Merge branch 'main' into feature/concat_hdf5_virtual_datasets

Author: selmanozleyen

.github/workflows/test-gpu.yml

@@ -32,7 +32,7 @@ jobs:
   # If neither is set, this job fails, `test` is skipped, and the whole workflow fails.
   check:
     name: "Triage: Check if GPU tests are allowed to run"
-    if: (!contains(github.event.pull_request.labels.*.name, 'skip-gpu-ci'))
+    if: ${{ !(github.event.pull_request.user.login == 'pre-commit-ci[bot]' || contains(github.event.pull_request.labels.*.name, 'skip-gpu-ci')) }}
     runs-on: ubuntu-latest
     steps:
       - uses: flying-sheep/check@v1

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.7
+    rev: v0.12.9
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -10,15 +10,15 @@ repos:
         id: ruff
         args: ["--preview", "--select=PLR0917"]
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.1.3
+    rev: v2.2.0
     hooks:
       - id: biome-format
   - repo: https://github.com/ComPWA/taplo-pre-commit
     rev: v0.9.3
     hooks:
       - id: taplo-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer

docs/release-notes/0.12.2.md

@@ -0,0 +1,6 @@
+(v0.12.2)=
+### 0.12.2 {small}`2025-08-11`
+
+### Bug fixes
+
+- Revert accidental change where {attr}`~anndata.AnnData.X` got written to disk when it was `None` {user}`flying-sheep` ({pr}`2054`)