diff --git a/science/py-spglib/Makefile b/science/py-spglib/Makefile
index bd88002a5b36..436d4b5d6165 100644
--- a/science/py-spglib/Makefile
+++ b/science/py-spglib/Makefile
@@ -1,38 +1,38 @@
 PORTNAME=	spglib
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.4.0
+DISTVERSION=	2.5.0
 CATEGORIES=	science python
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Library for finding and handling crystal symmetries (python binding)
 WWW=		https://spglib.readthedocs.io/en/stable/
 
 LICENSE=	BSD3CLAUSE
 
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scikit-build-core>0:devel/py-scikit-build-core@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pyproject-metadata>0:devel/py-pyproject-metadata@${PY_FLAVOR} \
 		cmake:devel/cmake-core \
 		${PYNUMPY} \
 		${PY_SETUPTOOLS}
 RUN_DEPENDS=	${PYNUMPY}
 
 USES=		python
 USE_PYTHON=	pep517 autoplist pytest # tests fail to run, see https://github.com/spglib/spglib/issues/192
 USE_GITHUB=	yes
 
 CMAKE_ARGS=	-DPython3_EXECUTABLE=${PYTHON_CMD}
 
 MAKE_ENV=	SETUPTOOLS_SCM_PRETEND_VERSION=${DISTVERSION}
 
 TEST_WRKSRC=	${WRKSRC}
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
 
 post-patch:
 	##@cd ${WRKSRC} && ${RLN} ../test .
 	#@cd ${WRKSRC} && ${CP} -r ../test .
 	# workaround for https://github.com/spglib/spglib/issues/429
 	@${REINPLACE_CMD} -i '' -e 's|^from ._version import|#&|' ${WRKSRC}/python/spglib/__init__.py
 
 .include <bsd.port.mk>
diff --git a/science/py-spglib/distinfo b/science/py-spglib/distinfo
index 9f8bce21d7f0..48711790a26d 100644
--- a/science/py-spglib/distinfo
+++ b/science/py-spglib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1712894995
-SHA256 (spglib-spglib-v2.4.0_GH0.tar.gz) = e33694b189c6864f719a59c31e2af55301a524fb68ba9fb65f08e95af471847d
-SIZE (spglib-spglib-v2.4.0_GH0.tar.gz) = 2921409
+TIMESTAMP = 1720768210
+SHA256 (spglib-spglib-v2.5.0_GH0.tar.gz) = b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914
+SIZE (spglib-spglib-v2.5.0_GH0.tar.gz) = 2926427
diff --git a/science/py-spglib/files/patch-pyproject.toml b/science/py-spglib/files/patch-pyproject.toml
new file mode 100644
index 000000000000..e4e8f702013c
--- /dev/null
+++ b/science/py-spglib/files/patch-pyproject.toml
@@ -0,0 +1,11 @@
+--- pyproject.toml.orig	2024-07-12 07:15:17 UTC
++++ pyproject.toml
+@@ -1,7 +1,7 @@
+ [build-system]
+ # Numpy build and runtime dependencies are linked to ABI compatibility
+ # A new wheel rebuild is needed when changing these
+-requires = ["scikit-build-core", "numpy~=2.0"]
++requires = ["scikit-build-core", "numpy"]
+ build-backend = "scikit_build_core.build"
+ 
+ [project]
diff --git a/science/spglib/Makefile b/science/spglib/Makefile
index f82431cf69ff..4615c4db21ff 100644
--- a/science/spglib/Makefile
+++ b/science/spglib/Makefile
@@ -1,35 +1,35 @@
 PORTNAME=	spglib
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.4.0
+DISTVERSION=	2.5.0
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	C library for finding and handling crystal symmetries
 WWW=		https://spglib.github.io/spglib/
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/COPYING
 
 USES=		cmake:testing
 USE_GITHUB=	yes
 USE_LDCONFIG=	yes
 
 TEST_DEPENDS=	googletest>0:devel/googletest
 
 CMAKE_OFF=	SPGLIB_WITH_TESTS
 CMAKE_TESTING_ON=	SPGLIB_WITH_TESTS
 
 .if !exists(/usr/include/omp.h)
 CMAKE_OFF+=	SPGLIB_USE_OMP
 .else
 FORTRAN_LDFLAGS=	-lomp # workaround for: undefined reference to `__kmpc_fork_call'
 .endif
 
 OPTIONS_DEFINE=		FORTRAN
 OPTIONS_DEFAULT=	FORTRAN
 OPTIONS_SUB=		yes
 
 FORTRAN_USES=		fortran
 FORTRAN_CMAKE_BOOL=	SPGLIB_WITH_Fortran
 
 .include <bsd.port.mk>
diff --git a/science/spglib/distinfo b/science/spglib/distinfo
index 4dc0d99ef754..07218b207bc7 100644
--- a/science/spglib/distinfo
+++ b/science/spglib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1712894917
-SHA256 (spglib-spglib-v2.4.0_GH0.tar.gz) = e33694b189c6864f719a59c31e2af55301a524fb68ba9fb65f08e95af471847d
-SIZE (spglib-spglib-v2.4.0_GH0.tar.gz) = 2921409
+TIMESTAMP = 1720768091
+SHA256 (spglib-spglib-v2.5.0_GH0.tar.gz) = b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914
+SIZE (spglib-spglib-v2.5.0_GH0.tar.gz) = 2926427
diff --git a/science/spglib/pkg-plist b/science/spglib/pkg-plist
index 4968e83ec22c..c3b5f01c8d33 100644
--- a/science/spglib/pkg-plist
+++ b/science/spglib/pkg-plist
@@ -1,19 +1,19 @@
 include/spglib.h
 %%FORTRAN%%include/spglib_f08.F90
 %%FORTRAN%%include/spglib_f08.mod
 lib/cmake/Spglib/PackageCompsHelper.cmake
 lib/cmake/Spglib/SpglibConfig.cmake
 lib/cmake/Spglib/SpglibConfigVersion.cmake
 %%FORTRAN%%lib/cmake/Spglib/SpglibTargets_fortran_shared-%%CMAKE_BUILD_TYPE%%.cmake
 %%FORTRAN%%lib/cmake/Spglib/SpglibTargets_fortran_shared.cmake
 lib/cmake/Spglib/SpglibTargets_shared-%%CMAKE_BUILD_TYPE%%.cmake
 lib/cmake/Spglib/SpglibTargets_shared.cmake
 %%FORTRAN%%lib/cmake/Spglib/try_compile.f90
 %%FORTRAN%%lib/libspglib_f08.so
 %%FORTRAN%%lib/libspglib_f08.so.2
-%%FORTRAN%%lib/libspglib_f08.so.2.4.0
+%%FORTRAN%%lib/libspglib_f08.so.2.5.0
 lib/libsymspg.so
 lib/libsymspg.so.2
-lib/libsymspg.so.2.4.0
+lib/libsymspg.so.2.5.0
 libdata/pkgconfig/spglib.pc
 %%FORTRAN%%libdata/pkgconfig/spglib_f08.pc