Upgrade to 1.23.

Approved by:	maintainer timeout

6 files changed, 1125 insertions, 1001 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>
diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
index 3704fe20f076..4279fd3841e3 100644
--- a/biology/py-biopython/distinfo
+++ b/biology/py-biopython/distinfo
@@ -1,2 +1 @@
-MD5 (biopython-1.00a4.tar.gz) = bca77b4242c9a8495f60c7475b884c5d
-MD5 (biopython-corba-0.3.0.tar.gz) = 4465f240d22b113314c70b1dc8ebc41c
+MD5 (biopython-1.23.tar.gz) = 45ea628621c6b04d471f029ef5873aaf
diff --git a/biology/py-biopython/files/corba.msg b/biology/py-biopython/files/corba.msg
deleted file mode 100644
index df7961e5b5a4..000000000000
--- a/biology/py-biopython/files/corba.msg
+++ /dev/null
@@ -1,12 +0,0 @@
----------------------------------------------------------------------------
-Biopython is currently being built without CORBA support.  If you wish to
-enable the optional CORBA support, set the WITH_CORBA variable, e.g.:
-
-  make WITH_CORBA=yes install
-
-If you set WITH_CORBA, you may optionally also set the CORBA_ORB variable
-to "omniorb", "fnorb" or "orbit".  If you do not, "omniorb" is assumed as
-default.
-
-Further details are provided in the comments in this port's Makefile.
----------------------------------------------------------------------------
diff --git a/biology/py-biopython/files/patch-setup.py b/biology/py-biopython/files/patch-setup.py
deleted file mode 100644
index 919aef5bfea3..000000000000
--- a/biology/py-biopython/files/patch-setup.py
+++ /dev/null
@@ -1,11 +0,0 @@
---- setup.py.orig	Fri Jul  6 01:55:51 2001
-+++ setup.py	Fri Jul  6 18:13:35 2001
-@@ -188,7 +188,7 @@
- # Martel -- for building parsers
- martel_packages = ['Martel']
- # a flag to determine if we should install Martel
--INSTALL_MARTEL = 1
-+INSTALL_MARTEL = 0
- 
- # -- setup the packages list
- all_packages = biopython_packages
diff --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist
index 71f0e6762633..f3348733d001 100644
--- a/biology/py-biopython/pkg-plist
+++ b/biology/py-biopython/pkg-plist
@@ -1,857 +1,1117 @@
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/Generic.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/Generic.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/Generic.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_BsanePOA.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_BsanePOA.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_BsanePOA.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_CollectionPOA.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_CollectionPOA.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_CollectionPOA.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_SeqcorePOA.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_SeqcorePOA.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_SeqcorePOA.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/Fasta/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/Fasta/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/Fasta/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/GenBank/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/GenBank/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/GenBank/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/Seq.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/Seq.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/Seq.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/SeqFeature.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/SeqFeature.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/SeqFeature.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/SeqRecord.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/SeqRecord.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/SeqRecord.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/BiocorbaConnect.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/BiocorbaConnect.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/BiocorbaConnect.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/Annotation.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/Annotation.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/Annotation.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/Base.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/Base.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/Base.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/CorbaExceptions.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/CorbaExceptions.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/CorbaExceptions.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaCollection.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaCollection.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaCollection.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaSeqFeature.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaSeqFeature.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaSeqFeature.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaSequence.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaSequence.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaSequence.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Bsane/Annotation.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Bsane/Annotation.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Bsane/Annotation.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Bsane/Base.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Bsane/Base.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Bsane/Base.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Bsane/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Bsane/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Bsane/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaCollection.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaCollection.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaCollection.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaSeqFeature.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaSeqFeature.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaSeqFeature.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaSequence.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaSequence.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaSequence.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/ServerFactory.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/ServerFactory.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/ServerFactory.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Share/SeqFeature.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Share/SeqFeature.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Share/SeqFeature.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Share/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Share/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Share/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/biocorbaconfig.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/biocorbaconfig.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/biocorbaconfig.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane.idl
