- Update the included (optional) Biopython-CORBA pacakge to version 0.3.0

- If CORBA support is included, the default ORB has changed from omniORB to
  ORBit
- PORTREVISION bump

5 files changed, 210 insertions, 263 deletions

diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index 2787d9a959ea..ec84861dd108 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	biopython
 PORTVERSION=	1.00.a3
+PORTREVISION=	1
 CATEGORIES=	biology python
 MASTER_SITES=	http://www.biopython.org/Download/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -21,6 +22,7 @@ RUN_DEPENDS=	${PYTHON_SITELIBDIR}/Martel/__init__.py:${PORTSDIR}/textproc/py-mar
 		${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
 
 USE_PYTHON=	yes
+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
@@ -36,13 +38,13 @@ EXAMPLESDIR=	${PREFIX}/share/examples/${PORTNAME}
 #   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.
-# Since Fnorb is distributed under a non-free licence and ORBit support in
-# Biopython-CORBA is reputedly not yet stable, "omniorb" is the default.
-CORBA_ORB?=	omniorb
+# Note:  If unspecified, "orbit" is assumed as default.
+CORBA_ORB?=	orbit
 
-CORBA_VERSION=	0.2.1
+CORBA_VERSION=	0.3.0
 CORBA_DISTNAME=	biopython-corba-${CORBA_VERSION}
 CORBA_WRKSRC=	${WRKDIR}/${CORBA_DISTNAME}
 DISTFILES+=	${CORBA_DISTNAME}${EXTRACT_SUFX}
@@ -57,7 +59,6 @@ PLIST_FNORB=	"@comment "
 BUILD_DEPENDS+=	${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
 RUN_DEPENDS+=	${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
 CORBA_ORBNAME=	Fnorb
-EXTRA_PATCHES+=	${PATCHDIR}/extra-patch-build_helper.py
 PLIST_OMNIORB=	"@comment "
 PLIST_FNORB=	""
 .elif ${CORBA_ORB} == "orbit"
@@ -81,48 +82,47 @@ pre-fetch:
 post-configure:
 .if defined(WITH_CORBA)
 	@ ${PERL} -pi.orig -e \
-	  "/^orb_implementation/ && s/omniORB/${CORBA_ORBNAME}/" \
+	  "/^orb_implementation/ && s/ORBit/${CORBA_ORBNAME}/" \
 	  ${CORBA_WRKSRC}/BioCorba/biocorbaconfig.py
 .endif
 
 do-build:
-	@ cd ${WRKSRC} && ${PYTHON_CMD} setup.py build
+	@ cd ${WRKSRC} && ${PYTHON_SETUP} build
 .if defined(WITH_CORBA)
-	@ cd ${CORBA_WRKSRC} && ${PYTHON_CMD} setup.py build
+	@ cd ${CORBA_WRKSRC} && ${PYTHON_SETUP} build
 .endif
 
 pre-install:
 	@ ${SH} ${PKGREQ} INSTALL
 
 do-install:
-	@ cd ${WRKSRC} && ${PYTHON_CMD} setup.py install -c -O1 \
+	@ cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 \
 	  --prefix=${PREFIX}
 .if defined(WITH_CORBA)
-	@ cd ${CORBA_WRKSRC} && ${PYTHON_CMD} setup.py install -c -O1 \
+	@ cd ${CORBA_WRKSRC} && ${PYTHON_SETUP} install -c -O1 \
 	  --prefix=${PREFIX}
 .endif
 
 post-install:
 .if !defined(NOPORTDOCS)
 	@ ${MKDIR} ${DOCSDIR}
-.for docfiles in *.txt *.tex *.py
+.for docfiles in *.pdf *.py *.tex *.txt
 	@ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCSDIR}
 .endfor
 	@ ${MKDIR} ${EXAMPLESDIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.py ${EXAMPLESDIR}
-	@ cd ${WRKSRC} && find Scripts \
+	@ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/* ${EXAMPLESDIR}
+	@ cd ${WRKSRC}/Scripts && find * \
 	  | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
 .if defined(WITH_CORBA)
 	@ ${MKDIR} ${DOCSDIR}/BioCorba
-.for docfiles in *.tex *.pdf
+.for docfiles in *.html *.pdf *.tex *.txt
 	@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCSDIR}/BioCorba
 .endfor
 	@ ${MKDIR} ${EXAMPLESDIR}/BioCorba
-	@ cd ${CORBA_WRKSRC}/Doc/examples && find * \
-	  | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}/BioCorba
-	@ ${MKDIR} ${EXAMPLESDIR}/BioCorba/Scripts
+	@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/examples/* \
+	  ${EXAMPLESDIR}/BioCorba
 	@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* \
-	  ${EXAMPLESDIR}/BioCorba/Scripts
+	  ${EXAMPLESDIR}/BioCorba
 .endif	# defined(WITH_CORBA)
 .endif	# !defined(NOPORTDOCS)
 
diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
index d88599879874..25df909a4e3f 100644
--- a/biology/py-biopython/distinfo
+++ b/biology/py-biopython/distinfo
@@ -1,2 +1,2 @@
 MD5 (biopython-1.00a3.tar.gz) = be59a12eeb2c0bcdd82a73dfd7bcc615
-MD5 (biopython-corba-0.2.1.tar.gz) = 3d6d3e4570ff2996bef84e08f6fabc25
+MD5 (biopython-corba-0.3.0.tar.gz) = 4465f240d22b113314c70b1dc8ebc41c
diff --git a/biology/py-biopython/files/extra-patch-build_helper.py b/biology/py-biopython/files/extra-patch-build_helper.py
deleted file mode 100644
index a30993dc5d3b..000000000000
--- a/biology/py-biopython/files/extra-patch-build_helper.py
+++ /dev/null
@@ -1,24 +0,0 @@
-Nasty, nasty workaround for an error which I can't quite explain.  This
-happens only if Fnorb is chosen as CORBA ORB.  Since CORBA support itself
-is optional in this port, this patch is added to EXTRA_PATCHES only if
-necessary.
-
--- Johann Visagie <wjv@FreeBSD.org>
-
-
---- ../biopython-corba-0.2.1/build_helper.py.orig	Sun Apr 15 15:19:31 2001
-+++ ../biopython-corba-0.2.1/build_helper.py	Thu Jun  7 16:25:05 2001
-@@ -125,7 +125,12 @@
-     # move the new file in place of the old
-     input_handle.close()
-     output_handle.close()
--    os.rename(output_file, file)
-+    input_handle = open(output_file, 'r')
-+    output_handle = open(file, 'w')
-+    S = input_handle.read()
-+    output_handle.write(S)
-+    input_handle.close()
-+    output_handle.close()
- 
- def generate_orbit_stubs(idl_name, remove_old = 1):
-     """Move adapters to act as stubs and skeletons for ORBit.
diff --git a/biology/py-biopython/pkg-descr b/biology/py-biopython/pkg-descr
index 08627102f68a..cce6195cfe2e 100644
--- a/biology/py-biopython/pkg-descr
+++ b/biology/py-biopython/pkg-descr
@@ -9,6 +9,9 @@ applications in the Python language.
 Note that the current release is alpha quality, and not yet deemed to be
 stable.
 
+This port includes optional support for Biopython-CORBA, a CORBA interface
+built to the BioCorba standard (http://biocorba.org/).
+
 Authors: <biopython-dev@biopython.org>
 WWW:     http://biopython.org/
 
