UPDATE biology/py-biopython [Re: numpy status update and help requested]

Martin Reindl Fri, 16 Oct 2020 00:00:29 -0700

On Sun, Oct 11, 2020 at 06:12:20PM -0400, Daniel Dickman wrote:
> - biology/py-biopython


Hello Daniel,

attached is an update for biopython to 1.78. I did an complete overhaul of
the port including switch to python3 with quirks and conflict markers. Tests
still run quite alright on amd64. Comments? OKs?

-m


Index: biology/py-biopython/Makefile
===================================================================
RCS file: /cvs/ports/biology/py-biopython/Makefile,v
retrieving revision 1.30
diff -u -p -r1.30 Makefile
--- biology/py-biopython/Makefile       12 Jul 2019 20:43:44 -0000      1.30
+++ biology/py-biopython/Makefile       16 Oct 2020 06:42:58 -0000
@@ -1,29 +1,35 @@
 # $OpenBSD: Makefile,v 1.30 2019/07/12 20:43:44 sthen Exp $
 
-COMMENT=               Python tools for computational molecular biology
+COMMENT =              Python tools for computational molecular biology
 
-MODPY_EGG_VERSION=     1.66
-DISTNAME=              biopython-${MODPY_EGG_VERSION}
-CATEGORIES=            biology
-REVISION=              2
+MODPY_EGG_VERSION =    1.78
+DISTNAME =             biopython-${MODPY_EGG_VERSION}
+CATEGORIES =           biology
+PKGNAME =              py-${DISTNAME}
 
-HOMEPAGE=              http://www.biopython.org/
+HOMEPAGE =             http://www.biopython.org/
 
-# BSD-like 
-PERMIT_PACKAGE=        Yes
+MAINTAINER =           Martin Reindl <mar...@catai.org>
 
-MASTER_SITES=  ${HOMEPAGE}DIST/
+# BSD-like
+PERMIT_PACKAGE =       Yes
 
-MODULES=       lang/python
+MODULES =      lang/python
 
-WANTLIB+=      ${MODPY_WANTLIB} pthread
+MODPY_PI =              Yes
+MODPY_SETUPTOOLS =      Yes
 
-BUILD_DEPENDS= devel/swig \
-               math/py-numpy
-RUN_DEPENDS=   math/py-numpy \
-               print/py-reportlab
+FLAVORS =              python3
+FLAVOR =               python3
 
-CFLAGS+=       -fPIC
+WANTLIB +=     pthread
+
+BUILD_DEPENDS =        devel/swig \
+               math/py-numpy${MODPY_FLAVOR}
+RUN_DEPENDS =  math/py-numpy${MODPY_FLAVOR} \
+               print/py-reportlab${MODPY_FLAVOR}
+
+CFLAGS +=      -fPIC
 
 post-install:
        ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/py-biopython/
Index: biology/py-biopython/distinfo
===================================================================
RCS file: /cvs/ports/biology/py-biopython/distinfo,v
retrieving revision 1.9
diff -u -p -r1.9 distinfo
--- biology/py-biopython/distinfo       29 Nov 2015 08:22:11 -0000      1.9
+++ biology/py-biopython/distinfo       16 Oct 2020 06:42:58 -0000
@@ -1,2 +1,2 @@
-SHA256 (biopython-1.66.tar.gz) = UXjqOzQ7HYcQ85IFOGCT5Tae1lOqAg4bDEt2IqWTRsE=
-SIZE (biopython-1.66.tar.gz) = 13724754
+SHA256 (biopython-1.78.tar.gz) = HuCgtsI3ZoD+pmQtUIC6pBn9c98QSmLViouveou+RWQ=
+SIZE (biopython-1.78.tar.gz) = 16895184
Index: biology/py-biopython/patches/patch-Tests_run_tests_py
===================================================================
RCS file: /cvs/ports/biology/py-biopython/patches/patch-Tests_run_tests_py,v
retrieving revision 1.4
diff -u -p -r1.4 patch-Tests_run_tests_py
--- biology/py-biopython/patches/patch-Tests_run_tests_py       18 Jul 2015 
22:24:48 -0000      1.4
+++ biology/py-biopython/patches/patch-Tests_run_tests_py       16 Oct 2020 
06:42:58 -0000
@@ -1,13 +1,16 @@
 $OpenBSD: patch-Tests_run_tests_py,v 1.4 2015/07/18 22:24:48 jasper Exp $
---- Tests/run_tests.py.orig    Sat Dec 17 11:34:46 2005
-+++ Tests/run_tests.py Sat Jul 18 15:18:10 2015
-@@ -196,11 +196,8 @@ def main(argv):
+Index: Tests/run_tests.py
+--- Tests/run_tests.py.orig
++++ Tests/run_tests.py
+@@ -150,13 +150,10 @@ def main(argv):
      # A. Because Martel may not be in ../build/lib.*
      test_path = sys.path[0] or "."
      source_path = os.path.abspath("%s/.." % test_path)
 -    sys.path.insert(1, source_path)
-     build_path = os.path.abspath("%s/../build/lib.%s-%s" % (
-         test_path, distutils.util.get_platform(), sys.version[:3]))
+     build_path = os.path.abspath(
+         "%s/../build/lib.%s-%s"
+         % (test_path, distutils.util.get_platform(), sys.version[:3])
+     )
 -    if os.access(build_path, os.F_OK):
 -        sys.path.insert(1, build_path)
  
