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biopython, py-biopython, py-cytoolz, py-guppy3: removed; already in base
Module Name: pkgsrc-wip
Committed By: Adam Ciarciński <aciarcinski%teonite.com@localhost>
Pushed By: adam
Date: Mon May 16 07:21:09 2022 +0200
Changeset: ec66c14d0f394f077d1c3d81352c045854998e36
Modified Files:
Makefile
py-anvio/Makefile
py-mdanalysis/Makefile
Removed Files:
biopython/DESCR
biopython/Makefile
biopython/PLIST
biopython/distinfo
py-biopython/DESCR
py-biopython/Makefile
py-biopython/PLIST
py-biopython/distinfo
py-cytoolz/DESCR
py-cytoolz/Makefile
py-cytoolz/PLIST
py-cytoolz/distinfo
py-guppy3/DESCR
py-guppy3/Makefile
py-guppy3/PLIST
py-guppy3/distinfo
Log Message:
biopython, py-biopython, py-cytoolz, py-guppy3: removed; already in base
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=ec66c14d0f394f077d1c3d81352c045854998e36
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 3 -
biopython/DESCR | 7 -
biopython/Makefile | 36 --
biopython/PLIST | 1299 ------------------------------------------------
biopython/distinfo | 4 -
py-anvio/Makefile | 3 +-
py-biopython/DESCR | 10 -
py-biopython/Makefile | 31 --
py-biopython/PLIST | 1282 -----------------------------------------------
py-biopython/distinfo | 5 -
py-cytoolz/DESCR | 15 -
py-cytoolz/Makefile | 17 -
py-cytoolz/PLIST | 102 ----
py-cytoolz/distinfo | 5 -
py-guppy3/DESCR | 10 -
py-guppy3/Makefile | 17 -
py-guppy3/PLIST | 226 ---------
py-guppy3/distinfo | 5 -
py-mdanalysis/Makefile | 4 +-
19 files changed, 3 insertions(+), 3078 deletions(-)
diffs:
diff --git a/Makefile b/Makefile
index a70b8c017b..7a10e996eb 100644
--- a/Makefile
+++ b/Makefile
@@ -284,7 +284,6 @@ SUBDIR+= bindgraph
SUBDIR+= binutils-gold-git
SUBDIR+= biolibc
SUBDIR+= biolibc-tools
-SUBDIR+= biopython
SUBDIR+= bioruby
SUBDIR+= bip
SUBDIR+= bitkeeper
@@ -3491,7 +3490,6 @@ SUBDIR+= py-bicho
SUBDIR+= py-bidict
SUBDIR+= py-bigfloat
SUBDIR+= py-biofrills
-SUBDIR+= py-biopython
SUBDIR+= py-bitsets
SUBDIR+= py-blake2
SUBDIR+= py-blaze
@@ -3652,7 +3650,6 @@ SUBDIR+= py-cymem
SUBDIR+= py-cysignals
SUBDIR+= py-cython-blis
SUBDIR+= py-cythongsl
-SUBDIR+= py-cytoolz
SUBDIR+= py-da
SUBDIR+= py-dana
SUBDIR+= py-dantic
diff --git a/biopython/DESCR b/biopython/DESCR
deleted file mode 100644
index 1efcadd89f..0000000000
--- a/biopython/DESCR
+++ /dev/null
@@ -1,7 +0,0 @@
-The Biopython package contains high-quality, reusable modules and
-scripts written in Python to make it as easy as possible to use Python
-for bioinformatics. The Biopython includes the follwing: the ability to
-parse bioinformatics files into python utilizable data structures,
-including support for the formats such as Blast output, Clustalw, FASTA,
-GenBank, PubMed and Medicine, various Expasy files, SCOP, Rebase,
-UniGene, and SwissProt.
diff --git a/biopython/Makefile b/biopython/Makefile
deleted file mode 100644
index 973db2dcb1..0000000000
--- a/biopython/Makefile
+++ /dev/null
@@ -1,36 +0,0 @@
-# $NetBSD: Makefile,v 1.18 2014/05/09 07:38:42 thomasklausner Exp $
-
-DISTNAME= biopython-1.63b
-PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
-CATEGORIES= biology
-MASTER_SITES= http://biopython.org/DIST/
-
-MAINTAINER= dprice%cs.nmsu.edu@localhost
-HOMEPAGE= https://biopython.org/
-COMMENT= Python libraries for computational molecular biology
-LICENSE= Biopython
-
-DEPENDS+= ${PYPKGPREFIX}-reportlab>=2.5:../../print/py-reportlab
-
-PYDISTUTILSPKG= YES
-
-post-install:
- ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/biopython
- ${INSTALL_DATA} ${WRKSRC}/Doc/*.pdf ${DESTDIR}${PREFIX}/share/doc/biopython
-.for f in README LICENSE CONTRIB
- ${INSTALL_DATA} ${WRKSRC}/${f} ${DESTDIR}${PREFIX}/share/doc/biopython
-.endfor
- ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/examples/biopython
- ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.py \
- ${DESTDIR}${PREFIX}/share/examples/biopython
- ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.fasta \
- ${DESTDIR}${PREFIX}/share/examples/biopython
- ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.aln \
- ${DESTDIR}${PREFIX}/share/examples/biopython
- ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/examples/biopython/nmr
- ${INSTALL_DATA} ${WRKSRC}/Doc/examples/nmr/* \
- ${DESTDIR}${PREFIX}/share/examples/biopython/nmr
-
-.include "../../math/py-numpy/buildlink3.mk"
-.include "../../lang/python/extension.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/biopython/PLIST b/biopython/PLIST
deleted file mode 100644
index 92b389f794..0000000000
--- a/biopython/PLIST
+++ /dev/null
@@ -1,1299 +0,0 @@
-@comment $NetBSD: PLIST,v 1.5 2013/12/02 09:46:01 jihbed Exp $
-${PYSITELIB}/Bio/Affy/CelFile.py
-${PYSITELIB}/Bio/Affy/CelFile.pyc
-${PYSITELIB}/Bio/Affy/CelFile.pyo
-${PYSITELIB}/Bio/Affy/__init__.py
-${PYSITELIB}/Bio/Affy/__init__.pyc
-${PYSITELIB}/Bio/Affy/__init__.pyo
-${PYSITELIB}/Bio/Align/AlignInfo.py
-${PYSITELIB}/Bio/Align/AlignInfo.pyc
-${PYSITELIB}/Bio/Align/AlignInfo.pyo
-${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.py
-${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.pyc
-${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.pyo
-${PYSITELIB}/Bio/Align/Applications/_Clustalw.py
-${PYSITELIB}/Bio/Align/Applications/_Clustalw.pyc
-${PYSITELIB}/Bio/Align/Applications/_Clustalw.pyo
-${PYSITELIB}/Bio/Align/Applications/_Dialign.py
-${PYSITELIB}/Bio/Align/Applications/_Dialign.pyc
-${PYSITELIB}/Bio/Align/Applications/_Dialign.pyo
-${PYSITELIB}/Bio/Align/Applications/_MSAProbs.py
-${PYSITELIB}/Bio/Align/Applications/_MSAProbs.pyc
-${PYSITELIB}/Bio/Align/Applications/_MSAProbs.pyo
-${PYSITELIB}/Bio/Align/Applications/_Mafft.py
-${PYSITELIB}/Bio/Align/Applications/_Mafft.pyc
-${PYSITELIB}/Bio/Align/Applications/_Mafft.pyo
-${PYSITELIB}/Bio/Align/Applications/_Muscle.py
-${PYSITELIB}/Bio/Align/Applications/_Muscle.pyc
