biology/crux: stage, modernize, add license (BSD[23]CLAUSE), cleanups

PR:		193026
Submitted by:	Ports Fury

4 files changed, 63 insertions, 46 deletions

diff --git a/biology/crux/Makefile b/biology/crux/Makefile
index 08f03465fa0f..a21d0a3c3504 100644
--- a/biology/crux/Makefile
+++ b/biology/crux/Makefile
@@ -3,41 +3,49 @@
 
 PORTNAME=	crux
 PORTVERSION=	1.2.0
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	biology python
 MASTER_SITES=	http://www.canonware.com/download/Crux/
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Software toolkit for phylogenetic inference
 
-USES=		fortran gmake tar:bzip2
-GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--with-python=${PYTHON_CMD} --disable-mpi
-USE_CSTD=	gnu99
-USE_PYTHON=	yes
+LICENSE=	BSD2CLAUSE BSD3CLAUSE
+LICENSE_COMB=	multi
 
-OPTIONS_DEFINE=	SYS_LINALG
-SYS_LINALG_DESC=	Enable system ATLAS/LAPACK
-
-NO_STAGE=	yes
+USES=		fortran gmake python tar:bzip2
+USE_CSTD=	gnu99
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--datadir=${PREFIX}/lib \
+		--with-python=${PYTHON_CMD} \
+		--disable-mpi
 
 CPPFLAGS+=	-I${LOCALBASE}/include
 LDFLAGS+=	-L${LOCALBASE}/lib
 
+OPTIONS_DEFINE=		SYS_LINALG
+SYS_LINALG_DESC=	Enable system ATLAS/LAPACK
+SYS_LINALG_LIB_DEPENDS=	libatlas.so:${PORTSDIR}/math/atlas
+SYS_LINALG_CONFIGURE_ENABLE=	sys-linalg
+
 .include <bsd.port.options.mk>
 
-.if ${PORT_OPTIONS:MSYS_LINALG}
-CONFIGURE_ARGS+=	--enable-sys-linalg
-LIB_DEPENDS+=	libatlas.so:${PORTSDIR}/math/atlas
-.else
-CONFIGURE_ARGS+=	--disable-sys-linalg
+.if ${OSVERSION} > 900000
+BROKEN_powerpc=	Does not build on powerpc-9: error in pthreads
 .endif
 
-.if ${ARCH} == "powerpc" && ${OSVERSION} > 900000
-BROKEN=		Does not build on powerpc-9: error in pthreads
-.endif
+post-patch:
+	@${REINPLACE_CMD} -e \
+		's|\([[:blank:]]\)\($$(BINDIR)\)|\1$$(DESTDIR)\2| ; \
+		 s|\([[:blank:]]\)\($$(DATADIR)\)|\1$$(DESTDIR)\2| ; \
+		 s|\(,\)\(@site_packages@\)|\1$$(DESTDIR)\2| ; \
+		 s|\([[:blank:]]\)\(@site_packages@\)|\1$$(DESTDIR)\2|' \
+		${WRKSRC}/Makefile.in
 
 post-install:
-	@${PREFIX}/bin/crux -b -q /dev/null
+	@(${FIND} ${STAGEDIR}${PREFIX}/lib/Crux/lib -maxdepth 1 -type f \
+		-name "*.so" | ${XARGS} ${STRIP_CMD})
+	@(${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} -maxdepth 3 -type f \
+		-name "*.so" | ${XARGS} ${STRIP_CMD})
 
 .include <bsd.port.mk>
diff --git a/biology/crux/files/pkg-install b/biology/crux/files/pkg-install
new file mode 100644
index 000000000000..c2e494752edd
--- /dev/null
+++ b/biology/crux/files/pkg-install
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+case $2 in
+POST-INSTALL)
+	${PKG_PREFIX}/bin/crux -b -q /dev/null
+	exit 0
+	;;
+esac
diff --git a/biology/crux/pkg-descr b/biology/crux/pkg-descr
index 044b39424386..5a27474d58b3 100644
--- a/biology/crux/pkg-descr
+++ b/biology/crux/pkg-descr
@@ -1,18 +1,19 @@
-Crux is a software toolkit for molecular phylogenetic inference.  It is
+Crux is a software toolkit for molecular phylogenetic inference. It is
 structured as a set of Python modules, which makes it possible to quickly
-develop Python scripts that perform unique, non-canned analyses.  Features
+develop Python scripts that perform unique, non-canned analyses. Features
 include:
-* Tree log-likelihoods can be computed under a variety of models, including all
-  specializations of GTR+I+G and mixture models.  Tree likelihoods can be
-  computed in parallel via pthreads.
-* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis coupling)
-  can sample among non-nested models using reversible model jumps.
-* Crux is capable of simulating character data under any model its likelihood
-  engine is capable of.
-* The neighbor joining (NJ) and relaxed neighbor joining (RNJ) implementations
-  are among the fastest in existence.
+* Tree log-likelihoods can be computed under a variety of models,
+  including all specializations of GTR+I+G and mixture models. Tree
+  likelihoods can be computed in parallel via pthreads.
+* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis
+  coupling) can sample among non-nested models using reversible model
+  jumps.
+* Crux is capable of simulating character data under any model its
+  likelihood engine is capable of.
+* The neighbor joining (NJ) and relaxed neighbor joining (RNJ)
+  implementations are among the fastest in existence.
 * Pairwise distances between sequences can be computed based on percent
-  identity, or using methods that correct for multiple hits (Jukes-Cantor,
-  Kimura, and logDet).
+  identity, or using methods that correct for multiple hits
+  (Jukes-Cantor, Kimura, and logDet).
 
 WWW: http://www.canonware.com/Crux/
diff --git a/biology/crux/pkg-plist b/biology/crux/pkg-plist
index 2f17b9c68f86..2ec46ccfc5e4 100644
--- a/biology/crux/pkg-plist
+++ b/biology/crux/pkg-plist
@@ -1,12 +1,15 @@
 bin/crux
 bin/redpoint
 bin/MrRogers
+lib/Crux/lib/libCx.so
+lib/Crux/parsers/Fasta.log
+lib/Crux/parsers/Fasta.pickle
 %%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so
 %%PYTHON_SITELIBDIR%%/Crux/Character.so
 %%PYTHON_SITELIBDIR%%/Crux/Config.py
-%%PYTHON_SITELIBDIR%%/Crux/Config.pyo
+@rmtry %%PYTHON_SITELIBDIR%%/Crux/Config.pyo
 %%PYTHON_SITELIBDIR%%/Crux/Copying.py
-%%PYTHON_SITELIBDIR%%/Crux/Copying.pyo
+@rmtry %%PYTHON_SITELIBDIR%%/Crux/Copying.pyo
 %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
 %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py
 %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so
@@ -51,22 +54,19 @@ bin/MrRogers
 %%PYTHON_SITELIBDIR%%/Crux/__init__.py
 %%PYTHON_SITELIBDIR%%/Crux/__init__.so
 %%PYTHON_SITELIBDIR%%/Parsing.so
-share/Crux/lib/libCx.so
-share/Crux/parsers/Fasta.log
-share/Crux/parsers/Fasta.pickle
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/Mc3
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/Tree
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/Mc3
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix
 @dirrm %%PYTHON_SITELIBDIR%%/Crux
-@dirrm share/Crux/lib
-@dirrm share/Crux/parsers
-@dirrm share/Crux
+@dirrm lib/Crux/parsers
+@dirrm lib/Crux/lib
+@dirrm lib/Crux