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-rw-r--r--science/py-DendroPy/Makefile2
-rw-r--r--science/py-DendroPy/distinfo6
-rw-r--r--science/py-DendroPy/files/patch-setup.py21
-rw-r--r--science/py-DendroPy/pkg-plist314
4 files changed, 16 insertions, 327 deletions
diff --git a/science/py-DendroPy/Makefile b/science/py-DendroPy/Makefile
index 1e135426a9f1..03f6d5428cd1 100644
--- a/science/py-DendroPy/Makefile
+++ b/science/py-DendroPy/Makefile
@@ -6,7 +6,7 @@
#
PORTNAME= DendroPy
-PORTVERSION= 3.0.2
+PORTVERSION= 3.0.5
CATEGORIES= science python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/science/py-DendroPy/distinfo b/science/py-DendroPy/distinfo
index 18f87fab87eb..0ab1bc517195 100644
--- a/science/py-DendroPy/distinfo
+++ b/science/py-DendroPy/distinfo
@@ -1,3 +1,3 @@
-MD5 (DendroPy-3.0.2.tar.gz) = d1e44937e5171fe864864f6cb8e629c1
-SHA256 (DendroPy-3.0.2.tar.gz) = 99304b4611f38da96370ca6470847e20a0ff01f78320438a872fdcebdb41f621
-SIZE (DendroPy-3.0.2.tar.gz) = 2233110
+MD5 (DendroPy-3.0.5.tar.gz) = 01d088b5184bdced992499fc0a6fbd12
+SHA256 (DendroPy-3.0.5.tar.gz) = 4688c28e771e448633354da31211f9078fed48701c991baa04b69cc04c39eed1
+SIZE (DendroPy-3.0.5.tar.gz) = 2238712
diff --git a/science/py-DendroPy/files/patch-setup.py b/science/py-DendroPy/files/patch-setup.py
index 455b04d52f80..4107230f620b 100644
--- a/science/py-DendroPy/files/patch-setup.py
+++ b/science/py-DendroPy/files/patch-setup.py
@@ -1,15 +1,16 @@
---- setup.py.orig 2010-01-09 13:22:53.000000000 +0800
-+++ setup.py 2010-01-09 13:23:15.000000000 +0800
-@@ -28,9 +28,9 @@
- import os
+--- 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
-- sys.stderr.write("using ez_setup ('%s')\n" % os.path.abspath(ez_setup.__file__))
+- 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 ez_setup
-+# sys.stderr.write("using ez_setup ('%s')\n" % os.path.abspath(ez_setup.__file__))
-+# ez_setup.use_setuptools()
import setuptools
- sys.stderr.write("using setuptools ('%s')\n" % os.path.abspath(setuptools.__file__))
- from setuptools import setup, find_packages
+ try:
+ setuptools_path = " ('" + os.path.abspath(setuptools.__file__) + "')"
diff --git a/science/py-DendroPy/pkg-plist b/science/py-DendroPy/pkg-plist
index d36cf1d5b021..db97df2e3274 100644
--- a/science/py-DendroPy/pkg-plist
+++ b/science/py-DendroPy/pkg-plist
@@ -2,316 +2,4 @@ bin/cattrees.py
bin/long_branch_symmdiff.py
bin/strict_consensus_merge.py
bin/sumtrees.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/PKG-INFO
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/SOURCES.txt
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/dependency_links.txt
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/not-zip-safe
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/requires.txt
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/scripts/cattrees.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/scripts/long_branch_symmdiff.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/scripts/strict_consensus_merge.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/scripts/sumtrees.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/EGG-INFO/top_level.txt
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/__init__.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/__init__.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/__init__.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/coalescent.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/coalescent.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/coalescent.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/continuous.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/continuous.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/continuous.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/__init__.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/__init__.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/__init__.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/dataschema.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/dataschema.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/dataschema.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/fasta.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/fasta.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/fasta.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/ioclient.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/ioclient.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/ioclient.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/newick.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/newick.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/newick.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/nexml.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/nexml.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/nexml.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/nexus.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/nexus.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/nexus.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/nexustokenizer.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/nexustokenizer.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/nexustokenizer.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/phylip.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/phylip.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/phylip.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/xmlparser.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/xmlparser.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataio/xmlparser.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/__init__.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/__init__.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/__init__.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/base.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/base.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/base.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/char.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/char.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/char.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/dataset.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/dataset.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/dataset.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/taxon.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/taxon.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/taxon.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/tree.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/tree.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/dataobject/tree.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/__init__.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/__init__.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/__init__.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/ape.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/ape.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/ape.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/biopython.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/biopython.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/biopython.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/paup.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/paup.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/interop/paup.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/popgensim.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/popgensim.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/popgensim.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/popgenstat.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/popgenstat.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/popgenstat.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/seqmodel.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/seqmodel.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/seqmodel.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/seqsim.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/seqsim.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/seqsim.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/__init__.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/__init__.pyc
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/__init__.pyo
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/angiosperms.chars.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/angiosperms.chars.txt
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/apternodus.chars.hacked-for-tests.txt
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/apternodus.chars.interleaved.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/apternodus.chars.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/bad_names.fasta
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/caenophidia_mos.chars.fasta
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/caenophidia_mos.chars.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/caenophidia_mos.chars.txt
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/primates.chars.csv
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/primates.chars.interleaved.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/primates.chars.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/primates.chars.simple.interleaved.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/primates.chars.simple.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/pythonidae-beast.xml
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/pythonidae_continuous.chars.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/pythonidae_continuous.chars.txt
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/pythonidae_cytb.chars.fasta
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/pythonidae_cytb.chars.interleaved.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/pythonidae_cytb.chars.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/pythonidae_cytb.chars.phylip
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/pythonidae_cytb.chars.txt
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/chars/pythonidae_cytb.mb
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/mixed/multitaxa_mesquite.nex
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/mixed/reference_single_taxonset_dataset.nex
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-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/bird_orders.nex
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/feb032009.splits.csv
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/feb032009.trees.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/maj-rule-bug1.trees.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/maj-rule-bug2.trees.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/primates.trees.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/pythonidae.beast-mcmc.trees
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-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/pythonidae.mle.nex
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/pythonidae.random.tre
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/pythonidae.reference-trees.newick
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-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/pythonidae.reference-trees.no-taxa-block.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/pythonidae.reference-trees.no-taxa-no-translate-block.nexus
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/data/trees/pythonidae_cytb.mb.con
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-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/test_ape.py
-%%PYTHON_SITELIBDIR%%/%%PYEASYINSTALL_EGG%%/dendropy/test/test_ape.pyc
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