-${PYSITELIB}/Bio/Align/Applications/_Muscle.pyo
-${PYSITELIB}/Bio/Align/Applications/_Prank.py
-${PYSITELIB}/Bio/Align/Applications/_Prank.pyc
-${PYSITELIB}/Bio/Align/Applications/_Prank.pyo
-${PYSITELIB}/Bio/Align/Applications/_Probcons.py
-${PYSITELIB}/Bio/Align/Applications/_Probcons.pyc
-${PYSITELIB}/Bio/Align/Applications/_Probcons.pyo
-${PYSITELIB}/Bio/Align/Applications/_TCoffee.py
-${PYSITELIB}/Bio/Align/Applications/_TCoffee.pyc
-${PYSITELIB}/Bio/Align/Applications/_TCoffee.pyo
-${PYSITELIB}/Bio/Align/Applications/__init__.py
-${PYSITELIB}/Bio/Align/Applications/__init__.pyc
-${PYSITELIB}/Bio/Align/Applications/__init__.pyo
-${PYSITELIB}/Bio/Align/Generic.py
-${PYSITELIB}/Bio/Align/Generic.pyc
-${PYSITELIB}/Bio/Align/Generic.pyo
-${PYSITELIB}/Bio/Align/__init__.py
-${PYSITELIB}/Bio/Align/__init__.pyc
-${PYSITELIB}/Bio/Align/__init__.pyo
-${PYSITELIB}/Bio/AlignIO/ClustalIO.py
-${PYSITELIB}/Bio/AlignIO/ClustalIO.pyc
-${PYSITELIB}/Bio/AlignIO/ClustalIO.pyo
-${PYSITELIB}/Bio/AlignIO/EmbossIO.py
-${PYSITELIB}/Bio/AlignIO/EmbossIO.pyc
-${PYSITELIB}/Bio/AlignIO/EmbossIO.pyo
-${PYSITELIB}/Bio/AlignIO/FastaIO.py
-${PYSITELIB}/Bio/AlignIO/FastaIO.pyc
-${PYSITELIB}/Bio/AlignIO/FastaIO.pyo
-${PYSITELIB}/Bio/AlignIO/Interfaces.py
-${PYSITELIB}/Bio/AlignIO/Interfaces.pyc
-${PYSITELIB}/Bio/AlignIO/Interfaces.pyo
-${PYSITELIB}/Bio/AlignIO/NexusIO.py
-${PYSITELIB}/Bio/AlignIO/NexusIO.pyc
-${PYSITELIB}/Bio/AlignIO/NexusIO.pyo
-${PYSITELIB}/Bio/AlignIO/PhylipIO.py
-${PYSITELIB}/Bio/AlignIO/PhylipIO.pyc
-${PYSITELIB}/Bio/AlignIO/PhylipIO.pyo
-${PYSITELIB}/Bio/AlignIO/StockholmIO.py
-${PYSITELIB}/Bio/AlignIO/StockholmIO.pyc
-${PYSITELIB}/Bio/AlignIO/StockholmIO.pyo
-${PYSITELIB}/Bio/AlignIO/__init__.py
-${PYSITELIB}/Bio/AlignIO/__init__.pyc
-${PYSITELIB}/Bio/AlignIO/__init__.pyo
-${PYSITELIB}/Bio/Alphabet/IUPAC.py
-${PYSITELIB}/Bio/Alphabet/IUPAC.pyc
-${PYSITELIB}/Bio/Alphabet/IUPAC.pyo
-${PYSITELIB}/Bio/Alphabet/Reduced.py
-${PYSITELIB}/Bio/Alphabet/Reduced.pyc
-${PYSITELIB}/Bio/Alphabet/Reduced.pyo
-${PYSITELIB}/Bio/Alphabet/__init__.py
-${PYSITELIB}/Bio/Alphabet/__init__.pyc
-${PYSITELIB}/Bio/Alphabet/__init__.pyo
-${PYSITELIB}/Bio/Application/__init__.py
-${PYSITELIB}/Bio/Application/__init__.pyc
-${PYSITELIB}/Bio/Application/__init__.pyo
-${PYSITELIB}/Bio/Blast/Applications.py
-${PYSITELIB}/Bio/Blast/Applications.pyc
-${PYSITELIB}/Bio/Blast/Applications.pyo
-${PYSITELIB}/Bio/Blast/NCBIStandalone.py
-${PYSITELIB}/Bio/Blast/NCBIStandalone.pyc
-${PYSITELIB}/Bio/Blast/NCBIStandalone.pyo
-${PYSITELIB}/Bio/Blast/NCBIWWW.py
-${PYSITELIB}/Bio/Blast/NCBIWWW.pyc
-${PYSITELIB}/Bio/Blast/NCBIWWW.pyo
-${PYSITELIB}/Bio/Blast/NCBIXML.py
-${PYSITELIB}/Bio/Blast/NCBIXML.pyc
-${PYSITELIB}/Bio/Blast/NCBIXML.pyo
-${PYSITELIB}/Bio/Blast/ParseBlastTable.py
-${PYSITELIB}/Bio/Blast/ParseBlastTable.pyc
-${PYSITELIB}/Bio/Blast/ParseBlastTable.pyo
-${PYSITELIB}/Bio/Blast/Record.py
-${PYSITELIB}/Bio/Blast/Record.pyc
-${PYSITELIB}/Bio/Blast/Record.pyo
-${PYSITELIB}/Bio/Blast/__init__.py
-${PYSITELIB}/Bio/Blast/__init__.pyc
-${PYSITELIB}/Bio/Blast/__init__.pyo
-${PYSITELIB}/Bio/CAPS/__init__.py
-${PYSITELIB}/Bio/CAPS/__init__.pyc
-${PYSITELIB}/Bio/CAPS/__init__.pyo
-${PYSITELIB}/Bio/Cluster/__init__.py
-${PYSITELIB}/Bio/Cluster/__init__.pyc
-${PYSITELIB}/Bio/Cluster/__init__.pyo
-${PYSITELIB}/Bio/Cluster/cluster.so
-${PYSITELIB}/Bio/Compass/__init__.py
-${PYSITELIB}/Bio/Compass/__init__.pyc
-${PYSITELIB}/Bio/Compass/__init__.pyo
-${PYSITELIB}/Bio/Crystal/__init__.py
-${PYSITELIB}/Bio/Crystal/__init__.pyc
-${PYSITELIB}/Bio/Crystal/__init__.pyo
-${PYSITELIB}/Bio/Data/CodonTable.py
-${PYSITELIB}/Bio/Data/CodonTable.pyc
-${PYSITELIB}/Bio/Data/CodonTable.pyo
-${PYSITELIB}/Bio/Data/IUPACData.py
-${PYSITELIB}/Bio/Data/IUPACData.pyc
-${PYSITELIB}/Bio/Data/IUPACData.pyo
-${PYSITELIB}/Bio/Data/SCOPData.py
-${PYSITELIB}/Bio/Data/SCOPData.pyc
-${PYSITELIB}/Bio/Data/SCOPData.pyo
-${PYSITELIB}/Bio/Data/__init__.py
-${PYSITELIB}/Bio/Data/__init__.pyc
-${PYSITELIB}/Bio/Data/__init__.pyo
-${PYSITELIB}/Bio/DocSQL.py
-${PYSITELIB}/Bio/DocSQL.pyc
-${PYSITELIB}/Bio/DocSQL.pyo
-${PYSITELIB}/Bio/Emboss/Applications.py
-${PYSITELIB}/Bio/Emboss/Applications.pyc
-${PYSITELIB}/Bio/Emboss/Applications.pyo
-${PYSITELIB}/Bio/Emboss/Primer3.py
-${PYSITELIB}/Bio/Emboss/Primer3.pyc
-${PYSITELIB}/Bio/Emboss/Primer3.pyo
-${PYSITELIB}/Bio/Emboss/PrimerSearch.py
-${PYSITELIB}/Bio/Emboss/PrimerSearch.pyc
-${PYSITELIB}/Bio/Emboss/PrimerSearch.pyo
-${PYSITELIB}/Bio/Emboss/__init__.py
-${PYSITELIB}/Bio/Emboss/__init__.pyc
-${PYSITELIB}/Bio/Emboss/__init__.pyo
-${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_0.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_1.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_2.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_3.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_4.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/EMBL_General.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/EMBL_General.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/GenBank_General.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/GenBank_General.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/HomoloGene.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/HomoloGene.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/INSD_INSDSeq.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/MMDB.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/MMDB.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Features.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Features.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Structural_model.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Access.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Access.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Biblio.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BioSource.