Attachment 233634 Details for Bug 263706 – patch

[patch] patch

py-DendroPy.patch (text/plain), 17.88 KB, created by Yuri Victorovich on 2022-05-01 18:19:32 UTC

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Creator: Yuri Victorovich

Created: 2022-05-01 18:19:32 UTC

Size: 17.88 KB

patch

obsolete

>diff --git a/science/py-DendroPy/Makefile b/science/py-DendroPy/Makefile
>index 6b90a05a82fc..2b962e3dc0c4 100644
>--- a/science/py-DendroPy/Makefile
>+++ b/science/py-DendroPy/Makefile
>@@ -1,7 +1,7 @@
> # Created by: Wen Heping <wenheping@gmail.com>
> 
> PORTNAME=	DendroPy
>-PORTVERSION=	4.4.0
>+PORTVERSION=	4.5.2
> CATEGORIES=	science python
> MASTER_SITES=	CHEESESHOP
> PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
>@@ -12,6 +12,6 @@ COMMENT=	Phylogenetic computing library
> LICENSE=	BSD3CLAUSE
> 
> USES=		python:3.6+
>-USE_PYTHON=	distutils py3kplist
>+USE_PYTHON=	distutils py3kplist autoplist
> 
> .include <bsd.port.mk>
>diff --git a/science/py-DendroPy/distinfo b/science/py-DendroPy/distinfo
>index 9c7677db26e1..6438e8d9edad 100644
>--- a/science/py-DendroPy/distinfo
>+++ b/science/py-DendroPy/distinfo
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1539118893
>-SHA256 (DendroPy-4.4.0.tar.gz) = f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c
>-SIZE (DendroPy-4.4.0.tar.gz) = 15166418
>+TIMESTAMP = 1651428912
>+SHA256 (DendroPy-4.5.2.tar.gz) = 3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101
>+SIZE (DendroPy-4.5.2.tar.gz) = 15201088
>diff --git a/science/py-DendroPy/pkg-plist b/science/py-DendroPy/pkg-plist
>deleted file mode 100644
>index 843368df223e..000000000000
>--- a/science/py-DendroPy/pkg-plist
>+++ /dev/null
>@@ -1,317 +0,0 @@
>-bin/sumlabels.py
>-bin/sumtrees.py
>-%%PYTHON_SITELIBDIR%%/dendropy/__init__.py
>-%%PYTHON_SITELIBDIR%%/dendropy/__init__.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/__main__.py
>-%%PYTHON_SITELIBDIR%%/dendropy/__main__.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/__main__.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/__init__.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/__init__.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/combinatorics.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/combinatorics.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/combinatorics.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/mathfn.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/mathfn.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/mathfn.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/phylogeneticdistance.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/phylogeneticdistance.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/phylogeneticdistance.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/popgenstat.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/popgenstat.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/popgenstat.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/probability.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/probability.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/probability.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/profiledistance.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/profiledistance.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/profiledistance.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/statistics.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/statistics.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/statistics.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treecompare.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treecompare.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treecompare.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treemeasure.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treemeasure.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treemeasure.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treescore.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treescore.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treescore.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treesum.py
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treesum.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/calculate/treesum.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/__init__.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/__init__.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/fastareader.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/fastareader.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/fastareader.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/fastawriter.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/fastawriter.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/fastawriter.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/ioservice.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/ioservice.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/ioservice.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newick.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newick.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newick.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newickreader.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newickreader.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newickreader.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newickwriter.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newickwriter.pyc
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>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newickyielder.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newickyielder.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/newickyielder.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexmlreader.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexmlreader.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexmlreader.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexmlwriter.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexmlwriter.pyc
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>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusprocessing.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusprocessing.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusprocessing.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusreader.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusreader.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusreader.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexuswriter.py
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>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusyielder.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusyielder.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusyielder.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/phylipreader.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/phylipreader.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/phylipreader.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/phylipwriter.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/phylipwriter.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/phylipwriter.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/tokenizer.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/tokenizer.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/tokenizer.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/xmlprocessing.py
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/xmlprocessing.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/dataio/xmlprocessing.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/__init__.py
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/__init__.pyc
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>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/basemodel.py
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/basemodel.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/basemodel.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/charmatrixmodel.py
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/charmatrixmodel.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/charmatrixmodel.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/charstatemodel.py
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/charstatemodel.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/charstatemodel.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/datasetmodel.py
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/datasetmodel.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/datasetmodel.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/taxonmodel.py
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/taxonmodel.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/taxonmodel.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/treecollectionmodel.py
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/treecollectionmodel.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/treecollectionmodel.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/treemodel.py
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/treemodel.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/datamodel/treemodel.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/__init__.py
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/__init__.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/ape.py
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/ape.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/ape.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/biopython.py
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/biopython.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/biopython.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/entrez.py
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/entrez.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/entrez.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/ete.py
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/ete.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/ete.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/gbif.py
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/gbif.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/gbif.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/genbank.py
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/genbank.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/genbank.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/muscle.py
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>-%%PYTHON_SITELIBDIR%%/dendropy/interop/muscle.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/paup.py
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>-%%PYTHON_SITELIBDIR%%/dendropy/interop/raxml.pyc
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>-%%PYTHON_SITELIBDIR%%/dendropy/interop/rspr.py
>-%%PYTHON_SITELIBDIR%%/dendropy/interop/rspr.pyc
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>-%%PYTHON_SITELIBDIR%%/dendropy/legacy/__init__.pyo
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>-%%PYTHON_SITELIBDIR%%/dendropy/legacy/ncbi.py
>-%%PYTHON_SITELIBDIR%%/dendropy/legacy/ncbi.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/legacy/ncbi.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/legacy/popgensim.py
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>-%%PYTHON_SITELIBDIR%%/dendropy/legacy/popgensim.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/legacy/popgenstat.py
>-%%PYTHON_SITELIBDIR%%/dendropy/legacy/popgenstat.pyc
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>-%%PYTHON_SITELIBDIR%%/dendropy/utility/cli.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/constants.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/constants.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/constants.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/container.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/container.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/container.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/debug.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/debug.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/debug.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/deprecate.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/deprecate.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/deprecate.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/error.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/error.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/error.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/filesys.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/filesys.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/filesys.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/libexec/__init__.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/libexec/__init__.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/libexec/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/messaging.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/messaging.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/messaging.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/metavar.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/metavar.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/metavar.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/processio.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/processio.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/processio.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/terminal.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/terminal.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/terminal.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/textprocessing.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/textprocessing.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/textprocessing.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/timeprocessing.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/timeprocessing.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/timeprocessing.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/urlio.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/urlio.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/urlio.pyo
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/vcsinfo.py
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/vcsinfo.pyc
>-%%PYTHON_SITELIBDIR%%/dendropy/utility/vcsinfo.pyo

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Attachments on bug 263706: 233634