[pre-commit.ci] pre-commit autoupdate (#483)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.0 → v0.13.3](astral-sh/ruff-pre-commit@v0.5.0...v0.13.3)
- [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v6.0.0](pre-commit/pre-commit-hooks@v4.6.0...v6.0.0)
- [github.com/codespell-project/codespell: v2.3.0 → v2.4.1](codespell-project/codespell@v2.3.0...v2.4.1)
- [github.com/kynan/nbstripout: 0.7.1 → 0.8.1](kynan/nbstripout@0.7.1...0.8.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix/rm broken links

* pre-commit fixes and linting

* add kaleido dep

* auto dependency upgrades

* new image export Plotly API

* auto dependency upgrades

* try to avoid circular import for version

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* dynamic module import

* fix dynamic import

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Patrick Huck <[email protected]>
Co-authored-by: github-actions <[email protected]>

Author: 3 people

.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()