Index: head/biology/py-biom-format/Makefile
===================================================================
--- head/biology/py-biom-format/Makefile	(revision 549976)
+++ head/biology/py-biom-format/Makefile	(revision 549977)
@@ -1,42 +1,34 @@
 # $FreeBSD$
 
 PORTNAME=	biom-format
-PORTVERSION=	2.1.7
-PORTREVISION=	3
+PORTVERSION=	2.1.8
 CATEGORIES=	biology python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Biological Observation Matrix (BIOM) Format Project
 
 LICENSE=	BSD3CLAUSE
 
-DEPRECATED=	Uses deprecated version of python
-EXPIRATION_DATE=	2020-08-15
-
 BUILD_DEPENDS=	${PYNUMPY}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}click>0:devel/py-click@${PY_FLAVOR} \
 		${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}future>=0.16.0:devel/py-future@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}scipy>=0.13.0:science/py-scipy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>=1.3.1:science/py-scipy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pandas>=0.20.0:math/py-pandas@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}h5py>=2.2.0:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}six>=1.10.0:devel/py-six@${PY_FLAVOR}
 
-USES=		python:-3.6
-USE_PYTHON=	autoplist concurrent distutils
+USES=		python:3.6+
+USE_PYTHON=	autoplist concurrent cython distutils
 
 .include <bsd.port.pre.mk>
-
-.if ${PYTHON_REL} < 3000
-RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}pyqi>0:devel/py-pyqi@${PY_FLAVOR}
-.endif
 
 post-extract:
 	${RM} -r ${WRKSRC}/tests
 
 post-install:
 	${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/biom/*.so
 
 .include <bsd.port.post.mk>
Index: head/biology/py-biom-format/distinfo
===================================================================
--- head/biology/py-biom-format/distinfo	(revision 549976)
+++ head/biology/py-biom-format/distinfo	(revision 549977)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1538769748
-SHA256 (biom-format-2.1.7.tar.gz) = b47e54282ef13cddffdb00aea9183a87175a2372c91a915259086a3f444c42f4
-SIZE (biom-format-2.1.7.tar.gz) = 11820666
+TIMESTAMP = 1579317018
+SHA256 (biom-format-2.1.8.tar.gz) = 4d8813f84f7a79ee8c367e6ef57e154a121198b3979b81c74e6514668b756827
+SIZE (biom-format-2.1.8.tar.gz) = 12206773