Pre-commit and minor CI updates

.github/workflows/ci.yml

@@ -35,21 +35,17 @@ jobs:
             - name: Check out app
               uses: actions/checkout@v6
 
-            - name: Set up Python
-              uses: actions/setup-python@v6
-              with:
-                  python-version: '3.11'
-
             - name: Setup uv
               uses: astral-sh/setup-uv@v7
               with:
-                  version: 0.4.20
+                  python-version: '3.12'
+                  activate-environment: 'true'
 
             - name: Install package test dependencies
               # Notebook tests happen in the container, here we only need to install
               # the pytest-docker dependency. Unfortunately, uv/pip does not allow to
               # only install [dev] dependencies so we end up installing all the rest as well.
-              run: uv pip install --system .[dev]
+              run: uv pip install .[dev]
 
             - name: Set jupyter token env
               run: echo "JUPYTER_TOKEN=$(openssl rand -hex 32)" >> $GITHUB_ENV

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
             exclude: miscellaneous/structures/SiO2.xyz
 
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.14.10
+      rev: v0.15.7
       hooks:
           - id: ruff-format
           - id: ruff
@@ -26,11 +26,11 @@ repos:
           - id: yamlfmt
 
     - repo: https://github.com/sirosen/check-jsonschema
-      rev: 0.36.0
+      rev: 0.37.0
       hooks:
           - id: check-github-workflows
 
     - repo: https://github.com/kynan/nbstripout
-      rev: 0.8.2
+      rev: 0.9.1
       hooks:
           - id: nbstripout