Index: biology/py-biopython/pkg/PLIST
===================================================================
RCS file: /cvs/ports/biology/py-biopython/pkg/PLIST,v
retrieving revision 1.9
diff -u -p -r1.9 PLIST
--- biology/py-biopython/pkg/PLIST      29 Nov 2015 08:22:11 -0000      1.9
+++ biology/py-biopython/pkg/PLIST      16 Oct 2020 06:42:58 -0000
@@ -1,113 +1,161 @@
 @comment $OpenBSD: PLIST,v 1.9 2015/11/29 08:22:11 ajacoutot Exp $
+@conflict biopython-*
+@pkgpath biology/py-biopython
 lib/python${MODPY_VERSION}/site-packages/Bio/
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 lib/python${MODPY_VERSION}/site-packages/Bio/Affy/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Affy/__init__.pyc
+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Affy/${MODPY_PYCACHE}/
+lib/python${MODPY_VERSION}/site-packages/Bio/Affy/${MODPY_PYCACHE}CelFile.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Affy/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
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-lib/python${MODPY_VERSION}/site-packages/Bio/Align/AlignInfo.pyc
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lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_ClustalOmega.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_ClustalOmega.pyc
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-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Clustalw.pyc
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-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Dialign.pyc
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-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_MSAProbs.pyc
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-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Mafft.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Muscle.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Muscle.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Prank.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Prank.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Probcons.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Probcons.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_TCoffee.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_TCoffee.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Generic.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/Generic.pyc
+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/${MODPY_PYCACHE}/
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/${MODPY_PYCACHE}_ClustalOmega.${MODPY_PYC_MAGIC_TAG}pyc
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+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/${MODPY_PYCACHE}_Muscle.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/${MODPY_PYCACHE}_Prank.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/${MODPY_PYCACHE}_Probcons.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/${MODPY_PYCACHE}_TCoffee.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/__init__.pyc
+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Align/${MODPY_PYCACHE}/
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/${MODPY_PYCACHE}AlignInfo.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/_aligners.c
+@so lib/python${MODPY_VERSION}/site-packages/Bio/Align/_aligners.so
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/substitution_matrices/
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/substitution_matrices/__init__.py
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-lib/python${MODPY_VERSION}/site-packages/Bio/AlignIO/Interfaces.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/AlignIO/MafIO.py
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-lib/python${MODPY_VERSION}/site-packages/Bio/AlignIO/__init__.pyc
+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/AlignIO/${MODPY_PYCACHE}/
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+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Alphabet/${MODPY_PYCACHE}/
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+lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/${MODPY_PYCACHE}Primer3.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/${MODPY_PYCACHE}PrimerSearch.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/Docsum_3_0.dtd
@@ -225,6 +273,7 @@ lib/python${MODPY_VERSION}/site-packages
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_Submit.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_Systems.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_TSeq.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_TxInit.dtd
@@ -303,13 +352,17 @@ lib/python${MODPY_VERSION}/site-packages
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/link.ent
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/list.ent
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/math.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/mathml-in-pubmed.mod
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/mathml2-qname-1.mod
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/mathml2.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/mathml3-qname1.mod
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/mathml3.dtd
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 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/modules.ent
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd
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 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/nlmcommon_080101.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/nlmcommon_090101.dtd
@@ -346,724 +399,714 @@ lib/python${MODPY_VERSION}/site-packages
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 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_140101.dtd
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+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_180101.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_180601.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_190101.dtd
