Fix incompatibility with scipy 1.12 (#484)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/mirrors-prettier: v3.0.3 → v4.0.0-alpha.8](pre-commit/mirrors-prettier@v3.0.3...v4.0.0-alpha.8)
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.14](astral-sh/ruff-pre-commit@v0.1.9...v0.1.14)

* Fix vstack for scipy 1.12

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Gregor Sturm <[email protected]>

.pre-commit-config.yaml

@@ -26,7 +26,7 @@ repos:
         language_version: "17.9.1"
         exclude: '^\.conda'
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.9
+    rev: v0.1.14
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixes
 
+-   Fix incompatibility with `scipy` 1.12 ([#484](https://github.com/scverse/scirpy/pull/484))
 -   Fix incompatibility with `adjustText` 1.0 ([#477](https://github.com/scverse/scirpy/pull/477))
 -   Reduce overall importtime by deferring the import of the `airr` package until it is actually used. ([#473](https://github.com/scverse/scirpy/pull/473))
 

src/scirpy/ir_dist/_clonotype_neighbors.py

@@ -228,7 +228,7 @@ def compute_distances(self) -> sp.csr_matrix:
                 tqdm_class=tqdm,
             )
 
-        dist = sp.vstack(dist_rows)
+        dist = sp.vstack(list(dist_rows))
         dist.eliminate_zeros()
         logging.hint("Done computing clonotype x clonotype distances. ", time=start)
         return dist  # type: ignore