Merge branch 'main' into add_lobster_integration

Author: tschaume

.github/dependabot.yml

@@ -1,8 +1,6 @@
 name: Monthly issue metrics
 on:
   workflow_dispatch:
-  schedule:
-    - cron: '3 2 1 * *'
 
 permissions:
   contents: read

.github/workflows/issue-metrics.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     steps:
       - uses: actions/checkout@v4
@@ -47,7 +47,7 @@ jobs:
           PERCY_TOKEN: ${{ secrets.PERCY_TOKEN }}
         run: python${{ matrix.python-version }} -m pytest --cov=crystal_toolkit --cov-report=xml --color=yes --webdriver Chrome --headless crystal_toolkit/apps/examples/tests/
       - uses: codecov/codecov-action@v1
-        if: matrix.python-version == 3.10
+        if: matrix.python-version == 3.11
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

.github/workflows/pull-request.yml

@@ -17,14 +17,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'

.github/workflows/pytest-docs.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     steps:
       - uses: actions/checkout@v4
@@ -39,7 +39,7 @@ jobs:
         run: python${{ matrix.python-version }} -m build
 
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@release/v1.5
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/release.yml

@@ -3,9 +3,6 @@ name: upgrade dependencies
 
 on:
   workflow_dispatch: # Allow running on-demand
-  schedule:
-    # Runs every Monday at 8:00 UTC (4:00 Eastern)
-    - cron: "0 8 * * 1"
 
 jobs:
   upgrade:
@@ -14,7 +11,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -71,6 +68,8 @@ jobs:
           git checkout -b auto-dependency-upgrades
           git branch -r | grep auto-dependency-upgrades- | xargs -I {} git merge {}
           git rebase ${GITHUB_REF##*/}
+          git reset $(git merge-base ${GITHUB_REF##*/} HEAD)
+          git commit -a -m "auto dependency upgrades"
           git push -f origin auto-dependency-upgrades
           git branch -r | grep auto-dependency-upgrades- | cut -d/ -f2 | xargs -I {} git push origin :{}
       - name: Open pull request if needed

.github/workflows/upgrade-dependencies.yml

@@ -14,7 +14,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Check for broken links
-        uses: lycheeverse/lychee-action@v1
+        uses: lycheeverse/lychee-action@v2.0.2
         with:
           # --exclude-loopback ensures we don't check localhost URLs
           args: --exclude-loopback './**/*.md' './**/*.rst'

.github/workflows/url-check.yml

@@ -11,7 +11,7 @@ exclude: ^(docs/.+|.*lock.*|jupyterlab-extension/.+|.*\.(svg|js|css))|_version.p
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.13.3
     hooks:
       - id: ruff
         args: [--fix, --ignore, D]
@@ -23,7 +23,7 @@ repos:
   #     - id: mypy
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-case-conflict
       - id: check-symlinks
@@ -33,14 +33,14 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         stages: [pre-commit, commit-msg]
         args: [--ignore-words-list, "nd,te,ois,dscribe", --check-filenames]
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]

.pre-commit-config.yaml

@@ -26,7 +26,6 @@ If you would like a new-contributor issue assigned, get in touch with project ma
 
 [![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/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)
 [![arXiv link](https://img.shields.io/badge/arXiv-2302.06147-blue)](https://arxiv.org/abs/2302.06147)
@@ -81,7 +80,7 @@ The [Crystal Toolkit Development Team](https://github.com/materialsproject/cryst
 * [Janosh Riebesell](https://github.com/janosh) contributed Phonon band structure component, [3 example apps](https://github.com/materialsproject/crystaltoolkit/blob/main/crystal_toolkit/apps/examples/matbench_dielectric_structure_on_hover.py), tests
 * [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
+* Guy Moore for contributing magnetic moment visualization
 * [Steve Zeltmann](https://github.com/sezelt) for contributing electron diffraction
 * [Patrick Huck](https://github.com/tschaume), releases, operations, bugfixes and POC for MP / MPContribs
 
@@ -101,7 +100,7 @@ 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](https://nersc.gov/systems/spin) service for
+Thank you to the [NERSC Spin](https://docs.nersc.gov/services/spin/) service for
 hosting the app and for their technical support.
 
 ## Contact

README.md

@@ -436,15 +436,15 @@ def get_search_layout(self, payload=None):
             "Surface Formula": unicodeify(contribution["formula"]),
             "Surface Material ID": dcc.Link(
                 contribution["data"]["mpid"],
-                href=f'/materials/{contribution["data"]["mpid"]}',
+                href=f"/materials/{contribution['data']['mpid']}",
             ),
             "Adsorbate SMILES": adsorbate_smiles,
             "Adsorbate IUPAC Formula": contribution["data"]["adsorbateIUPACFormula"],
             "Adsorption Energy": contribution["data"]["adsorptionEnergy"]["value"],
             "Miller Index": unicodeify_spacegroup(
-                f'({int(contribution["data"]["h"]["value"])} '
-                f'{int(contribution["data"]["k"]["value"])} '
-                f'{int(contribution["data"]["l"]["value"])})'
+                f"({int(contribution['data']['h']['value'])} "
+                f"{int(contribution['data']['k']['value'])} "
+                f"{int(contribution['data']['l']['value'])})"
             ),
             "Surface Shift": contribution["data"]["surfaceShift"]["value"],
         }