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-lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/Parser.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/XSDs/
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/XSDs/IPGReportSet.xsd
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-lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/__init__.pyc
+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/${MODPY_PYCACHE}/
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/${MODPY_PYCACHE}Parser.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
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+lib/python${MODPY_VERSION}/site-packages/Bio/codonalign/${MODPY_PYCACHE}codonalignment.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/codonalign/${MODPY_PYCACHE}codonseq.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/codonalign/chisq.py
-lib/python${MODPY_VERSION}/site-packages/Bio/codonalign/chisq.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/codonalign/codonalignment.py
-lib/python${MODPY_VERSION}/site-packages/Bio/codonalign/codonalignment.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/codonalign/codonalphabet.py
-lib/python${MODPY_VERSION}/site-packages/Bio/codonalign/codonalphabet.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/codonalign/codonseq.py
-lib/python${MODPY_VERSION}/site-packages/Bio/codonalign/codonseq.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/cpairwise2.so
+@so lib/python${MODPY_VERSION}/site-packages/Bio/cpairwise2.so
+lib/python${MODPY_VERSION}/site-packages/Bio/cpairwise2module.c
 lib/python${MODPY_VERSION}/site-packages/Bio/kNN.py
-lib/python${MODPY_VERSION}/site-packages/Bio/kNN.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/_pwm.so
+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}/
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}alignace.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}clusterbuster.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}mast.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}matrix.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}meme.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}minimal.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}pfm.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}thresholds.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}transfac.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/${MODPY_PYCACHE}xms.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/_pwm.c
+@so lib/python${MODPY_VERSION}/site-packages/Bio/motifs/_pwm.so
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/alignace.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/alignace.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/applications/
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/applications/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/applications/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/applications/_alignace.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/applications/_alignace.pyc
+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/motifs/applications/${MODPY_PYCACHE}/
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/applications/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/applications/${MODPY_PYCACHE}_xxmotif.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/applications/_xxmotif.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/applications/_xxmotif.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/clusterbuster.py
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/jaspar/
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/jaspar/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/jaspar/__init__.pyc
+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/motifs/jaspar/${MODPY_PYCACHE}/
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/jaspar/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/jaspar/${MODPY_PYCACHE}db.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/jaspar/db.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/jaspar/db.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/mast.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/mast.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/matrix.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/matrix.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/meme.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/meme.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/minimal.py
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/pfm.py
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/thresholds.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/thresholds.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/motifs/transfac.py
-lib/python${MODPY_VERSION}/site-packages/Bio/motifs/transfac.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/motifs/xms.py
 lib/python${MODPY_VERSION}/site-packages/Bio/pairwise2.py
-lib/python${MODPY_VERSION}/site-packages/Bio/pairwise2.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/trie.so
-lib/python${MODPY_VERSION}/site-packages/Bio/triefind.py
-lib/python${MODPY_VERSION}/site-packages/Bio/triefind.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/phenotype/
+lib/python${MODPY_VERSION}/site-packages/Bio/phenotype/__init__.py
+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/phenotype/${MODPY_PYCACHE}/
+lib/python${MODPY_VERSION}/site-packages/Bio/phenotype/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/phenotype/${MODPY_PYCACHE}phen_micro.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/phenotype/${MODPY_PYCACHE}pm_fitting.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/phenotype/phen_micro.py
