Merge branch 'main' into doc-for-mpcontrib-app

Author: mkhorton

.github/pull_request_template.md

@@ -0,0 +1,32 @@
+<!--
+
+All previous Crystal Toolkit contributors/co-authors are encouraged to merge their own PRs once CI passes.
+Crystal Toolkit is a community project, and merging your own PRs is encouraged to help
+maintain the overall health of the code. If you do not have the required permissions to merge
+your PR, contact @mkhorton or another repository admin.
+
+If you have concerns about your PR, or if it has expansive changes, please request review
+from @mkhorton or another active contributor.
+
+If you are a new contributor, your PR will be fully reviewed before merging by a previous
+contributor/co-author.
+
+-->
+
+## Checklist
+
+Work-in-progress pull requests are encouraged but please [mark your PR as draft](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/changing-the-stage-of-a-pull-request#converting-a-pull-request-to-a-draft).
+
+Usually the following items should be checked before merging a PR:
+
+- [ ] Doc strings have been added in the [Google docstring format](https://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings).
+- [ ] Type annotations are *highly* encouraged. Run [`mypy path/to/file.py`](https://github.com/python/mypy) to type check your code. Type checks are run in CI.
+- [ ] Tests for any new functionality as well as bug fixes, where appropriate.
+- [ ] Create a new [Issue](https://github.com/materialsproject/crystaltoolkit/issues) for any TODO items that will result from merging the PR.
+
+We recommended installing [`pre-commit`](https://pre-commit.com) to run all our linters locally. That will increase your development speed since you don't have to wait for our CI to tell about errors, your code will be checked at commit time.
+
+```sh
+pip install -U pre-commit
+pre-commit install
+```

.github/workflows/pull-request.yml

@@ -22,13 +22,15 @@ jobs:
           cache: 'pip'
           cache-dependency-path: '**/pyproject.toml'
       - name: Install webdriver
-        run: sudo apt-get update && sudo apt-get install firefox-geckodriver chromium-chromedriver
+        run: sudo apt-get update && sudo apt-get install chromium-chromedriver
       - name: Install dependencies
         run: |
-          python${{ matrix.python-version }} -m pip install --user --upgrade pip pip-tools numpy
-          python${{ matrix.python-version }} -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
-          python${{ matrix.python-version }} -m pip install --user --no-deps .
-      - name: Test with pytest
+          python -m pip install --user --upgrade pip pip-tools numpy
+          python -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
+          python -m pip install --user --no-deps .
+      - name: Test modules
+        run: pytest tests
+      - name: Test example apps
         env:
           PERCY_TOKEN: ${{ secrets.PERCY_TOKEN }}
         run: pytest --color=yes --webdriver Chrome --headless crystal_toolkit/apps/examples/tests/

.github/workflows/pytest-docs.yml

@@ -1,4 +1,4 @@
-name: pytest_and_docs
+name: Tests
 
 on: [release, workflow_dispatch]
 
@@ -23,9 +23,9 @@ jobs:
         run: sudo apt-get update && sudo apt-get install firefox-geckodriver
       - name: Install dependencies
         run: |
-          python${{ matrix.python-version }} -m pip install --user --upgrade pip pip-tools numpy
-          python${{ matrix.python-version }} -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
-          python${{ matrix.python-version }} -m pip install --user --no-deps .
+          python -m pip install --user --upgrade pip pip-tools numpy
+          python -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
+          python -m pip install --user --no-deps .
       - name: Build new docs
         run: |
           cd docs_rst
@@ -44,7 +44,7 @@ jobs:
           git add -A
           git commit -m "Automated doc build"
           git push
-      - name: Test with pytest
+      - name: pytest
         env:
           PERCY_TOKEN: ${{ secrets.PERCY_TOKEN }}
         run: pytest --color=yes --webdriver Firefox --headless crystal_toolkit/apps/examples/tests/

.github/workflows/release.yml

@@ -1,4 +1,4 @@
-name: release
+name: Release
 
 on: workflow_dispatch
 
@@ -37,23 +37,24 @@ jobs:
           echo "Next release: ${NEXT_RELEASE}"
           git config --local user.email "[email protected]"
           git config --local user.name "github-actions"
-          python${{ matrix.python-version }} -m pip install --upgrade pip
-          python${{ matrix.python-version }} -m pip install --user --upgrade pip build setuptools setuptools_scm wheel
-          SETUPTOOLS_SCM_PRETEND_VERSION=${NEXT_RELEASE} python${{ matrix.python-version }} -m setuptools_scm
+          python -m pip install --upgrade pip
+          python -m pip install --user --upgrade pip build setuptools setuptools_scm wheel
+          SETUPTOOLS_SCM_PRETEND_VERSION=${NEXT_RELEASE} python -m setuptools_scm
           git add crystal_toolkit/_version.py
           git commit -m "version bump: ${NEXT_RELEASE}"
           git push
           git tag ${NEXT_RELEASE}
           git push --tags
+          echo "NEXT_RELEASE=${NEXT_RELEASE}" >> $GITHUB_ENV
 
