Update instance repo (PR 498 -- chore: zizmor for pre-commit)

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-  "commit": "6cca9704e02edc716fa4665258aa2eb4518be78e",
+  "commit": "5a017ae9269e1f624da099f48903775fb3b468c7",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -36,7 +36,7 @@
         "trim_blocks": true
       },
       "_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-      "_commit": "6cca9704e02edc716fa4665258aa2eb4518be78e"
+      "_commit": "5a017ae9269e1f624da099f48903775fb3b468c7"
     }
   },
   "directory": null

.github/workflows/test.yaml

@@ -48,6 +48,7 @@ jobs:
     needs: get-environments
     permissions:
        id-token: write  # for codecov OIDC
+       contents: read
 
     strategy:
       fail-fast: false
@@ -85,7 +86,7 @@ jobs:
           uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
           uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
       - name: Upload coverage
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           fail_ci_if_error: true
           use_oidc: true

.pre-commit-config.yaml

@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.4.13
+    rev: v2.4.16
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.21.1
+    rev: v2.23.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.12
+    rev: v0.15.15
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
@@ -36,3 +36,8 @@ repos:
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
+
+  - repo: https://github.com/zizmorcore/zizmor-pre-commit
+    rev: v1.24.1
+    hooks:
+      - id: zizmor

pyproject.toml

@@ -60,11 +60,10 @@ doc = [
 [tool.hatch]
 envs.default.installer = "uv"
 envs.default.dependency-groups = [ "dev" ]
-envs.docs.dependency-groups = [ "doc" ]
 envs.docs.scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
-envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
-envs.hatch-test.dependency-groups = [ "dev", "test" ]
+envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+envs.docs.dependency-groups = [ "doc" ]
 envs.hatch-test.matrix = [
   # Test the lowest and highest supported Python versions with normal deps
   { deps = [ "stable" ], python = [ "3.11", "3.14" ] },
@@ -74,8 +73,9 @@ envs.hatch-test.matrix = [
 # If the matrix variable `deps` is set to "pre",
 # set the environment variable `UV_PRERELEASE` to "allow".
 envs.hatch-test.overrides.matrix.deps.env-vars = [
-  { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+  { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
 ]
+envs.hatch-test.dependency-groups = [ "dev", "test" ]
 
 [tool.ruff]
 line-length = 120
@@ -116,11 +116,11 @@ lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
 [tool.pytest]
-strict = true
-testpaths = [ "tests" ]
 addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
+strict = true
+testpaths = [ "tests" ]
 
 [tool.coverage]
 run.omit = [