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BioTree.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Blast4.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BlastDL.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Cdd.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Cn3d.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Entrez2.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_FeatDef.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_GBSeq.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Gene.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_General.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_General.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ID1Access.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ID2Access.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_MedArchive.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Medlars.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Medline.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Mim.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Mime.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Organism.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PCAssay.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Project.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Project.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Protein.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Pub.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PubMed.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_RNA.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Remap.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Rsite.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_SeqCode.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_SeqTable.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seq_split.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seqalign.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seqloc.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seqres.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seqset.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Sequence.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Submit.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_TSeq.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_TxInit.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Variation.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NCBI_all.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NSE.dtd
-${PYSITELIB}/Bio/Entrez/DTDs/NSE.mod.dtd
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-share/doc/biopython/CONTRIB
-share/doc/biopython/LICENSE
-share/doc/biopython/README
-share/doc/biopython/Tutorial.pdf
-share/doc/biopython/biopdb_faq.pdf
-share/examples/biopython/ACT_example.py
-share/examples/biopython/Proux_et_al_2002_Figure_6.py
-share/examples/biopython/clustal_run.py
-share/examples/biopython/fasta_dictionary.py
-share/examples/biopython/fasta_iterator.py
-share/examples/biopython/getgene.py
-share/examples/biopython/ls_orchid.fasta
-share/examples/biopython/m_cold.fasta
-share/examples/biopython/make_subsmat.py
-share/examples/biopython/nmr/noed.xpk
-share/examples/biopython/nmr/simplepredict.py
-share/examples/biopython/opuntia.fasta
-share/examples/biopython/protein.aln
-share/examples/biopython/swissprot.py
-share/examples/biopython/www_blast.py
diff --git a/biopython/distinfo b/biopython/distinfo
deleted file mode 100644
index af66c6204d..0000000000
--- a/biopython/distinfo
+++ /dev/null
@@ -1,4 +0,0 @@
-$NetBSD: distinfo,v 1.5 2013/12/02 09:46:01 jihbed Exp $
-
-RMD160 (biopython-1.63b.tar.gz) = f7eb4192a79fc052761e1050665abaf5ab00aa20
-Size (biopython-1.63b.tar.gz) = 11513224 bytes
diff --git a/py-anvio/Makefile b/py-anvio/Makefile
index 130124d486..90998bf6cf 100644
--- a/py-anvio/Makefile
+++ b/py-anvio/Makefile
@@ -39,8 +39,7 @@ DEPENDS= samtools>0:../../wip/samtools \
${PYPKGPREFIX}-psutil>0:../../sysutils/py-psutil \
${PYPKGPREFIX}-scikit-learn>0:../../math/py-scikit-learn \
${PYPKGPREFIX}-h5py>0:../../devel/py-h5py \
- ${PYPKGPREFIX}-biopython>0:../../wip/py-biopython \
- ${PYPKGPREFIX}-biopython>0:../../wip/py-biopython \
+ ${PYPKGPREFIX}-biopython>0:../../biology/py-biopython \
Prodigal>0:../../wip/prodigal \
centrifuge>0:../../wip/centrifuge \
mcl>0:../../wip/mcl \
diff --git a/py-biopython/DESCR b/py-biopython/DESCR
deleted file mode 100644
index 38b785a7de..0000000000
--- a/py-biopython/DESCR
+++ /dev/null
@@ -1,10 +0,0 @@
-The Biopython Project is an international association of developers who are
-providing freely available Python tools for use in areas of computational
-molecular biology such as bioinformatics and genomics.
-Biopython is a collection of Python packages and modules created by the
-Biopython Project, intended to provide the basis for building bioinformatics
-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/).
diff --git a/py-biopython/Makefile b/py-biopython/Makefile
deleted file mode 100644
index 594f7828d4..0000000000
--- a/py-biopython/Makefile
+++ /dev/null
@@ -1,31 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-# Generated by fbsd2pkg #
-# Mon Nov 5 14:38:46 CST 2018 #
-###########################################################
-
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-#pre-configure: # unbreak for python3: README.rst can't be decoded with the ascii codec: https://github.com/biopython/biopython/issues/1649
-# @truncate -s 0 ${WRKSRC}/README.rst
-
-DISTNAME= biopython-${PV}
-PKGNAME= ${PYPKGPREFIX}-biopython-${PV}
-CATEGORIES= biology
-MASTER_SITES= http://www.biopython.org/DIST/
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= https://biopython.org/
-COMMENT= Collection of Python modules for bioinformatics
-LICENSE= modified-bsd
-
-# Many dependencies. Option?
