git: a8ceb6491219 - main - math/polymake: Backport patch allowing to use external Nauty library instead of Nauty source tree
Yuri Victorovich
yuri at FreeBSD.org
Sat Aug 28 07:41:11 UTC 2021
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=a8ceb6491219baa95155e2b55a1ba5b1654757cb
commit a8ceb6491219baa95155e2b55a1ba5b1654757cb
Author: Philipp Ost <bsd at philippost.de>
AuthorDate: 2021-08-28 07:32:22 +0000
Commit: Yuri Victorovich <yuri at FreeBSD.org>
CommitDate: 2021-08-28 07:41:05 +0000
math/polymake: Backport patch allowing to use external Nauty library instead of Nauty source tree
Also fix stripping of ideal.so
---
math/polymake/Makefile | 22 ++--
math/polymake/files/patch-libnauty | 212 +++++++++++++++++++++++++++++++++++++
2 files changed, 225 insertions(+), 9 deletions(-)
diff --git a/math/polymake/Makefile b/math/polymake/Makefile
index 097714d1f003..e88745e92d98 100644
--- a/math/polymake/Makefile
+++ b/math/polymake/Makefile
@@ -2,6 +2,7 @@
PORTNAME= polymake
DISTVERSION= 4.4
+PORTREVISION= 1
CATEGORIES= math
MASTER_SITES= https://polymake.org/lib/exe/fetch.php/download/
DISTNAME= ${PORTNAME}-${DISTVERSION}-minimal
@@ -95,14 +96,9 @@ BLISS_CONFIGURE_OFF= --without-bliss
BLISS_BUILD_DEPENDS= bliss-graph-tool>=0.73:math/bliss
BLISS_RUN_DEPENDS= bliss-graph-tool>=0.73:math/bliss
-NAUTY_WRKSRC= ${:!${MAKE} -V WRKSRC -C ${.CURDIR:H:H}/math/nauty!}
-NAUTY_CONFIGURE_ON= --with-nauty-src=${NAUTY_WRKSRC}
-NAUTY_BUILD_DEPENDS= ${NONEXISTENT}:math/nauty:patch
-NAUTY_RUN_DEPENDS= nauty>=27:math/nauty
-# Do not explicitly disable nauty. polymake's configure script currently fails
-# if a reconfiguration is triggered. However, it is aware that bliss and nauty
-# are mutually exclusive and disables nauty if BLISS=on.
-#NAUTY_CONFIGURE_OFF= --without-nauty
+NAUTY_CONFIGURE_ON= --with-nauty=${LOCALBASE}
+NAUTY_CONFIGURE_OFF= --without-nauty
+NAUTY_LIB_DEPENDS= libnauty.so:math/nauty
LRS_CONFIGURE_ON= --with-lrs=${LOCALBASE} \
--with-lrs-include=${LOCALBASE}/include/lrslib
@@ -140,6 +136,8 @@ TESTS_VARS= USE_PERL5+=test
# Set WRKSRC accordingly.
WRKSRC= ${WRKDIR}/${PORTNAME}-${DISTVERSION}
+.include <bsd.port.options.mk>
+
# Deal with site specific installation directory
# polymake installs a perlxs module which depends on the perl configuration
PERL_ARCHNAME= ${:!${PERL} -E 'use Config; print "\$Config::Config{archname}";'!}
@@ -178,10 +176,16 @@ post-install:
${STRIP_CMD} ${STAGEDIR}${PREFIX}/libexec/polymake/perlx/${PERL_VERSION}/${PERL_ARCHNAME}/auto/Polymake/Ext/Ext.so
-.for l in common fan fulton graph group ideal matroid polytope topaz tropical
+.for l in common fan fulton graph group matroid polytope topaz tropical
${STRIP_CMD} ${STAGEDIR}${PREFIX}/libexec/polymake/lib/${l}.so
.endfor
+# only strip libexec/polymake/lib/ideal.so iff SINGULAR=on, if SINGULAR=off it
+# is an empty file and stripping fails
+.if ${PORT_OPTIONS:MSINGULAR}
+ ${STRIP_CMD} ${STAGEDIR}${PREFIX}/libexec/polymake/lib/ideal.so
+.endif
+
.for lp in libpolymake-apps libpolymake-apps-rt
${STRIP_CMD} ${STAGEDIR}${PREFIX}/libexec/polymake/lib/${lp}.so.${DISTVERSION}
.endfor
diff --git a/math/polymake/files/patch-libnauty b/math/polymake/files/patch-libnauty
new file mode 100644
index 000000000000..77eaf347b801
--- /dev/null
+++ b/math/polymake/files/patch-libnauty
@@ -0,0 +1,212 @@
+- patch from the upstream allowing to link to libnauty.so: https://github.com/polymake/polymake/issues/10#issuecomment-906184045
+
+commit 3d5f15812247c37e1821d30a24e69acc308bc54b
+Author: Benjamin Lorenz <lorenz at math.tu-berlin.de>
+Date: Tue Aug 24 21:20:40 2021 +0200
+
+ bundled/nauty: add support for libnauty installation to configuration
+
+ in addition to bundled and source-dir
+
+ without any options this will try to run a test-program and fall back
+ to the bundled nauty if that fails.
