Add patch for bliss 0.77, remove debug option

3 files changed, 193 insertions, 5 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 1d724db71265..b9132a7e8f7b 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -70,6 +70,7 @@ pkgbase = sagemath-git
 	optdepends = jupyter-jsmol: alternative 3D plot engine in the Jupyter notebook
 	optdepends = sagemath-doc: HTML documentation
 	optdepends = python-igraph: igraph backend for graph theory
+	optdepends = bliss: bliss backend for graph theory
 	optdepends = sage-numerical-backends-coin: COIN mixed integer linear programming backend
 	optdepends = sage-numerical-backends-gurobi: Gurobi mixed integer linear programming backend
 	optdepends = coin-or-csdp: for computing Lovász theta-function of graphs
@@ -95,8 +96,6 @@ pkgbase = sagemath-git
 	optdepends = python-database-knotinfo: interface to the KnotInfo and LinkInfo databases
 	provides = sagemath
 	conflicts = sagemath
-	options = debug
-	options = !strip
 	source = git://git.sagemath.org/sage.git#branch=develop
 	source = sagemath-optional-packages.patch
 	source = latte-count.patch
@@ -105,6 +104,7 @@ pkgbase = sagemath-git
 	source = sagemath-singular-4.2.1.p1.patch
 	source = sagemath-linbox-1.7.patch
 	source = sagemath-python3.10.patch
+	source = sagemath-bliss-0.77.patch
 	sha256sums = SKIP
 	sha256sums = eee5fa15d8c7be7e009166dbde3ea24bb10d7793dc12880516f278f86b1a6694
 	sha256sums = 2f310081357996b7d3bf813e63d07c0fc04d6724adbfbd1beeb554e9476e2e4c
@@ -113,5 +113,6 @@ pkgbase = sagemath-git
 	sha256sums = 1f0c44a4998ed239a3d77e3028b98b6f2c28a95e9bb4b8557523cc8f12ffba34
 	sha256sums = eacea27b214d32cb886a75695153dfc36b5bad2fd2517e8e4eee18e74220e9e3
 	sha256sums = b9ca4fb0e3083e73560df5f0aca7e87d7aa8c05eca3eea49c704bcee102919c7
+	sha256sums = 49ede468b8e1e7b8d7a390aab9ff1a6e899a0c5e487632cbf76902d80c637505
 
 pkgname = sagemath-git
diff --git a/PKGBUILD b/PKGBUILD
index efcd1cddb54a..6e4673a4185a 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -23,6 +23,7 @@ optdepends=('cython: to compile cython code'
   'jupyter-jsmol: alternative 3D plot engine in the Jupyter notebook'
   'sagemath-doc: HTML documentation'
   'python-igraph: igraph backend for graph theory'
+  'bliss: bliss backend for graph theory'
   'sage-numerical-backends-coin: COIN mixed integer linear programming backend'
   'sage-numerical-backends-gurobi: Gurobi mixed integer linear programming backend'
   'coin-or-csdp: for computing Lovász theta-function of graphs'
@@ -56,7 +57,8 @@ source=(git://git.sagemath.org/sage.git#branch=develop
         sagemath-lrcalc2.patch
         sagemath-singular-4.2.1.p1.patch
         sagemath-linbox-1.7.patch
-        sagemath-python3.10.patch)
+        sagemath-python3.10.patch
+        sagemath-bliss-0.77.patch)
 sha256sums=('SKIP'
             'eee5fa15d8c7be7e009166dbde3ea24bb10d7793dc12880516f278f86b1a6694'
             '2f310081357996b7d3bf813e63d07c0fc04d6724adbfbd1beeb554e9476e2e4c'
@@ -64,8 +66,8 @@ sha256sums=('SKIP'
             '8534700f78690a9f1b07df25b281138ed870fdfb70ab4df3818df79d5468ec9f'
             '1f0c44a4998ed239a3d77e3028b98b6f2c28a95e9bb4b8557523cc8f12ffba34'
             'eacea27b214d32cb886a75695153dfc36b5bad2fd2517e8e4eee18e74220e9e3'
-            'b9ca4fb0e3083e73560df5f0aca7e87d7aa8c05eca3eea49c704bcee102919c7')
-options=(debug !strip)
+            'b9ca4fb0e3083e73560df5f0aca7e87d7aa8c05eca3eea49c704bcee102919c7'
+            '49ede468b8e1e7b8d7a390aab9ff1a6e899a0c5e487632cbf76902d80c637505')
 
 pkgver() {
   cd sage
@@ -84,6 +86,8 @@ prepare(){
   patch -p1 -i ../sagemath-linbox-1.7.patch
 # Fix tests with Python 3.10 https://trac.sagemath.org/ticket/30766
   patch -p1 -i ../sagemath-python3.10.patch
+# Fix build with bliss 0.77 https://trac.sagemath.org/ticket/33010
+  patch -p1 -i ../sagemath-bliss-0.77.patch
 
 # Arch-specific patches
 # assume all optional packages are installed
diff --git a/sagemath-bliss-0.77.patch b/sagemath-bliss-0.77.patch
new file mode 100644
index 000000000000..2c0f11b56b81
--- /dev/null
+++ b/sagemath-bliss-0.77.patch
@@ -0,0 +1,183 @@
+diff --git a/build/pkgs/bliss/checksums.ini b/build/pkgs/bliss/checksums.ini
+index e97d89587b..0c1ebf647b 100644
+--- a/build/pkgs/bliss/checksums.ini
++++ b/build/pkgs/bliss/checksums.ini
+@@ -1,4 +1,5 @@
+-tarball=bliss-VERSION.tar.gz
+-sha1=1da8f098046824fbfff4c64c337e28b2a082f74f
+-md5=452aea8737d3c4ad0d8ff39180be8004
+-cksum=2193930007
++tarball=bliss-VERSION.zip
++sha1=c91c9dcbc11d66ffbcf6415e09ebe793df37be2a
++md5=5707cbfd9fd00980571c64ab3584c505
++cksum=1626493724
++upstream_url=https://users.aalto.fi/~tjunttil/bliss/downloads/bliss-VERSION.zip
+diff --git a/build/pkgs/bliss/dependencies b/build/pkgs/bliss/dependencies
+index 3546cda461..66d6773d90 100644
+--- a/build/pkgs/bliss/dependencies
++++ b/build/pkgs/bliss/dependencies
+@@ -1,4 +1,4 @@
+-# no dependencies
++| cmake
+ 
+ ----------
+ All lines of this file are ignored except the first.
+diff --git a/build/pkgs/bliss/package-version.txt b/build/pkgs/bliss/package-version.txt
+index e93ee1376f..9e1e206c41 100644
+--- a/build/pkgs/bliss/package-version.txt
++++ b/build/pkgs/bliss/package-version.txt
+@@ -1 +1 @@
+-0.73+debian-1+sage-2016-08-02.p0
++0.77
+diff --git a/build/pkgs/bliss/spkg-install.in b/build/pkgs/bliss/spkg-install.in
+index aaf4c3037b..ad1fe8176c 100644
+--- a/build/pkgs/bliss/spkg-install.in
++++ b/build/pkgs/bliss/spkg-install.in
+@@ -1,4 +1,6 @@
+ cd src
+-sdh_configure --disable-gmp
++sdh_cmake -DUSE_GMP=OFF -DCMAKE_VERBOSE_MAKEFILE=ON
+ sdh_make
+-sdh_make_install
++sdh_install src/*.hh $SAGE_LOCAL/include/bliss/
++sdh_install libbliss.so $SAGE_LOCAL/lib/
++sdh_install bliss $SAGE_LOCAL/bin/
+diff --git a/build/pkgs/bliss/spkg-src b/build/pkgs/bliss/spkg-src
+deleted file mode 100755
+index 90073233b7..0000000000
+--- a/build/pkgs/bliss/spkg-src
++++ /dev/null
+@@ -1,28 +0,0 @@
+-#!/bin/sh
+-#
+-# creates the tarball in the current dir, to be moved to ../../../upstream
+-#
+-# adapted from cliquer/spkg-src
+-
+-die () {
+-    echo >&2 "$@"
+-    exit 1
+-}
+-
+-rm -rf bliss/
+-git clone -b sage_package https://github.com/mkoeppe/bliss.git  || die "Failed to git clone"
+-cd bliss/
+-
+-VERSION=`autoconf --trace='AC_INIT:$2'`
+-libtoolize || die "Failed to autoreconf"
+-autoreconf -fi || die "Failed to autoreconf"
+-automake --add-missing --copy || die "automake failed"
+-./configure || die "configure failed"
+-
+-rm -f bliss-$VERSION.tar.gz
+-make dist || die "make dist failed"
+-mv bliss-$VERSION.tar.gz ../
+-cd ..
