKING:
     from crystal_toolkit.apps.examples.tests.typing import DashDuo
 
 
 def test_diffraction(dash_duo: DashDuo) -> None:
-    from crystal_toolkit.apps.examples.fermi_surface import app
-
     dash_duo.start_server(app)
     dash_duo.clear_storage()
 

crystal_toolkit/apps/examples/utils.py

@@ -1,14 +1,16 @@
 from __future__ import annotations
 
 import os
-from typing import TYPE_CHECKING
 
+import pandas as pd
 from dash import dcc
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from tqdm import tqdm
 
-if TYPE_CHECKING:
-    import pandas as pd
+try:
+    from matminer.datasets import load_dataset
+except ImportError:
+    load_dataset = None
 
 
 def load_and_store_matbench_dataset(dataset_name: str) -> pd.DataFrame:
@@ -18,34 +20,30 @@ def load_and_store_matbench_dataset(dataset_name: str) -> pd.DataFrame:
     data_path = os.path.join(os.path.dirname(__file__), f"{dataset_name}.json.gz")
 
     if os.path.isfile(data_path):
-        import pandas as pd
-
         df = pd.read_json(data_path)
     else:
-        try:
-            from matminer.datasets import load_dataset
+        if not load_dataset:
+            raise ImportError(
+                "matminer is not installed but needed to download a dataset. Run "
+                "`pip install matminer`"
+            )
 
-            df = load_dataset(dataset_name)
+        df = load_dataset(dataset_name)
 
-            if "structure" in df:
-                df[["spg_symbol", "spg_num"]] = [
-                    struct.get_space_group_info()
-                    for struct in tqdm(df.structure, desc="Getting space groups")
-                ]
+        if "structure" in df:
+            df[["spg_symbol", "spg_num"]] = [
+                struct.get_space_group_info()
+                for struct in tqdm(df.structure, desc="Getting space groups")
+            ]
 
-                df["crystal_sys"] = [
-                    SpacegroupAnalyzer(x).get_crystal_system() for x in df.structure
-                ]
+            df["crystal_sys"] = [
+                SpacegroupAnalyzer(x).get_crystal_system() for x in df.structure
+            ]
 
-                df["volume"] = [x.volume for x in df.structure]
-                df["formula"] = [x.formula for x in df.structure]
+            df["volume"] = [x.volume for x in df.structure]
+            df["formula"] = [x.formula for x in df.structure]
 
-            df.to_json(data_path, default_handler=lambda x: x.as_dict())
-        except ImportError:
-            print(
-                "matminer is not installed but needed to download a dataset. Run "
-                "`pip install matminer`"
-            )
+        df.to_json(data_path, default_handler=lambda x: x.as_dict())
 
     return df
 

crystal_toolkit/apps/examples/write_structure_screenshot_to_file.py

@@ -32,8 +32,6 @@
 
 
 def get_structure_for_mpid(mpid):
-    from pymatgen.ext.matproj import MPRester
-
     with MPRester() as mpr:
         structure = mpr.get_structure_by_material_id(mpid)
 

crystal_toolkit/apps/main.py

@@ -461,7 +461,7 @@ def perform_search_on_page_load(
     """
     # TODO: could be a client side callback
     if n_submit is None:
-        return 1, int(round(time() * 1000))
+        return 1, round(time() * 1000)
     raise PreventUpdate
 
 

crystal_toolkit/apps/tests/test_main.py

@@ -3,13 +3,13 @@
 import time
 from typing import TYPE_CHECKING
 
+from crystal_toolkit.apps.main import app
+
 if TYPE_CHECKING:
     from crystal_toolkit.apps.examples.tests.typing import DashDuo
 
 
 def test_main_app_startup(dash_duo: DashDuo):
-    from crystal_toolkit.apps.main import app
-
     dash_duo.start_server(app)
     # dash_duo.clear_storage()
 

crystal_toolkit/apps/tests/test_pourbaix.py

@@ -2,10 +2,10 @@
 
 from playwright.sync_api import Page
 
+from crystal_toolkit.apps.examples.pourbaix import app
 
-def test_pourbaix(page: Page):
-    from crystal_toolkit.apps.examples.pourbaix import app
 
+def test_pourbaix(page: Page):
     thread = threading.Thread(target=app.run)
     thread.start()
 

crystal_toolkit/apps/tests/test_structure.py

@@ -3,10 +3,10 @@
 
 from playwright.sync_api import Page, expect
 
+from crystal_toolkit.apps.examples.structure import app
 
-def test_structure(page: Page):
-    from crystal_toolkit.apps.examples.structure import app
 
+def test_structure(page: Page):
     thread = threading.Thread(target=app.run)
     thread.start()
 

crystal_toolkit/components/diffraction.py

@@ -205,7 +205,7 @@ def _sub_layouts(self) -> dict[str, Component]:
             help_str="This defines the wavelength of the incident X-ray radiation.",
             options=[
                 {
-                    "label": f'{name.replace("a", "α").replace("b", "β")} ({wavelength:.3f} Å)',  # noqa: RUF001
+                    "label": f"{name.replace('a', 'α').replace('b', 'β')} ({wavelength:.3f} Å)",  # noqa: RUF001
                     "value": name,
                 }
                 for name, wavelength in WAVELENGTHS.items()
@@ -375,9 +375,9 @@ def get_figure(
                 )
                 sigma = (alpha / np.sqrt(2 * np.log(2))).item()
 