-# DEPENDS+= ${PYPKGPREFIX}-reportlab>0:../../print/py-reportlab
-DEPENDS+= ${PYPKGPREFIX}-numpy>0:../../math/py-numpy
-
-PV= 1.72
-
-.include "../../lang/python/egg.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-biopython/PLIST b/py-biopython/PLIST
deleted file mode 100644
index 7715a6509b..0000000000
--- a/py-biopython/PLIST
+++ /dev/null
@@ -1,1282 +0,0 @@
-@comment $NetBSD$
-${PYSITELIB}/Bio/Affy/CelFile.py
-${PYSITELIB}/Bio/Affy/CelFile.pyc
-${PYSITELIB}/Bio/Affy/CelFile.pyo
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-${PYSITELIB}/Bio/UniGene/__init__.pyc
-${PYSITELIB}/Bio/UniGene/__init__.pyo
-${PYSITELIB}/Bio/UniProt/GOA.py
-${PYSITELIB}/Bio/UniProt/GOA.pyc
-${PYSITELIB}/Bio/UniProt/GOA.pyo
-${PYSITELIB}/Bio/UniProt/__init__.py
-${PYSITELIB}/Bio/UniProt/__init__.pyc
-${PYSITELIB}/Bio/UniProt/__init__.pyo
-${PYSITELIB}/Bio/Wise/__init__.py
-${PYSITELIB}/Bio/Wise/__init__.pyc
-${PYSITELIB}/Bio/Wise/__init__.pyo
-${PYSITELIB}/Bio/Wise/dnal.py
-${PYSITELIB}/Bio/Wise/dnal.pyc
-${PYSITELIB}/Bio/Wise/dnal.pyo
-${PYSITELIB}/Bio/Wise/psw.py
-${PYSITELIB}/Bio/Wise/psw.pyc
-${PYSITELIB}/Bio/Wise/psw.pyo
-${PYSITELIB}/Bio/__init__.py
-${PYSITELIB}/Bio/__init__.pyc
-${PYSITELIB}/Bio/__init__.pyo
-${PYSITELIB}/Bio/_py3k/__init__.py
-${PYSITELIB}/Bio/_py3k/__init__.pyc
-${PYSITELIB}/Bio/_py3k/__init__.pyo
-${PYSITELIB}/Bio/_utils.py
-${PYSITELIB}/Bio/_utils.pyc
-${PYSITELIB}/Bio/_utils.pyo
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-${PYSITELIB}/Bio/bgzf.pyc
-${PYSITELIB}/Bio/bgzf.pyo
-${PYSITELIB}/Bio/codonalign/__init__.py
-${PYSITELIB}/Bio/codonalign/__init__.pyc
-${PYSITELIB}/Bio/codonalign/__init__.pyo
-${PYSITELIB}/Bio/codonalign/chisq.py
-${PYSITELIB}/Bio/codonalign/chisq.pyc
-${PYSITELIB}/Bio/codonalign/chisq.pyo
-${PYSITELIB}/Bio/codonalign/codonalignment.py
-${PYSITELIB}/Bio/codonalign/codonalignment.pyc
-${PYSITELIB}/Bio/codonalign/codonalignment.pyo
-${PYSITELIB}/Bio/codonalign/codonalphabet.py
-${PYSITELIB}/Bio/codonalign/codonalphabet.pyc
-${PYSITELIB}/Bio/codonalign/codonalphabet.pyo
-${PYSITELIB}/Bio/codonalign/codonseq.py
-${PYSITELIB}/Bio/codonalign/codonseq.pyc
-${PYSITELIB}/Bio/codonalign/codonseq.pyo
-${PYSITELIB}/Bio/cpairwise2.so
-${PYSITELIB}/Bio/kNN.py
-${PYSITELIB}/Bio/kNN.pyc
-${PYSITELIB}/Bio/kNN.pyo
-${PYSITELIB}/Bio/motifs/__init__.py
-${PYSITELIB}/Bio/motifs/__init__.pyc
-${PYSITELIB}/Bio/motifs/__init__.pyo
-${PYSITELIB}/Bio/motifs/_pwm.so
-${PYSITELIB}/Bio/motifs/alignace.py
-${PYSITELIB}/Bio/motifs/alignace.pyc
-${PYSITELIB}/Bio/motifs/alignace.pyo
-${PYSITELIB}/Bio/motifs/applications/__init__.py
-${PYSITELIB}/Bio/motifs/applications/__init__.pyc
-${PYSITELIB}/Bio/motifs/applications/__init__.pyo
-${PYSITELIB}/Bio/motifs/applications/_xxmotif.py
-${PYSITELIB}/Bio/motifs/applications/_xxmotif.pyc
-${PYSITELIB}/Bio/motifs/applications/_xxmotif.pyo
-${PYSITELIB}/Bio/motifs/jaspar/__init__.py
-${PYSITELIB}/Bio/motifs/jaspar/__init__.pyc
-${PYSITELIB}/Bio/motifs/jaspar/__init__.pyo
-${PYSITELIB}/Bio/motifs/jaspar/db.py
-${PYSITELIB}/Bio/motifs/jaspar/db.pyc
-${PYSITELIB}/Bio/motifs/jaspar/db.pyo
-${PYSITELIB}/Bio/motifs/mast.py
-${PYSITELIB}/Bio/motifs/mast.pyc
-${PYSITELIB}/Bio/motifs/mast.pyo
-${PYSITELIB}/Bio/motifs/matrix.py
-${PYSITELIB}/Bio/motifs/matrix.pyc
-${PYSITELIB}/Bio/motifs/matrix.pyo
-${PYSITELIB}/Bio/motifs/meme.py
-${PYSITELIB}/Bio/motifs/meme.pyc
-${PYSITELIB}/Bio/motifs/meme.pyo
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-${PYSITELIB}/Bio/motifs/thresholds.pyc
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-${PYSITELIB}/Bio/motifs/transfac.py
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-${PYSITELIB}/Bio/pairwise2.pyc
-${PYSITELIB}/Bio/pairwise2.pyo
-${PYSITELIB}/Bio/phenotype/__init__.py
-${PYSITELIB}/Bio/phenotype/__init__.pyc
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-${PYSITELIB}/Bio/phenotype/phen_micro.py
-${PYSITELIB}/Bio/phenotype/phen_micro.pyc
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-${PYSITELIB}/Bio/phenotype/pm_fitting.pyc
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-${PYSITELIB}/Bio/trie.so
-${PYSITELIB}/Bio/triefind.py
-${PYSITELIB}/Bio/triefind.pyc
-${PYSITELIB}/Bio/triefind.pyo
-${PYSITELIB}/BioSQL/BioSeq.py
-${PYSITELIB}/BioSQL/BioSeq.pyc
-${PYSITELIB}/BioSQL/BioSeq.pyo
-${PYSITELIB}/BioSQL/BioSeqDatabase.py
-${PYSITELIB}/BioSQL/BioSeqDatabase.pyc
-${PYSITELIB}/BioSQL/BioSeqDatabase.pyo
-${PYSITELIB}/BioSQL/DBUtils.py
-${PYSITELIB}/BioSQL/DBUtils.pyc
-${PYSITELIB}/BioSQL/DBUtils.pyo
-${PYSITELIB}/BioSQL/Loader.py
-${PYSITELIB}/BioSQL/Loader.pyc
-${PYSITELIB}/BioSQL/Loader.pyo
-${PYSITELIB}/BioSQL/__init__.py
-${PYSITELIB}/BioSQL/__init__.pyc
-${PYSITELIB}/BioSQL/__init__.pyo
-${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
-${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
-${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
-${PYSITELIB}/${EGG_INFODIR}/requires.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
diff --git a/py-biopython/distinfo b/py-biopython/distinfo
deleted file mode 100644
index 100ecf004a..0000000000
--- a/py-biopython/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (biopython-1.72.tar.gz) = 8d3659c93a8d6c916ea242a2ae689609879454ce
-SHA512 (biopython-1.72.tar.gz) = e2ce74f4533c9c779c8fbafb73ed562c890209a4318fc9d8616ec98670ee5e97649b8c1b0207c91454b923faecf375f20bd6a0aaff52ccc73268fb0b1ea0b44c
-Size (biopython-1.72.tar.gz) = 16391360 bytes
diff --git a/py-cytoolz/DESCR b/py-cytoolz/DESCR
deleted file mode 100644
index 4869a36d94..0000000000
--- a/py-cytoolz/DESCR
+++ /dev/null
@@ -1,15 +0,0 @@
-Cython implementation of the toolz package, which provides high performance
-utility functions for iterables, functions, and dictionaries
-
-toolz is a pure Python package that borrows heavily from contemporary functional
-languanges.It is designed to interoperate seamlessly with other libraries
-including itertools, functools, and third party libraries. High performance
-functional data analysis is possible with builtin types like list and dict, and
-user-defined data structures; and low memory usage is achieved by using the
-iterator protocol and returning iterators whenever possible.
