From 6b18fdede56ec2b50edb970098f1115ee5fdca1c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 24 Jan 2024 13:12:53 +0100 Subject: [PATCH] Fix incompatibility with scipy 1.12 (#484) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/mirrors-prettier: v3.0.3 → v4.0.0-alpha.8](https://github.com/pre-commit/mirrors-prettier/compare/v3.0.3...v4.0.0-alpha.8) - [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/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 --- .pre-commit-config.yaml | 2 +- CHANGELOG.md | 1 + src/scirpy/ir_dist/_clonotype_neighbors.py | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 28566a5d2..7dc3910e3 100644 --- a/.pre-commit-config.yaml +++ b/.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] diff --git a/CHANGELOG.md b/CHANGELOG.md index 63893f31a..f6b9953b9 100644 --- a/CHANGELOG.md +++ b/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)) diff --git a/src/scirpy/ir_dist/_clonotype_neighbors.py b/src/scirpy/ir_dist/_clonotype_neighbors.py index 5176e35ff..7c4484249 100644 --- a/src/scirpy/ir_dist/_clonotype_neighbors.py +++ b/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