Merge remote-tracking branch 'origin/main' into fix-test-toml

.github/workflows/issue-metrics.yml

@@ -0,0 +1,42 @@
+name: Monthly issue metrics
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '3 2 1 * *'
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: issue metrics
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: read
+    steps:
+    - name: Get dates for last month
+      shell: bash
+      run: |
+        # Calculate the first day of the previous month
+        first_day=$(date -d "last month" +%Y-%m-01)
+
+        # Calculate the last day of the previous month
+        last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
+
+        #Set an environment variable with the date range
+        echo "$first_day..$last_day"
+        echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
+
+    - name: Run issue-metrics tool
+      uses: github/issue-metrics@v3
+      env:
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SEARCH_QUERY: 'repo:materialsproject/crystaltoolkit is:issue created:${{ env.last_month }} -reason:"not planned"'
+
+    - name: Create issue
+      uses: peter-evans/create-issue-from-file@v5
+      with:
+        title: Monthly issue metrics report
+        token: ${{ secrets.GITHUB_TOKEN }}
+        content-filepath: ./issue_metrics.md

.github/workflows/pull-request.yml

@@ -1,15 +1,24 @@
-name: pytest
+name: Testing
 
 on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
   pull_request:
-    branches: [main]
+    branches:
+      - main
+
+permissions:
+  contents: read
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v3
@@ -29,7 +38,7 @@ jobs:
           python${{ matrix.python-version }} -m pip install `grep numpy== requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt`
           python${{ matrix.python-version }} -m pip install -r requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
           python${{ matrix.python-version }} -m pip install --upgrade pip
-          python${{ matrix.python-version }} -m pip install --no-deps .
+          python${{ matrix.python-version }} -m pip install --no-deps .[server]
       - name: Test modules
         run: python${{ matrix.python-version }} -m pytest tests
       - name: Test example apps

.github/workflows/pytest-docs.yml

@@ -1,13 +1,23 @@
-name: Tests
+name: Build Docs
 
-on: [release, workflow_dispatch]
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+    branches:
+      - main
+  release:
+    types: [published]
 
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v3
@@ -20,18 +30,20 @@ jobs:
           cache: 'pip'
           cache-dependency-path: '**/pyproject.toml'
       - name: Install webdriver
-        run: sudo apt-get update && sudo apt-get install firefox-geckodriver
+        run: sudo apt-get update && sudo apt-get install chromium-chromedriver
       - name: Install dependencies
         run: |
           python${{ matrix.python-version }} -m pip install --upgrade pip packaging wheel
           python${{ matrix.python-version }} -m pip install `grep numpy== requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt`
           python${{ matrix.python-version }} -m pip install -r requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
+          python${{ matrix.python-version }} -m pip install --upgrade pip
           python${{ matrix.python-version }} -m pip install --no-deps .
       - name: Build new docs
         run: |
           cd docs_rst
           make html
-      - name: Detect changes
+      - name: Detect changes on release
+        if: startsWith(github.head_ref, 'releases/')
         id: changes
         shell: bash
         run: |
@@ -45,7 +57,3 @@ jobs:
           git add -A
           git commit -m "Automated doc build"
           git push
-      - name: pytest
-        env:
-          PERCY_TOKEN: ${{ secrets.PERCY_TOKEN }}
-        run: pytest --color=yes --webdriver Firefox --headless crystal_toolkit/apps/examples/tests/

.github/workflows/release.yml

@@ -1,62 +1,42 @@
 name: Release
 
-on: workflow_dispatch
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
           token: ${{ secrets.PAT }}
 
-      - uses: actions/setup-python@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
           cache-dependency-path: '**/pyproject.toml'
 
-      - name: bump version and create tag
-        env:
-          DATE_FORMAT: "%Y.%m.%d"
-        run: |
-          NEXT_RELEASE=$(date "+${DATE_FORMAT}")
-          LAST_RELEASE=$(git tag --sort=v:refname | grep "^20[^\-]*$" | tail -n 1)
-          echo "Last release : ${LAST_RELEASE}"
-          MAJOR_LAST_RELEASE=$(echo "${LAST_RELEASE}" | awk -v l=${#NEXT_RELEASE} '{ string=substr($0, 1, l); print string; }')
-          echo "Last major release : ${MAJOR_LAST_RELEASE}"
-          if [ "${MAJOR_LAST_RELEASE}" = "${NEXT_RELEASE}" ]; then
-            MINOR_LAST_RELEASE="$(echo "${LAST_RELEASE}" | awk -v l=$((${#NEXT_RELEASE} + 2)) '{ string=substr($0, l); print string; }')"
-            NEXT_RELEASE=${MAJOR_LAST_RELEASE}.$((MINOR_LAST_RELEASE + 1))
-          fi
-          echo "Next release: ${NEXT_RELEASE}"
-          git config --local user.email "github-actions@github.com"
-          git config --local user.name "github-actions"
-          python -m pip install --upgrade pip
-          python -m pip install --user --upgrade pip build setuptools setuptools_scm wheel
-          SETUPTOOLS_SCM_PRETEND_VERSION=${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}" >> $GITHUB_ENV
-
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install `grep numpy== requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt`
-          python -m pip install -r requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
-          python -m pip install --upgrade pip
-          python -m pip install --no-deps .[server]
+          python${{ matrix.python-version }} -m pip install --upgrade pip packaging wheel build
+          python${{ matrix.python-version }} -m pip install `grep numpy== requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt`
+          python${{ matrix.python-version }} -m pip install -r requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
+          python${{ matrix.python-version }} -m pip install --upgrade pip
+          python${{ matrix.python-version }} -m pip install --no-deps .[server]
 
