Update to 4.1.0

3 files changed, 35 insertions, 3 deletions

diff --git a/science/py-DendroPy/Makefile b/science/py-DendroPy/Makefile
index 45d2f62b3485..48f1bcd6e5c1 100644
--- a/science/py-DendroPy/Makefile
+++ b/science/py-DendroPy/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	DendroPy
-PORTVERSION=	4.0.3
+PORTVERSION=	4.1.0
 CATEGORIES=	science python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
diff --git a/science/py-DendroPy/distinfo b/science/py-DendroPy/distinfo
index 04a2d2263006..8735c5821409 100644
--- a/science/py-DendroPy/distinfo
+++ b/science/py-DendroPy/distinfo
@@ -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
diff --git a/science/py-DendroPy/pkg-plist b/science/py-DendroPy/pkg-plist
index 2b70dd776b7e..09dfc78f7e8a 100644
--- a/science/py-DendroPy/pkg-plist
+++ b/science/py-DendroPy/pkg-plist
@@ -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