+
+diff --git bundled/nauty/apps/graph/src/GraphIso.cc bundled/nauty/apps/graph/src/GraphIso.cc
+index 26779977ff..26a0b689bf 100644
+--- bundled/nauty/apps/graph/src/GraphIso.cc
++++ bundled/nauty/apps/graph/src/GraphIso.cc
+@@ -29,8 +29,8 @@
+ #define set nauty_set
+ #define permutation nauty_permutation
+
+-#include <nauty.h>
+-#include <naututil.h>
++#include <nauty/nauty.h>
++#include <nauty/naututil.h>
+ #include <memory>
+
+ namespace {
+diff --git bundled/nauty/apps/graph/src/build_flags.pl bundled/nauty/apps/graph/src/build_flags.pl
+index 1b6fac03e2..9efd0a0cd0 100644
+--- bundled/nauty/apps/graph/src/build_flags.pl
++++ bundled/nauty/apps/graph/src/build_flags.pl
+@@ -1,6 +1,6 @@
+ # input for generate_ninja_targets.pl
+
+-my $foreign_src = $ConfigFlags{'bundled.nauty.NautySrc'};
++my $foreign_src = $ConfigFlags{'bundled.nauty.NautySrc'} ne "bundled" && $ConfigFlags{'bundled.nauty.NautySrc'};
+ my $nauty_src = $foreign_src ? '${bundled.nauty.NautySrc}' : '${root}/bundled/nauty/external/nauty';
+ my $generated_dir = '${buildroot}/staticlib/nauty';
+ my @generated_headers = qw( nauty.h naututil.h gtools.h );
+@@ -9,17 +9,21 @@ my @generated_out = map { "$generated_dir/$_" } @generated_headers;
+ my $include_generated = ($foreign_src && grep { -f "$foreign_src/$_" } @generated_headers)
+ ? join(" ", map { "-include $_" } @generated_out)
+ : "-I$generated_dir";
++my $nauty_inc = $ConfigFlags{'bundled.nauty.NautySrc'}
++ ? " -I$generated_dir -I$nauty_src"
++ : "";
+
+-( CXXFLAGS => "-DBIGNAUTY -I$generated_dir -I$nauty_src",
++( 'GraphIso.cc' => $nauty_inc,
+
+- GENERATED => {
+- out => "@generated_out", in => "@generated_in",
+- command => "cd $generated_dir; CC=\"\${CC}\" CFLAGS=\"\${CFLAGS}\" $nauty_src/configure --quiet >/dev/null 2>/dev/null; rm -f makefile",
+- },
+-
+- staticlib => {
+- SOURCEDIR => $nauty_src,
+- SOURCES => [ qw(naugraph.c naurng.c nausparse.c nautaux.c nautil.c nautinv.c naututil.c nauty.c rng.c schreier.c) ],
+- CFLAGS => "-DBIGNAUTY $include_generated -I$nauty_src",
+- }
++ $ConfigFlags{'bundled.nauty.NautySrc'}
++ ? ( GENERATED => {
++ out => "@generated_out", in => "@generated_in",
++ command => "cd $generated_dir; CC=\"\${CC}\" CFLAGS=\"\${CFLAGS}\" $nauty_src/configure --quiet >/dev/null 2>/dev/null; rm -rf makefile nauty; ln -s . nauty",
++ },
++ staticlib => {
++ SOURCEDIR => $nauty_src,
++ SOURCES => [ qw(naugraph.c naurng.c nausparse.c nautaux.c nautil.c nautinv.c naututil.c nauty.c rng.c schreier.c) ],
++ CFLAGS => "$include_generated -I$nauty_src",
++ } )
++ : ()
+ )
+diff --git bundled/nauty/support/configure.pl bundled/nauty/support/configure.pl
+index 73ac8c2b22..e8b9eec126 100644
+--- bundled/nauty/support/configure.pl
++++ bundled/nauty/support/configure.pl
+@@ -14,19 +14,19 @@
+ # GNU General Public License for more details.
