- Update to 1.60 Fix: PORTNAME= biopython -PORTVERSION= 1.59 +PORTVERSION= 1.60 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -238,8 +229,8 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Entrez/DTDs/link.ent %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Entrez/DTDs/list.ent %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Entrez/DTDs/math.ent -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Entrez/DTDs/mathml2-qname-1.mod %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Entrez/DTDs/mathml2.dtd +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Entrez/DTDs/mathml2-qname-1.mod %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Entrez/DTDs/mathmlsetup.ent %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Entrez/DTDs/mmlalias.ent %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Entrez/DTDs/mmlextra.ent @@ -301,21 +292,21 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/FSSPTools.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/FSSPTools.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/FSSPTools.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/__init__.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/__init__.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/fssp_rec.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/fssp_rec.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/fssp_rec.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/__init__.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/__init__.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/FSSP/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/File.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/File.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/File.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/General.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/General.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/General.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/GeneralPoint.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/GeneralPoint.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/GeneralPoint.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/General.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/General.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/General.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/Point.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/Point.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/Crossover/Point.pyo @@ -367,15 +358,15 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/Record.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/Record.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/Record.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/Scanner.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/utils.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/utils.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/utils.pyo @@ -412,18 +403,18 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Diagram.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Diagram.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Diagram.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Feature.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Feature.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Feature.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_FeatureSet.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_FeatureSet.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_FeatureSet.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Graph.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Graph.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Graph.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Feature.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Feature.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Feature.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_GraphSet.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_GraphSet.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_GraphSet.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Graph.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Graph.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_Graph.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_LinearDrawer.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_LinearDrawer.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Graphics/GenomeDiagram/_LinearDrawer.pyo @@ -457,13 +448,13 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Index.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Index.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Index.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/KDTree.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/KDTree.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/KDTree.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/_CKDTree.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/_CKDTree.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/_CKDTree.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/_CKDTree.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/_CKDTree.so +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/KDTree.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/KDTree.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/KDTree.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/__init__.pyo @@ -491,15 +482,15 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Medline/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Medline/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Medline/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Applications/_AlignAce.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Applications/_AlignAce.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Applications/_AlignAce.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Applications/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Applications/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Applications/__init__.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_Motif.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_Motif.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_Motif.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Parsers/AlignAce.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Parsers/AlignAce.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Parsers/AlignAce.pyo @@ -515,12 +506,12 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Thresholds.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Thresholds.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Thresholds.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_Motif.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_Motif.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_Motif.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/__init__.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/NMR/NOEtools.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/NMR/NOEtools.pyc @@ -576,40 +567,13 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/Trees.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/Trees.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/Trees.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/__init__.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/__init__.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/cnexus.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/cnexus.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/cnexus.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/cnexus.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/__init__.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/__init__.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_baseml.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_baseml.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_baseml.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_codeml.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_codeml.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_codeml.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_paml.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_paml.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_paml.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/baseml.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/baseml.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/baseml.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/chi2.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/chi2.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/chi2.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/codeml.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/codeml.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/codeml.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/cnexus.so +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/__init__.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/__init__.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/AbstractPropertyMap.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/AbstractPropertyMap.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/AbstractPropertyMap.pyo @@ -667,24 +631,24 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Polypeptide.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Polypeptide.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Polypeptide.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Residue.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Residue.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Residue.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/ResidueDepth.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/ResidueDepth.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/ResidueDepth.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Residue.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Residue.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Residue.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Selection.