+lib/python${MODPY_VERSION}/site-packages/Bio/phenotype/pm_fitting.py
 lib/python${MODPY_VERSION}/site-packages/BioSQL/
 lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeq.py
-lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeq.pyc
 lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeqDatabase.py
-lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeqDatabase.pyc
 lib/python${MODPY_VERSION}/site-packages/BioSQL/DBUtils.py
-lib/python${MODPY_VERSION}/site-packages/BioSQL/DBUtils.pyc
 lib/python${MODPY_VERSION}/site-packages/BioSQL/Loader.py
-lib/python${MODPY_VERSION}/site-packages/BioSQL/Loader.pyc
 lib/python${MODPY_VERSION}/site-packages/BioSQL/__init__.py
-lib/python${MODPY_VERSION}/site-packages/BioSQL/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info
-share/doc/${MODPY_PY_PREFIX}biopython/
-share/doc/${MODPY_PY_PREFIX}biopython/Tutorial.pdf
-share/doc/${MODPY_PY_PREFIX}biopython/biopdb_faq.pdf
-share/examples/${MODPY_PY_PREFIX}biopython/
-share/examples/${MODPY_PY_PREFIX}biopython/ACT_example.py
-share/examples/${MODPY_PY_PREFIX}biopython/PF05371_seed.sth
-share/examples/${MODPY_PY_PREFIX}biopython/Proux_et_al_2002_Figure_6.py
-share/examples/${MODPY_PY_PREFIX}biopython/clustal_run.py
-share/examples/${MODPY_PY_PREFIX}biopython/fasta_dictionary.py
-share/examples/${MODPY_PY_PREFIX}biopython/fasta_iterator.py
-share/examples/${MODPY_PY_PREFIX}biopython/getgene.py
-share/examples/${MODPY_PY_PREFIX}biopython/ls_orchid.fasta
-share/examples/${MODPY_PY_PREFIX}biopython/ls_orchid.gbk
-share/examples/${MODPY_PY_PREFIX}biopython/ls_orchid.gbk.bgz
-share/examples/${MODPY_PY_PREFIX}biopython/m_cold.fasta
-share/examples/${MODPY_PY_PREFIX}biopython/make_subsmat.py
-share/examples/${MODPY_PY_PREFIX}biopython/my_blast.xml
-share/examples/${MODPY_PY_PREFIX}biopython/my_blat.psl
-share/examples/${MODPY_PY_PREFIX}biopython/nmr/
-share/examples/${MODPY_PY_PREFIX}biopython/nmr/noed.xpk
-share/examples/${MODPY_PY_PREFIX}biopython/nmr/simplepredict.py
-share/examples/${MODPY_PY_PREFIX}biopython/opuntia.aln
-share/examples/${MODPY_PY_PREFIX}biopython/opuntia.dnd
-share/examples/${MODPY_PY_PREFIX}biopython/opuntia.fasta
-share/examples/${MODPY_PY_PREFIX}biopython/protein.aln
-share/examples/${MODPY_PY_PREFIX}biopython/simple.dnd
-share/examples/${MODPY_PY_PREFIX}biopython/swissprot.py
-share/examples/${MODPY_PY_PREFIX}biopython/www_blast.py
+${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/BioSQL/${MODPY_PYCACHE}/
+lib/python${MODPY_VERSION}/site-packages/BioSQL/${MODPY_PYCACHE}BioSeq.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/BioSQL/${MODPY_PYCACHE}BioSeqDatabase.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/BioSQL/${MODPY_PYCACHE}DBUtils.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/BioSQL/${MODPY_PYCACHE}Loader.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/BioSQL/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/
+lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/PKG-INFO
+lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/SOURCES.txt
+lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/dependency_links.txt
+lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/requires.txt
+lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/top_level.txt
+share/doc/py-biopython/
+share/doc/py-biopython/Tutorial.pdf
+share/doc/py-biopython/biopdb_faq.pdf
+share/examples/py-biopython/
+share/examples/py-biopython/ACT_example.py
+share/examples/py-biopython/PF05371_seed.sth
+share/examples/py-biopython/Plates.csv
+share/examples/py-biopython/Proux_et_al_2002_Figure_6.py
+share/examples/py-biopython/alpha.faa
+share/examples/py-biopython/beta.faa
+share/examples/py-biopython/clustal_run.py
+share/examples/py-biopython/ec_5.4.2.2.txt
+share/examples/py-biopython/fasta_dictionary.py
+share/examples/py-biopython/fasta_iterator.py
+share/examples/py-biopython/getgene.py
+share/examples/py-biopython/ls_orchid.fasta
+share/examples/py-biopython/ls_orchid.gbk
+share/examples/py-biopython/ls_orchid.gbk.bgz
+share/examples/py-biopython/ls_orchid.gbk.bz2
+share/examples/py-biopython/ls_orchid.gbk.gz
+share/examples/py-biopython/m_cold.fasta
+share/examples/py-biopython/my_blast.xml
+share/examples/py-biopython/my_blat.psl
+share/examples/py-biopython/nmr/
+share/examples/py-biopython/nmr/noed.xpk
+share/examples/py-biopython/nmr/simplepredict.py
+share/examples/py-biopython/opuntia.aln
+share/examples/py-biopython/opuntia.dnd
+share/examples/py-biopython/opuntia.fasta
+share/examples/py-biopython/simple.dnd
+share/examples/py-biopython/swissprot.py
+share/examples/py-biopython/www_blast.py
Index: devel/quirks/Makefile
===================================================================
RCS file: /cvs/ports/devel/quirks/Makefile,v
retrieving revision 1.1066
diff -u -p -r1.1066 Makefile
--- devel/quirks/Makefile       14 Oct 2020 11:17:10 -0000      1.1066
+++ devel/quirks/Makefile       16 Oct 2020 06:42:58 -0000
@@ -5,7 +5,7 @@ CATEGORIES =    devel databases
 DISTFILES =
 
 # API.rev
-PKGNAME =      quirks-3.458
+PKGNAME =      quirks-3.459
 PKG_ARCH =     *
 MAINTAINER =   Marc Espie <es...@openbsd.org>
 
Index: devel/quirks/files/Quirks.pm
===================================================================
RCS file: /cvs/ports/devel/quirks/files/Quirks.pm,v
retrieving revision 1.1084
diff -u -p -r1.1084 Quirks.pm
--- devel/quirks/files/Quirks.pm        14 Oct 2020 11:17:10 -0000      1.1084
+++ devel/quirks/files/Quirks.pm        16 Oct 2020 06:42:58 -0000
@@ -493,6 +493,7 @@ my $stem_extensions = {
        'py-zmq' => 'py3-zmq',
        'py-kiwisolver' => 'py3-kiwisolver',
        'py-scipy' => 'py3-scipy',
+       'biopython' => 'py3-biopython',
 };
 
 my $obsolete_reason = {

UPDATE biology/py-biopython [Re: numpy status update and help requested]

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