math/nauty: Update 27r1 -> 27r3

PR:		258237
Approved by:	moritz@schmi.tt (maintainer)

12 files changed, 95 insertions, 36 deletions

diff --git a/math/casadi/Makefile b/math/casadi/Makefile
index 09b0d622afc6..17a8ddc0ba89 100644
--- a/math/casadi/Makefile
+++ b/math/casadi/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	casadi
 DISTVERSION=	3.5.5
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	math
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/math/cbc/Makefile b/math/cbc/Makefile
index 41791fc98aff..19d93066eacd 100644
--- a/math/cbc/Makefile
+++ b/math/cbc/Makefile
@@ -1,7 +1,7 @@
 PORTNAME=	cbc
 DISTVERSIONPREFIX=	releases/
 DISTVERSION=	2.10.5
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	math
 PKGNAMEPREFIX=	coin-or-
 
diff --git a/math/couenne/Makefile b/math/couenne/Makefile
index b2c61b658f58..2685f534ec3c 100644
--- a/math/couenne/Makefile
+++ b/math/couenne/Makefile
@@ -1,7 +1,7 @@
 PORTNAME=	couenne
 DISTVERSIONPREFIX=	releases/
 DISTVERSION=	0.5.8
-PORTREVISION=	6
+PORTREVISION=	7
 CATEGORIES=	math
 PKGNAMEPREFIX=	coin-or-
 
@@ -11,7 +11,6 @@ COMMENT=	Convex Over and Under Envelopes for NonliNear Estimation
 LICENSE=	EPL
 LICENSE_FILE=	${WRKSRC}/Couenne/LICENSE
 
-BUILD_DEPENDS=	${LOCALBASE}/lib/libnauty.a:math/nauty
 LIB_DEPENDS=	libbonmin.so:math/bonmin \
 		libCbc.so:math/cbc \
 		libCgl.so:math/cgl \
@@ -19,7 +18,9 @@ LIB_DEPENDS=	libbonmin.so:math/bonmin \
 		libcoinasl.so:math/asl \
 		libCoinUtils.so:math/coinutils \
 		libipopt.so:math/ipopt \
-		libopenblas.so:math/openblas
+		libnauty.so:math/nauty \
+		libopenblas.so:math/openblas \
+		libOsi.so:math/osi
 
 USES=		blaslapack:netlib fortran gmake libtool pkgconfig
 USE_LDCONFIG=	yes
@@ -29,7 +30,7 @@ GH_ACCOUNT=	coin-or
 GH_PROJECT=	Couenne
 
 GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--with-nauty-incdir=${LOCALBASE}/include/nauty --with-nauty-lib=${LOCALBASE}/lib/libnauty.a
+CONFIGURE_ARGS=	--with-nauty-incdir=${LOCALBASE}/include/nauty --with-nauty-lib=${LOCALBASE}/lib/libnauty.so # see https://github.com/coin-or/Couenne/issues/58
 
 INSTALL_TARGET=	install-strip
 
diff --git a/math/disco/Makefile b/math/disco/Makefile
index 0d0dafcc52be..919eb821f902 100644
--- a/math/disco/Makefile
+++ b/math/disco/Makefile
@@ -1,6 +1,7 @@
 PORTNAME=	disco
 DISTVERSIONPREFIX=	releases/
 DISTVERSION=	1.0.0-33
+PORTREVISION=	1
 DISTVERSIONSUFFIX=	-g68720be
 CATEGORIES=	math
 PKGNAMEPREFIX=	coin-or-
diff --git a/math/libnormaliz/Makefile b/math/libnormaliz/Makefile
index 64385b289c22..5fd9311f65c9 100644
--- a/math/libnormaliz/Makefile
+++ b/math/libnormaliz/Makefile
@@ -1,6 +1,7 @@
 # PORTNAME block
 PORTNAME=	libnormaliz
 DISTVERSION=	3.9.0
+PORTREVISION=	1
 CATEGORIES=	math
 MASTER_SITES=	https://github.com/Normaliz/Normaliz/releases/download/v${PORTVERSION}/
 DISTNAME=	normaliz-${PORTVERSION}
diff --git a/math/nauty/Makefile b/math/nauty/Makefile
index d2ce334366f6..8538cc39a9f1 100644
--- a/math/nauty/Makefile
+++ b/math/nauty/Makefile
@@ -1,51 +1,67 @@
 # Created by: bremner@unb.ca
 
 PORTNAME=	nauty
-PORTVERSION=	27r1
-PORTREVISION=	3
+PORTVERSION=	27r3
 CATEGORIES=	math
 MASTER_SITES=	https://users.cecs.anu.edu.au/~bdm/nauty/
 DISTNAME=	${PORTNAME}${PORTVERSION}
 
 MAINTAINER=	moritz@schmi.tt
-COMMENT=	Nauty & Traces are programs for computing graph automorphisms
+COMMENT=	Nauty & Traces are programs for computing graph automorphism
 
 LICENSE=	APACHE20
 
 USES=		gmake
 
 GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--enable-tls # math/libnormaliz requires nauty with tls
+CONFIGURE_ARGS=	--enable-tls # this makes nauty thread-safe, math/libnormaliz requires nauty with tls
 
 MAKEFILE=	makefile
+MAKE_ARGS=	includedir=${PREFIX}/include/${PORTNAME} # place headers into a dedicated directory
 
 TEST_TARGET=	check
 
-CFLAGS+=	-fPIC
+OPTIONS_DEFINE=	DOCS NATIVE
 
-OPTIONS_DEFINE=	DOCS
+NATIVE_DESC=		Build with native optimizations (-march=native, etc)
+NATIVE_CONFIGURE_ON=	--disable-generic --enable-clz --enable-popcnt
+NATIVE_CONFIGURE_OFF=	--enable-generic --disable-clz --disable-popcnt
 
-post-build:
-	@cd ${WRKSRC} && ${CC} ${LDFLAGS} -shared -o libnauty.so \
-		gtnauty.o gtools.o gutil1.o gutil2.o naugraph.o naugroup.o naurng.o nausparse.o nautil.o nautinv.o \
-		naututil.o nauty.o nautycliquer.o schreier.o traces.o
+post-build: # build shared libraries: based on how static libraries are created
+	# rebuild .o files with -fPIC
+	@cd ${WRKSRC} ; \
+		objects=$$(ls *.o) ; \
+		${RM} $${objects} ; \
+		${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${_MAKE_JOBS} ${MAKE_ARGS} FREEBSD_EXTRA_CFLAGS="-fPIC" $${objects}
+	# build libraries
+	cd ${WRKSRC} && ${CC} ${LDFLAGS} -shared -o libnauty.so -Wl,-soname,libnauty.so \
+		nauty.o nautil.o nausparse.o naugraph.o schreier.o naurng.o traces.o gtools.o naututil.o \
+		nautinv.o gutil1.o gutil2.o gtnauty.o naugroup.o nautycliquer.o
+	cd ${WRKSRC} && ${CC} ${LDFLAGS} -shared -o libnauty1.so -Wl,-soname,libnauty1.so \
+		nauty1.o nautil1.o nausparse.o naugraph1.o schreier.o naurng.o traces.o gtools.o naututil1.o \
+		nautinv1.o gutil1.o gutil2.o gtnauty.o naugroup.o nautycliquer.o
+	cd ${WRKSRC} && ${CC} ${LDFLAGS} -shared -o libnautyW.so -Wl,-soname,libnautyW.so \
+		nautyW.o nautilW.o nausparseW.o naugraphW.o schreierW.o naurng.o traces.o gtoolsW.o naututilW.o \
+		nautinvW.o gutil1W.o gutil2W.o gtnautyW.o naugroupW.o nautycliquerW.o
+	cd ${WRKSRC} && ${CC} ${LDFLAGS} -shared -o libnautyW1.so -Wl,-soname,libnautyW1.so \
+		nautyW1.o nautilW1.o nausparseW.o naugraphW1.o schreierW.o naurng.o traces.o gtoolsW.o naututilW1.o \
+		nautinvW1.o gutil1W1.o gutil2W1.o gtnautyW1.o naugroupW.o nautycliquerW.o
+	cd ${WRKSRC} && ${CC} ${LDFLAGS} -shared -o libnautyL.so -Wl,-soname,libnautyL.so \
+		nautyL.o nautilL.o nausparseL.o naugraphL.o schreierL.o naurng.o traces.o gtoolsL.o naututilL.o \
+		nautinvL.o gutil1L.o gutil2L.o gtnautyL.o naugroupL.o nautycliquerL.o
+	cd ${WRKSRC} && ${CC} ${LDFLAGS} -shared -o libnautyL1.so -Wl,-soname,libnautyL1.so \
+		nautyL1.o nautilL1.o nausparseL.o naugraphL1.o schreierL.o naurng.o traces.o gtoolsL.o naututilL1.o \
+		nautinvL1.o gutil1L1.o gutil2L1.o gtnautyL1.o naugroupL.o nautycliquerL.o
 
