diff --git a/science/py-pymatgen/Makefile b/science/py-pymatgen/Makefile
index 33b459c57ce1..65015aab2e14 100644
--- a/science/py-pymatgen/Makefile
+++ b/science/py-pymatgen/Makefile
@@ -1,64 +1,66 @@
 PORTNAME=	pymatgen
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2025.3.10
+DISTVERSION=	2025.5.28
 CATEGORIES=	science python
 #MASTER_SITES=	PYPI # no tests
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Python Materials Genomics is a robust materials analysis code
 WWW=		https://pymatgen.org/ \
 		https://github.com/materialsproject/pymatgen
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${PY_SETUPTOOLS} \
 		${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}beautifulsoup>0:www/py-beautifulsoup@${PY_FLAVOR} \
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}bibtexparser>=1.4.0:textproc/py-bibtexparser@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}joblib>=1:devel/py-joblib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>=3.8:math/py-matplotlib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}monty>=2025.1.9:devel/py-monty@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}networkx>=2.7:math/py-networkx@${PY_FLAVOR} \
 		${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}orjson>=3.10:devel/py-orjson@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}palettable>=3.3.3:misc/py-palettable@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pandas>=2:math/py-pandas@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}plotly>=4.5.0:graphics/py-plotly@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}plotly>=5.0.0:graphics/py-plotly@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pybtex>=0.24.0:textproc/py-pybtex@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}requests>=2.32:www/py-requests@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}ruamel.yaml>=0.17.0:devel/py-ruamel.yaml@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>=1.13.0:science/py-scipy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}spglib>=2.5.0:science/py-spglib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}spglib>=2.5:science/py-spglib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}sympy>=1.3:math/py-sympy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}tabulate>=0.9:devel/py-tabulate@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}tqdm>=4.60:misc/py-tqdm@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}uncertainties>=3.1.4:math/py-uncertainties@${PY_FLAVOR}
-RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}icet>0:science/py-icet@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}openbabel>0:science/py-openbabel@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}phonopy>0:science/py-phonopy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}seekpath>0:science/py-seekpath@${PY_FLAVOR} # optional dependencies
+RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}ase>=3.23.0:science/py-ase@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}beautifulsoup>0:www/py-beautifulsoup@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}h5py>=3.11.0:science/py-h5py@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}phonopy>=2.33.3:science/py-phonopy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}seekpath>=2.0.1:science/py-seekpath@${PY_FLAVOR} # optional dependencies
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pybtex>0:textproc/py-pybtex@${PY_FLAVOR}
 
 USES=		compiler:c++11-lang python
 USE_PYTHON=	pep517 cython concurrent autoplist pytest
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	materialsproject
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} \
 		PMG_TEST_FILES_DIR=${WRKSRC}/tests/files \
 		DISPLAY=${DISPLAY} \
 		XAUTHORITY=${XAUTHORITY}
 TEST_WRKSRC=	${WRKSRC}/tests
 
 post-install: # strip binaries
 	@cd ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/${PORTNAME} && ${STRIP_CMD} \
 		optimization/linear_assignment*.so \
 		optimization/neighbors*.so \
 		util/coord_cython*.so
 
 # tests as of 2025.2.18: 56 failed, 2912 passed, 149 skipped, 1980 warnings in 11080.55s (3:04:40), see https://github.com/materialsproject/pymatgen/issues/4264
+# tests as of 2025.5.28: 56 failed, 3015 passed, 161 skipped, 131 warnings, 7 errors in 5700.13s (1:35:00)
 
 .include <bsd.port.mk>
diff --git a/science/py-pymatgen/distinfo b/science/py-pymatgen/distinfo
index b86f67b1dd9f..0d9b3bdd4daa 100644
--- a/science/py-pymatgen/distinfo
+++ b/science/py-pymatgen/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1741670459
-SHA256 (materialsproject-pymatgen-v2025.3.10_GH0.tar.gz) = e04c32df88d92c46a07bf23205cd36f33e1c8b760ccf7d6c975abc2b2f1db238
-SIZE (materialsproject-pymatgen-v2025.3.10_GH0.tar.gz) = 271898854
+TIMESTAMP = 1748630766
+SHA256 (materialsproject-pymatgen-v2025.5.28_GH0.tar.gz) = 4e5c6d9a679b96b160e146b1ebcb3014201dfc668d0981d58e494961b9a5cceb
+SIZE (materialsproject-pymatgen-v2025.5.28_GH0.tar.gz) = 272197685