ports/71400: [PATCH] biology/py23-biopython: unbreak/update to 1.30

Stefan Walter sw at gegenunendlich.de
Sun Sep 5 13:00:33 UTC 2004 

>Number:         71400
>Category:       ports
>Synopsis:       [PATCH] biology/py23-biopython: unbreak/update to 1.30
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Sun Sep 05 13:00:33 GMT 2004
>Closed-Date:
>Last-Modified:
>Originator:     Stefan Walter
>Release:        FreeBSD 5.2-CURRENT i386
>Organization:
Infinity Approximation Task Force
>Environment:
System: FreeBSD kyuzo.dunkelkammer.void 5.2-CURRENT FreeBSD 5.2-CURRENT #0: Wed Jul 28 20:21:17 CEST 2004
>Description:
- Unbreak build by fixing dependency list
- Update to 1.30, which really honors PREFIX
- USE_PYDISTUTILS

Port maintainer (wjv at FreeBSD.org) is cc'd.

Generated with FreeBSD Port Tools 0.50
>How-To-Repeat:
>Fix:

--- py23-biopython-1.30.patch begins here ---
diff -ruN --exclude=CVS /usr/ports/biology/py-biopython.old/Makefile /usr/ports/biology/py-biopython/Makefile
--- /usr/ports/biology/py-biopython.old/Makefile	Sun Sep  5 13:44:19 2004
+++ /usr/ports/biology/py-biopython/Makefile	Sun Sep  5 14:16:13 2004
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	biopython
-PORTVERSION=	1.23
+PORTVERSION=	1.30
 CATEGORIES=	biology python
 MASTER_SITES=	http://www.biopython.org/files/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -16,26 +16,16 @@
 
 CONFLICTS=	py*-martel-*
 
-BROKEN=		"Does not build"
-
-BUILD_DEPENDS=	${PYDISTUTILS}
-RUN_DEPENDS=	${PYNUMERIC} \
+BUILD_DEPENDS=	${PYNUMERIC} \
 		${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
+RUN_DEPENDS=	${BUILD_DEPENDS}
 
-USE_PERL5_BUILD=yes
-USE_PYTHON=	2.0+
-PYTHON_SETUP=	${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py
-CPIO=		cpio --quiet -pdum -R
-EXAMPLESDIR=	${PREFIX}/share/examples/${PORTNAME}
+USE_PYTHON=	2.2+
+USE_PYDISTUTILS=yes
 
 .if !defined(WITHOUT_REPORTLAB)
+BUILD_DEPENDS+=	${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab
 RUN_DEPENDS+=	${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab
 .endif
-
-do-build:
-	(cd ${WRKSRC} && ${PYTHON_SETUP} build)
-
-do-install:
-	(cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 --prefix=${PREFIX})
 