-
-cytoolz implements the same API as toolz. The main differences are that cytoolz
-is faster (typically 2-5x faster with a few spectactular exceptions) and cytoolz
-offers a C API that is accessible to other projects developed in Cython. Since
-toolz is able to process very large (potentially infinite) data sets, the
-performance increase gained by using cytoolz can be significant
diff --git a/py-cytoolz/Makefile b/py-cytoolz/Makefile
deleted file mode 100644
index 5257e4e3ab..0000000000
--- a/py-cytoolz/Makefile
+++ /dev/null
@@ -1,17 +0,0 @@
-# $NetBSD: Makefile,v 1.1 2014/05/05 23:50:47 jihbed Exp $
-
-DISTNAME= cytoolz-0.10.1
-PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
-CATEGORIES= devel python
-MASTER_SITES= ${MASTER_SITE_PYPI:=c/cytoolz/}
-
-MAINTAINER= jihbed.research%gmail.com@localhost
-HOMEPAGE= https://github.com/pytoolz/cytoolz
-COMMENT= Cython Toolz High performance functional utilities
-LICENSE= modified-bsd
-
-PYDISTUTILSPKG= yes
-
-.include "../../devel/py-cython/buildlink3.mk"
-.include "../../lang/python/egg.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-cytoolz/PLIST b/py-cytoolz/PLIST
deleted file mode 100644
index df0bfe255a..0000000000
--- a/py-cytoolz/PLIST
+++ /dev/null
@@ -1,102 +0,0 @@
-@comment $NetBSD$
-${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
-${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
-${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
-${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
-${PYSITELIB}/${EGG_INFODIR}/requires.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
-${PYSITELIB}/cytoolz/__init__.pxd
-${PYSITELIB}/cytoolz/__init__.py
-${PYSITELIB}/cytoolz/__init__.pyc
-${PYSITELIB}/cytoolz/__init__.pyo
-${PYSITELIB}/cytoolz/_signatures.py
-${PYSITELIB}/cytoolz/_signatures.pyc
-${PYSITELIB}/cytoolz/_signatures.pyo
-${PYSITELIB}/cytoolz/_version.py
-${PYSITELIB}/cytoolz/_version.pyc
-${PYSITELIB}/cytoolz/_version.pyo
-${PYSITELIB}/cytoolz/compatibility.py
-${PYSITELIB}/cytoolz/compatibility.pyc
-${PYSITELIB}/cytoolz/compatibility.pyo
-${PYSITELIB}/cytoolz/cpython.pxd
-${PYSITELIB}/cytoolz/curried/__init__.py
-${PYSITELIB}/cytoolz/curried/__init__.pyc
-${PYSITELIB}/cytoolz/curried/__init__.pyo
-${PYSITELIB}/cytoolz/curried/exceptions.py
-${PYSITELIB}/cytoolz/curried/exceptions.pyc
-${PYSITELIB}/cytoolz/curried/exceptions.pyo
-${PYSITELIB}/cytoolz/curried/operator.py
-${PYSITELIB}/cytoolz/curried/operator.pyc
-${PYSITELIB}/cytoolz/curried/operator.pyo
-${PYSITELIB}/cytoolz/dicttoolz.pxd
-${PYSITELIB}/cytoolz/dicttoolz.pyx
-${PYSITELIB}/cytoolz/dicttoolz.so
-${PYSITELIB}/cytoolz/functoolz.pxd
-${PYSITELIB}/cytoolz/functoolz.pyx
-${PYSITELIB}/cytoolz/functoolz.so
-${PYSITELIB}/cytoolz/itertoolz.pxd
-${PYSITELIB}/cytoolz/itertoolz.pyx
-${PYSITELIB}/cytoolz/itertoolz.so
-${PYSITELIB}/cytoolz/recipes.pxd
-${PYSITELIB}/cytoolz/recipes.pyx
-${PYSITELIB}/cytoolz/recipes.so
-${PYSITELIB}/cytoolz/tests/dev_skip_test.py
-${PYSITELIB}/cytoolz/tests/dev_skip_test.pyc
-${PYSITELIB}/cytoolz/tests/dev_skip_test.pyo
-${PYSITELIB}/cytoolz/tests/test_compatibility.py
-${PYSITELIB}/cytoolz/tests/test_compatibility.pyc
-${PYSITELIB}/cytoolz/tests/test_compatibility.pyo
-${PYSITELIB}/cytoolz/tests/test_curried.py
-${PYSITELIB}/cytoolz/tests/test_curried.pyc
-${PYSITELIB}/cytoolz/tests/test_curried.pyo
-${PYSITELIB}/cytoolz/tests/test_curried_toolzlike.py
-${PYSITELIB}/cytoolz/tests/test_curried_toolzlike.pyc
-${PYSITELIB}/cytoolz/tests/test_curried_toolzlike.pyo
-${PYSITELIB}/cytoolz/tests/test_dev_skip_test.py
-${PYSITELIB}/cytoolz/tests/test_dev_skip_test.pyc
-${PYSITELIB}/cytoolz/tests/test_dev_skip_test.pyo
-${PYSITELIB}/cytoolz/tests/test_dicttoolz.py
-${PYSITELIB}/cytoolz/tests/test_dicttoolz.pyc
-${PYSITELIB}/cytoolz/tests/test_dicttoolz.pyo
-${PYSITELIB}/cytoolz/tests/test_docstrings.py
-${PYSITELIB}/cytoolz/tests/test_docstrings.pyc
-${PYSITELIB}/cytoolz/tests/test_docstrings.pyo
-${PYSITELIB}/cytoolz/tests/test_doctests.py
-${PYSITELIB}/cytoolz/tests/test_doctests.pyc
-${PYSITELIB}/cytoolz/tests/test_doctests.pyo
-${PYSITELIB}/cytoolz/tests/test_embedded_sigs.py
-${PYSITELIB}/cytoolz/tests/test_embedded_sigs.pyc
-${PYSITELIB}/cytoolz/tests/test_embedded_sigs.pyo
-${PYSITELIB}/cytoolz/tests/test_functoolz.py
-${PYSITELIB}/cytoolz/tests/test_functoolz.pyc
-${PYSITELIB}/cytoolz/tests/test_functoolz.pyo
-${PYSITELIB}/cytoolz/tests/test_inspect_args.py