       - name: Build package
-        run: SETUPTOOLS_SCM_PRETEND_VERSION=${{env.NEXT_RELEASE}} python -m build
+        run: python${{ matrix.python-version }} -m build
 
       - name: Publish package
         uses: pypa/gh-action-pypi-publish@release/v1.5

.github/workflows/upgrade-dependencies.yml

@@ -13,20 +13,20 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ['ubuntu-latest', 'macos-latest']
-        python-version: ["3.8", "3.9", "3.10"]
+        os: ['ubuntu-latest']
+        python-version: ["3.9", "3.10", "3.11"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
       - name: Upgrade Python dependencies
         shell: bash
         run: |
-          python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools
+          python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools wheel cython setuptools
           python${{ matrix.python-version }} -m pip install `grep numpy== requirements/${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt`
           python${{ matrix.python-version }} -m piptools compile -q --upgrade --resolver=backtracking -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}.txt pyproject.toml
           python${{ matrix.python-version }} -m piptools compile -q --upgrade --resolver=backtracking --all-extras -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt pyproject.toml
@@ -43,7 +43,7 @@ jobs:
           git config user.name github-actions
           git config user.email github-actions@github.com
           git add requirements
-          git commit -m "update dependencies for ${{ matrix.os }}/py${{ matrix.python-version }}"
+          git commit --allow-empty -m "update dependencies for ${{ matrix.os }}/py${{ matrix.python-version }}"
           git push -f origin ${{ github.ref_name }}:auto-dependency-upgrades-${{ matrix.os }}-py${{ matrix.python-version }}
 
   pull_request:
@@ -54,10 +54,10 @@ jobs:
       matrix:
         python-version: ["3.9"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: detect auto-upgrade-dependency branches

.pre-commit-config.yaml

@@ -7,27 +7,23 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 # ignore generated docs and dependency lock files, the directory
 # jupyterlab-extension/ and all SVG, JS and CSS files
-exclude: ^(docs/.+|.*lock.*|jupyterlab-extension/.+|.*\.(svg|js|css))$
+exclude: ^(docs/.+|.*lock.*|jupyterlab-extension/.+|.*\.(svg|js|css))|_version.py$
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.277
+    rev: v0.4.8
     hooks:
       - id: ruff
         args: [--fix, --ignore, D]
-
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black-jupyter
+      - id: ruff-format
 
   # - repo: https://github.com/pre-commit/mirrors-mypy
   #   rev: v1.3.0
   #   hooks:
   #     - id: mypy
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-case-conflict
       - id: check-symlinks
@@ -37,19 +33,14 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.3.0
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
-        args: [--ignore-words-list, "nd,te,ois"]
-
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
-    hooks:
-      - id: nbqa-ruff
+        args: [--ignore-words-list, "nd,te,ois,dscribe", --check-filenames]
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]

README.md

@@ -25,7 +25,7 @@ If you would like a new-contributor issue assigned, get in touch with project ma
 ## Status
 
 [![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)
+[![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)

crystal_toolkit/__init__.py

@@ -5,12 +5,9 @@
 
 from monty.json import MSONable
 
-from crystal_toolkit.msonable import (
-    _ipython_display_,
-    _repr_mimebundle_,
-    show_json,
-    to_plotly_json,
-)
+import crystal_toolkit.helpers.layouts as ctl
+from crystal_toolkit.core.jupyter import patch_msonable
+from crystal_toolkit.core.plugin import CrystalToolkitPlugin
 from crystal_toolkit.renderables import (
     Lattice,
     Molecule,
@@ -22,10 +19,7 @@
     VolumetricData,
 )
 
-MSONable.to_plotly_json = to_plotly_json
-MSONable._repr_mimebundle_ = _repr_mimebundle_
-MSONable.show_json = show_json
-MSONable._ipython_display_ = _ipython_display_
+patch_msonable()
 
 MODULE_PATH = Path(__file__).parents[0]
 

crystal_toolkit/apps/examples/bandstructure.py

@@ -32,13 +32,13 @@
 )
 
 # example layout to demonstrate capabilities of component
-my_layout = Container(
+layout = Container(
     [H1("Band Structure and Density of States Example"), bsdos_component.layout()]
 )
 
 # wrap your app.layout with crystal_toolkit_layout()
 # to ensure all necessary components are loaded into layout
-ctc.register_crystal_toolkit(app, layout=my_layout)
+ctc.register_crystal_toolkit(app, layout=layout)
 
 
 # run this app with "python path/to/this/file.py"

crystal_toolkit/apps/examples/basic_hello_structure.py

@@ -15,9 +15,9 @@
 structure_component = ctc.StructureMoleculeComponent(structure, id="hello_structure")
 
 # add the component's layout to our app's layout
-my_layout = html.Div([structure_component.layout()])
+layout = html.Div([structure_component.layout()])
 
 # as explained in "preamble" section in documentation
-ctc.register_crystal_toolkit(app=app, layout=my_layout)
+ctc.register_crystal_toolkit(app=app, layout=layout)
 if __name__ == "__main__":
     app.run(debug=True, port=8050)

crystal_toolkit/apps/examples/basic_hello_structure_interactive.py

@@ -28,9 +28,9 @@
 
 # now we have two entries in our app layout,
 # the structure component's layout and the button
-my_layout = html.Div([structure_component.layout(), my_button])
+layout = html.Div([structure_component.layout(), my_button])
 
-ctc.register_crystal_toolkit(app=app, layout=my_layout)
+ctc.register_crystal_toolkit(app=app, layout=layout)
 
 
 # for the interactivity, we use a standard Dash callback