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Merge pull request #272 from materialsproject/pre-commit
`pre-commit` hooks
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‎.github/workflows/pytest_docs.yml

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PERCY_TOKEN: ${{ secrets.PERCY_TOKEN }}
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run: |
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poetry run pytest --color=yes --webdriver Firefox --headless crystal_toolkit/apps/examples/tests/
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‎.github/workflows/release.yml

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name: release
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on:
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on:
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workflow_dispatch
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jobs:

‎.pre-commit-config.yaml

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ci:
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autoupdate_schedule: quarterly
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default_stages: [commit]
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default_install_hook_types: [pre-commit, commit-msg]
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# ignore generated doc and dependency lock files
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exclude: ^(docs/.+|.*lock.*)$
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repos:
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- repo: https://github.com/ambv/black
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- repo: https://github.com/PyCQA/isort
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rev: 5.10.1
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hooks:
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- id: isort
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- repo: https://github.com/psf/black
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rev: 22.6.0
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hooks:
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- id: black
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- id: black-jupyter
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- repo: https://github.com/PyCQA/flake8
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rev: 4.0.1
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hooks:
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- id: flake8
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- repo: https://github.com/asottile/pyupgrade
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rev: v2.34.0
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hooks:
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- id: pyupgrade
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args: [--py38-plus]
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v0.961
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hooks:
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- id: mypy
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.3.0
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hooks:
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- id: check-case-conflict
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- id: check-symlinks
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- id: check-yaml
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- id: destroyed-symlinks
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- id: end-of-file-fixer
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exclude: ^assets/.+\.(svg|html)$
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- id: mixed-line-ending
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- id: trailing-whitespace
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- repo: https://github.com/codespell-project/codespell
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rev: v2.1.0
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hooks:
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- id: codespell
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stages: [commit, commit-msg]
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exclude_types: [csv, svg, html, yaml, jupyter]
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- repo: local
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hooks:
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- id: svg-assets
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name: SVG assets
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entry: Files under assets/* must end in .(svg|html)
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language: fail
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files: ^assets/.*(?<!\.svg)(?<!\.html)$
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- repo: https://github.com/myint/autoflake
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rev: v1.4
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hooks:
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- id: autoflake
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args:
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- --in-place
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- --remove-unused-variables
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- --remove-all-unused-imports
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- --expand-star-imports
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- --ignore-init-module-imports
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- repo: https://github.com/nbQA-dev/nbQA
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rev: 1.3.1
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hooks:
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- id: nbqa-pyupgrade
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args: [--py38-plus]
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- id: nbqa-isort
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- id: nbqa-flake8
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args: [--ignore=E402]

‎README.md

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@@ -41,16 +41,16 @@ New contributors are welcome, please see our [Code of Conduct.](code-of-conduct.
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The Crystal Toolkit repo currently contains three major parts:
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* An object-orientated Python framework for rendering materials science data based on the schema employed by the Materials Proejct
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* An object-orientated Python framework for rendering materials science data based on the schema employed by the Materials Project
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* A few custom Plotly Dash components (Simple3DSceneComponent, JSONComponent, GraphComponent)
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* Some example apps using these components
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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.
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## Acknowledgements
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Thank you to all the authors and maintainers of the libraries Crystal Toolkit
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depends upon, and in particular [pymatgen](http://pymatgen.org) for crystallographic
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Thank you to all the authors and maintainers of the libraries Crystal Toolkit
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depends upon, and in particular [pymatgen](http://pymatgen.org) for crystallographic
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analysis and [Dash from Plotly](https://plot.ly/products/dash/) for their web app framework.
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Thank you to the [NERSC Spin](http://www.nersc.gov/users/data-analytics/spin/) service for

‎code-of-conduct.md

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

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

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body, html, .body {
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background: #f3f3f3 !important;
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}
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‎crystal_toolkit/apps/assets/doi_cache.json

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{"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"}
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"}

‎crystal_toolkit/apps/assets/task_ids_on_load.json

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‎crystal_toolkit/apps/examples/GaN_bs.json

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‎crystal_toolkit/apps/examples/GaN_dos.json

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‎crystal_toolkit/apps/examples/Si_bs.json

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‎crystal_toolkit/apps/examples/Si_dos.json

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‎crystal_toolkit/apps/examples/bandstructure.py

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# standard Dash imports
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import dash
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from dash import html
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from dash import dcc
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import os
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# standard Crystal Toolkit import
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import crystal_toolkit.components as ctc
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from crystal_toolkit.settings import SETTINGS
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from crystal_toolkit.helpers.layouts import H1, H2, Container
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import dash
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# dos and bs data from local jsons
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from monty.serialization import loadfn
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import os
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# standard Crystal Toolkit import
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import crystal_toolkit.components as ctc
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from crystal_toolkit.helpers.layouts import H1, Container
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from crystal_toolkit.settings import SETTINGS
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# create Dash app as normal, assets folder set for visual styles only
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app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH)
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# example layout to demonstrate capabilities of component
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my_layout = Container(
38-
[H1("Band Structure and Density of States Example"), bsdos_component.layout(),]
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[H1("Band Structure and Density of States Example"), bsdos_component.layout()]
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)
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# wrap your app.layout with crystal_toolkit_layout()

‎crystal_toolkit/apps/examples/basic_hello_world.py

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# standard Dash imports
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import dash
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from dash import html
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from dash import dcc
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# standard Crystal Toolkit import
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import crystal_toolkit.components as ctc