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Selection.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Selection.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Structure.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Structure.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Structure.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/StructureAlignment.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/StructureAlignment.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/StructureAlignment.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/StructureBuilder.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/StructureBuilder.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/StructureBuilder.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Structure.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Structure.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Structure.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Superimposer.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Superimposer.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/Superimposer.pyo @@ -694,6 +658,10 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/__init__.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/MMCIFlex.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/MMCIFlex.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/MMCIFlex.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/MMCIFlex.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/__init__.pyo @@ -718,30 +686,60 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Pathway/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Pathway/__init__.pyc 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+%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PhyloXMLIO.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PhyloXMLIO.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PhyloXMLIO.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PhyloXML.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PhyloXML.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PhyloXML.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/__init__.pyo @@ -802,9 +800,6 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/Template.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/Template.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/Template.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/__init__.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/__init__.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/data/bottle.par %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/data/decline_lambda.par %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/data/decline_split.par @@ -815,6 +810,9 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/data/split_ssm_2d.par %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/data/ssm_1d.par %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/data/ssm_2d.par +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/__init__.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/__init__.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/SimCoal/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PopGen/__init__.pyo @@ -824,12 +822,12 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/RanaConfig.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/RanaConfig.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/RanaConfig.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/Restriction.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/Restriction.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/Restriction.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/Restriction_Dictionary.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/Restriction_Dictionary.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/Restriction_Dictionary.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/Restriction.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/Restriction.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/Restriction.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/_Update/RestrictionCompiler.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/_Update/RestrictionCompiler.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/_Update/RestrictionCompiler.pyo @@ -863,6 +861,24 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/__init__.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/three_to_one_dict.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/three_to_one_dict.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/three_to_one_dict.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeqDatabase.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeqDatabase.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeqDatabase.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeq.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeq.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeq.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/DBUtils.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/DBUtils.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/DBUtils.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/Loader.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/Loader.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/Loader.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/__init__.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/__init__.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SVDSuperimposer/SVDSuperimposer.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SVDSuperimposer/SVDSuperimposer.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SVDSuperimposer/SVDSuperimposer.pyo @@ -872,9 +888,6 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Search.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Search.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Search.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Seq.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Seq.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Seq.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqFeature.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqFeature.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqFeature.pyo @@ -920,45 +933,48 @@ 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+%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqIO/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqRecord.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqRecord.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqRecord.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/CheckSum.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/CheckSum.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/CheckSum.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/CodonUsage.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/CodonUsage.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/CodonUsage.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/CodonUsageIndices.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/CodonUsageIndices.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/CodonUsageIndices.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/CodonUsage.py 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%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/ProtParamData.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/ProtParam.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/ProtParam.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/ProtParam.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/lcc.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/lcc.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils/lcc.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Seq.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Seq.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Seq.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Sequencing/Ace.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Sequencing/Ace.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Sequencing/Ace.pyo @@ -1004,44 +1020,47 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/UniGene/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/UniGene/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/UniGene/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/__init__.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/__init__.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/dnal.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/dnal.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/dnal.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/__init__.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/__init__.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/psw.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/psw.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise/psw.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/bgzf.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/bgzf.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/bgzf.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/kNN.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/kNN.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/kNN.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/pairwise2.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/pairwise2.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/pairwise2.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.so +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/_py3k.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/_py3k.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/_py3k.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/triefind.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/triefind.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/triefind.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeq.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeq.