From owner-svn-ports-all@freebsd.org Thu Apr 7 20:30:13 2016 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 60BEAB0688C; Thu, 7 Apr 2016 20:30:13 +0000 (UTC) (envelope-from cs@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 1E7D7197E; Thu, 7 Apr 2016 20:30:13 +0000 (UTC) (envelope-from cs@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id u37KUCM4015304; Thu, 7 Apr 2016 20:30:12 GMT (envelope-from cs@FreeBSD.org) Received: (from cs@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u37KUCVm015301; Thu, 7 Apr 2016 20:30:12 GMT (envelope-from cs@FreeBSD.org) Message-Id: <201604072030.u37KUCVm015301@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: cs set sender to cs@FreeBSD.org using -f From: Carlo Strub Date: Thu, 7 Apr 2016 20:30:12 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r412694 - head/science/py-DendroPy X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 07 Apr 2016 20:30:13 -0000 Author: cs Date: Thu Apr 7 20:30:11 2016 New Revision: 412694 URL: https://svnweb.freebsd.org/changeset/ports/412694 Log: Update to 4.1.0 Modified: head/science/py-DendroPy/Makefile head/science/py-DendroPy/distinfo head/science/py-DendroPy/pkg-plist Modified: head/science/py-DendroPy/Makefile ============================================================================== --- head/science/py-DendroPy/Makefile Thu Apr 7 20:23:55 2016 (r412693) +++ head/science/py-DendroPy/Makefile Thu Apr 7 20:30:11 2016 (r412694) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= DendroPy -PORTVERSION= 4.0.3 +PORTVERSION= 4.1.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} Modified: head/science/py-DendroPy/distinfo ============================================================================== --- head/science/py-DendroPy/distinfo Thu Apr 7 20:23:55 2016 (r412693) +++ head/science/py-DendroPy/distinfo Thu Apr 7 20:30:11 2016 (r412694) @@ -1,2 +1,2 @@ -SHA256 (DendroPy-4.0.3.tar.gz) = a2c074eb91e2866120521c076587983900c5b312879832c3559effb730bd4465 -SIZE (DendroPy-4.0.3.tar.gz) = 16330973 +SHA256 (DendroPy-4.1.0.tar.gz) = c3d4b2780b84fb6ad64a8350855b2d762cabe45ecffbc04318f07214ee3bdfc9 +SIZE (DendroPy-4.1.0.tar.gz) = 16492139 Modified: head/science/py-DendroPy/pkg-plist ============================================================================== --- head/science/py-DendroPy/pkg-plist Thu Apr 7 20:23:55 2016 (r412693) +++ head/science/py-DendroPy/pkg-plist Thu Apr 7 20:30:11 2016 (r412694) @@ -8,9 +8,15 @@ bin/sumtrees.py %%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 @@ -283,6 +289,7 @@ bin/sumtrees.py %%PYTHON_SITELIBDIR%%/dendropy/test/data/chars/caenophidia_mos.chars.txt %%PYTHON_SITELIBDIR%%/dendropy/test/data/chars/cetaceans.nex %%PYTHON_SITELIBDIR%%/dendropy/test/data/chars/codons.nexml +%%PYTHON_SITELIBDIR%%/dendropy/test/data/chars/community.data.tsv %%PYTHON_SITELIBDIR%%/dendropy/test/data/chars/crotaphytus_bicinctores.cytb.aligned.nexml %%PYTHON_SITELIBDIR%%/dendropy/test/data/chars/crotaphytus_bicinctores.nd2.aligned.nexml %%PYTHON_SITELIBDIR%%/dendropy/test/data/chars/interleaved-charsets-all.nex @@ -360,6 +367,20 @@ bin/sumtrees.py %%PYTHON_SITELIBDIR%%/dendropy/test/data/mixed/multitaxa_mesquite.nex %%PYTHON_SITELIBDIR%%/dendropy/test/data/mixed/reference_single_taxonset_dataset.nex %%PYTHON_SITELIBDIR%%/dendropy/test/data/mixed/standard-test-mixed.1.basic.nexus +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/community.data.tsv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/community.data.weighted.unnormalized.ses.mntd.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/community.data.weighted.unnormalized.ses.mpd.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/hiv1.distances.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/hiv1.node-to-node-dists.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/hiv1.unweighted.node-to-node-dists.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/laurasiatherian.distances.ml.