Update to 4.0.3

author: Carlo Strub <cs@FreeBSD.org> 2015-12-25 12:30:50 +0000
committer: Carlo Strub <cs@FreeBSD.org> 2015-12-25 12:30:50 +0000
commit: 182898838c3dce0a7df6ec5a7d8d586a125f04da (patch)
tree: 116e85a902be71e25862cba38df43559bb8079ca /science
parent: - Update to version 1.4.3 (diff)
4 files changed, 791 insertions, 291 deletions
diff --git a/science/py-DendroPy/Makefile b/science/py-DendroPy/Makefile
index 759497923df4..45d2f62b3485 100644
--- a/science/py-DendroPy/Makefile
+++ b/science/py-DendroPy/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	DendroPy
-PORTVERSION=	3.12.0
-PORTREVISION=	1
+PORTVERSION=	4.0.3
 CATEGORIES=	science python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
diff --git a/science/py-DendroPy/distinfo b/science/py-DendroPy/distinfo
index aa957a397125..04a2d2263006 100644
--- a/science/py-DendroPy/distinfo
+++ b/science/py-DendroPy/distinfo
@@ -1,2 +1,2 @@
-SHA256 (DendroPy-3.12.0.tar.gz) = 38a0f36f2f7aae43ec5599408b0d0a4c80996b749589f025940d955a70fc82d4
-SIZE (DendroPy-3.12.0.tar.gz) = 6631147
+SHA256 (DendroPy-4.0.3.tar.gz) = a2c074eb91e2866120521c076587983900c5b312879832c3559effb730bd4465
+SIZE (DendroPy-4.0.3.tar.gz) = 16330973
diff --git a/science/py-DendroPy/files/patch-setup.py b/science/py-DendroPy/files/patch-setup.py
deleted file mode 100644
index 4107230f620b..000000000000
--- a/science/py-DendroPy/files/patch-setup.py
+++ /dev/null
@@ -1,16 +0,0 @@
---- setup.py.orig	2010-01-15 12:55:37.000000000 +0800
-+++ setup.py	2010-01-15 12:55:53.000000000 +0800
-@@ -31,13 +31,6 @@
- # setuptools/distutils/etc. import and configuration
- 
- try:
--    import ez_setup
--    try:
--        ez_setup_path = " ('" + os.path.abspath(ez_setup.__file__) + "')"
--    except OSError:
--        ez_setup_path = ""
--    sys.stderr.write("using ez_setup%s\n" %  ez_setup_path)
--    ez_setup.use_setuptools()
-     import setuptools
-     try:
-         setuptools_path = " ('" +  os.path.abspath(setuptools.__file__) + "')"
diff --git a/science/py-DendroPy/pkg-plist b/science/py-DendroPy/pkg-plist
index d5458c621eef..2b70dd776b7e 100644
--- a/science/py-DendroPy/pkg-plist
+++ b/science/py-DendroPy/pkg-plist
@@ -1,77 +1,118 @@
-bin/cattrees.py
-bin/long_branch_symmdiff.py
-bin/strict_consensus_merge.py
-bin/sumlabels.py
 bin/sumtrees.py
 %%PYTHON_SITELIBDIR%%/dendropy/__init__.py
 %%PYTHON_SITELIBDIR%%/dendropy/__init__.pyc
 %%PYTHON_SITELIBDIR%%/dendropy/__init__.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/coalescent.py
-%%PYTHON_SITELIBDIR%%/dendropy/coalescent.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/coalescent.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/continuous.py
-%%PYTHON_SITELIBDIR%%/dendropy/continuous.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/continuous.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/mathfn.py
+%%PYTHON_SITELIBDIR%%/dendropy/calculate/mathfn.pyc
+%%PYTHON_SITELIBDIR%%/dendropy/calculate/mathfn.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/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/beast.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/beast.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/beast.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/dataschema.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/dataschema.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/dataschema.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/fasta.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/fasta.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/fasta.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/ioclient.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/ioclient.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/ioclient.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/nexml.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexml.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexml.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusreader_ncl.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusreader_ncl.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusreader_ncl.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusreader_py.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusreader_py.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexusreader_py.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexustokenizer.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexustokenizer.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexustokenizer.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexustreeiter.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexustreeiter.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexustreeiter.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
