Merge branch 'devel' into lmp-spin

.github/workflows/benchmark.yml

@@ -13,7 +13,12 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: 3.12
-    - run: curl -LsSf https://astral.sh/uv/install.sh | sh
+    - uses: astral-sh/setup-uv@v3
+      with:
+        enable-cache: true
+        cache-dependency-glob: |
+          **/requirements*.txt
+          **/pyproject.toml
     - name: Install dependencies
       run: uv pip install --system .[test,amber,ase,pymatgen,benchmark] rdkit openbabel-wheel
     - name: Run benchmarks

.github/workflows/test.yml

@@ -18,7 +18,13 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - run: curl -LsSf https://astral.sh/uv/install.sh | sh
+    - uses: astral-sh/setup-uv@v3
+      with:
+        enable-cache: true
+        cache-dependency-glob: |
+          **/requirements*.txt
+          **/pyproject.toml
+        cache-suffix: "py${{ matrix.python-version }}"
     - name: Install dependencies
       run: uv pip install --system .[test,amber,ase,pymatgen] coverage ./tests/plugin rdkit openbabel-wheel
     - name: Test

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     # there are many log files in tests
     # TODO: seperate py files and log files
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.7
+    rev: v0.6.9
     hooks:
     - id: ruff
       args: ["--fix"]
@@ -36,7 +36,7 @@ repos:
       args: ["--write"]
 # Python inside docs
 -   repo: https://github.com/asottile/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.0
     hooks:
     -   id: blacken-docs
 ci: