Add patch BitMatrix_AdjacencyMatrix_Deleted_Vertex.patch.

The patch is taken from the upstream 0.9721 release, and fixes BitMatrix and
AdjacencyMatrix problems in combination with deleted vertices.

Thanks: Ian Jackson for the bug report with reproducer, which is now part of the testsuite.
Closes: #987095

debian/patches/BitMatrix_AdjacencyMatrix_Deleted_Vertex.patch

+Description: fix BitMatrix and AdjacencyMatrix problems
+Origin: upstream git, diff 0.9720..0.9721
+Bug: https://github.com/graphviz-perl/Graph/issues/20
+Bug-Debian: https://bugs.debian.org/987095
+Author: Ed J <mohawk2@users.noreply.github.com>
+Reviewed-by: gregor herrmann <gregoa@debian.org>
+Last-Update: 2021-04-18
+
+--- a/lib/Graph.pm
++++ b/lib/Graph.pm
+@@ -356,6 +356,7 @@
+ sub _vertex_ids_maybe_ensure {
+     my $ensure = pop;
+     my ($g, @args) = @_;
++    __carp_confess "Graph: given undefined vertex" if grep !defined, @args;
+     my $V = $g->[ _V ];
+     if (($V->[ _f ] & _LIGHT)) {
+ 	my $s = $V->[ _s ];
+--- a/lib/Graph/AdjacencyMatrix.pm
++++ b/lib/Graph/AdjacencyMatrix.pm
+@@ -29,31 +29,22 @@
+     my $m = Graph::BitMatrix->new($g);
+     my $self = bless [ $m, undef, \@V ], $class;
+     return $self if !$want_distance;
+-    # for my $u (@V) {
+-    #     for my $v (@V) {
+-    #         if ($g->has_edge($u, $v)) {
+-    #             $n->set($u, $v,
+-    #                    $g->get_edge_attribute($u, $v, $d));
+-    #        }
+-    #     }
+-    # }
+     my $n = $self->[ _DM ] = Graph::Matrix->new($g);
+     $n->set($_, $_, 0) for @V;
+-    my $Ei = $g->[_E][_i];
+     my $n0 = $n->[0];
+     my $n1 = $n->[1];
+     my $undirected = $g->is_undirected;
+     my $multiedged = $g->multiedged;
+-    for my $t (grep defined, @$Ei) {
+-	my ($i0, $j0) = @$t;
+-	my $u = $V[ $i0 ];
+-	my $v = $V[ $j0 ];
+-	$n0->[ $i0 ]->[ $j0 ] = $multiedged
++    for my $e ($g->edges) {
++	my ($u, $v) = @$e;
++        $n->set($u, $v, $multiedged
+ 	    ? _multiedged_distances($g, $u, $v, $d)
+-	    : $g->get_edge_attribute($u, $v, $d);
+-	$n0->[ $j0 ]->[ $i0 ] = $multiedged
++	    : $g->get_edge_attribute($u, $v, $d)
++        );
++        $n->set($v, $u, $multiedged
+ 	    ? _multiedged_distances($g, $v, $u, $d)
+-	    : $g->get_edge_attribute($v, $u, $d) if $undirected;
++	    : $g->get_edge_attribute($v, $u, $d)
++        ) if $undirected;
+     }
+     $self;
+ }
+--- a/lib/Graph/BitMatrix.pm
++++ b/lib/Graph/BitMatrix.pm
+@@ -30,19 +30,12 @@
+     #	vec($bm0->[$i], $j, 1) = 1 if $g->has_edge($u, $V[$j]);
+     #    }
+     # }
+-    my $Ei = $g->[_E]->[_i];
+-    if ($g->is_undirected) {
+-	for my $e (grep defined, @{ $Ei }) {
+-	    my ($i0, $j0) = @$e;
+-	    vec($bm0->[$i0], $j0, 1) = 1;
+-	    vec($bm0->[$j0], $i0, 1) = 1;
+-	}
+-    } else {
+-	for my $e (grep defined, @{ $Ei }) {
+-	    my ($i0, $j0) = @$e;
+-            ($j0, $i0) = ($i0, $j0) if $transpose;
+-	    vec($bm0->[$i0], $j0, 1) = 1;
+-	}
++    my $undirected = $g->is_undirected;
++    for my $e ($g->edges) {
++	my ($i0, $j0) = map $V{$_}, @$e;
++	($j0, $i0) = ($i0, $j0) if $transpose;
++	vec($bm0->[$i0], $j0, 1) = 1;
++	vec($bm0->[$j0], $i0, 1) = 1 if $undirected;
+     }
+     $bm;
+ }
+--- a/t/72_transitive.t
++++ b/t/72_transitive.t
+@@ -1,5 +1,5 @@
+ use strict; use warnings;
+-use Test::More tests => 235;
++use Test::More tests => 237;
+ 
+ use Graph::Directed;
+ use Graph::Undirected;
+@@ -506,3 +506,14 @@
+ EOF
+     ok $tcg->is_reachable(7, 8), '7-8 reachable when on cycle';
+ }
++
++{
++  my $g = Graph::Directed->new(edges => [
++    [qw(A C)], [qw(A NOTA)], [qw(B A)], [qw(B C)], [qw(B NOTA)],
++  ]);
++  $g->delete_vertex('C');
++  my $tc = $g->transitive_closure;
++  is $tc, 'A-A,A-NOTA,B-A,B-B,B-NOTA,NOTA-NOTA';
++  $tc->delete_edge($_,$_) for qw(A B C N);
++  is $tc, 'A-NOTA,B-A,B-NOTA,NOTA-NOTA';
++}
+--- a/t/83_bitmatrix.t
++++ b/t/83_bitmatrix.t
+@@ -6,10 +6,12 @@
+ 
+ my $g = Graph->new;
+ 
++$g->add_edge(qw(e a));
+ $g->add_edge(qw(a b));
+ $g->add_edge(qw(b c));
+ $g->add_edge(qw(b d));
+ $g->add_edge(qw(d d));
++$g->delete_vertex('e');
+ 
+ my $m = Graph::BitMatrix->new($g);
+ 

debian/patches/series

+BitMatrix_AdjacencyMatrix_Deleted_Vertex.patch