-${PYSITELIB}/cytoolz/tests/test_inspect_args.pyc
-${PYSITELIB}/cytoolz/tests/test_inspect_args.pyo
-${PYSITELIB}/cytoolz/tests/test_itertoolz.py
-${PYSITELIB}/cytoolz/tests/test_itertoolz.pyc
-${PYSITELIB}/cytoolz/tests/test_itertoolz.pyo
-${PYSITELIB}/cytoolz/tests/test_none_safe.py
-${PYSITELIB}/cytoolz/tests/test_none_safe.pyc
-${PYSITELIB}/cytoolz/tests/test_none_safe.pyo
-${PYSITELIB}/cytoolz/tests/test_recipes.py
-${PYSITELIB}/cytoolz/tests/test_recipes.pyc
-${PYSITELIB}/cytoolz/tests/test_recipes.pyo
-${PYSITELIB}/cytoolz/tests/test_serialization.py
-${PYSITELIB}/cytoolz/tests/test_serialization.pyc
-${PYSITELIB}/cytoolz/tests/test_serialization.pyo
-${PYSITELIB}/cytoolz/tests/test_signatures.py
-${PYSITELIB}/cytoolz/tests/test_signatures.pyc
-${PYSITELIB}/cytoolz/tests/test_signatures.pyo
-${PYSITELIB}/cytoolz/tests/test_tlz.py
-${PYSITELIB}/cytoolz/tests/test_tlz.pyc
-${PYSITELIB}/cytoolz/tests/test_tlz.pyo
-${PYSITELIB}/cytoolz/tests/test_utils.py
-${PYSITELIB}/cytoolz/tests/test_utils.pyc
-${PYSITELIB}/cytoolz/tests/test_utils.pyo
-${PYSITELIB}/cytoolz/utils.pxd
-${PYSITELIB}/cytoolz/utils.pyx
-${PYSITELIB}/cytoolz/utils.so
-${PYSITELIB}/cytoolz/utils_test.py
-${PYSITELIB}/cytoolz/utils_test.pyc
-${PYSITELIB}/cytoolz/utils_test.pyo
diff --git a/py-cytoolz/distinfo b/py-cytoolz/distinfo
deleted file mode 100644
index 786325a293..0000000000
--- a/py-cytoolz/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD: distinfo,v 1.1 2014/05/05 23:50:47 jihbed Exp $
-
-RMD160 (cytoolz-0.10.1.tar.gz) = 1093edea2b7306f75f46d7ce04268320ed9fa09c
-SHA512 (cytoolz-0.10.1.tar.gz) = 55c4fca8d4ace766a8241a25a6c4924971b7e7068ee79ad65fa8aac136aa1f88e57337c0ec278ee9e8544c6e96dd31138b39d7cc28cd91ff0e53a71f8dec55d1
-Size (cytoolz-0.10.1.tar.gz) = 475647 bytes
diff --git a/py-guppy3/DESCR b/py-guppy3/DESCR
deleted file mode 100644
index fad6c545cd..0000000000
--- a/py-guppy3/DESCR
+++ /dev/null
@@ -1,10 +0,0 @@
-A Python Programming Environment & Heap analysis toolset.
-
-This package contains the following subpackages:
-
- etc - Support modules. Contains especially the Glue protocol module.
- gsl - The Guppy Specification Language implementation. This can be
- used to create documents and tests from a common source.
- heapy - The heap analysis toolset. It can be used to find information
- about the objects in the heap and display the information in various ways.
- sets - Bitsets and 'nodesets' implemented in C
\ No newline at end of file
diff --git a/py-guppy3/Makefile b/py-guppy3/Makefile
deleted file mode 100644
index c7dd0b967c..0000000000
--- a/py-guppy3/Makefile
+++ /dev/null
@@ -1,17 +0,0 @@
-# $NetBSD$
-
-DISTNAME= guppy3-3.0.10.post1
-PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
-CATEGORIES= devel python
-MASTER_SITES= https://files.pythonhosted.org/packages/58/a6/6b7ab2dba33a8f32d1639c6a52d10d111255062dedc87a45ca5c6381bd0a/
-
-MAINTAINER= kamelderouiche%yahoo.com@localhost
-HOMEPAGE= https://github.com/zhuyifei1999/guppy3/
-COMMENT= Python Programming Environment & Heap analysis toolset
-LICENSE= mit
-
-
-PYTHON_VERSIONS_INCOMPATIBLE= 27
-
-.include "../../lang/python/egg.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-guppy3/PLIST b/py-guppy3/PLIST
deleted file mode 100644
index 39411d7d67..0000000000
--- a/py-guppy3/PLIST
+++ /dev/null
@@ -1,226 +0,0 @@
-@comment $NetBSD$
-${PYSITELIB}/guppy/__init__.py
-${PYSITELIB}/guppy/__init__.pyc
-${PYSITELIB}/guppy/__init__.pyo
-${PYSITELIB}/guppy/etc/Cat.py
-${PYSITELIB}/guppy/etc/Cat.pyc
-${PYSITELIB}/guppy/etc/Cat.pyo
-${PYSITELIB}/guppy/etc/Code.py
-${PYSITELIB}/guppy/etc/Code.pyc
-${PYSITELIB}/guppy/etc/Code.pyo
-${PYSITELIB}/guppy/etc/Descriptor.py
-${PYSITELIB}/guppy/etc/Descriptor.pyc
-${PYSITELIB}/guppy/etc/Descriptor.pyo
-${PYSITELIB}/guppy/etc/FSA.py
-${PYSITELIB}/guppy/etc/FSA.pyc
-${PYSITELIB}/guppy/etc/FSA.pyo
-${PYSITELIB}/guppy/etc/Glue.py
-${PYSITELIB}/guppy/etc/Glue.pyc
-${PYSITELIB}/guppy/etc/Glue.pyo
-${PYSITELIB}/guppy/etc/Help.py
-${PYSITELIB}/guppy/etc/Help.pyc
-${PYSITELIB}/guppy/etc/Help.pyo
-${PYSITELIB}/guppy/etc/IterPermute.py
-${PYSITELIB}/guppy/etc/IterPermute.pyc
-${PYSITELIB}/guppy/etc/IterPermute.pyo
-${PYSITELIB}/guppy/etc/KanExtension.py
-${PYSITELIB}/guppy/etc/KanExtension.pyc
-${PYSITELIB}/guppy/etc/KanExtension.pyo
-${PYSITELIB}/guppy/etc/KnuthBendix.py
-${PYSITELIB}/guppy/etc/KnuthBendix.pyc
-${PYSITELIB}/guppy/etc/KnuthBendix.pyo
-${PYSITELIB}/guppy/etc/RE.py