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/collection.idl
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/seqcore.idl
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/types.idl
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Types/__init__.py
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Types/__init__.pyc
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Types/__init__.pyo
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Types_skel/__init__.py
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Types_skel/__init__.pyc
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Types_skel/__init__.pyo
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/__init__.py
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/__init__.pyc
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/__init__.pyo
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/collection/__init__.py
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/collection/__init__.pyc
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/collection/__init__.pyo
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/comparison/__init__.py
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/comparison/__init__.pyc
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/comparison/__init__.pyo
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/seqcore/__init__.py
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/seqcore/__init__.pyc
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/seqcore/__init__.pyo
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/__init__.py
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/__init__.pyc
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/__init__.pyo
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/collection/__init__.py
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/collection/__init__.pyc
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/collection/__init__.pyo
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/seqcore/__init__.py
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/seqcore/__init__.pyc
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/seqcore/__init__.pyo
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane_skel/__init__.py
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane_skel/__init__.pyc
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane_skel/__init__.pyo
-%%PLIST_FNORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane_skel/collection_skel/__init__.py
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+%%PYTHON_SITELIBDIR%%/Bio/expressions/embl/embl65.py
+%%PYTHON_SITELIBDIR%%/Bio/expressions/embl/embl65.pyc
+%%PYTHON_SITELIBDIR%%/Bio/expressions/embl/embl65.pyo
+%%PYTHON_SITELIBDIR%%/Bio/expressions/fasta.py
+%%PYTHON_SITELIBDIR%%/Bio/expressions/fasta.pyc
+%%PYTHON_SITELIBDIR%%/Bio/expressions/fasta.pyo
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+%%PYTHON_SITELIBDIR%%/Bio/expressions/genbank.pyo
+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/speclist.py
+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/speclist.pyc
+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/speclist.pyo
+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot38.py
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+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot40.py
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+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot40.pyo
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/__init__.pyo
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+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/embl.pyc
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/embl.pyo
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/genbank.py
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/genbank.pyc
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/genbank.pyo
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/search.py
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/search.pyc
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/search.pyo
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/sequence.py
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/sequence.pyc
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/sequence.pyo
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.py
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.pyc
+%%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.pyo
+%%PYTHON_SITELIBDIR%%/Bio/kMeans.py
+%%PYTHON_SITELIBDIR%%/Bio/kMeans.pyc
+%%PYTHON_SITELIBDIR%%/Bio/kMeans.pyo
+%%PYTHON_SITELIBDIR%%/Bio/kNN.py
+%%PYTHON_SITELIBDIR%%/Bio/kNN.pyc
+%%PYTHON_SITELIBDIR%%/Bio/kNN.pyo
+%%PYTHON_SITELIBDIR%%/Bio/lcc.py
+%%PYTHON_SITELIBDIR%%/Bio/lcc.pyc
+%%PYTHON_SITELIBDIR%%/Bio/lcc.pyo
+%%PYTHON_SITELIBDIR%%/Bio/listfns.py
+%%PYTHON_SITELIBDIR%%/Bio/listfns.pyc
+%%PYTHON_SITELIBDIR%%/Bio/listfns.pyo
+%%PYTHON_SITELIBDIR%%/Bio/mathfns.py
+%%PYTHON_SITELIBDIR%%/Bio/mathfns.pyc
+%%PYTHON_SITELIBDIR%%/Bio/mathfns.pyo
+%%PYTHON_SITELIBDIR%%/Bio/pairwise2.py
+%%PYTHON_SITELIBDIR%%/Bio/pairwise2.pyc
+%%PYTHON_SITELIBDIR%%/Bio/pairwise2.pyo
+%%PYTHON_SITELIBDIR%%/Bio/sequtils.py
+%%PYTHON_SITELIBDIR%%/Bio/sequtils.pyc
+%%PYTHON_SITELIBDIR%%/Bio/sequtils.pyo
+%%PYTHON_SITELIBDIR%%/Bio/stringfns.py
+%%PYTHON_SITELIBDIR%%/Bio/stringfns.pyc
+%%PYTHON_SITELIBDIR%%/Bio/stringfns.pyo
+%%PYTHON_SITELIBDIR%%/Bio/trie.so
+%%PYTHON_SITELIBDIR%%/Bio/triefind.py
+%%PYTHON_SITELIBDIR%%/Bio/triefind.pyc
