Merge pull request #272 from materialsproject/pre-commit

`pre-commit` hooks

Author: janosh

.github/workflows/pytest_docs.yml

@@ -50,4 +50,3 @@ jobs:
         PERCY_TOKEN: ${{ secrets.PERCY_TOKEN }}
       run: |
         poetry run pytest --color=yes --webdriver Firefox --headless crystal_toolkit/apps/examples/tests/
-

.github/workflows/release.yml

@@ -1,6 +1,6 @@
 name: release
 
-on: 
+on:
   workflow_dispatch
 
 jobs:

.pre-commit-config.yaml

@@ -1,5 +1,83 @@
+ci:
+  autoupdate_schedule: quarterly
+
+default_stages: [commit]
+
+default_install_hook_types: [pre-commit, commit-msg]
+
+# ignore generated doc and dependency lock files
+exclude: ^(docs/.+|.*lock.*)$
+
 repos:
-  - repo: https://github.com/ambv/black
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/psf/black
     rev: 22.6.0
     hooks:
-    - id: black
+      - id: black-jupyter
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.34.0
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.961
+    hooks:
+      - id: mypy
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - 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
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.1.0
+    hooks:
+      - id: codespell
+        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:
+      - id: autoflake
+        args:
+          - --in-place
+          - --remove-unused-variables
+          - --remove-all-unused-imports
+          - --expand-star-imports
+          - --ignore-init-module-imports
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.3.1
+    hooks:
+      - id: nbqa-pyupgrade
+        args: [--py38-plus]
+      - id: nbqa-isort
+      - id: nbqa-flake8
+        args: [--ignore=E402]

README.md

@@ -41,16 +41,16 @@ New contributors are welcome, please see our [Code of Conduct.](code-of-conduct.
 
 The Crystal Toolkit repo currently contains three major parts:
 
-* An object-orientated Python framework for rendering materials science data based on the schema employed by the Materials Proejct
+* An object-orientated Python framework for rendering materials science data based on the schema employed by the Materials Project
 * A few custom Plotly Dash components (Simple3DSceneComponent, JSONComponent, GraphComponent)
 * Some example apps using these components
 
 It is likely the custom Plotly Dash components might be spun off into a separate repo at some point to reduce the complexity of the Crystal Toolkit repo itself.
 
 ## Acknowledgements
 
-Thank you to all the authors and maintainers of the libraries Crystal Toolkit 
-depends upon, and in particular [pymatgen](http://pymatgen.org) for crystallographic 
+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](http://www.nersc.gov/users/data-analytics/spin/) service for

code-of-conduct.md

@@ -46,4 +46,3 @@ This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 1.3.0, available at https://www.contributor-covenant.org/version/1/3/0/code-of-conduct.html
 
 [homepage]: https://www.contributor-covenant.org
-

crystal_toolkit/__init__.py

@@ -1,12 +1,24 @@
+from __future__ import annotations
+
 import json
 import os as _os
 from collections import defaultdict
 from pathlib import Path
+from typing import Any
 
 # pleasant hack to support MSONable objects in Dash callbacks natively
 from monty.json import MSONable
 
-from crystal_toolkit.renderables import *
+from crystal_toolkit.renderables import (
+    Lattice,
+    Molecule,
+    MoleculeGraph,
+    PhaseDiagram,
+    Site,
+    Structure,
+    StructureGraph,
+    VolumetricData,
+)
 
 __version__ = "2022.07.25"
 
@@ -21,7 +33,7 @@ def to_plotly_json(self):
 
 
 # Populate the default values from the JSON file
-_DEFAULTS = defaultdict(lambda: None)
+_DEFAULTS: dict[str, Any] = defaultdict()
 default_js = _os.path.join(
     _os.path.join(_os.path.dirname(_os.path.abspath(__file__))), "./", "defaults.json"
 )
@@ -43,8 +55,8 @@ def _repr_mimebundle_(self, include=None, exclude=None):
 This only works in Jupyter Lab 3.x or above.\n\n
 """
 
-    help_text_plotly = """If you see this text, the Plotly Jupyter Lab extension 
-is not installed, please consult Plotly documentation for information on how to 
+    help_text_plotly = """If you see this text, the Plotly Jupyter Lab extension
+is not installed, please consult Plotly documentation for information on how to
 install.
 """
 

crystal_toolkit/apps/assets/crystaltoolkit.css

@@ -1,7 +1,3 @@
-
-
-
 body, html, .body {
   background: #f3f3f3 !important;
 }
-

crystal_toolkit/apps/assets/doi_cache.json

@@ -1 +1 @@
-{"10.26434/chemrxiv.11294480.v1": "D. Waroquiers, J. George, M. Horton, S. Schenk, K. Persson, G.-M. Rignanese, X. Gonze, and G. Hautier, \u201cChemEnv\u202f: A Fast and Robust Coordination Environment Identification Tool,\u201d Dec. 2019.\n", "10.3389/fmats.2017.00034": "N. E. R. Zimmermann, M. K. Horton, A. Jain, and M. Haranczyk, \u201cAssessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization,\u201d Frontiers in Materials, vol. 4, Nov. 2017.\n"}
+{"10.26434/chemrxiv.11294480.v1": "D. Waroquiers, J. George, M. Horton, S. Schenk, K. Persson, G.-M. Rignanese, X. Gonze, and G. Hautier, \u201cChemEnv\u202f: A Fast and Robust Coordination Environment Identification Tool,\u201d Dec. 2019.\n", "10.3389/fmats.2017.00034": "N. E. R. Zimmermann, M. K. Horton, A. Jain, and M. Haranczyk, \u201cAssessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization,\u201d Frontiers in Materials, vol. 4, Nov. 2017.\n"}