From 6f83ceb6f5c32d2848de10ceb0134b6f39788946 Mon Sep 17 00:00:00 2001
From: Tiago Gomes <tgomes@fc.up.pt>
Date: Thu, 7 Feb 2013 23:53:13 +0000
Subject: [PATCH] Put the code inside a horus namespace

---
 packages/CLPBN/horus/BayesBall.cpp        |  4 ++
 packages/CLPBN/horus/BayesBall.h          |  3 +
 packages/CLPBN/horus/BayesBallGraph.cpp   |  4 ++
 packages/CLPBN/horus/BayesBallGraph.h     |  4 ++
 packages/CLPBN/horus/BeliefProp.cpp       |  4 ++
 packages/CLPBN/horus/BeliefProp.h         |  4 ++
 packages/CLPBN/horus/ConstraintTree.cpp   |  4 ++
 packages/CLPBN/horus/ConstraintTree.h     |  4 ++
 packages/CLPBN/horus/CountingBp.cpp       |  4 ++
 packages/CLPBN/horus/CountingBp.h         | 14 ++++-
 packages/CLPBN/horus/ElimGraph.cpp        |  5 ++
 packages/CLPBN/horus/ElimGraph.h          |  4 ++
 packages/CLPBN/horus/Factor.cpp           |  4 ++
 packages/CLPBN/horus/Factor.h             |  5 ++
 packages/CLPBN/horus/FactorGraph.cpp      |  4 ++
 packages/CLPBN/horus/FactorGraph.h        |  4 ++
 packages/CLPBN/horus/GroundSolver.cpp     |  4 ++
 packages/CLPBN/horus/GroundSolver.h       |  4 ++
 packages/CLPBN/horus/Histogram.cpp        |  4 ++
 packages/CLPBN/horus/Histogram.h          |  4 ++
 packages/CLPBN/horus/Horus.h              |  9 ++-
 packages/CLPBN/horus/HorusCli.cpp         | 73 ++++++++++++-----------
 packages/CLPBN/horus/HorusYap.cpp         |  3 +
 packages/CLPBN/horus/Indexer.h            |  4 ++
 packages/CLPBN/horus/LiftedBp.cpp         |  4 ++
 packages/CLPBN/horus/LiftedBp.h           |  4 ++
 packages/CLPBN/horus/LiftedKc.cpp         |  4 ++
 packages/CLPBN/horus/LiftedKc.h           |  4 ++
 packages/CLPBN/horus/LiftedOperations.cpp |  4 ++
 packages/CLPBN/horus/LiftedOperations.h   |  5 ++
 packages/CLPBN/horus/LiftedSolver.h       |  4 ++
 packages/CLPBN/horus/LiftedUtils.cpp      |  4 ++
 packages/CLPBN/horus/LiftedUtils.h        | 17 ++++--
 packages/CLPBN/horus/LiftedVe.cpp         |  4 ++
 packages/CLPBN/horus/LiftedVe.h           |  4 ++
 packages/CLPBN/horus/LiftedWCNF.cpp       |  4 ++
 packages/CLPBN/horus/LiftedWCNF.h         |  4 ++
 packages/CLPBN/horus/Parfactor.cpp        |  4 ++
 packages/CLPBN/horus/Parfactor.h          |  4 ++
 packages/CLPBN/horus/ParfactorList.cpp    |  4 ++
 packages/CLPBN/horus/ParfactorList.h      |  5 ++
 packages/CLPBN/horus/ProbFormula.cpp      |  5 ++
 packages/CLPBN/horus/ProbFormula.h        |  5 ++
 packages/CLPBN/horus/TinySet.h            |  4 ++
 packages/CLPBN/horus/Util.cpp             | 12 ++--
 packages/CLPBN/horus/Util.h               | 11 ++--
 packages/CLPBN/horus/Var.cpp              |  4 ++
 packages/CLPBN/horus/Var.h                |  4 ++
 packages/CLPBN/horus/VarElim.cpp          |  4 ++
 packages/CLPBN/horus/VarElim.h            |  4 ++
 packages/CLPBN/horus/WeightedBp.cpp       |  3 +
 packages/CLPBN/horus/WeightedBp.h         |  4 ++
 52 files changed, 270 insertions(+), 53 deletions(-)

diff --git a/packages/CLPBN/horus/BayesBall.cpp b/packages/CLPBN/horus/BayesBall.cpp
index 01da5edc0..be3abc309 100644
--- a/packages/CLPBN/horus/BayesBall.cpp
+++ b/packages/CLPBN/horus/BayesBall.cpp
@@ -3,6 +3,8 @@
 #include "BayesBall.h"
 
