Update py-biothyon to 1.78. Take maintainer and completely overhaul the

port including the switch to python3-only.

ok kmos

biology/py-biopython/Makefile

@@ -1,29 +1,35 @@
-# $OpenBSD: Makefile,v 1.30 2019/07/12 20:43:44 sthen Exp $
+# $OpenBSD: Makefile,v 1.31 2020/10/25 18:12:58 martin Exp $
 
-COMMENT=		Python tools for computational molecular biology
+COMMENT =		Python tools for computational molecular biology
 
-MODPY_EGG_VERSION=	1.66
-DISTNAME=		biopython-${MODPY_EGG_VERSION}
-CATEGORIES=		biology
-REVISION=		2
+MODPY_EGG_VERSION =	1.78
+DISTNAME =		biopython-${MODPY_EGG_VERSION}
+CATEGORIES =		biology
+PKGNAME =		py-${DISTNAME}
 
-HOMEPAGE=		http://www.biopython.org/
+HOMEPAGE =		http://www.biopython.org/
 
-# BSD-like 
-PERMIT_PACKAGE=	Yes
+MAINTAINER =		Martin Reindl <martin@catai.org>
 
-MASTER_SITES=	${HOMEPAGE}DIST/
+# BSD-like
+PERMIT_PACKAGE =	Yes
 
-MODULES=	lang/python
+MODULES =	lang/python
 
-WANTLIB+=	${MODPY_WANTLIB} pthread
+MODPY_PI =              Yes
+MODPY_SETUPTOOLS =      Yes
 
-BUILD_DEPENDS=	devel/swig \
-		math/py-numpy
-RUN_DEPENDS=	math/py-numpy \
-		print/py-reportlab
+FLAVORS =		python3
+FLAVOR =		python3
 
-CFLAGS+=	-fPIC
+WANTLIB +=	pthread
+
+BUILD_DEPENDS =	devel/swig \
+		math/py-numpy${MODPY_FLAVOR}
+RUN_DEPENDS =	math/py-numpy${MODPY_FLAVOR} \
+		print/py-reportlab${MODPY_FLAVOR}
+
+CFLAGS +=	-fPIC
 
 post-install:
 	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/py-biopython/

biology/py-biopython/distinfo

@@ -1,2 +1,2 @@
-SHA256 (biopython-1.66.tar.gz) = UXjqOzQ7HYcQ85IFOGCT5Tae1lOqAg4bDEt2IqWTRsE=
-SIZE (biopython-1.66.tar.gz) = 13724754
+SHA256 (biopython-1.78.tar.gz) = HuCgtsI3ZoD+pmQtUIC6pBn9c98QSmLViouveou+RWQ=
+SIZE (biopython-1.78.tar.gz) = 16895184

biology/py-biopython/patches/patch-Tests_run_tests_py

@@ -1,13 +1,16 @@
-$OpenBSD: patch-Tests_run_tests_py,v 1.4 2015/07/18 22:24:48 jasper Exp $
---- Tests/run_tests.py.orig	Sat Dec 17 11:34:46 2005
-+++ Tests/run_tests.py	Sat Jul 18 15:18:10 2015
-@@ -196,11 +196,8 @@ def main(argv):
+$OpenBSD: patch-Tests_run_tests_py,v 1.5 2020/10/25 18:12:58 martin Exp $
+Index: Tests/run_tests.py
+--- Tests/run_tests.py.orig
++++ Tests/run_tests.py
+@@ -150,13 +150,10 @@ def main(argv):
      # A. Because Martel may not be in ../build/lib.*
      test_path = sys.path[0] or "."
      source_path = os.path.abspath("%s/.." % test_path)
 -    sys.path.insert(1, source_path)
-     build_path = os.path.abspath("%s/../build/lib.%s-%s" % (
-         test_path, distutils.util.get_platform(), sys.version[:3]))
+     build_path = os.path.abspath(
+         "%s/../build/lib.%s-%s"
+         % (test_path, distutils.util.get_platform(), sys.version[:3])
+     )
 -    if os.access(build_path, os.F_OK):
 -        sys.path.insert(1, build_path)
  

devel/quirks/Makefile

@@ -1,11 +1,11 @@
-# $OpenBSD: Makefile,v 1.1075 2020/10/23 18:22:21 jasper Exp $
+# $OpenBSD: Makefile,v 1.1076 2020/10/25 18:12:58 martin Exp $
 
 COMMENT =	exceptions to pkg_add rules
 CATEGORIES =	devel databases
 DISTFILES =
 
 # API.rev
-PKGNAME =	quirks-3.467
+PKGNAME =	quirks-3.468
 PKG_ARCH =	*
 MAINTAINER =	Marc Espie <espie@openbsd.org>
 

devel/quirks/files/Quirks.pm

@@ -1,7 +1,7 @@
 #! /usr/bin/perl
 
 # ex:ts=8 sw=4:
-# $OpenBSD: Quirks.pm,v 1.1093 2020/10/23 18:22:21 jasper Exp $
+# $OpenBSD: Quirks.pm,v 1.1094 2020/10/25 18:12:58 martin Exp $
 #
 # Copyright (c) 2009 Marc Espie <espie@openbsd.org>
 #
@@ -496,6 +496,7 @@ my $stem_extensions = {
 	'spidermonkey68' => 'spidermonkey78',
 	'py-relatorio' => 'py3-relatorio',
 	'py-croniter' => 'py3-croniter',
+	'biopython' => 'py3-biopython',
 };
 
 my $obsolete_reason = {