+%%PYTHON_SITELIBDIR%%/dendropy/dataio/newickwriter.pyo
+%%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
+%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexmlwriter.pyo
+%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexmlyielder.py
+%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexmlyielder.pyc
+%%PYTHON_SITELIBDIR%%/dendropy/dataio/nexmlyielder.pyo
+%%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
 %%PYTHON_SITELIBDIR%%/dendropy/dataio/nexuswriter.pyc
 %%PYTHON_SITELIBDIR%%/dendropy/dataio/nexuswriter.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/phylip.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/phylip.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/phylip.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/xmlparser.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/xmlparser.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataio/xmlparser.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/__init__.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/__init__.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/__init__.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/base.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/base.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/base.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/char.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/char.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/char.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/dataset.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/dataset.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/dataset.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/taxon.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/taxon.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/taxon.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/tree.py
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/tree.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/dataobject/tree.pyo
+%%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
+%%PYTHON_SITELIBDIR%%/dendropy/datamodel/__init__.pyo
+%%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
@@ -96,55 +137,138 @@ bin/sumtrees.py
 %%PYTHON_SITELIBDIR%%/dendropy/interop/muscle.py
 %%PYTHON_SITELIBDIR%%/dendropy/interop/muscle.pyc
 %%PYTHON_SITELIBDIR%%/dendropy/interop/muscle.pyo
-%%PYTHON_SITELIBDIR%%/dendropy/interop/ncbi.py
-%%PYTHON_SITELIBDIR%%/dendropy/interop/ncbi.pyc
-%%PYTHON_SITELIBDIR%%/dendropy/interop/ncbi.pyo
 %%PYTHON_SITELIBDIR%%/dendropy/interop/paup.py
 %%PYTHON_SITELIBDIR%%/dendropy/interop/paup.pyc
 %%PYTHON_SITELIBDIR%%/dendropy/interop/paup.pyo
 %%PYTHON_SITELIBDIR%%/dendropy/interop/raxml.py
 %%PYTHON_SITELIBDIR%%/dendropy/interop/raxml.pyc
 %%PYTHON_SITELIBDIR%%/dendropy/interop/raxml.pyo
+%%PYTHON_SITELIBDIR%%/dendropy/interop/rstats.py
+%%PYTHON_SITELIBDIR%%/dendropy/interop/rstats.pyc
+%%PYTHON_SITELIBDIR%%/dendropy/interop/rstats.pyo
 %%PYTHON_SITELIBDIR%%/dendropy/interop/seqgen.py
 %%PYTHON_SITELIBDIR%%/dendropy/interop/seqgen.pyc
 %%PYTHON_SITELIBDIR%%/dendropy/interop/seqgen.pyo
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/__init__.py
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/__init__.pyc
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/__init__.pyo
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/coalescent.py
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/coalescent.pyc
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/coalescent.pyo
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/continuous.py
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/continuous.pyc
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/continuous.pyo
+%%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
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+%%PYTHON_SITELIBDIR%%/dendropy/legacy/treemanip.py
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+%%PYTHON_SITELIBDIR%%/dendropy/legacy/treemanip.pyo
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/treesim.py
+%%PYTHON_SITELIBDIR%%/dendropy/legacy/treesim.pyc
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author	Carlo Strub <cs@FreeBSD.org>	2015-12-25 12:30:50 +0000
committer	Carlo Strub <cs@FreeBSD.org>	2015-12-25 12:30:50 +0000
commit	182898838c3dce0a7df6ec5a7d8d586a125f04da (patch)
tree	116e85a902be71e25862cba38df43559bb8079ca /science
parent	- Update to version 1.4.3 (diff)