Bug#860310: unblock pre-apptoval request for yade/2017.01a-8

[Anton Gladky <gladk@debian.org>]

Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock

Please unblock package yade

Yade upstream have found a critical bug in so-called periodic
boundaries contact detection [1]. It would be good to have this
fix in Debian as well. I cherry-picked the upstream's patch,
which is attached to this mail.

unblock yade/2017.01a-8

[1] http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg12355.html


Thanks,

Anton

diff -Nru yade-2017.01a/debian/changelog yade-2017.01a/debian/changelog
--- yade-2017.01a/debian/changelog	2017-02-28 22:03:24.000000000 +0100
+++ yade-2017.01a/debian/changelog	2017-04-14 12:43:59.000000000 +0200
@@ -1,3 +1,10 @@
+yade (2017.01a-8) unstable; urgency=medium
+
+  [ Bruno Chareyre ]
+  * [be08409] Critical bugfix for periodic boundaries.
+
+ -- Anton Gladky <gladk@debian.org>  Fri, 14 Apr 2017 12:43:59 +0200
+
 yade (2017.01a-7) unstable; urgency=medium
 
   * [31387da] Add missing dependency on python-pyqt5.qtsvg in python-yade.
diff -Nru yade-2017.01a/debian/patches/09_fix_periodic_boundaries.patch yade-2017.01a/debian/patches/09_fix_periodic_boundaries.patch
--- yade-2017.01a/debian/patches/09_fix_periodic_boundaries.patch	1970-01-01 01:00:00.000000000 +0100
+++ yade-2017.01a/debian/patches/09_fix_periodic_boundaries.patch	2017-04-14 12:42:33.000000000 +0200
@@ -0,0 +1,28 @@
+From c7c8e6f62d452c81a31415f05a12587a6cc8c452 Mon Sep 17 00:00:00 2001
+From: bchareyre <bruno.chareyre@grenoble-inp.fr>
+Date: Fri, 14 Apr 2017 12:04:32 +0200
+Subject: [PATCH] Critical bugfix for collision detection in periodic boundary
+ conditions. Bounds lists were left partially unordered,  then some
+ interactions were never detected (my toughest yade debugging until now).
+
+---
+ pkg/common/InsertionSortCollider.cpp | 6 ++++--
+ 1 file changed, 4 insertions(+), 2 deletions(-)
+
+diff --git a/pkg/common/InsertionSortCollider.cpp b/pkg/common/InsertionSortCollider.cpp
+index dc5d7ac..163a4f4 100644
+--- a/pkg/common/InsertionSortCollider.cpp
++++ b/pkg/common/InsertionSortCollider.cpp
+@@ -410,8 +410,10 @@ Real InsertionSortCollider::cellWrapRel(const Real x, const Real x0, const Real
+ void InsertionSortCollider::insertionSortPeri(VecBounds& v, InteractionContainer* interactions, Scene*, bool doCollide){
+ 	assert(periodic);
+ 	long &loIdx=v.loIdx; const long &size=v.size;
+-	for(long _i=0; _i<size; _i++){
+-		const long i=v.norm(_i);
++	/* We have to visit each bound at least once (first condition), but this is not enough. The correct ordering in the begining of the list needs a second pass to connect begin and end consistently (the second condition). Strictly the second condition should include "+ (v.norm(j+1)==loIdx ? v.cellDim : 0)" but it is ok as is since the shift is added inside the loop. */
++	long _i=0;
++	for(; (_i<size) || (v[v.norm(_i)].coord <  v[v.norm(_i-1)].coord); _i++){
++		const long i=v.norm(_i);//FIXME: useless, and many others can probably be removed
+ 		const long i_1=v.norm(i-1);
+ 		//switch period of (i) if the coord is below the lower edge cooridnate-wise and just above the split
+ 		if(i==loIdx && v[i].coord<0){ v[i].period-=1; v[i].coord+=v.cellDim; loIdx=v.norm(loIdx+1); }
diff -Nru yade-2017.01a/debian/patches/series yade-2017.01a/debian/patches/series
--- yade-2017.01a/debian/patches/series	2017-02-26 20:21:22.000000000 +0100
+++ yade-2017.01a/debian/patches/series	2017-04-14 12:42:59.000000000 +0200
@@ -1,3 +1,4 @@
 01_remove_google_analytics.patch
 08_fix_gui.patch
+09_fix_periodic_boundaries.patch