-do-install:
-	${MKDIR} ${STAGEDIR}${PREFIX}/include/nauty
-.for h in  nauty.h nautycliquer.h nausparse.h traces.h naugroup.h
-	${INSTALL_DATA} ${WRKSRC}/${h} ${STAGEDIR}${PREFIX}/include/nauty
-.endfor
-	# Do not use ${INSTALL_LIB} to strip the library!
-	${INSTALL_DATA} ${WRKSRC}/nauty.a ${STAGEDIR}${PREFIX}/lib/libnauty.a
-	${INSTALL_LIB} ${WRKSRC}/libnauty.so ${STAGEDIR}${PREFIX}/lib
-.for e in \
-	NRswitchg addedgeg amtog assembleg biplabg catg complg converseg copyg countg \
-	cubhamg deledgeg delptg directg dreadnaut dretodot dretog edgetransg genbg genbgL \
-	geng gengL genquarticg genrang genspecialg gentourng gentreeg hamheuristic labelg linegraphg \
-	listg multig newedgeg pickg planarg ranlabg shortg showg subdivideg twohamg \
-	underlyingg vcolg watercluster2
-	${INSTALL_PROGRAM} ${WRKSRC}/${e} ${STAGEDIR}${PREFIX}/bin
+post-install:
+	# install shared libraries
+.for l in libnauty.so libnauty1.so libnautyW.so libnautyW1.so libnautyL.so libnautyL1.so
+	${INSTALL_LIB} ${WRKSRC}/${l} ${STAGEDIR}${PREFIX}/lib
 .endfor
+	# correct the include path in .pc files
+	@${REINPLACE_CMD} -i '' -e 's|-I$${includedir}|&/${PORTNAME}|' ${STAGEDIR}${PREFIX}/libdata/pkgconfig/*.pc
+	# strip executables
+	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*
 
