diff --git a/science/py-mdp/Makefile b/science/py-mdp/Makefile
index e047cd0fa30e..e9c465e1257b 100644
--- a/science/py-mdp/Makefile
+++ b/science/py-mdp/Makefile
@@ -1,29 +1,31 @@
 PORTNAME=	mdp
-PORTVERSION=	3.5
-PORTREVISION=	7
+DISTVERSION=	3.6
 CATEGORIES=	science python
-MASTER_SITES=	SF/${PORTNAME}-toolkit/${PORTNAME}-toolkit/${PORTVERSION}
+MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
-DISTNAME=	${PORTNAME:tu}-${PORTVERSION}
+DISTNAME=	${PORTNAME:tu}-${DISTVERSION}
 
 MAINTAINER=	bofh@FreeBSD.org
 COMMENT=	Modular toolkit for Data Processing
 WWW=		https://mdp-toolkit.sourceforge.net/
 
 LICENSE=	BSD3CLAUSE
 
+DEPRECATED=	No upstream activity since 2020
+EXPIRATION_DATE=	2026-08-31
+
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR}
 
 USES=		python
-USE_PYTHON=	distutils autoplist
+USE_PYTHON=	autoplist distutils
 
 OPTIONS_DEFINE=	LIBSVM SCIPY
 
 LIBSVM_DESC=	Provide the LibSVMClassifier node
 SCIPY_DESC=	Instal SciPy versions of eigensolver, FFT and convolution
 
 LIBSVM_RUN_DEPENDS=	libsvm>2.91:science/libsvm \
 			libsvm-python>2.91:science/libsvm-python
 SCIPY_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}scipy>=0.5.2:science/py-scipy@${PY_FLAVOR}
 
 .include <bsd.port.mk>
diff --git a/science/py-mdp/distinfo b/science/py-mdp/distinfo
index 98248ae01f50..00dbe9e803d3 100644
--- a/science/py-mdp/distinfo
+++ b/science/py-mdp/distinfo
@@ -1,2 +1,3 @@
-SHA256 (MDP-3.5.tar.gz) = 33f13804d32a2430caeef04f5cf3a11209a854ab78f5686b75cff4ed6bff812b
-SIZE (MDP-3.5.tar.gz) = 335420
+TIMESTAMP = 1783275387
+SHA256 (MDP-3.6.tar.gz) = ac52a652ccbaed1857ff1209862f03bf9b06d093b12606fb410787da3aa65a0e
+SIZE (MDP-3.6.tar.gz) = 411998
diff --git a/science/py-mdp/files/patch-mdp__configuration.py b/science/py-mdp/files/patch-mdp__configuration.py
deleted file mode 100644
index 3a15968aa3b3..000000000000
--- a/science/py-mdp/files/patch-mdp__configuration.py
+++ /dev/null
@@ -1,11 +0,0 @@
---- mdp/configuration.py.orig	2016-03-04 08:39:38 UTC
-+++ mdp/configuration.py
-@@ -388,7 +388,7 @@ def set_configuration():
-     try:
-         import svm as libsvm
-         libsvm.libsvm
--    except ImportError as exc:
-+    except (ImportError, OSError) as exc:
-         config.ExternalDepFailed('libsvm', exc)
-     except AttributeError as exc:
-         config.ExternalDepFailed('libsvm', 'libsvm version >= 2.91 required')