diff options
| -rw-r--r-- | science/py-DendroPy/Makefile | 3 | ||||
| -rw-r--r-- | science/py-DendroPy/distinfo | 4 | ||||
| -rw-r--r-- | science/py-DendroPy/files/patch-setup.py | 16 | ||||
| -rw-r--r-- | science/py-DendroPy/pkg-plist | 1059 |
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 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-%%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 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