 .include <bsd.port.mk>
diff -ruN --exclude=CVS /usr/ports/biology/py-biopython.old/distinfo /usr/ports/biology/py-biopython/distinfo
--- /usr/ports/biology/py-biopython.old/distinfo	Sun Sep  5 13:44:19 2004
+++ /usr/ports/biology/py-biopython/distinfo	Sun Sep  5 14:17:08 2004
@@ -1,2 +1,2 @@
-MD5 (biopython-1.23.tar.gz) = 45ea628621c6b04d471f029ef5873aaf
-SIZE (biopython-1.23.tar.gz) = 2241300
+MD5 (biopython-1.30.tar.gz) = d8df866a40be20962b8ef52baa5376c1
+SIZE (biopython-1.30.tar.gz) = 3186467
diff -ruN --exclude=CVS /usr/ports/biology/py-biopython.old/pkg-plist /usr/ports/biology/py-biopython/pkg-plist
--- /usr/ports/biology/py-biopython.old/pkg-plist	Sun Sep  5 13:44:19 2004
+++ /usr/ports/biology/py-biopython/pkg-plist	Sun Sep  5 14:29:33 2004
@@ -1,3 +1,10 @@
+%%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.py
+%%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Affy/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Affy/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Affy/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Affy/_cel.so
 %%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.pyo
@@ -37,6 +44,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/Alphabet/IUPAC.py
 %%PYTHON_SITELIBDIR%%/Bio/Alphabet/IUPAC.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Alphabet/IUPAC.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Alphabet/Reduced.py
+%%PYTHON_SITELIBDIR%%/Bio/Alphabet/Reduced.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Alphabet/Reduced.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Alphabet/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Alphabet/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Alphabet/__init__.pyo
@@ -52,6 +62,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIWWW.py
 %%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIWWW.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIWWW.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIXML.py
+%%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIXML.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIXML.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Blast/ParseBlastTable.py
 %%PYTHON_SITELIBDIR%%/Bio/Blast/ParseBlastTable.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Blast/ParseBlastTable.pyo
@@ -83,6 +96,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/Cluster/data.py
 %%PYTHON_SITELIBDIR%%/Bio/Cluster/data.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Cluster/data.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Compass/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Compass/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Compass/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.pyo
@@ -119,24 +135,30 @@
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DBIdsClient.py
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DBIdsClient.pyc
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DBIdsClient.pyo
+%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/LinkOut.dtd
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/LinkOut.py
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/LinkOut.pyc
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/LinkOut.pyo
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eInfo_020511.dtd
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eInfo_020511.py
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eInfo_020511.pyc
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eInfo_020511.pyo
+%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eLink_020511.dtd
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eLink_020511.py
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eLink_020511.pyc
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eLink_020511.pyo
+%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/ePost_020511.dtd
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/ePost_020511.py
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/ePost_020511.pyc
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/ePost_020511.pyo
+%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSearch_020511.dtd
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSearch_020511.py
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSearch_020511.pyc
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSearch_020511.pyo
+%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSummary_020511.dtd
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSummary_020511.py
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSummary_020511.pyc
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSummary_020511.pyo
@@ -176,6 +198,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/sourcegen.py
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/sourcegen.pyc
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/sourcegen.pyo
+%%PYTHON_SITELIBDIR%%/Bio/EZRetrieve.py
+%%PYTHON_SITELIBDIR%%/Bio/EZRetrieve.pyc
+%%PYTHON_SITELIBDIR%%/Bio/EZRetrieve.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.py
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.pyo
@@ -302,9 +327,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/GenBank/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/GenBank/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/GenBank/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/GenBank/genbank_format.py
-%%PYTHON_SITELIBDIR%%/Bio/GenBank/genbank_format.pyc
-%%PYTHON_SITELIBDIR%%/Bio/GenBank/genbank_format.pyo
 %%PYTHON_SITELIBDIR%%/Bio/GenBank/utils.py
 %%PYTHON_SITELIBDIR%%/Bio/GenBank/utils.pyc
 %%PYTHON_SITELIBDIR%%/Bio/GenBank/utils.pyo
@@ -368,9 +390,13 @@
 %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/KDTree/_KDTree.py
-%%PYTHON_SITELIBDIR%%/Bio/KDTree/_KDTree.pyc
-%%PYTHON_SITELIBDIR%%/Bio/KDTree/_KDTree.pyo
+%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.py
+%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.pyc
+%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.pyo
+%%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.py
+%%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.pyc
+%%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.pyo
+%%PYTHON_SITELIBDIR%%/Bio/KDTree/_CKDTree.so
 %%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.pyo
@@ -500,6 +526,15 @@
 %%PYTHON_SITELIBDIR%%/Bio/NBRF/nbrf_format.py
 %%PYTHON_SITELIBDIR%%/Bio/NBRF/nbrf_format.pyc
 %%PYTHON_SITELIBDIR%%/Bio/NBRF/nbrf_format.pyo
+%%PYTHON_SITELIBDIR%%/Bio/NMR/NOEtools.py
+%%PYTHON_SITELIBDIR%%/Bio/NMR/NOEtools.pyc
+%%PYTHON_SITELIBDIR%%/Bio/NMR/NOEtools.pyo
+%%PYTHON_SITELIBDIR%%/Bio/NMR/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/NMR/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/NMR/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/NMR/xpktools.py
+%%PYTHON_SITELIBDIR%%/Bio/NMR/xpktools.pyc
+%%PYTHON_SITELIBDIR%%/Bio/NMR/xpktools.pyo
 %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.py
 %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.pyc
 %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.pyo
@@ -548,9 +583,18 @@
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Chain.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Chain.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Chain.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PDB/DSSP.py
+%%PYTHON_SITELIBDIR%%/Bio/PDB/DSSP.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PDB/DSSP.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Entity.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Entity.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Entity.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PDB/FragmentMapper.py