-${PYSITELIB}/guppy/etc/RE.pyc
-${PYSITELIB}/guppy/etc/RE.pyo
-${PYSITELIB}/guppy/etc/RE_Rect.py
-${PYSITELIB}/guppy/etc/RE_Rect.pyc
-${PYSITELIB}/guppy/etc/RE_Rect.pyo
-${PYSITELIB}/guppy/etc/__init__.py
-${PYSITELIB}/guppy/etc/__init__.pyc
-${PYSITELIB}/guppy/etc/__init__.pyo
-${PYSITELIB}/guppy/etc/cmd.py
-${PYSITELIB}/guppy/etc/cmd.pyc
-${PYSITELIB}/guppy/etc/cmd.pyo
-${PYSITELIB}/guppy/etc/etc.py
-${PYSITELIB}/guppy/etc/etc.pyc
-${PYSITELIB}/guppy/etc/etc.pyo
-${PYSITELIB}/guppy/etc/textView.py
-${PYSITELIB}/guppy/etc/textView.pyc
-${PYSITELIB}/guppy/etc/textView.pyo
-${PYSITELIB}/guppy/etc/tkcursors.py
-${PYSITELIB}/guppy/etc/tkcursors.pyc
-${PYSITELIB}/guppy/etc/tkcursors.pyo
-${PYSITELIB}/guppy/etc/xterm.py
-${PYSITELIB}/guppy/etc/xterm.pyc
-${PYSITELIB}/guppy/etc/xterm.pyo
-${PYSITELIB}/guppy/gsl/Document.py
-${PYSITELIB}/guppy/gsl/Document.pyc
-${PYSITELIB}/guppy/gsl/Document.pyo
-${PYSITELIB}/guppy/gsl/DottedTree.py
-${PYSITELIB}/guppy/gsl/DottedTree.pyc
-${PYSITELIB}/guppy/gsl/DottedTree.pyo
-${PYSITELIB}/guppy/gsl/Exceptions.py
-${PYSITELIB}/guppy/gsl/Exceptions.pyc
-${PYSITELIB}/guppy/gsl/Exceptions.pyo
-${PYSITELIB}/guppy/gsl/FileIO.py
-${PYSITELIB}/guppy/gsl/FileIO.pyc
-${PYSITELIB}/guppy/gsl/FileIO.pyo
-${PYSITELIB}/guppy/gsl/Filer.py
-${PYSITELIB}/guppy/gsl/Filer.pyc
-${PYSITELIB}/guppy/gsl/Filer.pyo
-${PYSITELIB}/guppy/gsl/Gsml.py
-${PYSITELIB}/guppy/gsl/Gsml.pyc
-${PYSITELIB}/guppy/gsl/Gsml.pyo
-${PYSITELIB}/guppy/gsl/Help.py
-${PYSITELIB}/guppy/gsl/Help.pyc
-${PYSITELIB}/guppy/gsl/Help.pyo
-${PYSITELIB}/guppy/gsl/Html.py
-${PYSITELIB}/guppy/gsl/Html.pyc
-${PYSITELIB}/guppy/gsl/Html.pyo
-${PYSITELIB}/guppy/gsl/Latex.py
-${PYSITELIB}/guppy/gsl/Latex.pyc
-${PYSITELIB}/guppy/gsl/Latex.pyo
-${PYSITELIB}/guppy/gsl/Main.py
-${PYSITELIB}/guppy/gsl/Main.pyc
-${PYSITELIB}/guppy/gsl/Main.pyo
-${PYSITELIB}/guppy/gsl/SpecNodes.py
-${PYSITELIB}/guppy/gsl/SpecNodes.pyc
-${PYSITELIB}/guppy/gsl/SpecNodes.pyo
-${PYSITELIB}/guppy/gsl/Tester.py
-${PYSITELIB}/guppy/gsl/Tester.pyc
-${PYSITELIB}/guppy/gsl/Tester.pyo
-${PYSITELIB}/guppy/gsl/Text.py
-${PYSITELIB}/guppy/gsl/Text.pyc
-${PYSITELIB}/guppy/gsl/Text.pyo
-${PYSITELIB}/guppy/gsl/XHTML.py
-${PYSITELIB}/guppy/gsl/XHTML.pyc
-${PYSITELIB}/guppy/gsl/XHTML.pyo
-${PYSITELIB}/guppy/gsl/__init__.py
-${PYSITELIB}/guppy/gsl/__init__.pyc
-${PYSITELIB}/guppy/gsl/__init__.pyo
-${PYSITELIB}/guppy/heapy/Classifiers.py
-${PYSITELIB}/guppy/heapy/Classifiers.pyc
-${PYSITELIB}/guppy/heapy/Classifiers.pyo
-${PYSITELIB}/guppy/heapy/Console.py
-${PYSITELIB}/guppy/heapy/Console.pyc
-${PYSITELIB}/guppy/heapy/Console.pyo
-${PYSITELIB}/guppy/heapy/Doc.py
-${PYSITELIB}/guppy/heapy/Doc.pyc
-${PYSITELIB}/guppy/heapy/Doc.pyo
-${PYSITELIB}/guppy/heapy/ImpSet.py
-${PYSITELIB}/guppy/heapy/ImpSet.pyc
-${PYSITELIB}/guppy/heapy/ImpSet.pyo
-${PYSITELIB}/guppy/heapy/Monitor.py
-${PYSITELIB}/guppy/heapy/Monitor.pyc
-${PYSITELIB}/guppy/heapy/Monitor.pyo
-${PYSITELIB}/guppy/heapy/OutputHandling.py
-${PYSITELIB}/guppy/heapy/OutputHandling.pyc
-${PYSITELIB}/guppy/heapy/OutputHandling.pyo
-${PYSITELIB}/guppy/heapy/Part.py
-${PYSITELIB}/guppy/heapy/Part.pyc
-${PYSITELIB}/guppy/heapy/Part.pyo
-${PYSITELIB}/guppy/heapy/Path.py
-${PYSITELIB}/guppy/heapy/Path.pyc
-${PYSITELIB}/guppy/heapy/Path.pyo
-${PYSITELIB}/guppy/heapy/Prof.py
-${PYSITELIB}/guppy/heapy/Prof.pyc
-${PYSITELIB}/guppy/heapy/Prof.pyo
-${PYSITELIB}/guppy/heapy/RM.py
-${PYSITELIB}/guppy/heapy/RM.pyc
-${PYSITELIB}/guppy/heapy/RM.pyo
-${PYSITELIB}/guppy/heapy/RefPat.py
-${PYSITELIB}/guppy/heapy/RefPat.pyc
-${PYSITELIB}/guppy/heapy/RefPat.pyo
-${PYSITELIB}/guppy/heapy/Remote.py
-${PYSITELIB}/guppy/heapy/Remote.pyc
-${PYSITELIB}/guppy/heapy/Remote.pyo
-${PYSITELIB}/guppy/heapy/RemoteConstants.py
-${PYSITELIB}/guppy/heapy/RemoteConstants.pyc
-${PYSITELIB}/guppy/heapy/RemoteConstants.pyo
-${PYSITELIB}/guppy/heapy/Spec.py
-${PYSITELIB}/guppy/heapy/Spec.pyc
-${PYSITELIB}/guppy/heapy/Spec.pyo
-${PYSITELIB}/guppy/heapy/Target.py
-${PYSITELIB}/guppy/heapy/Target.pyc
-${PYSITELIB}/guppy/heapy/Target.pyo
-${PYSITELIB}/guppy/heapy/UniSet.py
-${PYSITELIB}/guppy/heapy/UniSet.pyc
-${PYSITELIB}/guppy/heapy/UniSet.pyo
-${PYSITELIB}/guppy/heapy/Use.py
-${PYSITELIB}/guppy/heapy/Use.pyc
-${PYSITELIB}/guppy/heapy/Use.pyo
-${PYSITELIB}/guppy/heapy/View.py
-${PYSITELIB}/guppy/heapy/View.pyc
-${PYSITELIB}/guppy/heapy/View.pyo
-${PYSITELIB}/guppy/heapy/__init__.py
-${PYSITELIB}/guppy/heapy/__init__.pyc
