New ports: math/gfan, math/gfanlib

Gfan is a software package for computing Groebner fans and tropical
varieties. These are polyhedral fans associated to polynomial ideals.
The maximal cones of a Groebner fan are in bijection with the marked
reduced Groebner bases of its defining ideal. The software computes
all marked reduced Groebner bases of an ideal. Their union is a
universal Greobner basis. The tropical variety of a polynomial ideal
is a certain subcomplex of the Groebner fan. Gfan contains algorithms
for computing this complex for general ideals and specialized
algorithms for tropical curves, tropical hypersurfaces and tropical
varieties of prime ideals.  In addition to the above core functions
the package contains many tools which are useful in the study of
Groebner bases, initial ideals and tropical geometry.

WWW: http://home.math.au.dk/jensen/software/gfan/gfan.html

PR:		231186
Submitted by:	Lorenzo Salvadore <phascolarctos@protonmail.ch>

12 files changed, 385 insertions, 0 deletions

diff --git a/math/Makefile b/math/Makefile
index 058c79a378f9..f217bbe2c7d0 100644
--- a/math/Makefile
+++ b/math/Makefile
@@ -234,6 +234,8 @@
     SUBDIR += geogram
     SUBDIR += geonext
     SUBDIR += gexpr
+    SUBDIR += gfan
+    SUBDIR += gfanlib
     SUBDIR += ggobi
     SUBDIR += gh-bc
     SUBDIR += giacxcas
diff --git a/math/gfan/Makefile b/math/gfan/Makefile
new file mode 100644
index 000000000000..a56106f32e55
--- /dev/null
+++ b/math/gfan/Makefile
@@ -0,0 +1,46 @@
+# Created by: Lorenzo Salvadore
+# $FreeBSD$
+
+PORTNAME=	gfan
+DISTVERSION=	0.6.2
+CATEGORIES=	math
+MASTER_SITES=	http://home.math.au.dk/jensen/software/gfan/
+DISTNAME=	${PORTNAME}${DISTVERSION}
+
+MAINTAINER=	phascolarctos@protonmail.ch
+COMMENT=	Software for computing Groebner fans and tropical varieties
+
+LICENSE=	GPLv2+
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+LIB_DEPENDS=	libcddgmp.so:math/cddlib \
+		libgmp.so:math/gmp
+
+USES=		gmake
+
+CFLAGS+=	-I${LOCALBASE}/include -DGMPRATIONAL
+
+OPTIONS_DEFINE=	DOCS EXAMPLES
+
+post-patch:
+	@${REINPLACE_CMD} \
+		's,ADDITIONALLINKOPTIONS = ,ADDITIONALLINKOPTIONS = -L${LOCALBASE}/lib ,' \
+		${WRKSRC}/Makefile
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/gfan ${STAGEDIR}${PREFIX}/bin
+	cd ${STAGEDIR}${PREFIX}/bin && ./gfan installlinks
+
+post-install-DOCS-on:
+	@${MKDIR} ${STAGEDIR}${DOCSDIR}
+	${INSTALL_MAN} ${WRKSRC}/doc/manual.dvi ${STAGEDIR}${DOCSDIR}
+	${INSTALL_MAN} ${WRKSRC}/doc/*.eps ${STAGEDIR}${DOCSDIR}
+
+post-install-EXAMPLES-on:
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
+
+do-test:
+	cd ${WRKSRC} && ./gfan _test
+
+.include <bsd.port.mk>
diff --git a/math/gfan/distinfo b/math/gfan/distinfo
new file mode 100644
index 000000000000..dd07fa419d7c
--- /dev/null
+++ b/math/gfan/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1535465532
+SHA256 (gfan0.6.2.tar.gz) = a674d5e5dc43634397de0d55dd5da3c32bd358d05f72b73a50e62c1a1686f10a
