Merge branch 'main' into devel

Author: mkhorton

.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
-    rev: stable
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
     hooks:
-    - id: black
+      - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+      - 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

@@ -1,6 +1,14 @@
 # Crystal Toolkit
 
-**Crystal Toolkit is not ready for the public yet! Please wait for a release announcement soon, thank you :-)**   
+# Call for new contributors
+
+Crystal Toolkit is an academic project. A manuscript is in preparation to detail the design goals of Crystal Toolkit and achievements to date.
+
+**If you are interested in getting involved in Crystal Toolkit and are not already, it is not too late to be included in this manuscript, but please get in touch with [email protected] ASAP.** Include information on the specific contributions that you would like to make (e.g. this may include adding features, addressing bugs, writing documentation, manuscript preparation, community engagement, writing tests, and the like), and if these align with the project we can formally add you to the development team.
+
+Following a discussion with a potential contributor, "new contributor" issues are assigned. A current list of new contributor issues can be seen [here](https://github.com/materialsproject/crystaltoolkit/labels/new-contributor).
+
+## Status
 
 [![Pytest Status](https://github.com/materialsproject/crystaltoolkit/workflows/pytest_and_docs/badge.svg)](https://github.com/materialsproject/crystaltoolkit/actions?query=workflow%3Apytest_and_docs)
 [![Visual Regression Test Status](https://percy.io/static/images/percy-badge.svg)](https://percy.io/Materials-Project/crystaltoolkit)
@@ -33,16 +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

@@ -1,14 +1,26 @@
+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__ = "2022.06.08"
+__version__ = "2022.07.25"
 
 MODULE_PATH = Path(__file__).parents[0]
 
@@ -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"}