Date: Tue, 19 Mar 2019 16:04:10 +0000 (UTC) From: Steve Wills <swills@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r496268 - in head/math: . frobby frobby/files Message-ID: <201903191604.x2JG4Amo009384@repo.freebsd.org>
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Author: swills Date: Tue Mar 19 16:04:10 2019 New Revision: 496268 URL: https://svnweb.freebsd.org/changeset/ports/496268 Log: math/frobby: create port Frobby is a software system and project for computations with monomial ideals. Frobby is free software and it is intended as a vehicle for computational and mathematical research on monomial ideals. The current functionality includes Euler characteristic, Hilbert series, maximal standard monomials, combinatorial optimization on monomial ideals, primary decomposition, irreducible decomposition, Alexander dual, associated primes, minimization and intersection of monomial ideals as well as the computation of Frobenius problems (using 4ti2) with very large numbers. Frobby is also able to translate between formats that can be used with several different computer systems, such as Macaulay 2, Monos, 4ti2, CoCoA4 and Singular. Thus Frobby can be used with any of those systems. WWW: http://www.broune.com/frobby/ PR: 231208 Submitted by: Lorenzo Salvadore <phascolarctos@protonmail.ch> Added: head/math/frobby/ head/math/frobby/Makefile (contents, props changed) head/math/frobby/distinfo (contents, props changed) head/math/frobby/files/ head/math/frobby/files/patch-Makefile (contents, props changed) head/math/frobby/files/patch-src_HashMap.h (contents, props changed) head/math/frobby/files/patch-src_StatisticsStrategy.cpp (contents, props changed) head/math/frobby/files/patch-src_main.cpp (contents, props changed) head/math/frobby/files/patch-src_randomDataGenerators.cpp (contents, props changed) head/math/frobby/files/patch-test_runSplitTests (contents, props changed) head/math/frobby/files/patch-test_runTests (contents, props changed) head/math/frobby/pkg-descr (contents, props changed) head/math/frobby/pkg-help (contents, props changed) head/math/frobby/pkg-plist (contents, props changed) Modified: head/math/Makefile (contents, props changed) Modified: head/math/Makefile ============================================================================== --- head/math/Makefile Tue Mar 19 15:26:00 2019 (r496267) +++ head/math/Makefile Tue Mar 19 16:04:10 2019 (r496268) @@ -227,6 +227,7 @@ SUBDIR += fpc-numlib SUBDIR += fplll SUBDIR += fricas + SUBDIR += frobby SUBDIR += fxt SUBDIR += g2o SUBDIR += galculator Added: head/math/frobby/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/Makefile Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,100 @@ +# $FreeBSD$ + +PORTNAME= frobby +DISTVERSIONPREFIX= v +DISTVERSION= 0.9.0 +CATEGORIES= math +MASTER_SITES= http://www.broune.com/frobby/ +DISTNAME= ${PORTNAME}_${DISTVERSIONPREFIX}${DISTVERSION} + +MAINTAINER= phascolarctos@protonmail.ch +COMMENT= Software system and project for computations with monomial ideals + +LICENSE= GPLv2+ +LICENSE_FILE= ${WRKSRC}/COPYING + +LIB_DEPENDS= libgmp.so:math/gmp + +USES= gmake shebangfix + +BINARY_ALIAS= make=gmake +USE_LDCONFIG= yes + +SHEBANG_FILES= test/testScripts/* \ + test/latticeFormats/runtest* + +OPTIONS_DEFINE= EXEDOCS LIBDOCS TEST +OPTIONS_DEFAULT= STATIC SHARED +OPTIONS_MULTI= INSTALL +OPTIONS_MULTI_INSTALL= EXECUTABLE \ + SHARED \ + STATIC +EXEDOCS_DESC= Build and install documentation for frobby executable +LIBDOCS_DESC= Build and install documentation for frobby library +EXECUTABLE_DESC= Build and install frobby executable +SHARED_DESC= Build and install libfrobby.so +STATIC_DESC= Build and install libfrobby.a +EXEDOCS_BUILD_DEPENDS= latex:print/tex-formats \ + dvips:print/tex-dvipsk +LIBDOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ + epstopdf:print/texlive-base +TEST_BUILD_DEPENDS= bash:shells/bash +OPTIONS_SUB= yes + +MAKE_ARGS+= GMP_INC_DIR=${LOCALBASE}/include +LDFLAGS+= -L${LOCALBASE}/lib + +.include <bsd.port.options.mk> + +.if ${PORT_OPTIONS:MSHARED} || ${PORT_OPTIONS:MSTATIC} +PLIST_SUB+= LIBRARY="" NO_LIBRARY="@comment " +.else +PLIST_SUB+= LIBRARY="@comment " NO_LIBRARY="" +.endif + +do-build: + +do-build-EXEDOCS-on: + cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} doc + +do-build-EXECUTABLE-on: + cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} + +do-build-LIBDOCS-on: + cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} develDoc + +do-build-STATIC-on: + cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} library + +post-build-SHARED-on: + cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} MODE=shared library + +post-build-TEST-on: do-build-EXECUTABLE-on + cd ${WRKSRC} && test/runTests _full + cd ${WRKSRC} && test/runSplitTests _full + +do-install: + +do-install-EXECUTABLE-on: + ${INSTALL_PROGRAM} ${WRKSRC}/bin/release/frobby ${STAGEDIR}${PREFIX}/bin + +do-install-SHARED-on: + ${INSTALL_DATA} ${WRKSRC}/src/frobby.h ${STAGEDIR}${PREFIX}/include + ${INSTALL_DATA} ${WRKSRC}/bin/libfrobby.so ${STAGEDIR}${PREFIX}/lib + +do-install-STATIC-on: + ${INSTALL_DATA} ${WRKSRC}/src/frobby.h ${STAGEDIR}${PREFIX}/include + ${INSTALL_LIB} ${WRKSRC}/bin/libfrobby.a ${STAGEDIR}${PREFIX}/lib + +do-install-EXEDOCS-on: + ${MKDIR} ${STAGEDIR}${DOCSDIR} + ${INSTALL_MAN} ${WRKSRC}/bin/manual.ps ${STAGEDIR}${DOCSDIR} + ${INSTALL_MAN} ${WRKSRC}/bin/manual.pdf ${STAGEDIR}${DOCSDIR} + +do-install-LIBDOCS-on: + ${MKDIR} ${STAGEDIR}${DOCSDIR} + ${INSTALL_MAN} ${WRKSRC}/bin/develDoc/develDoc.ps ${STAGEDIR}${DOCSDIR} + ${INSTALL_MAN} ${WRKSRC}/bin/develDoc/develDoc.pdf ${STAGEDIR}${DOCSDIR} + cd ${WRKSRC}/bin/develDoc && ${COPYTREE_SHARE} html ${STAGEDIR}${DOCSDIR} + +.include <bsd.port.mk> Added: head/math/frobby/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/distinfo Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,3 @@ +TIMESTAMP = 1535898606 +SHA256 (frobby_v0.9.0.tar.gz) = af092383e6dc849c86f4e79747ae0e5cd309a690747230e10aa38d60640062df +SIZE (frobby_v0.9.0.tar.gz) = 852524 Added: head/math/frobby/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/files/patch-Makefile Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,26 @@ +--- Makefile.orig 2011-09-23 20:09:12 UTC ++++ Makefile +@@ -87,7 +87,6 @@ endif + MATCH=false + ifeq ($(MODE), release) + outdir = bin/release/ +- cflags += -O2 + MATCH=true + endif + ifeq ($(MODE), debug) +@@ -99,13 +98,13 @@ ifeq ($(MODE), debug) + endif + ifeq ($(MODE), shared) + outdir = bin/shared/ +- cflags += -O2 -fPIC ++ cflags += -fPIC + library = libfrobby.so + MATCH=true + endif + ifeq ($(MODE), profile) + outdir = bin/profile/ +- cflags += -g -pg -O2 -D PROFILE ++ cflags += -g -pg -D PROFILE + ldflags += -pg + MATCH=true + benchArgs = _profile $(FROBBYARGS) Added: head/math/frobby/files/patch-src_HashMap.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/files/patch-src_HashMap.h Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,58 @@ +--- src/HashMap.h.orig 2018-09-05 21:12:33 UTC ++++ src/HashMap.h +@@ -34,55 +34,10 @@ + template<class Key> + class FrobbyHash {}; + +-// ********************************************************* +-#ifdef __GNUC__ // Only GCC defines this macro +-#include "hash_map/hash_map" +-#include <string> +- +-template<> +-class FrobbyHash<string> : public __gnu_cxx::hash<string> { +-}; +- +-template<class Key, class Value> +-class HashMap : public __gnu_cxx::hash_map<Key, Value, +- FrobbyHash<Key> > { +-}; +- +-#else +- +-// ********************************************************* +-#ifdef _MSC_VER // Only Microsoft C++ defines this macro +-#include <hash_map> +-#include <string> +- +-template<class Key> +-class HashWrapper : public stdext::hash_compare<Key, ::std::less<Key> >, FrobbyHash<Key> { +-public: +- size_t operator()(const Key& key) const { +- return FrobbyHash<typename Key>::operator()(key); +- } +- +- bool operator()(const Key& a, const Key& b) const { +- return stdext::hash_compare<Key, ::std::less<Key> >::operator()(a, b); +- } +-}; +- +-template<> +-class HashWrapper<string> : public stdext::hash_compare<string, ::std::less<string> > { +-}; +- +-template<class Key, class Value> +-class HashMap : public stdext::hash_map<Key, Value, HashWrapper<Key> > { +-}; +- +-// ********************************************************* +-#else // Fall-back for unknown compilers + #include <map> + template<class Key, class Value> + class HashMap : public std::map<Key, Value> { + }; +-#endif +-#endif + + + #endif Added: head/math/frobby/files/patch-src_StatisticsStrategy.