diff --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist
index 8a4749f0eb0b..8d71f3c0cb88 100644
--- a/biology/py-biopython/pkg-plist
+++ b/biology/py-biopython/pkg-plist
@@ -4,33 +4,15 @@
 %%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_EnsemblPOA.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_EnsemblPOA.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_EnsemblPOA.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_GnomePOA.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_GnomePOA.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/fnorb_GnomePOA.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/Adapters/orbit_Ensembl.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_Ensembl.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_Ensembl.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_EnsemblPOA.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_EnsemblPOA.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_EnsemblPOA.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_Gnome.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_Gnome.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_Gnome.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_GnomePOA.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_GnomePOA.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_GnomePOA.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_Seqcore.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_Seqcore.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_Seqcore.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_SeqcorePOA.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_SeqcorePOA.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters/orbit_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
@@ -52,93 +34,51 @@
 %%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/Ensembl/Exon.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Exon.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Exon.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Gene.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Gene.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Gene.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Transcript.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Transcript.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Transcript.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Translation.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Translation.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/Translation.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/VirtualContig.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/VirtualContig.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/VirtualContig.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/GnomeMemory/CorbaUnknown.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/GnomeMemory/CorbaUnknown.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/GnomeMemory/CorbaUnknown.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/GnomeMemory/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/GnomeMemory/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/GnomeMemory/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaAnonymousSeq.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaAnonymousSeq.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaAnonymousSeq.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaBioEnv.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaBioEnv.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaBioEnv.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaExceptions.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaExceptions.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaExceptions.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaPrimarySeq.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaPrimarySeq.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaPrimarySeq.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaSeq.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaSeq.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaSeq.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/CorbaUpdatableSeqDB.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaUpdatableSeqDB.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore/CorbaUpdatableSeqDB.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/GNOME/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/GNOME/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/GNOME/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/GNOME__POA/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/GNOME__POA/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/GNOME__POA/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/GnomeMemory/CorbaUnknown.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/GnomeMemory/CorbaUnknown.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/GnomeMemory/CorbaUnknown.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/GnomeMemory/__init__.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/GnomeMemory/__init__.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/GnomeMemory/__init__.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaAnonymousSeq.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaAnonymousSeq.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaAnonymousSeq.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaBioEnv.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaBioEnv.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaBioEnv.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaPrimarySeq.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaPrimarySeq.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaPrimarySeq.pyo
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaSeq.py
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaSeq.pyc
-%%PLIST_CORBA%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore/CorbaSeq.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
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-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gb_bioenv.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gbclient.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gbsrv.pl
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/genbank_db_server.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/collection_server.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/genbank_client.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/genbank_server.py
 %%PORTDOCS%%share/doc/biopython/Blast.txt
 %%PORTDOCS%%share/doc/biopython/Enzyme.txt
 %%PORTDOCS%%share/doc/biopython/Fasta.txt
@@ -241,34 +210,38 @@
 %%PORTDOCS%%share/doc/biopython/References.txt
 %%PORTDOCS%%share/doc/biopython/SCOP.txt
 %%PORTDOCS%%share/doc/biopython/SwissProt.txt
+%%PORTDOCS%%share/doc/biopython/Tutorial.pdf
 %%PORTDOCS%%share/doc/biopython/Tutorial.tex
 %%PORTDOCS%%share/doc/biopython/Tutorial.txt
 %%PORTDOCS%%share/doc/biopython/make_api_docs.py
-%%PORTDOCS%%share/examples/biopython/Scripts/SeqGui/SeqGui.py
-%%PORTDOCS%%share/examples/biopython/Scripts/query_pubmed.py
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/README
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/nextorf.py
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/test.fas
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/testrp.fas
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_blast.py
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_blastbg.py
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_io.py
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_sequence.py
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_translations.py
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_utils.py
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_widget.py
-%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbbtools.py
+%%PORTDOCS%%share/examples/biopython/SeqGui/SeqGui.py
 %%PORTDOCS%%share/examples/biopython/clustal_run.py
 %%PORTDOCS%%share/examples/biopython/fasta_consumer.py
 %%PORTDOCS%%share/examples/biopython/fasta_dictionary.py
 %%PORTDOCS%%share/examples/biopython/fasta_iterator.py
 %%PORTDOCS%%share/examples/biopython/getgene.py
 %%PORTDOCS%%share/examples/biopython/local_blast.py
+%%PORTDOCS%%share/examples/biopython/ls_orchid.fasta
+%%PORTDOCS%%share/examples/biopython/m_cold.fasta
 %%PORTDOCS%%share/examples/biopython/make_subsmat.py
+%%PORTDOCS%%share/examples/biopython/opuntia.fasta
 %%PORTDOCS%%share/examples/biopython/pubmed_search.py
 %%PORTDOCS%%share/examples/biopython/query_entrez.py
+%%PORTDOCS%%share/examples/biopython/query_pubmed.py
 %%PORTDOCS%%share/examples/biopython/swissprot.py
 %%PORTDOCS%%share/examples/biopython/www_blast.py
+%%PORTDOCS%%share/examples/biopython/xbbtools/README
+%%PORTDOCS%%share/examples/biopython/xbbtools/nextorf.py
+%%PORTDOCS%%share/examples/biopython/xbbtools/test.fas
+%%PORTDOCS%%share/examples/biopython/xbbtools/testrp.fas
+%%PORTDOCS%%share/examples/biopython/xbbtools/xbb_blast.py
+%%PORTDOCS%%share/examples/biopython/xbbtools/xbb_blastbg.py
+%%PORTDOCS%%share/examples/biopython/xbbtools/xbb_io.py
+%%PORTDOCS%%share/examples/biopython/xbbtools/xbb_sequence.py
+%%PORTDOCS%%share/examples/biopython/xbbtools/xbb_translations.py
+%%PORTDOCS%%share/examples/biopython/xbbtools/xbb_utils.py
+%%PORTDOCS%%share/examples/biopython/xbbtools/xbb_widget.py
+%%PORTDOCS%%share/examples/biopython/xbbtools/xbbtools.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.pyo
@@ -593,49 +566,44 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Align
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/Scripts
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers__POA
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient
 %%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba
 %%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/doc/biopython/BioCorba
-%%PORTDOCS%%@dirrm share/examples/biopython/Scripts/xbbtools
-%%PORTDOCS%%@dirrm share/examples/biopython/Scripts/SeqGui
-%%PORTDOCS%%@dirrm share/examples/biopython/Scripts
+%%PORTDOCS%%@dirrm share/examples/biopython/xbbtools
+%%PORTDOCS%%@dirrm share/examples/biopython/SeqGui
 %%PORTDOCS%%@dirrm share/examples/biopython
 %%PORTDOCS%%@dirrm share/doc/biopython
-%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/ensembl_skel
-%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/biocorba_skel/seqcore_skel
-%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/biocorba_skel
-%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel
-%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/GNOME_skel
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org__POA/ensembl
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org__POA/biocorba/seqcore
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org__POA/biocorba
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org__POA
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org/ensembl
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org/biocorba/seqcore
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org/biocorba
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org
+%%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/seqcore
+%%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/comparison
+%%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/collection
+%%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA
+%%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/seqcore
+%%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/comparison
+%%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/collection
+%%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane
+%%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Types__POA
+%%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Types
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane_skel/seqcore_skel
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane_skel/comparison_skel
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane_skel/collection_skel
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane_skel
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/seqcore
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/collection
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/seqcore
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/comparison
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane/collection
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Types_skel
+%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Types
+%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Share
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Seqcore
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/GnomeMemory
+%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server/Bsane
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Server
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/GNOME__POA
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/GNOME
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Seqcore
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/GnomeMemory
-%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Ensembl
+%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client/Bsane
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Client
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/GenBank
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio/Fasta
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba
-