+%%PYTHON_SITELIBDIR%%/Bio/PDB/FragmentMapper.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PDB/FragmentMapper.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PDB/HSExposure.py
+%%PYTHON_SITELIBDIR%%/Bio/PDB/HSExposure.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PDB/HSExposure.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PDB/MMCIF2Dict.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/MMCIF2Dict.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/MMCIF2Dict.pyo
@@ -569,6 +613,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBIO.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBIO.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PDB/PDBList.py
+%%PYTHON_SITELIBDIR%%/Bio/PDB/PDBList.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PDB/PDBList.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBParser.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBParser.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBParser.pyo
@@ -578,15 +625,27 @@
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Residue.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Residue.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Residue.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PDB/ResidueDepth.py
+%%PYTHON_SITELIBDIR%%/Bio/PDB/ResidueDepth.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PDB/ResidueDepth.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Selection.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Selection.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Selection.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Structure.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Structure.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/Structure.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PDB/StructureAlignment.py
+%%PYTHON_SITELIBDIR%%/Bio/PDB/StructureAlignment.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PDB/StructureAlignment.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PDB/StructureBuilder.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/StructureBuilder.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/StructureBuilder.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PDB/Superimposer.py
+%%PYTHON_SITELIBDIR%%/Bio/PDB/Superimposer.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PDB/Superimposer.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PDB/Vector.py
+%%PYTHON_SITELIBDIR%%/Bio/PDB/Vector.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PDB/Vector.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.pyo
@@ -594,6 +653,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PDB/parse_pdb_header.py
+%%PYTHON_SITELIBDIR%%/Bio/PDB/parse_pdb_header.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PDB/parse_pdb_header.pyo
 %%PYTHON_SITELIBDIR%%/Bio/ParserSupport.py
 %%PYTHON_SITELIBDIR%%/Bio/ParserSupport.pyc
 %%PYTHON_SITELIBDIR%%/Bio/ParserSupport.pyo
@@ -633,9 +695,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/PubMed.py
 %%PYTHON_SITELIBDIR%%/Bio/PubMed.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PubMed.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Rebase/Rebase.py
-%%PYTHON_SITELIBDIR%%/Bio/Rebase/Rebase.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Rebase/Rebase.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.pyo
@@ -669,30 +728,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testCla.py
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testCla.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testCla.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDes.py
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDes.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDes.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDom.py
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDom.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDom.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testHie.py
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testHie.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testHie.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testRaf.py
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testRaf.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testRaf.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testResidues.py
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testResidues.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testResidues.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testScop.py
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testScop.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testScop.pyo
 %%PYTHON_SITELIBDIR%%/Bio/SGMLExtractor.py
 %%PYTHON_SITELIBDIR%%/Bio/SGMLExtractor.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SGMLExtractor.pyo
@@ -735,9 +770,42 @@
 %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsageIndices.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsageIndices.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsageIndices.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/IsoelectricPoint.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/IsoelectricPoint.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/IsoelectricPoint.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/MeltingTemp.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/MeltingTemp.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/MeltingTemp.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParam.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParam.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParam.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParamData.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParamData.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParamData.pyo
 %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.py
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.py
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Statistics/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Statistics/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Statistics/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Statistics/lowess.py
+%%PYTHON_SITELIBDIR%%/Bio/Statistics/lowess.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Statistics/lowess.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Std.py
 %%PYTHON_SITELIBDIR%%/Bio/Std.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Std.pyo
@@ -786,6 +854,15 @@
 %%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Wise/dnal.py
+%%PYTHON_SITELIBDIR%%/Bio/Wise/dnal.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Wise/dnal.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Wise/psw.py
+%%PYTHON_SITELIBDIR%%/Bio/Wise/psw.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Wise/psw.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Writer.py
 %%PYTHON_SITELIBDIR%%/Bio/Writer.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Writer.pyo
@@ -851,12 +928,18 @@
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/embl.py
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/embl.pyc
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/embl.pyo
+%%PYTHON_SITELIBDIR%%/Bio/dbdefs/fasta.py
+%%PYTHON_SITELIBDIR%%/Bio/dbdefs/fasta.pyc
+%%PYTHON_SITELIBDIR%%/Bio/dbdefs/fasta.pyo
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/genbank.py
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/genbank.pyc
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/genbank.pyo
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/interpro.py
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/interpro.pyc
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/interpro.pyo
+%%PYTHON_SITELIBDIR%%/Bio/dbdefs/medline.py
+%%PYTHON_SITELIBDIR%%/Bio/dbdefs/medline.pyc