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeq.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeqDatabase.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeqDatabase.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/BioSeqDatabase.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/DBUtils.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/DBUtils.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/DBUtils.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/Loader.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/Loader.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/Loader.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/__init__.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/__init__.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/__init__.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.so +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/PKG-INFO +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/SOURCES.txt +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/dependency_links.txt +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/native_libs.txt +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/not-zip-safe +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/top_level.txt @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Affy @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Align/Applications @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Align @@ -1099,6 +1118,7 @@ @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction/_Update @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Restriction @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP +@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SVDSuperimposer @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqIO @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SeqUtils @@ -1111,12 +1131,5 @@ @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/UniGene @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Wise @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio -@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/SOURCES.txt -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/PKG-INFO -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/dependency_links.txt -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/native_libs.txt -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/not-zip-safe -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/top_level.txt--KOnnpSJLOV7fW0ZpgJ8UbFwZTzegX60Y5L0EAZ5rJQSFOaWH Content-Type: text/plain; name="file.diff" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="file.diff" --- Makefile.orig 2012-08-27 15:39:19.000000000 +0800 +++ Makefile 2012-08-27 11:29:53.000000000 +0800 @@ -2,11 +2,11 @@ # Date created: 28 July 2000 # Whom: Johann Visagie <johann@egenetics.com> # -# $FreeBSD: head/biology/py-biopython/Makefile 300895 2012-07-14 12:56:14Z beat $ +# $FreeBSD: ports/biology/py-biopython/Makefile,v 1.33 2012/03/06 06:40:50 wen Exp $ #
Responsible Changed From-To: freebsd-ports-bugs->freebsd-python freebsd-python@ wants this port PRs (via the GNATS Auto Assign Tool)
Maintainer of biology/py-biopython, Please note that PR ports/171115 has just been submitted. If it contains a patch for an upgrade, an enhancement or a bug fix you agree on, reply to this email stating that you approve the patch and a committer will take care of it. The full text of the PR can be found at: http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/171115 -- Edwin Groothuis via the GNATS Auto Assign Tool edwin@FreeBSD.org
State Changed From-To: open->feedback Awaiting maintainers feedback (via the GNATS Auto Assign Tool)
The patch for the Makefile doesn't work right: [root@freebsd9-vm] /usr/ports/biology/py-biopython # patch < Makefile.diff Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |--- Makefile.orig 2012-08-27 15:39:19.000000000 +0800 |+++ Makefile 2012-08-27 11:29:53.000000000 +0800 -------------------------- Patching file Makefile using Plan A... patch: **** unexpected end of file in patch Please put the diff for all the port in a single file and submit again. Thanks. Mauricio ________________________________ From: Edwin Groothuis <edwin@FreeBSD.org> To: mauricio@arareko.net Cc: bug-followup@FreeBSD.org Sent: Monday, August 27, 2012 7:10 AM Subject: Re: ports/171115: [Update]biology/py-biopython:update to 1.60 Maintainer of biology/py-biopython, Please note that PR ports/171115 has just been submitted. If it contains a patch for an upgrade, an enhancement or a bug fix you agree on, reply to this email stating that you approve the patch and a committer will take care of it. The full text of the PR can be found at: http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/171115 -- Edwin Groothuis via the GNATS Auto Assign Tool edwin@FreeBSD.org
Responsible Changed From-To: freebsd-python->rm Take. Hi Mauricio. Here is 'assembled' patch (that was mangled by gnats) from Wen plus some of my changes: 1. trim Makefile header 2. remove undefined article from COMMENT 3. change USE_PYTHON to just -2.7 4. remove reportlab from BUILD_DEPENDS 5. remove deprecated Authors: field from pkg-descr 6. tab -> space change in pkg-descr:WWW. Here is the patch: http://people.freebsd.org/~rm/biopython-1.60.diff.txt and here is the buildlog: http://people.freebsd.org/~rm/py27-biopython-1.60.log. Would you approve?
You are right. Here is updated patch: http://people.freebsd.org/~rm/py-biopython2.diff.txt -- Regards, Ruslan Tinderboxing kills... the drives.
Author: rm Date: Tue Sep 25 08:06:42 2012 New Revision: 304822 URL: http://svn.freebsd.org/changeset/ports/304822 Log: - update to 1.60 while here: - convert Makefile header into two-line format - update COMMENT (indefinite article removed) - change USE_PYTHON to just -2.7 - remove py-reportlab from BUILD_DEPENDS and kick PYTHON_SITELIBDIR from there - tab -> space change in pkg-descr:WWW PR: 171115 Submitted by: wen Approved by: Mauricio Herrera Cuadra <mauricio at arareko dot net> (maintainer) Modified: head/biology/py-biopython/Makefile head/biology/py-biopython/distinfo head/biology/py-biopython/pkg-descr head/biology/py-biopython/pkg-plist Modified: head/biology/py-biopython/Makefile ============================================================================== --- head/biology/py-biopython/Makefile Tue Sep 25 07:58:59 2012 (r304821) +++ head/biology/py-biopython/Makefile Tue Sep 25 08:06:42 2012 (r304822) @@ -1,29 +1,24 @@ -# New ports collection makefile for: py-biopython -# Date created: 28 July 2000 -# Whom: Johann Visagie <johann@egenetics.com> -# +# Created by: Johann Visagie <johann@egenetics.com> # $FreeBSD$ -# PORTNAME= biopython -PORTVERSION= 1.59 +PORTVERSION= 1.60 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= mauricio@arareko.net -COMMENT= A collection of Python modules for bioinformatics +COMMENT= Collection of Python modules for bioinformatics BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${PYNUMPY} -USE_PYTHON= 2.5-2.7 +USE_PYTHON= -2.7 USE_PYDISTUTILS= easy_install PYEASYINSTALL_ARCHDEP= 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 +RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}reportlab>0:${PORTSDIR}/print/py-reportlab .endif .include <bsd.port.mk> Modified: head/biology/py-biopython/distinfo ============================================================================== --- head/biology/py-biopython/distinfo Tue Sep 25 07:58:59 2012 (r304821) +++ head/biology/py-biopython/distinfo Tue Sep 25 08:06:42 2012 (r304822) @@ -1,2 +1,2 @@ -SHA256 (biopython-1.59.tar.gz) = 588abf55de3d8e4deac611a0f810a9c5d9ce7e5868d3064f79efe6cabd18cacb -SIZE (biopython-1.59.tar.gz) = 8577492 +SHA256 (biopython-1.60.tar.gz) = 73a2e6d700c8735832b6fc15dd08a9baa4136b072ff18760b9d22f563579d733 +SIZE (biopython-1.60.tar.gz) = 9501707 Modified: head/biology/py-biopython/pkg-descr ============================================================================== --- head/biology/py-biopython/pkg-descr Tue Sep 25 07:58:59 2012 (r304821) +++ head/biology/py-biopython/pkg-descr Tue Sep 25 08:06:42 2012 (r304822) @@ -12,5 +12,4 @@ 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/ +WWW: http://biopython.org/ Modified: head/biology/py-biopython/pkg-plist ============================================================================== --- head/biology/py-biopython/pkg-plist Tue Sep 25 07:58:59 2012 (r304821) +++ head/biology/py-biopython/pkg-plist Tue Sep 25 08:06:42 2012 (r304822) @@ -1,12 +1,3 @@ -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/_py3k.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/_py3k.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/_py3k.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Affy/CelFile.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Affy/CelFile.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Affy/CelFile.pyo @@ -112,10 +103,10 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Cluster/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Cluster/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Cluster/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Cluster/cluster.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Cluster/cluster.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Cluster/cluster.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Cluster/cluster.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Cluster/cluster.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Compass/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Compass/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Compass/__init__.pyo @@ -367,15 +358,15 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GA/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/Record.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/Record.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/Record.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/Scanner.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/Scanner.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/Scanner.