+ #-------------------------------------------------------------------------------
+
+- at conf_vars=qw( NautySrc );
++ at conf_vars=qw( NautySrc CXXFLAGS LDFLAGS LIBS );
+
+ sub allowed_options {
+ my ($allowed_options, $allowed_with)=@_;
+- @$allowed_with{ qw( nauty-src ) }=();
++ @$allowed_with{ qw( nauty-src nauty ) }=();
+ }
+
+
+ sub usage {
+- print STDERR " --with-nauty-src=PATH Source directory of nauty.\n",
+- " By default polymake will use the bundled nauty source files,\n",
+- " for the minimal tarball this option allows using a custom\n",
+- " directory containing the nauty sources.\n";
++ print STDERR " By default polymake will use the bundled nauty source files,\n",
++ " these options allow using a custom nauty source or installation:\n",
++ " --with-nauty-src=PATH Source directory of nauty.\n",
++ " --with-nauty=PATH Installation prefix of nauty.\n";
+ }
+
+ sub check_nauty {
+@@ -36,17 +36,100 @@ sub check_nauty {
+
+ sub proceed {
+ my ($options)=@_;
+- my $nautysrc;
+- if (defined ($nautysrc=$options->{"nauty-src"})) {
+- check_nauty($nautysrc) or
+- die "Specified nauty source directory invalid, could not find 'nauty-h.in'.";
+- $NautySrc = $nautysrc;
+- } elsif (!check_nauty()) {
++ my $nauty_path;
++ my $nauty_src;
++ my $nautyver;
++ $NautySrc = "bundled";
++ if (defined ($nauty_path=$options->{nauty}) && $nauty_path ne "bundled") {
++ my $nauty_inc="$nauty_path/include";
++ my $nauty_lib=Polymake::Configure::get_libdir($nauty_path, "nauty");
++ unless (-f "$nauty_inc/nauty/nauty.h"
++ && ( -f "$nauty_lib/libnauty.$Config::Config{dlext}"
++ || -f "$nauty_lib/libnauty.a" ) ) {
++ die "Invalid installation location of nauty library: header file nauty/nauty.h and/or library libnauty.$Config::Config{dlext} / libnauty.a not found\n";
++ }
++ $LDFLAGS.=" -Wl,-rpath,$nauty_lib"
++ if $nauty_path !~ m|^/usr$| && -f "$nauty_lib/libnauty.$Config::Config{dlext}";
++ $CXXFLAGS = "-I$nauty_inc";
++ $LDFLAGS = "-L$nauty_lib";
++ undef $NautySrc;
++ } elsif (defined ($nauty_src=$options->{"nauty-src"}) && $nauty_src ne "bundled") {
++ check_nauty($nauty_src) or
++ die "Specified nauty source directory invalid, could not find 'nauty-h.in' in $nauty_src.";
++ $NautySrc = "$nauty_src";
++ }
++
++ if (!$nauty_src && $nauty_path ne "bundled" && $options->{prereq} ne ".none.") {
++ # compile test-program, soft-fail
++ my $testcode = <<'---';
++// simplified example from nautyex1.c from the nauty source
++
++#define MAXN 1000 /* Define this before including nauty.h */
++#include <nauty/nauty.h>
++#include <iostream>
++
++int
++main(int argc, char *argv[])
++{
++ graph g[MAXN*MAXM];
++ int lab[MAXN],ptn[MAXN],orbits[MAXN];
++ static DEFAULTOPTIONS_GRAPH(options);
++ statsblk stats;
++ int n = 5;
++ int m = 1;
++ int v;
++
++ options.writeautoms = FALSE;
++
++ /* The following optional call verifies that we are linking
++ to compatible versions of the nauty routines. */
++
++ nauty_check(WORDSIZE,m,n,NAUTYVERSIONID);
++ EMPTYGRAPH(g,m,n);
++ for (v = 0; v < n; ++v) ADDONEEDGE(g,v,(v+1)%n,m);
++
++ densenauty(g,lab,ptn,orbits,&options,&stats,m,n,NULL);
++ std::cout << "VERSION " << NAUTYVERSIONID << std::endl;
++
++ exit(0);
++}
++---
++ my $error=Polymake::Configure::build_test_program($testcode, LIBS => "-lnauty", CXXFLAGS => "$CXXFLAGS", LDFLAGS => "$LDFLAGS");
++
++ if ($? == 0) {
++ my $message=Polymake::Configure::run_test_program();
++ if ($?) {
++ check_nauty() and !defined($nauty_path) or
++ die "Could not run a test program checking for nauty library.\n",
++ "The complete error log follows:\n\n$message\n",
++ "Please investigate the reasons and fix the installation.\n";
++ } else {
++ ($nautyver) = $message =~ /VERSION (\d+)/;
++ my $nautymin = 25000; # version*10000
++ if ($nautyver < $nautymin) {
++ check_nauty() and !defined($nauty_path) or
++ die "Your nauty version $nautyver is too old, at least version $nautymin is required.\n";
++ } else {
++ $LIBS = "-lnauty";
++ undef $NautySrc;
++ }
++ }
++ } else {
++ check_nauty() and !defined($nauty_path) or
++ die "Could not compile a test program checking for nauty.\n",
++ "The most probable reasons are that the library is installed at a non-standard location,\n",
++ "is not configured to build a shared module, or missing at all.\n",
++ "The complete error log follows:\n\n$error\n",
++ "Please install the library and specify its location using --with-nauty option, if needed.\n";
++ }
++ }
++
++ if ($NautySrc eq "bundled" && !check_nauty()) {
+ die "Bundled nauty directory seems to be missing, to use the nauty interface\n",
+ "with the minimal tarball please specify a nauty source directory\n",
+- "via --with-nauty-src=PATH.";
++ "via --with-nauty-src=PATH, or a nauty installation with --with-nauty=PATH.";
+ }
+
+- return $NautySrc ? "$NautySrc" : "bundled";
++ return $NautySrc ? "source: $NautySrc" : ("version $nautyver @ ".($nauty_path//"system"));
+ }
+
More information about the dev-commits-ports-all
mailing list