+-rm -rf bliss/
+-
+-
+diff --git a/src/sage/graphs/bliss.pyx b/src/sage/graphs/bliss.pyx
+index 22e861a587..fa426e3d11 100644
+--- a/src/sage/graphs/bliss.pyx
++++ b/src/sage/graphs/bliss.pyx
+@@ -47,22 +47,27 @@ cdef extern from "bliss/graph.hh" namespace "bliss":
+     cdef cppclass Graph(AbstractGraph):
+         Graph(const unsigned int)
+         void add_edge(const unsigned int, const unsigned int)
+-        void find_automorphisms(Stats&, void (*)(void* , unsigned int,
+-                    const unsigned int*), void*)
++        #void find_automorphisms(Stats&, void (*)(void* , unsigned int,
++                    #const unsigned int*), void*)
+         void change_color(const unsigned int, const unsigned int);
+-        const unsigned int* canonical_form(Stats&, void (*)(void*,unsigned int,
+-                    const unsigned int*), void*)
++        const unsigned int* canonical_form(Stats&)
++
++cdef extern from "bliss/digraph.hh" namespace "bliss":
+ 
+     cdef cppclass Digraph(AbstractGraph):
+         Digraph(const unsigned int)
+         void add_edge(const unsigned int, const unsigned int)
+-        void find_automorphisms(Stats&, void (*)(void* , unsigned int,
+-                    const unsigned int*), void*)
++        #void find_automorphisms(Stats&, void (*)(void* , unsigned int,
++                    #const unsigned int*), void*)
+         void change_color(const unsigned int, const unsigned int);
+-        const unsigned int* canonical_form(Stats&, void (*)(void*,unsigned int,
+-                    const unsigned int*), void*)
++        const unsigned int* canonical_form(Stats&)
+         unsigned int get_hash()
+ 
++cdef extern from "bliss_find_automorphisms.h":
++
++    void bliss_find_automorphisms(Graph*, void (*)(void*, unsigned int, const unsigned int*), void*, Stats&)
++    void bliss_find_automorphisms(Digraph*, void (*)(void*, unsigned int, const unsigned int*), void*, Stats&)
++
+ 
+ cdef int encoding_numbits(int n):
+     r"""
+@@ -124,9 +129,6 @@ cdef void add_gen(void *user_param, unsigned int n, const unsigned int *aut):
+ 
+     sig_free(done)
+ 
+-cdef void empty_hook(void *user_param , unsigned int n, const unsigned int *aut):
+-    return
+-
+ #####################################################
+ # constructing bliss graphs from edge lists
+ #####################################################
+@@ -345,10 +347,10 @@ cdef canonical_form_from_edge_list(int Vnr, list Vout, list Vin, int Lnr=1, list
+ 
+     if directed:
+         d = bliss_digraph_from_labelled_edges(Vnr, Lnr, Vout, Vin, labels, partition)
+-        aut = d.canonical_form(s, empty_hook, NULL)
++        aut = d.canonical_form(s)
+     else:
+         g = bliss_graph_from_labelled_edges(Vnr, Lnr, Vout, Vin, labels, partition)
+-        aut = g.canonical_form(s, empty_hook, NULL)
++        aut = g.canonical_form(s)
+ 
+     for i in range(len(Vout)):
+         x = Vout[i]
+@@ -640,11 +642,11 @@ cdef automorphism_group_gens_from_edge_list(int Vnr, Vout, Vin, int Lnr=1, label
+ 
+     if directed:
+         d = bliss_digraph_from_labelled_edges(Vnr, Lnr, Vout, Vin, labels, partition)
+-        d.find_automorphisms(s, add_gen, <void*>data)
++        bliss_find_automorphisms(d, add_gen, <void*>data, s)
+         del d
+     else:
+         g = bliss_graph_from_labelled_edges(Vnr, Lnr, Vout, Vin, labels, partition)
+-        g.find_automorphisms(s, add_gen, <void*>data)
++        bliss_find_automorphisms(g, add_gen, <void*>data, s)
+         del g
+ 
+     return [[cyc for cyc in gen if cyc[0] is not None] for gen in gens]
+diff --git a/src/sage/graphs/bliss_find_automorphisms.h b/src/sage/graphs/bliss_find_automorphisms.h
+new file mode 100644
+index 0000000000..a2c084a163
+--- /dev/null
++++ b/src/sage/graphs/bliss_find_automorphisms.h
+@@ -0,0 +1,22 @@
++#include <bliss/graph.hh>
++#include <bliss/digraph.hh>
++
++inline void bliss_find_automorphisms(bliss::Graph *graph, void (*hook)(void *user_param, unsigned int n, const unsigned int *aut), void *hook_user_param, bliss::Stats s)
++{
++  auto report_aut = [&](unsigned int n, const unsigned int *aut) -> void {
++    if(hook)
++      (*hook)(hook_user_param, n, aut);
++  };
++
++  graph->find_automorphisms(s, report_aut);
++}
++
++inline void bliss_find_automorphisms(bliss::Digraph *graph, void (*hook)(void *user_param, unsigned int n, const unsigned int *aut), void *hook_user_param, bliss::Stats s)
++{
++  auto report_aut = [&](unsigned int n, const unsigned int *aut) -> void {
++    if(hook)
++      (*hook)(hook_user_param, n, aut);
++  };
++
++  graph->find_automorphisms(s, report_aut);
++}