6 files changed, 46 insertions, 8 deletions

diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index 2d398e090842..e59a64a4cae6 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	biopython
-PORTVERSION=	1.00.a1
+PORTVERSION=	1.00.a2
 CATEGORIES=	biology python
 MASTER_SITES=	http://www.biopython.org/Download/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -62,7 +62,7 @@ EXTRA_PATCHES+=	${PATCHDIR}/extra-patch-build_helper.py
 PLIST_OMNIORB=	"@comment "
 PLIST_FNORB=	""
 .elif ${CORBA_ORB} == "orbit"
-RUN_DEPENDS+=	${PREFIX}/include/orbit-python/orbit-python.h:${PORTSDIR}/devel/py-orbit
+RUN_DEPENDS+=	${LOCALBASE}/include/orbit-python/orbit-python.h:${PORTSDIR}/devel/py-orbit
 CORBA_ORBNAME=	ORBit
 PLIST_OMNIORB=	"@comment "
 PLIST_FNORB=	"@comment "
diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
index a0b94229746a..5627a525c266 100644
--- a/biology/py-biopython/distinfo
+++ b/biology/py-biopython/distinfo
@@ -1,2 +1,2 @@
-MD5 (biopython-1.00a1.tar.gz) = 054baa272e2885e17512964215817119
+MD5 (biopython-1.00a2.tar.gz) = 416fb1ab08dfdd7f3d4d75bc0043ace8
 MD5 (biopython-corba-0.2.1.tar.gz) = 3d6d3e4570ff2996bef84e08f6fabc25
diff --git a/biology/py-biopython/files/extra-patch-build_helper.py b/biology/py-biopython/files/extra-patch-build_helper.py
index 777e20947f5d..a30993dc5d3b 100644
--- a/biology/py-biopython/files/extra-patch-build_helper.py
+++ b/biology/py-biopython/files/extra-patch-build_helper.py
@@ -3,7 +3,7 @@ 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 <johann@egenetics.com>
+-- Johann Visagie <wjv@FreeBSD.org>
 
 
 --- ../biopython-corba-0.2.1/build_helper.py.orig	Sun Apr 15 15:19:31 2001
diff --git a/biology/py-biopython/files/patch-setup.py b/biology/py-biopython/files/patch-setup.py
new file mode 100644
index 000000000000..919aef5bfea3
--- /dev/null
+++ b/biology/py-biopython/files/patch-setup.py
@@ -0,0 +1,11 @@
+--- 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-descr b/biology/py-biopython/pkg-descr
index c122f25cc2d3..08627102f68a 100644
--- a/biology/py-biopython/pkg-descr
+++ b/biology/py-biopython/pkg-descr
@@ -12,4 +12,4 @@ stable.
 Authors: <biopython-dev@biopython.org>
 WWW:     http://biopython.org/
 
--- Johann Visagie <johann@egenetics.com>
+-- Johann Visagie <wjv@FreeBSD.org>
diff --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist
index 0682a5f9fa13..a7b709a312f1 100644
--- a/biology/py-biopython/pkg-plist
+++ b/biology/py-biopython/pkg-plist
@@ -322,6 +322,15 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Encodings/__init__.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Enzyme/__init__.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Enzyme/__init__.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Enzyme/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP/FSSPTools.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP/FSSPTools.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP/FSSPTools.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP/fssp_rec.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP/fssp_rec.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP/fssp_rec.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta/FastaAlign.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta/FastaAlign.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta/FastaAlign.pyo
@@ -349,6 +358,15 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase/__init__.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/kabat_format.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/kabat_format.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/kabat_format.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/PubMed.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/PubMed.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/PubMed.pyo
@@ -379,6 +397,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Rebase/Rebase.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Rebase/__init__.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Rebase/__init__.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Rebase/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/RecordFile.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/RecordFile.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/RecordFile.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Dom.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Dom.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Dom.pyo
@@ -406,9 +427,6 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqIO/__init__.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqRecord.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqRecord.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqRecord.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Bio/Sequence.py
-lib/%%PYTHON_VERSION%%/site-packages/Bio/Sequence.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Bio/Sequence.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SubsMat/FreqTable.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SubsMat/FreqTable.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SubsMat/FreqTable.pyo
@@ -440,6 +458,12 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/cSVM.so
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/kNN.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/kNN.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/kNN.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.pyo
@@ -504,6 +528,7 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/UniGene
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Parsers
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt
@@ -514,9 +539,11 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Prosite
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/PDB
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Enzyme
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Encodings
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Data