-${PYSITELIB}/guppy/heapy/__init__.pyo
-${PYSITELIB}/guppy/heapy/heapyc.so
-${PYSITELIB}/guppy/heapy/pbhelp.py
-${PYSITELIB}/guppy/heapy/pbhelp.pyc
-${PYSITELIB}/guppy/heapy/pbhelp.pyo
-${PYSITELIB}/guppy/heapy/test/__init__.py
-${PYSITELIB}/guppy/heapy/test/__init__.pyc
-${PYSITELIB}/guppy/heapy/test/__init__.pyo
-${PYSITELIB}/guppy/heapy/test/support.py
-${PYSITELIB}/guppy/heapy/test/support.pyc
-${PYSITELIB}/guppy/heapy/test/support.pyo
-${PYSITELIB}/guppy/heapy/test/test_Classifiers.py
-${PYSITELIB}/guppy/heapy/test/test_Classifiers.pyc
-${PYSITELIB}/guppy/heapy/test/test_Classifiers.pyo
-${PYSITELIB}/guppy/heapy/test/test_ER.py
-${PYSITELIB}/guppy/heapy/test/test_ER.pyc
-${PYSITELIB}/guppy/heapy/test/test_ER.pyo
-${PYSITELIB}/guppy/heapy/test/test_OutputHandling.py
-${PYSITELIB}/guppy/heapy/test/test_OutputHandling.pyc
-${PYSITELIB}/guppy/heapy/test/test_OutputHandling.pyo
-${PYSITELIB}/guppy/heapy/test/test_Part.py
-${PYSITELIB}/guppy/heapy/test/test_Part.pyc
-${PYSITELIB}/guppy/heapy/test/test_Part.pyo
-${PYSITELIB}/guppy/heapy/test/test_Path.py
-${PYSITELIB}/guppy/heapy/test/test_Path.pyc
-${PYSITELIB}/guppy/heapy/test/test_Path.pyo
-${PYSITELIB}/guppy/heapy/test/test_RefPat.py
-${PYSITELIB}/guppy/heapy/test/test_RefPat.pyc
-${PYSITELIB}/guppy/heapy/test/test_RefPat.pyo
-${PYSITELIB}/guppy/heapy/test/test_RetaGraph.py
-${PYSITELIB}/guppy/heapy/test/test_RetaGraph.pyc
-${PYSITELIB}/guppy/heapy/test/test_RetaGraph.pyo
-${PYSITELIB}/guppy/heapy/test/test_Spec.py
-${PYSITELIB}/guppy/heapy/test/test_Spec.pyc
-${PYSITELIB}/guppy/heapy/test/test_Spec.pyo
-${PYSITELIB}/guppy/heapy/test/test_UniSet.py
-${PYSITELIB}/guppy/heapy/test/test_UniSet.pyc
-${PYSITELIB}/guppy/heapy/test/test_UniSet.pyo
-${PYSITELIB}/guppy/heapy/test/test_View.py
-${PYSITELIB}/guppy/heapy/test/test_View.pyc
-${PYSITELIB}/guppy/heapy/test/test_View.pyo
-${PYSITELIB}/guppy/heapy/test/test_all.py
-${PYSITELIB}/guppy/heapy/test/test_all.pyc
-${PYSITELIB}/guppy/heapy/test/test_all.pyo
-${PYSITELIB}/guppy/heapy/test/test_dependencies.py
-${PYSITELIB}/guppy/heapy/test/test_dependencies.pyc
-${PYSITELIB}/guppy/heapy/test/test_dependencies.pyo
-${PYSITELIB}/guppy/heapy/test/test_gsl.py
-${PYSITELIB}/guppy/heapy/test/test_gsl.pyc
-${PYSITELIB}/guppy/heapy/test/test_gsl.pyo
-${PYSITELIB}/guppy/heapy/test/test_heapyc.py
-${PYSITELIB}/guppy/heapy/test/test_heapyc.pyc
-${PYSITELIB}/guppy/heapy/test/test_heapyc.pyo
-${PYSITELIB}/guppy/heapy/test/test_menuleak.py
-${PYSITELIB}/guppy/heapy/test/test_menuleak.pyc
-${PYSITELIB}/guppy/heapy/test/test_menuleak.pyo
-${PYSITELIB}/guppy/heapy/test/test_sf.py
-${PYSITELIB}/guppy/heapy/test/test_sf.pyc
-${PYSITELIB}/guppy/heapy/test/test_sf.pyo
-${PYSITELIB}/guppy/sets/__init__.py
-${PYSITELIB}/guppy/sets/__init__.pyc
-${PYSITELIB}/guppy/sets/__init__.pyo
-${PYSITELIB}/guppy/sets/setsc.so
-${PYSITELIB}/guppy/sets/test.py
-${PYSITELIB}/guppy/sets/test.pyc
-${PYSITELIB}/guppy/sets/test.pyo
-${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
-${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
-${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
diff --git a/py-guppy3/distinfo b/py-guppy3/distinfo
deleted file mode 100644
index 7da1563d89..0000000000
--- a/py-guppy3/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (guppy3-3.0.10.post1.tar.gz) = 967fbb20f29dab51a808794b8da787e144693540
-SHA512 (guppy3-3.0.10.post1.tar.gz) = 9fc25775a26a6b8d0576c33eb02fb14d34139d23b44ef479df6af5a559012a15046c92a2156f2a8e5c22610c1e7f7217db201c0d6f6cda7d2492faf413305223
-Size (guppy3-3.0.10.post1.tar.gz) = 328698 bytes
diff --git a/py-mdanalysis/Makefile b/py-mdanalysis/Makefile
index 03a22a9113..9bcdae8b92 100644
--- a/py-mdanalysis/Makefile
+++ b/py-mdanalysis/Makefile
@@ -2,7 +2,7 @@
DISTNAME= MDAnalysis-0.15.0
PKGNAME= ${PYPKGPREFIX}-${DISTNAME:tl}
-CATEGORIES= biology
+CATEGORIES= biology python
MASTER_SITES= ${MASTER_SITE_PYPI:=M/MDAnalysis/}
MAINTAINER= jihbed.research%gmail.com@localhost
@@ -10,7 +10,7 @@ HOMEPAGE= https://www.mdanalysis.org/
COMMENT= Library to analyze and manipulate molecular dynamics trajectories
LICENSE= gnu-gpl-v2
-DEPENDS+= ${PYPKGPREFIX}-biopython>=1.63:../../wip/biopython
+DEPENDS+= ${PYPKGPREFIX}-biopython>=1.63:../../biology/biopython
DEPENDS+= ${PYPKGPREFIX}-networkx-[0-9]*:../../math/py-networkx
DEPENDS+= ${PYPKGPREFIX}-six-[0-9]*:../../lang/py-six
# also needs unpackaged GridDataFormats
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