‎crystal_toolkit/apps/examples/diffraction.py

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# standard Dash imports
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import dash
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from dash import html
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from dash import dcc
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# create our crystal structure using pymatgen
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from pymatgen.core.lattice import Lattice
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from pymatgen.core.structure import Structure
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# standard Crystal Toolkit import
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import crystal_toolkit.components as ctc
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from crystal_toolkit.settings import SETTINGS
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from crystal_toolkit.helpers.layouts import H1, H3, Container
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# import for this example
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from pymatgen.ext.matproj import MPRester
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from pymatgen.analysis.phase_diagram import PhaseDiagram
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from pymatgen.analysis.diffraction.xrd import XRDCalculator
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from crystal_toolkit.settings import SETTINGS
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# create Dash app as normal
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app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH)
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# create our crystal structure using pymatgen
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from pymatgen.core.structure import Structure
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from pymatgen.core.lattice import Lattice
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structure = Structure(Lattice.cubic(4.2), ["Na", "K"], [[0, 0, 0], [0.5, 0.5, 0.5]])
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‎crystal_toolkit/apps/examples/diffraction_dynamic.py

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# standard Dash imports
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import dash
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from dash.dependencies import Input, Output
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‎crystal_toolkit/apps/examples/diffraction_empty.py

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# standard Dash imports
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import dash
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from dash import html
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from dash import dcc
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# create our crystal structure using pymatgen
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from pymatgen.core.lattice import Lattice
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from pymatgen.core.structure import Structure
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# standard Crystal Toolkit import
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import crystal_toolkit.components as ctc
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from crystal_toolkit.helpers.layouts import H1, Container
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from crystal_toolkit.settings import SETTINGS
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from crystal_toolkit.helpers.layouts import H1, H2, Container
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# import for this example
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from pymatgen.core.structure import Structure
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from pymatgen.core.lattice import Lattice
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from pymatgen.ext.matproj import MPRester
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from pymatgen.analysis.phase_diagram import PhaseDiagram
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from pymatgen.analysis.diffraction.xrd import XRDCalculator
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# create Dash app as normal
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app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH)
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# create our crystal structure using pymatgen
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from pymatgen.core.structure import Structure
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from pymatgen.core.lattice import Lattice
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2515
structure = Structure(Lattice.cubic(4.2), ["Na", "K"], [[0, 0, 0], [0.5, 0.5, 0.5]])
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xrd_component = ctc.XRayDiffractionComponent()
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# example layout to demonstrate capabilities of component
3020
my_layout = Container(
31-
[H1("XRDComponent Example (Empty, No Structure Defined)"), xrd_component.layout(),]
21+
[H1("XRDComponent Example (Empty, No Structure Defined)"), xrd_component.layout()]
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)
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# as explained in "preamble" section in documentation

‎crystal_toolkit/apps/examples/kwarg_inputs.py

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import random
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import dash
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from dash import html, dcc, Input, Output
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from dash import Input, Output, dcc, html
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from dash.exceptions import PreventUpdate
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import crystal_toolkit.components as ctc

‎crystal_toolkit/apps/examples/phase_diagram.py

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# standard Dash imports
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import dash
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from dash import dcc
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from dash import html
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# import for this example
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from pymatgen.ext.matproj import MPRester
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from dash import dcc, html
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from pymatgen.analysis.phase_diagram import PhaseDiagram
4+
from pymatgen.ext.matproj import MPRester
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# standard Crystal Toolkit import
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import crystal_toolkit.components as ctc

‎crystal_toolkit/apps/examples/pourbaix.py

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# standard Dash imports
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import dash
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from dash import dcc
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from dash import html
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# import for this example
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from pymatgen.ext.matproj import MPRester
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# standard Crystal Toolkit import
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html.H1("PourbaixDiagramComponent Example"),
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html.Button("Get Pourbaix Diagram", id="get-pourbaix"),
3228
pourbaix_component.layout(),
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html.Div(id="pourbaix-output")
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html.Div(id="pourbaix-output"),
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]
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)
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‎crystal_toolkit/apps/examples/structure.py

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# standard Dash imports
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import dash
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from dash import html
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# import for this example
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from pymatgen.core.lattice import Lattice
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from pymatgen.core.structure import Structure
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‎crystal_toolkit/apps/examples/structure_magnetic.py

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# standard Dash imports
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import dash
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from dash import dcc
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from dash import html
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# import for this example
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from pymatgen.core.structure import Structure
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from pymatgen.core.lattice import Lattice
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from pymatgen.electronic_structure.core import Magmom
4+
from pymatgen.core.structure import Structure
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# standard Crystal Toolkit import
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import crystal_toolkit.components as ctc

‎crystal_toolkit/apps/examples/tests/test_bandstructure.py

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from crystal_toolkit.apps.examples.bandstructure import app
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import time
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from crystal_toolkit.apps.examples.bandstructure import app
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def test_bs(dash_duo):
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‎crystal_toolkit/apps/examples/tests/test_basic.py

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from crystal_toolkit.apps.examples.basic_hello_world import app as hello_world_app
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from crystal_toolkit.apps.examples.basic_hello_structure import (
3-
app as hello_structure_app,
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)
1+
import time
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53
from crystal_toolkit.apps.examples.basic_hello_structure_interactive import (
64
app as hello_structure_interactive_app,
75
)
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import time
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#
128
# def test_hello_scientist(dash_duo):
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#

‎crystal_toolkit/apps/examples/tests/test_structure.py

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from crystal_toolkit.apps.examples.structure import app
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import time
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from crystal_toolkit.apps.examples.structure import app
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def test_structure(dash_duo):
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