diff --git a/math/py-pynndescent/Makefile b/math/py-pynndescent/Makefile
index 8380d43868e4..336784d4c4f9 100644
--- a/math/py-pynndescent/Makefile
+++ b/math/py-pynndescent/Makefile
@@ -1,26 +1,26 @@
 PORTNAME=	pynndescent
-DISTVERSION=	0.5.12
+DISTVERSION=	0.5.13
 CATEGORIES=	math python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Python nearest neighbor descent for approximate nearest neighbors
 WWW=		https://github.com/lmcinnes/pynndescent
 
 LICENSE=	APACHE20
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 RUN_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}joblib>0.11:devel/py-joblib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}llvmlite>=0.30:devel/py-llvmlite@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numba>=0.51.2:devel/py-numba@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.18:science/py-scikit-learn@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>=1.0:science/py-scipy@${PY_FLAVOR}
 
 USES=		python
 USE_PYTHON=	distutils autoplist pytest # 1 test fails, see https://github.com/lmcinnes/pynndescent/issues/239
 
 NO_ARCH=	yes
 
 .include <bsd.port.mk>
diff --git a/math/py-pynndescent/distinfo b/math/py-pynndescent/distinfo
index c7d1017b9ba2..109a263dc925 100644
--- a/math/py-pynndescent/distinfo
+++ b/math/py-pynndescent/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1714296173
-SHA256 (pynndescent-0.5.12.tar.gz) = 0736291fcbbedfd5e0a3a280f71a63f8eb2f8bd9670d4c0b51ac1b4d081adf70
-SIZE (pynndescent-0.5.12.tar.gz) = 2975875
+TIMESTAMP = 1724602082
+SHA256 (pynndescent-0.5.13.tar.gz) = d74254c0ee0a1eeec84597d5fe89fedcf778593eeabe32c2f97412934a9800fb
+SIZE (pynndescent-0.5.13.tar.gz) = 2975955