+SIZE (gfan0.6.2.tar.gz) = 1321059
diff --git a/math/gfan/files/patch-Makefile b/math/gfan/files/patch-Makefile
new file mode 100644
index 000000000000..386e4a353358
--- /dev/null
+++ b/math/gfan/files/patch-Makefile
@@ -0,0 +1,40 @@
+--- Makefile.orig	2017-09-28 13:44:12 UTC
++++ Makefile
+@@ -110,13 +110,13 @@ MKDIR=mkdir -p
+ PREFIX =
+ SHELL       = /bin/sh
+ #ARCH        = LINUX
+-CC          = $(PREFIX)gcc
++CC          ?= $(PREFIX)gcc
+ CLINKER     = $(CC)
+-CXX         = $(PREFIX)g++
++CXX         ?= $(PREFIX)g++
+ CCLINKER    = $(CXX)
+ #OPTFLAGS    = -O2 -DGMPRATIONAL -DNDEBUG
+ # Note that gcc produces wrong code with -O3
+-OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2	 #-O3 -fno-guess-branch-probability #-DNDEBUG
++#OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2	 #-O3 -fno-guess-branch-probability #-DNDEBUG
+ #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O3 -mavx -msse2  -finline-limit=1000 -ffast-math -Wuninitialized # -fno-guess-branch-probability #-DNDEBUG -ftree-vectorizer-verbose=2
+ #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O1             -fno-guess-branch-probability
+  #-DNDEBUG
+@@ -125,9 +125,9 @@ OPTFLAGS    =  -DGMPRATIONAL -Wuninitial
+ #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O3 -msse2 -ftree-vectorizer-verbose=2 -ffast-math #-DNDEBUG
+ #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O3 -mavx -msse2 -ftree-vectorizer-verbose=2 -ffast-math #-DNDEBUG
+ 
+-CFLAGS	  = $(OPTFLAGS) $(GPROFFLAG) $(STACTDUMP_OPTIONS) $(ADDITIONALINCLUDEOPTIONS) -std=c++0x -g $(CDDDEFINE_PREFIX) #-pedantic
++CFLAGS	  += $(OPTFLAGS) $(GPROFFLAG) $(STACTDUMP_OPTIONS) $(ADDITIONALINCLUDEOPTIONS) -std=c++0x -g $(CDDDEFINE_PREFIX) #-pedantic
+ #CFLAGS	  = $(OPTFLAGS) $(GPROFFLAG) $(STACTDUMP_OPTIONS) $(ADDITIONALINCLUDEOPTIONS) -D_GLIBCXX_DEBUG -std=c++0x -g $(CDDDEFINE_PREFIX) #-pedantic
+-CCFLAGS	  = $(CFLAGS)
++CCFLAGS	  += $(CFLAGS)
+ FFLAGS	  = $(OPTFLAGS)
+ 
+ CATSOBJECTS =	lp_cdd.o \
+@@ -394,7 +394,7 @@ EXECS	  = $(MAIN)
+ # (compiling with gcc version 4.7.2 and running gfan _tropicaltraverse on a starting cone for Grassmann3_7)
+ # Either this is a bug in the code or in the compiler. The bug disappears by compiling with -fno-guess-branch-probability
+ src/symmetrictraversal.o: src/symmetrictraversal.cpp
+-	$(CXX) $(CFLAGS) -fno-guess-branch-probability  -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
++	$(CXX) $(CFLAGS) -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
+ # If compiling with clang, use the line below instead:
+ #	$(CXX) $(CFLAGS) -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
+ 
diff --git a/math/gfan/files/patch-testsuite_0008PolynomialSetUnion_output b/math/gfan/files/patch-testsuite_0008PolynomialSetUnion_output
new file mode 100644
index 000000000000..32067e9162a4
--- /dev/null
+++ b/math/gfan/files/patch-testsuite_0008PolynomialSetUnion_output
