Combined ci updates

.github/workflows/ci.yml

@@ -18,7 +18,7 @@ jobs:
   check-manifest:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - run: pipx run check-manifest
 
   test:
@@ -39,8 +39,8 @@ jobs:
       UV_PYTHON: ${{ matrix.python-version }}
       UV_NO_SYNC: 1
     steps:
-      - uses: actions/checkout@v5
-      - uses: astral-sh/setup-uv@v6
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
         with:
           enable-cache: true
 
@@ -51,7 +51,7 @@ jobs:
 
       - run: uv run coverage run -p -m pytest --color=yes -v
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v6
         with:
           name: covreport-${{ matrix.os }}-py${{ matrix.python-version }}-${{ matrix.min }}
           path: ./.coverage*
@@ -69,7 +69,7 @@ jobs:
     needs: test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - uses: hynek/build-and-inspect-python-package@v2
 
   upload-to-pypi:
@@ -82,7 +82,7 @@ jobs:
       contents: write
     steps:
       - name: Download built artifact to dist/
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v7
         with:
           name: Packages
           path: dist

.github/workflows/docs.yml

@@ -14,14 +14,14 @@ jobs:
     if: github.event_name == 'pull_request'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
-      - uses: astral-sh/setup-uv@v6
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
       - run: uv run --group docs mkdocs build --strict
 
   deploy:
     if: github.ref == 'refs/heads/main'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
-      - uses: astral-sh/setup-uv@v6
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
       - run: uv run --group docs mkdocs gh-deploy --force

.pre-commit-config.yaml

@@ -10,19 +10,19 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/adhtruong/mirrors-typos
-    rev: v1.35.5
+    rev: v1.40.0
     hooks:
       - id: typos
         args: [--force-exclude]  # omitting --write-changes
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.11
+    rev: v0.14.7
     hooks:
       - id: ruff-check
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.17.1
+    rev: v1.19.0
     hooks:
       - id: mypy
         files: "^src/"

src/microsim/schema/_validators.py

@@ -45,7 +45,7 @@ def validate_unit(value: Any) -> PlainQuantity[MagnitudeT]:
             raise ValueError(f"Expected a quantity with units {units}, got {quant}")
         with suppress(pint.UndefinedUnitError):
             # try to cast to the given units.
-            # This may fail, even if quant.check() passed, if `units` is just a dimenson
+            # This may fail even if quant.check() passed if units is just a dimension
             quant = quant.to(units)
         return quant
 

src/microsim/schema/sample/fluorophore.py

@@ -66,7 +66,7 @@ def _vmodel(cls, value: Any) -> Any:
     def plot(self, show: bool = True) -> None:
         import matplotlib.pyplot as plt
 
-        fig, ax = plt.subplots(figsize=(12, 3))
+        _fig, ax = plt.subplots(figsize=(12, 3))
         ax.plot(
             self.excitation_spectrum.wavelength,
             self.excitation_spectrum.intensity,