Index: head/science/py-phonopy/Makefile
===================================================================
--- head/science/py-phonopy/Makefile	(revision 500997)
+++ head/science/py-phonopy/Makefile	(revision 500998)
@@ -1,32 +1,32 @@
 # $FreeBSD$
 
 PORTNAME=	phonopy
-DISTVERSION=	2.0.0
+DISTVERSION=	2.1.3
 CATEGORIES=	science python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Package for phonon calculations at harmonic and quasi-harmonic levels
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR}
 RUN_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR}
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}nose>=0:devel/py-nose@${PY_FLAVOR}
 
 USES=		python
 USE_PYTHON=	distutils cython autoplist
 
-do-test: # One test fails: https://github.com/atztogo/phonopy/issues/79
+do-test:
 	@cd ${WRKSRC} && \
 		${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} test
 
 .include <bsd.port.mk>
Index: head/science/py-phonopy/distinfo
===================================================================
--- head/science/py-phonopy/distinfo	(revision 500997)
+++ head/science/py-phonopy/distinfo	(revision 500998)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1557294961
-SHA256 (phonopy-2.0.0.tar.gz) = 46baf7c4571fe75374071674727c2beb0388cf57073e0623d8457f04b1c54495
-SIZE (phonopy-2.0.0.tar.gz) = 6653497
+TIMESTAMP = 1557297164
+SHA256 (phonopy-2.1.3.tar.gz) = 92fd6ae20af4742745a45274e48ae4ba1eafd6f3fe562ca97267471349a530ac
+SIZE (phonopy-2.1.3.tar.gz) = 6737218