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/files/patch-src_StatisticsStrategy.cpp Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,11 @@ +--- src/StatisticsStrategy.cpp.orig 2011-09-23 20:09:12 UTC ++++ src/StatisticsStrategy.cpp +@@ -140,7 +140,7 @@ double StatisticsStrategy::StatTracker::getAvgSubGenCo + if (_nodeCount == 0) + return 0.0; + else { +- mpz_class q = mpq_class(_subGenSum) / _nodeCount; ++ mpq_class q = mpq_class(_subGenSum) / _nodeCount; + return q.get_d(); + } + } Added: head/math/frobby/files/patch-src_main.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/files/patch-src_main.cpp Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,10 @@ +--- src/main.cpp.orig 2011-09-23 20:09:12 UTC ++++ src/main.cpp +@@ -24,6 +24,7 @@ + + #include <ctime> + #include <cstdlib> ++#include <unistd.h> + + /** This function runs the Frobby console interface. the ::main + function calls this function after having set up DEBUG-specific Added: head/math/frobby/files/patch-src_randomDataGenerators.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/files/patch-src_randomDataGenerators.cpp Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,10 @@ +--- src/randomDataGenerators.cpp.orig 2018-09-05 21:14:15 UTC ++++ src/randomDataGenerators.cpp +@@ -25,6 +25,7 @@ + + #include <limits> + #include <ctime> ++#include <unistd.h> + + void generateLinkedListIdeal(BigIdeal& ideal, size_t variableCount) { + VarNames names(variableCount); Added: head/math/frobby/files/patch-test_runSplitTests ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/files/patch-test_runSplitTests Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,48 @@ +--- test/runSplitTests.orig 2018-09-08 10:55:55 UTC ++++ test/runSplitTests +@@ -30,6 +30,8 @@ params="$*" + testhelper=../testScripts/testhelper + paths="specialIdeals commonIdeals frob" + ++failed="" ++ + runTests () { + action="$1"; shift; + splits="$*"; +@@ -41,8 +43,9 @@ runTests () { + for path in $paths; do + cd test/$path; + ../testScripts/runtests $action $params -split $split; +- if [ $? != 0 ]; then exit 1; fi ++ if [ $? != 0 ]; then cd ../..; return 1; fi + cd ../..; ++return 0 + + if [ "$testLevel" = "few" ]; then + if [ "$action" != "frob" ]; then +@@ -57,19 +60,25 @@ runTests () { + for action in $bigattiActions; + do + runTests "$action" $bigattiSplits ++if [ $? -eq 1 ]; then failed="$failed $action"; continue; fi + done + + for action in $labelActions; + do + runTests "$action" $labelSplits ++if [ $? -eq 1 ]; then failed="$failed $action"; continue; fi + done + + for action in $pivotActions; + do + runTests "$action" $pivotSplits ++if [ $? -eq 1 ]; then failed="$failed $action"; continue; fi + done + + for action in $frobActions; + do + runTests "$action" $frobSplits ++if [ $? -eq 1 ]; then failed="$failed $action"; continue; fi + done ++echo -e "\nFailed tests:$failed." ++echo "But test hilbert_bigatti was expected to fail because simplification is broken for it." Added: head/math/frobby/files/patch-test_runTests ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/files/patch-test_runTests Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,60 @@ +--- test/runTests.orig 2011-09-23 20:09:12 UTC ++++ test/runTests +@@ -15,20 +15,23 @@ normalTests="euler alexdual hilbert_deform hilbert_big + + specialTests="internal idealFormats polyFormats latticeFormats messages" + params="$*" ++failed="" + + runNormalTests () { + action="$1"; shift; + path="$1"; shift; + cd test/$path; + ../testScripts/runtests $action $params +- if [ $? != 0 ]; then exit 1; fi ++ if [ $? != 0 ]; then cd ../..; return 1; fi + cd ../..; ++return 0 + } + + for t in $normalTests; do + echo -n "$t " + + runNormalTests $t specialIdeals ++if [ $? -eq 1 ]; then failed="$failed $t"; continue; fi + if [ "$testLevel" = "few" ]; then + if [ "$t" != "frob" ]; then + echo; +@@ -37,15 +40,19 @@ for t in $normalTests; do + fi + + runNormalTests $t commonIdeals ++if [ $? -eq 1 ]; then failed="$failed $t"; continue; fi + + runNormalTests $t frob ++if [ $? -eq 1 ]; then failed="$failed $t"; continue; fi + + if [ "$t" == "euler" ]; then + runNormalTests $t bigIdeals ++if [ $? -eq 1 ]; then failed="$failed $t"; continue; fi + fi + + if [ -e "$t" ]; then + runNormalTests $t $t ++if [ $? -eq 1 ]; then failed="$failed $t"; continue; fi + fi + + echo +@@ -56,9 +63,10 @@ do + echo -n "$t " + cd test/$t + ./runtests $* +- if [ $? != 0 ]; then exit 1; fi ++ if [ $? != 0 ]; then failed="$failed $t"; continue; fi + echo + cd ../.. + done + +-echo "All normal tests passed." ++echo "Failed tests:$failed." ++echo "But tests hilbert_deform and hilbert_bigatti were expected to fail because simplification is broken for them." Added: head/math/frobby/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/pkg-descr Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,15 @@ +Frobby is a software system and project for computations with monomial +ideals. Frobby is free software and it is intended as a vehicle for +computational and mathematical research on monomial ideals. + +The current functionality includes Euler characteristic, Hilbert +series, maximal standard monomials, combinatorial optimization on +monomial ideals, primary decomposition, irreducible decomposition, +Alexander dual, associated primes, minimization and intersection of +monomial ideals as well as the computation of Frobenius problems +(using 4ti2) with very large numbers. Frobby is also able to translate +between formats that can be used with several different computer +systems, such as Macaulay 2, Monos, 4ti2, CoCoA4 and Singular. Thus +Frobby can be used with any of those systems. + +WWW: http://www.broune.com/frobby/ Added: head/math/frobby/pkg-help ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/pkg-help Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,18 @@ +If you are installing Frobby as a dependency, most probably you only +need the static library and maybe the shared library, but certainly +not the executable. + +---------------------------------------------------------------------- + +Warning: the library documentation is very incomplete. +Warning: installing documentation might require high build times due +to heavy build dependencies. + +---------------------------------------------------------------------- + +Warning: hilbert_deform and hilbert_bigatti tests are known to fail +because simplifications do not work for action "hilbert" with +algorithm "deform" or "bigatti", i.e. output polynomials present +expressions such as "a*b*c + a*b*c" or "a - a". Nevertheless results +seem to be correct. +Please report if you get wrong results. Added: head/math/frobby/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/frobby/pkg-plist Tue Mar 19 16:04:10 2019 (r496268) @@ -0,0 +1,1658 @@ +%%EXECUTABLE%%bin/frobby +%%EXEDOCS%%%%DOCSDIR%%/manual.pdf +%%EXEDOCS%%%%DOCSDIR%%/manual.ps +%%LIBDOCS%%%%DOCSDIR%%/develDoc.pdf +%%LIBDOCS%%%%DOCSDIR%%/develDoc.ps +%%LIBDOCS%%%%DOCSDIR%%/html/ActionPrinter_8cpp.html +%%LIBDOCS%%%%DOCSDIR%%/html/ActionPrinter_8cpp_source.html +%%LIBDOCS%%%%DOCSDIR%%/html/ActionPrinter_8h.html +%%LIBDOCS%%%%DOCSDIR%%/html/ActionPrinter_8h_source.html +%%LIBDOCS%%%%DOCSDIR%%/html/Action_8cpp.html +%%LIBDOCS%%%%DOCSDIR%%/html/Action_8cpp_source.html +%%LIBDOCS%%%%DOCSDIR%%/html/Action_8h.html +%%LIBDOCS%%%%DOCSDIR%%/html/Action_8h_source.html +%%LIBDOCS%%%%DOCSDIR%%/html/AlexanderDualAction_8cpp.html +%%LIBDOCS%%%%DOCSDIR%%/html/AlexanderDualAction_8cpp_source.html 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