diff --git a/biology/py-scikit-bio/Makefile b/biology/py-scikit-bio/Makefile
index 03efdcfe9af3..4297e08f2c1c 100644
--- a/biology/py-scikit-bio/Makefile
+++ b/biology/py-scikit-bio/Makefile
@@ -1,56 +1,61 @@
 PORTNAME=	scikit-bio
-DISTVERSION=	0.6.2
+DISTVERSION=	0.6.3
 CATEGORIES=	biology education python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Data structures, algorithms, educational resources for bioinformatics
 WWW=		http://scikit-bio.org/
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 BROKEN_aarch64=	fails to build: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size, see https://github.com/biocore/scikit-bio/issues/1816
 .if !exists(/usr/include/omp.h)
 BROKEN=		requires OpenMP support that is missing on this architecture
 .endif
 
 BUILD_DEPENDS=	${PYNUMPY} \
 		${PY_SETUPTOOLS} \
 		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}biom-format>0:biology/py-biom-format@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}decorator>=3.4.2:devel/py-decorator@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}h5py>=3.6.0:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}hdmedians>=0.14.1:math/py-hdmedians@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}ipython>=3.2.0:devel/ipython@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>=1.4.3:math/py-matplotlib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}natsort>=4.0.3:devel/py-natsort@${PY_FLAVOR} \
 		${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}pandas>=1.5.0:math/py-pandas@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}requests>=2.20.0:www/py-requests@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.19.1:science/py-scikit-learn@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>=1.9.0:science/py-scipy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}statsmodels>=0.14.0:math/py-statsmodels@${PY_FLAVOR}
 
 USES=		python
-USE_PYTHON=	pep517 cython autoplist pytest # tests fail to run, see https://github.com/biocore/scikit-bio/issues/1846
+USE_PYTHON=	pep517 cython autoplist pytest
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
-TEST_WRKSRC=	${WRKSRC}/skbio/tests
 
 CONFLICTS_INSTALL=	${PYTHON_PKGNAMEPREFIX}ddtrace # lib/python3.8/site-packages/benchmarks/__init__.py
 
 .include <bsd.port.options.mk>
 
 .if ${ARCH} == i386
 CFLAGS+=	-msse2 # workaround for https://github.com/biocore/scikit-bio/issues/1727
 CXXFLAGS+=	-msse2
 .endif
 
 post-install:
 	@${STRIP_CMD} \
 		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*${PYTHON_EXT_SUFFIX}.so \
 		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*/*${PYTHON_EXT_SUFFIX}.so
 
+do-test: # tests fail to run in a regular way, see https://github.com/biocore/scikit-bio/issues/1846
+	@cd ${STAGEDIR}${PYTHON_SITELIBDIR} && \
+		${SETENV} ${TEST_ENV} pytest .
+
+# tests as of 0.6.3: 2792 passed, 30 skipped, 56 warnings in 250.28s (0:04:10)
+
 .include <bsd.port.mk>
diff --git a/biology/py-scikit-bio/distinfo b/biology/py-scikit-bio/distinfo
index fa11401cb467..370eba0445bd 100644
--- a/biology/py-scikit-bio/distinfo
+++ b/biology/py-scikit-bio/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1720838021
-SHA256 (scikit-bio-0.6.2.tar.gz) = af217ad12243cdaeef74a8f3bebe0d04aefda2a22d963d634201a36318b1a404
-SIZE (scikit-bio-0.6.2.tar.gz) = 2699488
+TIMESTAMP = 1736808587
+SHA256 (scikit-bio-0.6.3.tar.gz) = f06cc87a1823902906821819e66f7cd704563a9f8cdf6720296a42dcbc2fe1c2
+SIZE (scikit-bio-0.6.3.tar.gz) = 5356619