svn commit: r356177 - head/science/py-DendroPy

Carlo Strub cs at FreeBSD.org
Sun Jun 1 21:30:41 UTC 2014


Author: cs
Date: Sun Jun  1 21:30:40 2014
New Revision: 356177
URL: http://svnweb.freebsd.org/changeset/ports/356177
QAT: https://qat.redports.org/buildarchive/r356177/

Log:
  - Support staging
  - Minor edits

Modified:
  head/science/py-DendroPy/Makefile
  head/science/py-DendroPy/pkg-plist

Modified: head/science/py-DendroPy/Makefile
==============================================================================
--- head/science/py-DendroPy/Makefile	Sun Jun  1 21:29:40 2014	(r356176)
+++ head/science/py-DendroPy/Makefile	Sun Jun  1 21:30:40 2014	(r356177)
@@ -3,6 +3,7 @@
 
 PORTNAME=	DendroPy
 PORTVERSION=	3.12.0
+PORTREVISION=	1
 CATEGORIES=	science python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -10,12 +11,11 @@ PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 MAINTAINER=	cs at FreeBSD.org
 COMMENT=	Phylogenetic computing library
 
-LICENSE=	BSD
+LICENSE=	BSD3CLAUSE
 
 USE_PYTHON=	yes
-USE_PYDISTUTILS=	easy_install
+USE_PYDISTUTILS=yes
 
-NO_STAGE=	yes
 post-install:
 	@${CAT} ${PKGMESSAGE}
 

Modified: head/science/py-DendroPy/pkg-plist
==============================================================================
--- head/science/py-DendroPy/pkg-plist	Sun Jun  1 21:29:40 2014	(r356176)
+++ head/science/py-DendroPy/pkg-plist	Sun Jun  1 21:30:40 2014	(r356177)
@@ -3,4 +3,489 @@ bin/long_branch_symmdiff.py
 bin/strict_consensus_merge.py
 bin/sumlabels.py
 bin/sumtrees.py
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+ at dirrmtry %%PYTHON_SITELIBDIR%%/dendropy/mathlib
+ at dirrmtry %%PYTHON_SITELIBDIR%%/dendropy/test/data/chars
+ at dirrmtry %%PYTHON_SITELIBDIR%%/dendropy/test/data/mixed
+ at dirrmtry %%PYTHON_SITELIBDIR%%/dendropy/test/data/trees
+ at dirrmtry %%PYTHON_SITELIBDIR%%/dendropy/test/data
+ at dirrmtry %%PYTHON_SITELIBDIR%%/dendropy/test/support
+ at dirrmtry %%PYTHON_SITELIBDIR%%/dendropy/test
+ at dirrmtry %%PYTHON_SITELIBDIR%%/dendropy/utility
+ at dirrmtry %%PYTHON_SITELIBDIR%%/dendropy


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