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/utils.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/utils.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/GenBank/utils.pyo @@ -460,10 +451,10 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/KDTree.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/KDTree.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/KDTree.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/_CKDTree.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/_CKDTree.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/_CKDTree.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/_CKDTree.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/_CKDTree.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/KDTree/__init__.pyo @@ -491,9 +482,6 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Medline/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Medline/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Medline/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Applications/_AlignAce.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Applications/_AlignAce.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/Applications/_AlignAce.pyo @@ -521,6 +509,9 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/__init__.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Motif/_pwm.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/NMR/NOEtools.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/NMR/NOEtools.pyc @@ -579,37 +570,10 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/cnexus.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/cnexus.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/cnexus.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/cnexus.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/__init__.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/__init__.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_baseml.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_baseml.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_baseml.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_codeml.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_codeml.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_codeml.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_paml.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_paml.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_paml.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/baseml.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/baseml.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/baseml.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/chi2.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/chi2.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/chi2.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/codeml.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/codeml.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/codeml.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Nexus/cnexus.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/AbstractPropertyMap.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/AbstractPropertyMap.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/AbstractPropertyMap.pyo @@ -694,6 +658,10 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/__init__.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/MMCIFlex.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/MMCIFlex.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/MMCIFlex.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/MMCIFlex.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/PDB/mmCIF/__init__.pyo @@ -718,12 +686,15 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Pathway/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Pathway/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Pathway/__init__.pyo -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/__init__.py -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/__init__.pyc -%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/_Phyml.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/_Phyml.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/_Phyml.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/_Raxml.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/_Raxml.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/_Raxml.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/__init__.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/__init__.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/Applications/__init__.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/BaseTree.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/BaseTree.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/BaseTree.pyo @@ -736,6 +707,33 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/NexusIO.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/NexusIO.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/NexusIO.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/__init__.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/__init__.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/__init__.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_paml.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_paml.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_paml.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_baseml.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_baseml.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_baseml.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_codeml.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_codeml.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_codeml.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/_parse_yn00.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/baseml.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/baseml.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/baseml.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/chi2.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/chi2.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/chi2.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/codeml.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/codeml.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/codeml.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PAML/yn00.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PhyloXML.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PhyloXML.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Phylo/PhyloXML.pyo @@ -863,6 +861,9 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/__init__.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/three_to_one_dict.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/three_to_one_dict.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SCOP/three_to_one_dict.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SVDSuperimposer/SVDSuperimposer.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SVDSuperimposer/SVDSuperimposer.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/SVDSuperimposer/SVDSuperimposer.pyo @@ -1016,6 +1017,15 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/__init__.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/_py3k.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/_py3k.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/_py3k.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/bgzf.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/bgzf.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/bgzf.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/cpairwise2.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/kNN.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/kNN.pyc @@ -1023,6 +1033,9 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/pairwise2.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/pairwise2.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/pairwise2.pyo +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.py +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.pyc +%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.pyo %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/trie.so %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/triefind.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/triefind.pyc @@ -1042,81 +1055,81 @@ %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/__init__.py %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/__init__.pyc %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/BioSQL/__init__.pyo -@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Affy -@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Align/Applications -@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Align -@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/AlignIO -@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Alphabet -@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Application -@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Blast -@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/CAPS -@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Cluster -@dirrm 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%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Blast +@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Application +@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Alphabet +@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/AlignIO +@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Align/Applications +@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Align +@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio/Affy +@dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/Bio @dirrm %%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%% _______________________________________________ svn-ports-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/svn-ports-all To unsubscribe, send any mail to "svn-ports-all-unsubscribe@freebsd.org"
State Changed From-To: feedback->closed Committed, thank you!