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/pythonidae.mle.node-to-node-dists.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/pythonidae.mle.unweighted.node-to-node-dists.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/pythonidae.mle.unweighted.pdm.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/pythonidae.mle.weighted.pdm.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/saitou_and_nei_1987_table1.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/wpnjex.csv +%%PYTHON_SITELIBDIR%%/dendropy/test/data/other/wpupgmaex.csv %%PYTHON_SITELIBDIR%%/dendropy/test/data/splits/cetaceans.mb.no-clock.mcmc.trees.is-rooted-False.use-tree-weights-False.burnin-0.splits.txt %%PYTHON_SITELIBDIR%%/dendropy/test/data/splits/cetaceans.mb.no-clock.mcmc.trees.is-rooted-False.use-tree-weights-False.burnin-150.splits.txt %%PYTHON_SITELIBDIR%%/dendropy/test/data/splits/cetaceans.mb.no-clock.mcmc.trees.is-rooted-False.use-tree-weights-None.burnin-0.splits.txt @@ -621,6 +642,7 @@ bin/sumtrees.py %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/cetaceans.raxml.bootstraps.weighted-02.trees %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/cetaceans.raxml.bootstraps.weighted-03.trees %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/cetaceans.taxa.nex +%%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/community.tree.newick %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/curated-with-translate-block-and-internal-taxa.nex %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/curated-with-translate-block-and-no-taxa-block-and-untranslated-internal-taxa.nex %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/curated-with-translate-block-and-no-taxa-block.nex @@ -717,6 +739,7 @@ bin/sumtrees.py %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/pythonidae.mlboots.nexus.tre %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/pythonidae.mle.newick %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/pythonidae.mle.nex +%%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/pythonidae.mle.numbered-nodes.newick %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/pythonidae.random.bd0301.midpoint-rooted.tre %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/pythonidae.random.bd0301.randomly-rooted.tre %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees/pythonidae.random.bd0301.tre @@ -913,9 +936,15 @@ bin/sumtrees.py %%PYTHON_SITELIBDIR%%/dendropy/test/test_paup.py %%PYTHON_SITELIBDIR%%/dendropy/test/test_paup.pyc %%PYTHON_SITELIBDIR%%/dendropy/test/test_paup.pyo +%%PYTHON_SITELIBDIR%%/dendropy/test/test_phylogenetic_distance_matrix.py +%%PYTHON_SITELIBDIR%%/dendropy/test/test_phylogenetic_distance_matrix.pyc +%%PYTHON_SITELIBDIR%%/dendropy/test/test_phylogenetic_distance_matrix.pyo %%PYTHON_SITELIBDIR%%/dendropy/test/test_popgenstat.py %%PYTHON_SITELIBDIR%%/dendropy/test/test_popgenstat.pyc %%PYTHON_SITELIBDIR%%/dendropy/test/test_popgenstat.pyo +%%PYTHON_SITELIBDIR%%/dendropy/test/test_protractedspeciation.py +%%PYTHON_SITELIBDIR%%/dendropy/test/test_protractedspeciation.pyc +%%PYTHON_SITELIBDIR%%/dendropy/test/test_protractedspeciation.pyo %%PYTHON_SITELIBDIR%%/dendropy/test/test_statistics.py %%PYTHON_SITELIBDIR%%/dendropy/test/test_statistics.pyc %%PYTHON_SITELIBDIR%%/dendropy/test/test_statistics.pyo @@ -931,6 +960,9 @@ bin/sumtrees.py %%PYTHON_SITELIBDIR%%/dendropy/test/test_tree_reconciliation_and_discordance.py %%PYTHON_SITELIBDIR%%/dendropy/test/test_tree_reconciliation_and_discordance.pyc %%PYTHON_SITELIBDIR%%/dendropy/test/test_tree_reconciliation_and_discordance.pyo +%%PYTHON_SITELIBDIR%%/dendropy/test/test_tree_shape_kernel.py +%%PYTHON_SITELIBDIR%%/dendropy/test/test_tree_shape_kernel.pyc +%%PYTHON_SITELIBDIR%%/dendropy/test/test_tree_shape_kernel.pyo %%PYTHON_SITELIBDIR%%/dendropy/test/test_tree_split_compatibility.py %%PYTHON_SITELIBDIR%%/dendropy/test/test_tree_split_compatibility.pyc %%PYTHON_SITELIBDIR%%/dendropy/test/test_tree_split_compatibility.pyo