svn commit: r492416 - in head/math: . gfan gfan/files gfanlib
Tobias Kortkamp
tobik at FreeBSD.org
Fri Feb 8 09:27:35 UTC 2019
Author: tobik
Date: Fri Feb 8 09:27:32 2019
New Revision: 492416
URL: https://svnweb.freebsd.org/changeset/ports/492416
Log:
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 at protonmail.ch>
Added:
head/math/gfan/
head/math/gfan/Makefile (contents, props changed)
head/math/gfan/distinfo (contents, props changed)
head/math/gfan/files/
head/math/gfan/files/patch-Makefile (contents, props changed)
head/math/gfan/files/patch-testsuite_0008PolynomialSetUnion_output (contents, props changed)
head/math/gfan/pkg-descr (contents, props changed)
head/math/gfan/pkg-message (contents, props changed)
head/math/gfan/pkg-plist (contents, props changed)
head/math/gfanlib/
head/math/gfanlib/Makefile (contents, props changed)
head/math/gfanlib/distinfo (contents, props changed)
head/math/gfanlib/pkg-descr (contents, props changed)
head/math/gfanlib/pkg-plist (contents, props changed)
Modified:
head/math/Makefile
Modified: head/math/Makefile
==============================================================================
--- head/math/Makefile Fri Feb 8 09:00:43 2019 (r492415)
+++ head/math/Makefile Fri Feb 8 09:27:32 2019 (r492416)
@@ -234,6 +234,8 @@
SUBDIR += geogram
SUBDIR += geonext
SUBDIR += gexpr
+ SUBDIR += gfan
+ SUBDIR += gfanlib
SUBDIR += ggobi
SUBDIR += gh-bc
SUBDIR += giacxcas
Added: head/math/gfan/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfan/Makefile Fri Feb 8 09:27:32 2019 (r492416)
@@ -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 at 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>
Added: head/math/gfan/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfan/distinfo Fri Feb 8 09:27:32 2019 (r492416)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1535465532
+SHA256 (gfan0.6.2.tar.gz) = a674d5e5dc43634397de0d55dd5da3c32bd358d05f72b73a50e62c1a1686f10a
+SIZE (gfan0.6.2.tar.gz) = 1321059
Added: head/math/gfan/files/patch-Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfan/files/patch-Makefile Fri Feb 8 09:27:32 2019 (r492416)
@@ -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
+
Added: head/math/gfan/files/patch-testsuite_0008PolynomialSetUnion_output
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfan/files/patch-testsuite_0008PolynomialSetUnion_output Fri Feb 8 09:27:32 2019 (r492416)
@@ -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]
++{
Added: head/math/gfan/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfan/pkg-descr Fri Feb 8 09:27:32 2019 (r492416)
@@ -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
Added: head/math/gfan/pkg-message
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfan/pkg-message Fri Feb 8 09:27:32 2019 (r492416)
@@ -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.
Added: head/math/gfan/pkg-plist
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfan/pkg-plist Fri Feb 8 09:27:32 2019 (r492416)
@@ -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
Added: head/math/gfanlib/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfanlib/Makefile Fri Feb 8 09:27:32 2019 (r492416)
@@ -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 at 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>
Added: head/math/gfanlib/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfanlib/distinfo Fri Feb 8 09:27:32 2019 (r492416)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1535465532
+SHA256 (gfan0.6.2.tar.gz) = a674d5e5dc43634397de0d55dd5da3c32bd358d05f72b73a50e62c1a1686f10a
+SIZE (gfan0.6.2.tar.gz) = 1321059
Added: head/math/gfanlib/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfanlib/pkg-descr Fri Feb 8 09:27:32 2019 (r492416)
@@ -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
Added: head/math/gfanlib/pkg-plist
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/gfanlib/pkg-plist Fri Feb 8 09:27:32 2019 (r492416)
@@ -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
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