-                center_idx = int(round((xp - first) * N_density))
+                center_idx = round((xp - first) * N_density)
                 # total broadening window of 2 * num_sigma
-                half_window = int(round(num_sigma * sigma * N_density))
+                half_window = round(num_sigma * sigma * N_density)
 
                 lb = max(0, (center_idx - half_window))
                 ub = min(N, (center_idx + half_window))

crystal_toolkit/components/diffraction_tem.py

@@ -294,7 +294,7 @@ def get_plot_2d(
                 pattern, thickness=thickness, zone_axis_lattice=beam_direction
             )
 
-        print(f"Generated pattern in {time()-t0:.3f} seconds")
+        print(f"Generated pattern in {time() - t0:.3f} seconds")
 
         # generate plotly Figure
         return self.pointlist_to_spots(pattern, beam_direction, gamma)

crystal_toolkit/components/fermi_surface.py

@@ -4,6 +4,7 @@
 
 import matplotlib.pyplot as plt
 from dash import Input, Output
+from ifermi.plot import FermiSurfacePlotter
 
 from crystal_toolkit.core.mpcomponent import MPComponent
 from crystal_toolkit.helpers.layouts import Box, Column, Columns, Loading, dcc
@@ -43,8 +44,6 @@ def get_figure(fermi_surface: FermiSurface, **kwargs) -> Figure:
         Returns:
             A plotly Figure object.
         """
-        from ifermi.plot import FermiSurfacePlotter
-
         plotter = FermiSurfacePlotter(fermi_surface)
         fig = plotter.get_plot(plot_type="plotly", **kwargs)
 

crystal_toolkit/components/structure.py

@@ -385,7 +385,7 @@ def update_scene(graph, display_options, scene_additions):
                 raise PreventUpdate
             display_options = self.from_data(display_options)
             graph = self.from_data(graph)
-            scene, legend = self.get_scene_and_legend(
+            scene, _ = self.get_scene_and_legend(
                 graph, **display_options, scene_additions=scene_additions
             )
             return scene
@@ -402,7 +402,7 @@ def update_legend_and_colors(graph, display_options, scene_additions):
                 raise PreventUpdate
             display_options = self.from_data(display_options)
             graph = self.from_data(graph)
-            scene, legend = self.get_scene_and_legend(
+            _, legend = self.get_scene_and_legend(
                 graph, **display_options, scene_additions=scene_additions
             )
             return legend
@@ -643,9 +643,11 @@ def _make_title(self, legend):
                 formula = composition.reduced_formula
                 formula_parts = re.findall(r"[^\d_]+|\d+", formula)
                 formula_components = [
-                    html.Sub(part.strip())
-                    if part.isnumeric()
-                    else html.Span(part.strip())
+                    (
+                        html.Sub(part.strip())
+                        if part.isnumeric()
+                        else html.Span(part.strip())
+                    )
                     for part in formula_parts
                 ]
             except Exception:

crystal_toolkit/components/submit_snl.py

@@ -109,14 +109,14 @@ def generate_description(structure, comments, panel_open, url):
             contents = get_token_response(token)
 
             structure = self.from_data(structure)
-            if type(structure) != Structure:
+            if not isinstance(structure, Structure):
                 raise PreventUpdate
 
             description = dcc.Markdown(
                 f"""
 > **Structure to upload:** {structure.composition.reduced_formula} ({len(structure)} sites)
-> **Name:** {contents['first_name']} {contents['last_name']}
-> **Email:** {contents['email']}
+> **Name:** {contents["first_name"]} {contents["last_name"]}
+> **Email:** {contents["email"]}
 > **Comment:** {comments}
 
 This information is stored so that we can give credit to you on the Materials
@@ -144,7 +144,7 @@ def submit_snl(n_clicks, structure, comments, url):
                 raise PreventUpdate
 
             structure = self.from_data(structure)
-            if type(structure) != Structure:
+            if not isinstance(structure, Structure):
                 message = (
                     f"Can only submit structures to Materials Project, "
                     f"not {type(structure)}"

crystal_toolkit/components/transformations/core.py

@@ -198,7 +198,7 @@ def update_preview(transformation_data, input_structure):
                 if (not transformation_data) or (not input_structure):
                     return html.Div()
                 input_structure = self.from_data(input_structure)
-                output_structure, error = apply_transformation(
+                output_structure, _ = apply_transformation(
                     transformation_data, input_structure
                 )
                 if len(output_structure) > 64:

crystal_toolkit/components/upload.py

@@ -101,7 +101,7 @@ def callback_update_structure(contents, filename, last_modified):
                 raise PreventUpdate
 
             # assume we only want the first input for now
-            content_type, content_string = contents.split(",")
+            _, content_string = contents.split(",")
             decoded_contents = b64decode(content_string)
 
             error = None

crystal_toolkit/components/xas.py

@@ -5,6 +5,7 @@
 from dash.dependencies import Component, Input, Output, State
 from dash.exceptions import PreventUpdate
 from frozendict import frozendict
+from mp_api.client import MPRester
 
 from crystal_toolkit.core.mpcomponent import MPComponent
 from crystal_toolkit.core.panelcomponent import PanelComponent
@@ -154,8 +155,6 @@ def pattern_from_mpid(element, mpid, elements):
 
             url_path = f"/materials/{mpid['mpid']}/xas/{element}"
 
-            from mp_api.client import MPRester
-
             with MPRester() as mpr:
                 data = mpr._make_request(url_path)  # querying MP database via MAPI