 do-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
diff --git a/math/nauty/distinfo b/math/nauty/distinfo
index ef813103aef8..cc840a0e25f0 100644
--- a/math/nauty/distinfo
+++ b/math/nauty/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1601648114
-SHA256 (nauty27r1.tar.gz) = 76ca5d196e402c83a987f90c28ff706bcc5a333bb4a8fbb979a62d3b99c34e77
-SIZE (nauty27r1.tar.gz) = 3428473
+TIMESTAMP = 1630783130
+SHA256 (nauty27r3.tar.gz) = 4f0665b716a53f7a14ea2ae30059f23d064ce3fe4c12c013404ef6e1ee0b88c2
+SIZE (nauty27r3.tar.gz) = 1721200
diff --git a/math/nauty/files/patch-makefile.in b/math/nauty/files/patch-makefile.in
new file mode 100644
index 000000000000..76dc49de9aac
--- /dev/null
+++ b/math/nauty/files/patch-makefile.in
@@ -0,0 +1,13 @@
+- allow to add additional CFLAGS to build shared libraries
+
+--- makefile.in.orig	2021-09-03 17:45:35 UTC
++++ makefile.in
+@@ -3,7 +3,7 @@
+ 
+ SHELL=@SHELL@
+ CC=@CC@
+-CFLAGS=@CFLAGS@ @MORECFLAGS@
++CFLAGS=@CFLAGS@ @MORECFLAGS@ ${FREEBSD_EXTRA_CFLAGS}
+ SAFECFLAGS=@CFLAGS@
+ LDFLAGS=@LDFLAGS@ @LIBS@
+ THREADLIB=@threadlib@
diff --git a/math/nauty/pkg-plist b/math/nauty/pkg-plist
index 0ad268c2c22b..ef85048ffd07 100644
--- a/math/nauty/pkg-plist
+++ b/math/nauty/pkg-plist
@@ -30,6 +30,7 @@ bin/labelg
 bin/linegraphg
 bin/listg
 bin/multig
+bin/nbrhoodg
 bin/newedgeg
 bin/pickg
 bin/planarg
@@ -41,11 +42,36 @@ bin/twohamg
 bin/underlyingg
 bin/vcolg
 bin/watercluster2
+include/nauty/gtools.h
+include/nauty/gutils.h
 include/nauty/naugroup.h
+include/nauty/naugstrings.h
+include/nauty/naurng.h
 include/nauty/nausparse.h
+include/nauty/nautinv.h
+include/nauty/naututil.h
 include/nauty/nauty.h
 include/nauty/nautycliquer.h
+include/nauty/planarity.h
+include/nauty/quarticirred28.h
+include/nauty/schreier.h
 include/nauty/traces.h
 lib/libnauty.a
 lib/libnauty.so
+lib/libnauty1.a
+lib/libnauty1.so
+lib/libnautyL.a
+lib/libnautyL.so
+lib/libnautyL1.a
+lib/libnautyL1.so
+lib/libnautyW.a
+lib/libnautyW.so
+lib/libnautyW1.a
+lib/libnautyW1.so
+libdata/pkgconfig/nauty.pc
+libdata/pkgconfig/nauty1.pc
+libdata/pkgconfig/nautyL.pc
+libdata/pkgconfig/nautyL1.pc
+libdata/pkgconfig/nautyW.pc
+libdata/pkgconfig/nautyW1.pc
 %%PORTDOCS%%%%DOCSDIR%%/nug27.pdf
diff --git a/math/or-tools/Makefile b/math/or-tools/Makefile
index f120e7681230..6760ff201816 100644
--- a/math/or-tools/Makefile
+++ b/math/or-tools/Makefile
@@ -1,6 +1,7 @@
 PORTNAME=	or-tools
 DISTVERSIONPREFIX=	v
 DISTVERSION=	9.0
+PORTREVISION=	1
 CATEGORIES=	math
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/math/polymake/Makefile b/math/polymake/Makefile
index e88745e92d98..36b3127b7bc1 100644
--- a/math/polymake/Makefile
+++ b/math/polymake/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	polymake
 DISTVERSION=	4.4
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 MASTER_SITES=	https://polymake.org/lib/exe/fetch.php/download/
 DISTNAME=	${PORTNAME}-${DISTVERSION}-minimal
diff --git a/math/sage/Makefile b/math/sage/Makefile
index f8d30a68a1ff..f86bdc0bc60f 100644
--- a/math/sage/Makefile
+++ b/math/sage/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	sage
 PORTVERSION=	9.2
-PORTREVISION=	18
+PORTREVISION=	19
 CATEGORIES=	math
 MASTER_SITES=	https://mirrors.xmission.com/sage/src/		\
 		http://mirrors.xmission.com/sage/src/		\