@@ -0,0 +1,94 @@
+--- testsuite/0008PolynomialSetUnion/output.orig	2013-09-23 12:03:23 UTC
++++ testsuite/0008PolynomialSetUnion/output
+@@ -1,62 +1,62 @@
+-{
++Q[a,b,c]
++a*b-c^6,
++a*b^2-c^3,
++a*b^4-b,
++a*c-b^6,
++a*c^2-b,
++a*c^6-c,
++a-b^11,
++a-b^2*c,
++a-c^9,
+ a^11-c,
+ a^15-a,
++a^2*b-c,
+ a^2*b^3-a,
++a^2*c-b^3,
+ a^2-b^8,
+-a^2*b-c,
+ a^2-c^4,
+-a^2*c-b^3,
+-a^3-b^5,
+-a^3-b*c^2,
+ a^3*c^2-c}
+-a^4-b^2,
++a^3-b*c^2,
++a^3-b^5,
+ a^4*c-a,
++a^4-b^2,
+ a^5-c^3,
+ a^6*b-a,
+ a^6-b*c,
+ a^8-c^2,
+ a^9-b,
+-a-b^11,
+-a-b^2*c,
+-a*b^2-c^3,
+-a*b^4-b,
+-a*b-c^6,
+-a*c^2-b,
+-a*c^6-c,
+-a-c^9,
+-a*c-b^6,
++b*c-a^6,
++b*c^2-a^3,
++b*c^4-c,
++b-a*c^2,
++b-a^9,
++b-c^11,
+ b^11-a,
+ b^15-b,
+-b^2-a^4,
++b^2*c-a,
+ b^2*c^3-b,
++b^2-a^4,
+ b^2-c^8,
+-b^2*c-a,
+ b^3-a^2*c,
+ b^3-c^5,
+ b^4-c^2,
+ b^5-a^3,
+-b^6-a*c,
+ b^6*c-b,
++b^6-a*c,
+ b^8-a^2,
+ b^9-c,
+-b-a^9,
+-b-a*c^2,
+-b-c^11,
+-b*c^2-a^3,
+-b*c^4-c,
+-b*c-a^6,
++c-a^11,
++c-a^2*b,
++c-b^9,
+ c^11-b,
+ c^15-c,
+ c^2-a^8,
+ c^2-b^4,
+-c^3-a^5,
+ c^3-a*b^2,
++c^3-a^5,
+ c^4-a^2,
+ c^5-b^3,
+ c^6-a*b,
+ c^8-b^2,
+ c^9-a,
+-c-a^11,
+-c-a^2*b,
+-c-b^9,
+-Q[a,b,c]
++{
diff --git a/math/gfan/pkg-descr b/math/gfan/pkg-descr
new file mode 100644
index 000000000000..04b25c5406f0
--- /dev/null
+++ b/math/gfan/pkg-descr
@@ -0,0 +1,17 @@
+Gfan is a software package for computing Groebner fans and tropical
+varieties. These are polyhedral fans associated to polynomial ideals.
+The maximal cones of a Groebner fan are in bijection with the marked
+reduced Groebner bases of its defining ideal. The software computes
+all marked reduced Groebner bases of an ideal. Their union is a
+universal Greobner basis. The tropical variety of a polynomial ideal
+is a certain subcomplex of the Groebner fan. Gfan contains algorithms
+for computing this complex for general ideals and specialized
+algorithms for tropical curves, tropical hypersurfaces and tropical
+varieties of prime ideals.  In addition to the above core functions
+the package contains many tools which are useful in the study of
+Groebner bases, initial ideals and tropical geometry.
+
+This port provides gfan together with some handy symlinks. The static
+library libgfan.a is provided by the port math/gfanlib.
+
+WWW: http://home.math.au.dk/jensen/software/gfan/gfan.html
diff --git a/math/gfan/pkg-message b/math/gfan/pkg-message
new file mode 100644
index 000000000000..098c54d4f3bb
--- /dev/null
+++ b/math/gfan/pkg-message
@@ -0,0 +1,10 @@
+Gfan can also be linked to Sage, Singular or Soplex. I refrain to
+include those optional dependencies because Sage and Singular support
+is not documented in gfan's manual and Soplex has a very restrictive
+license (you can use or distribute it only if you are a member of a
+noncommercial and academic institution).
+
+If you feel you need any of those optional dependencies, please let
+me know and I will do my best to provide it as fast as possible.
