1 files changed, 7 insertions, 102 deletions

diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index 90cb82af858c..d9666a65b962 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -6,129 +6,34 @@
 #
 
 PORTNAME=	biopython
-PORTVERSION=	1.00.a4
+PORTVERSION=	1.23
 CATEGORIES=	biology python
-MASTER_SITES=	http://www.biopython.org/Download/
+MASTER_SITES=	http://www.biopython.org/files/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
-DISTNAME=	${PORTNAME}-${PORTVERSION:S/.a/a/}
-DISTFILES=	${DISTNAME}${EXTRACT_SUFX}
 
 MAINTAINER=	wjv@FreeBSD.org
 COMMENT=	A collection of Python modules for bioinformatics
 
+CONFLICTS=	py*-martel-*
+
 BUILD_DEPENDS=	${PYDISTUTILS}
 RUN_DEPENDS=	${PYNUMERIC} \
-		${PYTHON_SITELIBDIR}/Martel/__init__.py:${PORTSDIR}/textproc/py-martel \
 		${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
 
 USE_PERL5_BUILD=yes
-USE_PYTHON=	yes
+USE_PYTHON=	2.0+
 PYTHON_SETUP=	${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py
-PLIST_SUB+=	PLIST_CORBA=${PLIST_CORBA} PLIST_OMNIORB=${PLIST_OMNIORB} \
-		PLIST_FNORB=${PLIST_FNORB}
 CPIO=		cpio --quiet -pdum -R
 EXAMPLESDIR=	${PREFIX}/share/examples/${PORTNAME}
 
-# CORBA support (a.k.a Biopython-CORBA):
-# Set WITH_CORBA to enable CORBA support for the Biopython port.
-.if defined(WITH_CORBA)
-
-# CORBA_ORB may be set from the command line to either "omniorb", "fnorb"
-# or "orbit".
-# - omniORB is a commercial quality, high speed ORB.  The installation is
-#   huge and building the C++ source is a lengthy process.  The omniORBpy
-#   Python bindings are used.
-# - Fnorb is a tiny, lightweight ORB and is excellent for testing purposes.
-#   Its licence is non-free.
-# - ORBit is a very popular and elegant ORB.  The ORBit-Python bindings are
-#   used.
-# Note:  If unspecified, "orbit" is assumed as default.
-CORBA_ORB?=	orbit
-
-CORBA_VERSION=	0.3.0
-CORBA_DISTNAME=	biopython-corba-${CORBA_VERSION}
-CORBA_WRKSRC=	${WRKDIR}/${CORBA_DISTNAME}
-DISTFILES+=	${CORBA_DISTNAME}${EXTRACT_SUFX}
-PLIST_CORBA=	""
-
-.if ${CORBA_ORB} == "omniorb"
-RUN_DEPENDS+=	${PYTHON_SITELIBDIR}/omniORB/__init__.py:${PORTSDIR}/devel/py-omniorb
-CORBA_ORBNAME=	omniORB
-PLIST_OMNIORB=	""
-PLIST_FNORB=	"@comment "
-.elif ${CORBA_ORB} == "fnorb"
-BUILD_DEPENDS+=	${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
-RUN_DEPENDS+=	${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
-CORBA_ORBNAME=	Fnorb
-PLIST_OMNIORB=	"@comment "
-PLIST_FNORB=	""
-.elif ${CORBA_ORB} == "orbit"
-RUN_DEPENDS+=	${LOCALBASE}/include/orbit-python/orbit-python.h:${PORTSDIR}/devel/py-orbit
-CORBA_ORBNAME=	ORBit
-PLIST_OMNIORB=	"@comment "
-PLIST_FNORB=	"@comment "
-.endif
-
-.else
-PLIST_CORBA=	"@comment "
-PLIST_OMNIORB=	"@comment "
-PLIST_FNORB=	"@comment "
-.endif	# defined(WITH_CORBA)
-
 .if !defined(WITHOUT_REPORTLAB)
 RUN_DEPENDS+=	${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab
 .endif
 
-pre-fetch:
-.if !defined(BATCH) && !defined(WITH_CORBA)
-	@ ${CAT} ${FILESDIR}/corba.msg
-.endif
-
-post-configure:
-.if defined(WITH_CORBA)
-	@ ${PERL} -pi.orig -e \
-	  "/^orb_implementation/ && s/ORBit/${CORBA_ORBNAME}/" \
-	  ${CORBA_WRKSRC}/BioCorba/biocorbaconfig.py
-.endif
-
 do-build:
-	@ cd ${WRKSRC} && ${PYTHON_SETUP} build
-.if defined(WITH_CORBA)
-	@ cd ${CORBA_WRKSRC} && ${PYTHON_SETUP} build
-.endif
-
-pre-install:
-	@ ${SH} ${PKGREQ} INSTALL
+	(cd ${WRKSRC} && ${PYTHON_SETUP} build)
 
 do-install:
-	@ cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 \
-	  --prefix=${PREFIX}
-.if defined(WITH_CORBA)
-	@ cd ${CORBA_WRKSRC} && ${PYTHON_SETUP} install -c -O1 \
-	  --prefix=${PREFIX}
-.endif
-
-post-install:
-.if !defined(NOPORTDOCS)
-	@ ${MKDIR} ${DOCSDIR}
-.for docfiles in *.pdf *.py *.tex *.txt
-	@ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCSDIR}
-.endfor
-	@ ${MKDIR} ${EXAMPLESDIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/* ${EXAMPLESDIR}
-	@ cd ${WRKSRC}/Scripts && ${FIND} * \
-	  | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
-.if defined(WITH_CORBA)
-	@ ${MKDIR} ${DOCSDIR}/BioCorba
-.for docfiles in *.html *.pdf *.tex *.txt
-	@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCSDIR}/BioCorba
-.endfor
-	@ ${MKDIR} ${EXAMPLESDIR}/BioCorba
-	@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/examples/* \
-	  ${EXAMPLESDIR}/BioCorba
-	@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* \
-	  ${EXAMPLESDIR}/BioCorba
-.endif	# defined(WITH_CORBA)
-.endif	# !defined(NOPORTDOCS)
+	(cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 --prefix=${PREFIX})
 
 .include <bsd.port.mk>