diff --git a/science/py-phonopy/Makefile b/science/py-phonopy/Makefile
index d00bcb62bb2d..50ea96f6b5d9 100644
--- a/science/py-phonopy/Makefile
+++ b/science/py-phonopy/Makefile
@@ -1,37 +1,37 @@
 PORTNAME=	phonopy
-DISTVERSION=	4.0.0
+DISTVERSION=	4.2.0
 CATEGORIES=	science python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Package for phonon calculations at harmonic and quasi-harmonic levels
 WWW=		https://phonopy.github.io/phonopy/ \
 		https://github.com/phonopy/phonopy
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	cmake:devel/cmake-core \
 		${PYTHON_PKGNAMEPREFIX}nanobind>0:devel/py-nanobind@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numpy>=1.17:math/py-numpy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scikit-build-core>0:devel/py-scikit-build-core@${PY_FLAVOR} \
 		${PY_SETUPTOOLS} \
 		${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}h5py>=3.0:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>=2.2.2:math/py-matplotlib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numpy>=1.17:math/py-numpy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pyyaml>=5.3:devel/py-pyyaml@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}spglib>=2.5:science/py-spglib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}symfc>=1.7:science/py-symfc@${PY_FLAVOR}
 
 USES=		python
 USE_PYTHON=	pep517 autoplist pytest
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
 TEST_WRKSRC=	${WRKSRC}/test
 
 post-install:
 	@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/phonopy/_phonopy${PYTHON_TAG}.so
 
 .include <bsd.port.mk>
diff --git a/science/py-phonopy/distinfo b/science/py-phonopy/distinfo
index 3262ecd4144c..b2c7516502a4 100644
--- a/science/py-phonopy/distinfo
+++ b/science/py-phonopy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1779007076
-SHA256 (phonopy-4.0.0.tar.gz) = 650907380f4dd6c9ac6156651231c25d4d814cb4eca0bf06ec62b2263a8115a2
-SIZE (phonopy-4.0.0.tar.gz) = 5244720
+TIMESTAMP = 1780982078
+SHA256 (phonopy-4.2.0.tar.gz) = 1cebfacaf98ba584aba0be3401a50413bcc03cb44f4a9f6946a439ff6f706f15
+SIZE (phonopy-4.2.0.tar.gz) = 5262805
diff --git a/science/py-phonopy/files/patch-test_conftest.py b/science/py-phonopy/files/patch-test_conftest.py
deleted file mode 100644
index ea2d202b2f41..000000000000
--- a/science/py-phonopy/files/patch-test_conftest.py
+++ /dev/null
@@ -1,22 +0,0 @@
--- Force non-interactive matplotlib backend in tests.
--- Prevents crashes in headless FreeBSD test environments that otherwise select
--- a GUI backend.
--- Upstream: not yet submitted
-
---- test/conftest.py.orig	2022-11-09 12:37:21 UTC
-+++ test/conftest.py
-@@ -4,11 +4,14 @@
- 
- import pathlib
- from collections.abc import Callable
- 
-+import matplotlib
- import numpy as np
- import pytest
- 
- import phonopy
-+
-+matplotlib.use("Agg")
- from phonopy import Phonopy
- from phonopy.interface.phonopy_yaml import read_cell_yaml
- from phonopy.structure.atoms import PhonopyAtoms