+
+The mantainer.
diff --git a/math/gfan/pkg-plist b/math/gfan/pkg-plist
new file mode 100644
index 000000000000..eaedc0ba38f0
--- /dev/null
+++ b/math/gfan/pkg-plist
@@ -0,0 +1,92 @@
+bin/gfan
+bin/gfan_bases
+bin/gfan_buchberger
+bin/gfan_combinerays
+bin/gfan_doesidealcontain
+bin/gfan_fancommonrefinement
+bin/gfan_fanhomology
+bin/gfan_fanisbalanced
+bin/gfan_fanlink
+bin/gfan_fanproduct
+bin/gfan_fansubfan
+bin/gfan_genericlinearchange
+bin/gfan_groebnercone
+bin/gfan_groebnerfan
+bin/gfan_homogeneityspace
+bin/gfan_homogenize
+bin/gfan_initialforms
+bin/gfan_interactive
+bin/gfan_ismarkedgroebnerbasis
+bin/gfan_krulldimension
+bin/gfan_latticeideal
+bin/gfan_leadingterms
+bin/gfan_list
+bin/gfan_markpolynomialset
+bin/gfan_minkowskisum
+bin/gfan_minors
+bin/gfan_mixedvolume
+bin/gfan_overintegers
+bin/gfan_padic
+bin/gfan_polynomialsetunion
+bin/gfan_render
+bin/gfan_renderstaircase
+bin/gfan_resultantfan
+bin/gfan_saturation
+bin/gfan_secondaryfan
+bin/gfan_stats
+bin/gfan_substitute
+bin/gfan_symmetries
+bin/gfan_tolatex
+bin/gfan_topolyhedralfan
+bin/gfan_tropicalbasis
+bin/gfan_tropicalbruteforce
+bin/gfan_tropicalcurve
+bin/gfan_tropicalevaluation
+bin/gfan_tropicalfunction
+bin/gfan_tropicalhypersurface
+bin/gfan_tropicalintersection
+bin/gfan_tropicallifting
+bin/gfan_tropicallinearspace
+bin/gfan_tropicalmultiplicity
+bin/gfan_tropicalrank
+bin/gfan_tropicalstartingcone
+bin/gfan_tropicaltraverse
+bin/gfan_tropicalweildivisor
+bin/gfan_version
+%%PORTDOCS%%%%DOCSDIR%%/manual.dvi
+%%PORTDOCS%%%%DOCSDIR%%/gfan.eps
+%%PORTDOCS%%%%DOCSDIR%%/nonconst.eps
+%%PORTDOCS%%%%DOCSDIR%%/polyformat.eps
+%%PORTDOCS%%%%DOCSDIR%%/staircase.eps
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2x2of2x3
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2x2of2x4
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2x2of3x3
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2x2of4x4
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3x3of3x4
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3x3of3x5
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3x3of3x5.cone
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3x3of4x4
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3x3of4x4sym.cone
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4x4of4x5
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4x4of5x5
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/6x6-subPfaffians
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/commat2x2
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/commat2x2.cone
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclic4
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclic5
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/examplePaper
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/grassmann2_5
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/grassmann2_5.cone
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/grassmann2_6
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/grassmann2_6.cone
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/grassmann3_6
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/grassmann3_6.cone
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hankel3x3of4x4
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hankel3x3of4x4.cone
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hankel3x3of4x5
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hankel3x3of4x5.cone
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/linhyper5_2
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/linhyper5_2.cone
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pablo
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sturmfels3.9
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/symmetryTest
