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Update biopython to 1.79.

This commit is contained in:
martin 2021-06-23 10:46:49 +00:00
parent c94afe48d1
commit 17931fe70d
3 changed files with 14 additions and 27 deletions
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7
biology/py-biopython/Makefile
View File

@ -1,12 +1,11 @@
# $OpenBSD: Makefile,v 1.32 2021/01/04 14:06:27 sthen Exp $
# $OpenBSD: Makefile,v 1.33 2021/06/23 10:46:49 martin Exp $
COMMENT = Python tools for computational molecular biology
MODPY_EGG_VERSION = 1.78
MODPY_EGG_VERSION = 1.79
DISTNAME = biopython-${MODPY_EGG_VERSION}
CATEGORIES = biology
PKGNAME = py-${DISTNAME}
REVISION = 0
HOMEPAGE = http://www.biopython.org/
@ -39,7 +38,7 @@ post-install:
cd ${WRKSRC}/Doc/examples; tar cf - * | \
tar xf - -C ${PREFIX}/share/examples/py-biopython
do-test: fake
do-test:
@cd ${WRKSRC}/Tests && \
PYTHONPATH=${WRKINST}${MODPY_SITEPKG} \
${MODPY_BIN} ./run_tests.py

4
biology/py-biopython/distinfo
View File

@ -1,2 +1,2 @@
SHA256 (biopython-1.78.tar.gz) = HuCgtsI3ZoD+pmQtUIC6pBn9c98QSmLViouveou+RWQ=
SIZE (biopython-1.78.tar.gz) = 16895184
SHA256 (biopython-1.79.tar.gz) = 7bB+rJnTuKvXulb/S+3skmP3bfw8P0UOfS4rzez4VZs=
SIZE (biopython-1.79.tar.gz) = 16738730

30
biology/py-biopython/pkg/PLIST
View File

@ -1,6 +1,6 @@
@comment $OpenBSD: PLIST,v 1.11 2021/01/04 14:06:27 sthen Exp $
@conflict biopython-*
@pkgpath biology/py-biopython
@comment $OpenBSD: PLIST,v 1.12 2021/06/23 10:46:49 martin Exp $
lib/python${MODPY_VERSION}/
lib/python${MODPY_VERSION}/site-packages/
lib/python${MODPY_VERSION}/site-packages/Bio/
lib/python${MODPY_VERSION}/site-packages/Bio/Affy/
lib/python${MODPY_VERSION}/site-packages/Bio/Affy/CelFile.py
@ -132,10 +132,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Compass/
lib/python${MODPY_VERSION}/site-packages/Bio/Compass/__init__.py
${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Compass/${MODPY_PYCACHE}/
lib/python${MODPY_VERSION}/site-packages/Bio/Compass/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/Crystal/
lib/python${MODPY_VERSION}/site-packages/Bio/Crystal/__init__.py
${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Crystal/${MODPY_PYCACHE}/
lib/python${MODPY_VERSION}/site-packages/Bio/Crystal/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/Data/
lib/python${MODPY_VERSION}/site-packages/Bio/Data/CodonTable.py
lib/python${MODPY_VERSION}/site-packages/Bio/Data/IUPACData.py
@ -427,14 +423,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/ExPASy/${MODPY_PYCACHE}ScanProsite.
lib/python${MODPY_VERSION}/site-packages/Bio/ExPASy/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/ExPASy/${MODPY_PYCACHE}cellosaurus.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/ExPASy/cellosaurus.py
lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/
lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/FSSPTools.py
lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/__init__.py
${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/${MODPY_PYCACHE}/
lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/${MODPY_PYCACHE}FSSPTools.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/${MODPY_PYCACHE}fssp_rec.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/fssp_rec.py
lib/python${MODPY_VERSION}/site-packages/Bio/File.py
lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/
lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Record.py
@ -595,6 +583,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.c
@so lib/python${MODPY_VERSION}/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.${MODPY_PYC_MAGIC_TAG}so
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Residue.py
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/ResidueDepth.py
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/SASA.py
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/SCADIO.py
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Selection.py
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Structure.py
@ -625,6 +614,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}PSEA.${MODPY_PY
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}Polypeptide.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}Residue.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}ResidueDepth.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}SASA.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}SCADIO.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}Selection.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}Structure.${MODPY_PYC_MAGIC_TAG}pyc
@ -876,6 +866,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SffIO.py
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SnapGeneIO.py
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SwissIO.py
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/TabIO.py
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/TwoBitIO.py
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/UniprotIO.py
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/XdnaIO.py
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/__init__.py
@ -897,11 +888,14 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}SffIO.${MODPY
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}SnapGeneIO.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}SwissIO.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}TabIO.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}TwoBitIO.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}UniprotIO.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}XdnaIO.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}_index.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/_index.py
lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/_twoBitIO.c
@so lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/_twoBitIO.${MODPY_PYC_MAGIC_TAG}so
lib/python${MODPY_VERSION}/site-packages/Bio/SeqRecord.py
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/
lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CheckSum.py
@ -941,12 +935,6 @@ ${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/${MODPY_
lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/${MODPY_PYCACHE}Ace.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/${MODPY_PYCACHE}Phd.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/Statistics/
lib/python${MODPY_VERSION}/site-packages/Bio/Statistics/__init__.py
${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Statistics/${MODPY_PYCACHE}/
lib/python${MODPY_VERSION}/site-packages/Bio/Statistics/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/Statistics/${MODPY_PYCACHE}lowess.${MODPY_PYC_MAGIC_TAG}pyc
lib/python${MODPY_VERSION}/site-packages/Bio/Statistics/lowess.py
lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/
lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/FreqTable.py
lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/MatrixInfo.py