       - name: Install dependencies
         run: |
-          python${{ matrix.python-version }} -m pip install --user `grep numpy== requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt`
-          python${{ matrix.python-version }} -m pip install --user -r requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
-          python${{ matrix.python-version }} -m pip install --user --no-deps .[server]
+          python -m pip install --user `grep numpy== requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt`
+          python -m pip install --user -r requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
+          python -m pip install --user --no-deps .[server]
 
       - name: Build package
-        run: python${{ matrix.python-version }} -m build
+        run: SETUPTOOLS_SCM_PRETEND_VERSION=${{env.NEXT_RELEASE}} python -m build
 
       - name: Publish package
         uses: pypa/gh-action-pypi-publish@release/v1.5

.github/workflows/upgrade-dependencies.yml

@@ -26,9 +26,9 @@ jobs:
       - name: Upgrade Python dependencies
         shell: bash
         run: |
-          python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools numpy
-          python${{ matrix.python-version }} -m piptools compile -q --upgrade -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}.txt pyproject.toml
-          python${{ matrix.python-version }} -m piptools compile -q --upgrade --all-extras -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt pyproject.toml
+          python -m pip install --upgrade pip pip-tools numpy
+          python -m piptools compile -q --upgrade -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}.txt pyproject.toml
+          python -m piptools compile -q --upgrade --all-extras -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt pyproject.toml
       - name: Detect changes
         id: changes
         shell: bash

.gitignore

@@ -12,3 +12,4 @@ docs_rst/_build
 build/*
 *.egg-info
 dist/*
+.vscode

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 ci:
   autoupdate_schedule: quarterly
-  skip: [mypy, flake8]
+  skip: [mypy, flake8, docformatter]
 
 default_stages: [commit]
 
@@ -12,34 +12,35 @@ exclude: ^(docs/.+|.*lock.*|jupyterlab-extension/.+|.*\.(svg|js|css))$
 
 repos:
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
 
   - repo: https://github.com/psf/black
-    rev: 22.8.0
+    rev: 23.1.0
     hooks:
       - id: black-jupyter
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+    rev: 6.0.0
     hooks:
       - id: flake8
         additional_dependencies: [flake8-bugbear]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.38.2
+    rev: v3.3.1
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
+        exclude: ^crystal_toolkit/settings.py$
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.981
+    rev: v0.991
     hooks:
       - id: mypy
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: check-case-conflict
       - id: check-symlinks
@@ -49,18 +50,18 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.1
+    rev: v2.2.2
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v1.6.1
+    rev: v2.0.1
     hooks:
       - id: autoflake
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.5.2
+    rev: 1.6.1
     hooks:
       - id: nbqa-pyupgrade
         args: [--py38-plus]
@@ -75,7 +76,7 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.5.0
+    rev: v1.6.0.rc1
     hooks:
       - id: docformatter
         args: [--config, setup.cfg]

README.md

@@ -10,12 +10,18 @@ Following a discussion with a potential contributor, "new contributor" issues ar
 
 ## 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)
+[![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/Materials-Project/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/workflows/release/badge.svg)](https://github.com/materialsproject/crystaltoolkit/actions?query=workflow%3Arelease)
+[![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)
 
+## Installation
+
+```sh
+pip install crystal-toolkit
+```
+
 ## Documentation
 
 [Documentation can be found at docs.crystaltoolkit.org](https://docs.crystaltoolkit.org)
@@ -60,6 +66,7 @@ The [Crystal Toolkit Development Team](https://github.com/materialsproject/cryst
 * [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
+* [Steve Zeltmann](https://github.com/sezelt) for contributing electron diffraction
 
 New contributors are welcome, please see our [Code of Conduct.](code-of-conduct.md) If you are a new contributor please modify this README in your Pull Request to add your name to the list.
 

crystal_toolkit/_version.py

@@ -1 +1,3 @@
-__version__ = "2022.11.30.dev8"
+from __future__ import annotations
+
+__version__ = "2023.02.01"

crystal_toolkit/apps/constants.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from collections import defaultdict
 
 from monty.serialization import loadfn
@@ -7,15 +9,15 @@
 
 APP_METADATA = loadfn(SETTINGS.APP_METADATA)
 
-# List of URLs available in the website
+# list of URLs available in the website
 _BASE_URL = "https://materialsproject.org/"
 _apps_sitemap = []
 
 # Construct a nested dictionary showing the relationship between apps
 # based on their urls, used for About page etc.
 APP_TREE = {}
 for app_class_name, metadata in APP_METADATA.items():
-    if metadata["url"] and (not metadata["url"].startswith("http")):
+    if metadata["url"] and not metadata["url"].startswith("http"):
         _apps_sitemap.append(_BASE_URL + metadata["url"])
         path = metadata["url"].replace("/", ".")
         if not get(APP_TREE, path):