diff --git a/math/gfanlib/Makefile b/math/gfanlib/Makefile
new file mode 100644
index 000000000000..1b9adc5457ed
--- /dev/null
+++ b/math/gfanlib/Makefile
@@ -0,0 +1,41 @@
+# Created by: Lorenzo Salvadore
+# $FreeBSD$
+
+PORTNAME=	gfanlib
+DISTVERSION=	0.6.2
+CATEGORIES=	math
+MASTER_SITES=	http://home.math.au.dk/jensen/software/gfan/
+DISTNAME=	gfan${DISTVERSION}
+
+MAINTAINER=	phascolarctos@protonmail.ch
+COMMENT=	Static library for computing Groebner fans and tropical varieties
+
+LICENSE=	GPLv2+
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+BUILD_DEPENDS=	${LOCALBASE}/include/cdd/cdd.h:math/cddlib
+LIB_DEPENDS=	libgmp.so:math/gmp
+
+USES=		gmake
+
+GNU_CONFIGURE=	yes
+CPPFLAGS+=	-I${LOCALBASE}/include \
+		-I${LOCALBASE}/include/cdd
+
+CONFIGURE_WRKSRC=	${WRKSRC}/gfanlib
+BUILD_WRKSRC=		${WRKSRC}/gfanlib
+
+pre-configure:
+	for x in ${WRKSRC}/src/gfanlib*; do ${MV} $$x ${WRKSRC}/gfanlib; done
+# this is not supported yet, see ${WRKSRC}/Makefile: gfanlib_tableau.h
+# is commented in GFANLIBFILES' declaration
+	${RM} ${WRKSRC}/gfanlib/gfanlib_tableau.h
+
+do-install:
+	@${MKDIR} ${STAGEDIR}${PREFIX}/include/gfanlib
+	${INSTALL_DATA} ${WRKSRC}/gfanlib/gfanlib*.h \
+		${STAGEDIR}${PREFIX}/include/gfanlib
+	${INSTALL_DATA} ${WRKSRC}/gfanlib/libgfan.a \
+		${STAGEDIR}${PREFIX}/lib/libgfan.a
+
+.include <bsd.port.mk>
diff --git a/math/gfanlib/distinfo b/math/gfanlib/distinfo
new file mode 100644
index 000000000000..dd07fa419d7c
--- /dev/null
+++ b/math/gfanlib/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1535465532
+SHA256 (gfan0.6.2.tar.gz) = a674d5e5dc43634397de0d55dd5da3c32bd358d05f72b73a50e62c1a1686f10a
+SIZE (gfan0.6.2.tar.gz) = 1321059
diff --git a/math/gfanlib/pkg-descr b/math/gfanlib/pkg-descr
new file mode 100644
index 000000000000..689f577c7b13
--- /dev/null
+++ b/math/gfanlib/pkg-descr
@@ -0,0 +1,17 @@
+Gfan is a software package for computing Groebner fans and tropical
+varieties. These are polyhedral fans associated to polynomial ideals.
+The maximal cones of a Groebner fan are in bijection with the marked
+reduced Groebner bases of its defining ideal. The software computes
+all marked reduced Groebner bases of an ideal. Their union is a
+universal Greobner basis. The tropical variety of a polynomial ideal
+is a certain subcomplex of the Groebner fan. Gfan contains algorithms
+for computing this complex for general ideals and specialized
+algorithms for tropical curves, tropical hypersurfaces and tropical
+varieties of prime ideals.  In addition to the above core functions
+the package contains many tools which are useful in the study of
+Groebner bases, initial ideals and tropical geometry.
+
+This port provides only the static library libgfan.a: you can get the
+rest of the software package from the port math/gfan.
+
+WWW: http://home.math.au.dk/jensen/software/gfan/gfan.html
diff --git a/math/gfanlib/pkg-plist b/math/gfanlib/pkg-plist
new file mode 100644
index 000000000000..b4607203f1ed
--- /dev/null
+++ b/math/gfanlib/pkg-plist
@@ -0,0 +1,20 @@
+include/gfanlib/gfanlib.h
+include/gfanlib/gfanlib_circuittableint.h
+include/gfanlib/gfanlib_field.h
+include/gfanlib/gfanlib_matrix.h
+include/gfanlib/gfanlib_mixedvolume.h
+include/gfanlib/gfanlib_ordering.h
+include/gfanlib/gfanlib_paralleltraverser.h
+include/gfanlib/gfanlib_polyhedralfan.h
+include/gfanlib/gfanlib_polymakefile.h
+include/gfanlib/gfanlib_q.h
+include/gfanlib/gfanlib_symmetriccomplex.h
+include/gfanlib/gfanlib_symmetry.h
+include/gfanlib/gfanlib_traversal.h
+include/gfanlib/gfanlib_tropicalhomotopy.h
+include/gfanlib/gfanlib_tropicalintersection.h
+include/gfanlib/gfanlib_vector.h
+include/gfanlib/gfanlib_z.h
+include/gfanlib/gfanlib_zcone.h
+include/gfanlib/gfanlib_zfan.h
+lib/libgfan.a