+%%PYTHON_SITELIBDIR%%/Bio/triefind.pyo
+%%PYTHON_SITELIBDIR%%/Bio/utils.py
+%%PYTHON_SITELIBDIR%%/Bio/utils.pyc
+%%PYTHON_SITELIBDIR%%/Bio/utils.pyo
+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/empty.py
+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/empty.pyc
+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/empty.pyo
+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/fasta.py
+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/fasta.pyc
+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/fasta.pyo
+%%PYTHON_SITELIBDIR%%/Bio/writers/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/writers/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/writers/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/xkMeans.py
+%%PYTHON_SITELIBDIR%%/Bio/xkMeans.pyc
+%%PYTHON_SITELIBDIR%%/Bio/xkMeans.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.py
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.py
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.py
+%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/Loader.py
+%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/__init__.py
+%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Martel/Dispatch.py
+%%PYTHON_SITELIBDIR%%/Martel/Dispatch.pyc
+%%PYTHON_SITELIBDIR%%/Martel/Dispatch.pyo
+%%PYTHON_SITELIBDIR%%/Martel/Expression.py
+%%PYTHON_SITELIBDIR%%/Martel/Expression.pyc
+%%PYTHON_SITELIBDIR%%/Martel/Expression.pyo
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+%%PYTHON_SITELIBDIR%%/Martel/Generate.pyc
+%%PYTHON_SITELIBDIR%%/Martel/Generate.pyo
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+%%PYTHON_SITELIBDIR%%/Martel/IterParser.pyc
+%%PYTHON_SITELIBDIR%%/Martel/IterParser.pyo
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+%%PYTHON_SITELIBDIR%%/Martel/Iterator.pyc
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+%%PYTHON_SITELIBDIR%%/Martel/msre_constants.py
+%%PYTHON_SITELIBDIR%%/Martel/msre_constants.pyc
+%%PYTHON_SITELIBDIR%%/Martel/msre_constants.pyo
+%%PYTHON_SITELIBDIR%%/Martel/msre_parse.py
+%%PYTHON_SITELIBDIR%%/Martel/msre_parse.pyc
+%%PYTHON_SITELIBDIR%%/Martel/msre_parse.pyo
+%%PYTHON_SITELIBDIR%%/Martel/optimize.py
+%%PYTHON_SITELIBDIR%%/Martel/optimize.pyc
+%%PYTHON_SITELIBDIR%%/Martel/optimize.pyo
+%%PYTHON_SITELIBDIR%%/Martel/setup.py
+%%PYTHON_SITELIBDIR%%/Martel/setup.pyc
+%%PYTHON_SITELIBDIR%%/Martel/setup.pyo
+@dirrm %%PYTHON_SITELIBDIR%%/Martel
+@dirrm %%PYTHON_SITELIBDIR%%/BioSQL
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/formatdefs
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/embl
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/blast
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/dbdefs
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/config
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/Search
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/WWW
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/UniGene
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SwissProt
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SubsMat
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqUtils
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqIO
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Saf
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SCOP/tests
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SCOP
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Rebase
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Prosite
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/Gene
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Ndb
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/NBRF
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/MultiProc
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Mindy
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/MetaTool
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Medline
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/LocusLink
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Kabat
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/KDTree
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/InterPro
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/HMM
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Graphics
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Gobase
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Geo
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GenBank
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GFF
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Selection
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Repair
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Mutation
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Encodings
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Emboss
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/ECell
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Data
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Crystal
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Cluster
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Clustalw
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/CDD
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Blast
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Application
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Alphabet
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Align
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Ais
+@dirrm %%PYTHON_SITELIBDIR%%/Bio
diff --git a/biology/py-biopython/pkg-req b/biology/py-biopython/pkg-req
deleted file mode 100644
index 1a2bc48824e3..000000000000
--- a/biology/py-biopython/pkg-req
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/sh
-
-PATH=$PATH:/usr/local/bin
-
-if [ "x$1" = "xINSTALL" -o "x$2" = "xINSTALL" ]; then
-  PYTHON_GT=`python -c 'import string, sys; \
-                        print string.split(sys.version)[0] >= "2.0" and 1'`
-  if [ "x${PYTHON_GT}" = "x1" ]; then
-    exit 0
-  else
-    echo "-----------------------------------------------------------"
-    echo "Biopython requires Python version 2.0 or greater -         "
-    echo "  please update your Python installation before proceeding."
-    echo "-----------------------------------------------------------"
-    exit 1
-  fi
-fi