+%%PYTHON_SITELIBDIR%%/Bio/dbdefs/medline.pyo
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/pdb.py
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/pdb.pyc
 %%PYTHON_SITELIBDIR%%/Bio/dbdefs/pdb.pyo
@@ -899,6 +982,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/expressions/genbank.py
 %%PYTHON_SITELIBDIR%%/Bio/expressions/genbank.pyc
 %%PYTHON_SITELIBDIR%%/Bio/expressions/genbank.pyo
+%%PYTHON_SITELIBDIR%%/Bio/expressions/hmmpfam.py
+%%PYTHON_SITELIBDIR%%/Bio/expressions/hmmpfam.pyc
+%%PYTHON_SITELIBDIR%%/Bio/expressions/hmmpfam.pyo
 %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.pyo
@@ -1035,83 +1121,88 @@
 %%PYTHON_SITELIBDIR%%/Martel/setup.py
 %%PYTHON_SITELIBDIR%%/Martel/setup.pyc
 %%PYTHON_SITELIBDIR%%/Martel/setup.pyo
- at dirrm %%PYTHON_SITELIBDIR%%/Martel
- at dirrm %%PYTHON_SITELIBDIR%%/BioSQL
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/writers
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/formatdefs
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/embl
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/blast
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/dbdefs
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/config
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/Search
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/builders
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/WWW
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/UniGene
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/SwissProt
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/SubsMat
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqUtils
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqIO
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Saf
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/SCOP/tests
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/SCOP
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Rebase
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Prosite
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/Gene
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Ndb
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/NBRF
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/MultiProc
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Mindy
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/MetaTool
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Medline
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/LocusLink
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Kabat
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/KDTree
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/InterPro
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/HMM
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Graphics
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Gobase
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Geo
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/GenBank
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/GFF
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Selection
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Repair
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Mutation
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/GA
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Encodings
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Emboss
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Ais
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Align
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Alphabet
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Application
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Blast
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/CDD
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Clustalw
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Cluster
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Compass
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Crystal
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Data
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/ECell
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/ECell
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Data
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Crystal
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Cluster
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Clustalw
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/CDD
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Blast
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Application
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Alphabet
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Align
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Ais
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Emboss
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Encodings
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Mutation
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Repair
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Selection
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/GA
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/GFF
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/GenBank
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Geo
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Gobase
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Graphics
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/HMM
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/InterPro
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/KDTree
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Kabat
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/LocusLink
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Medline
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/MetaTool
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Mindy
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/MultiProc
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/NBRF
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/NMR
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Ndb
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/Gene
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Prosite
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Rebase
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/SCOP
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Saf
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqIO
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqUtils
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Sequencing
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Statistics
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/SubsMat
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/SwissProt
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/UniGene
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/WWW
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Wise
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/Search
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/builders
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/config
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/dbdefs
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/blast
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/embl
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/formatdefs
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/writers
 @dirrm %%PYTHON_SITELIBDIR%%/Bio
+ at dirrm %%PYTHON_SITELIBDIR%%/BioSQL
+ at dirrm %%PYTHON_SITELIBDIR%%/Martel
--- py23-biopython-1.30.patch ends here ---

>Release-Note:
>Audit-Trail:
>Unformatted:

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