 
+namespace horus {
+
 BayesBall::BayesBall (FactorGraph& fg)
     : fg_(fg) , dag_(fg.getStructure())
 {
@@ -93,3 +95,5 @@ BayesBall::constructGraph (FactorGraph* fg) const
   }
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/BayesBall.h b/packages/CLPBN/horus/BayesBall.h
index b8101231e..367bfe67d 100644
--- a/packages/CLPBN/horus/BayesBall.h
+++ b/packages/CLPBN/horus/BayesBall.h
@@ -9,6 +9,7 @@
 #include "BayesBallGraph.h"
 #include "Horus.h"
 
+namespace horus {
 
 struct ScheduleInfo
 {
@@ -69,5 +70,7 @@ BayesBall::scheduleChilds (const BBNode* n, Scheduling& sch) const
   }
 }
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_BAYESBALL_H_
 
diff --git a/packages/CLPBN/horus/BayesBallGraph.cpp b/packages/CLPBN/horus/BayesBallGraph.cpp
index 18b93b86f..c4500076a 100644
--- a/packages/CLPBN/horus/BayesBallGraph.cpp
+++ b/packages/CLPBN/horus/BayesBallGraph.cpp
@@ -8,6 +8,8 @@
 #include "Util.h"
 
 
+namespace horus {
+
 void
 BayesBallGraph::addNode (BBNode* n)
 {
@@ -103,3 +105,5 @@ BayesBallGraph::exportToGraphViz (const char* fileName)
   out.close();
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/BayesBallGraph.h b/packages/CLPBN/horus/BayesBallGraph.h
index e6c82467c..abc434a87 100644
--- a/packages/CLPBN/horus/BayesBallGraph.h
+++ b/packages/CLPBN/horus/BayesBallGraph.h
@@ -7,6 +7,8 @@
 #include "Var.h"
 #include "Horus.h"
 
+namespace horus {
+
 class BBNode : public Var
 {
   public:
@@ -76,5 +78,7 @@ class BayesBallGraph
     std::unordered_map<VarId, BBNode*> varMap_;
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_BAYESBALLGRAPH_H_
 
diff --git a/packages/CLPBN/horus/BeliefProp.cpp b/packages/CLPBN/horus/BeliefProp.cpp
index 2b4aa6a6d..d170840e6 100644
--- a/packages/CLPBN/horus/BeliefProp.cpp
+++ b/packages/CLPBN/horus/BeliefProp.cpp
@@ -9,6 +9,8 @@
 #include "Horus.h"
 
 
+namespace horus {
+
 BpLink::BpLink (FacNode* fn, VarNode* vn)
 {
   fac_ = fn;
@@ -570,3 +572,5 @@ BeliefProp::printLinkInformation (void) const
   }
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/BeliefProp.h b/packages/CLPBN/horus/BeliefProp.h
index 77783069f..385966985 100644
--- a/packages/CLPBN/horus/BeliefProp.h
+++ b/packages/CLPBN/horus/BeliefProp.h
@@ -9,6 +9,8 @@
 #include "FactorGraph.h"
 
 
+namespace horus {
+
 enum MsgSchedule {
   SEQ_FIXED,
   SEQ_RANDOM,
@@ -168,5 +170,7 @@ BeliefProp::ninf (const FacNode* fac) const
   return facsI_[fac->getIndex()];
 }
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_BELIEFPROP_H_
 
diff --git a/packages/CLPBN/horus/ConstraintTree.cpp b/packages/CLPBN/horus/ConstraintTree.cpp
index fa4797add..f7f8cb88c 100644
--- a/packages/CLPBN/horus/ConstraintTree.cpp
+++ b/packages/CLPBN/horus/ConstraintTree.cpp
@@ -7,6 +7,8 @@
 #include "Util.h"
 
 
+namespace horus {
+
 void
 CTNode::mergeSubtree (CTNode* n, bool updateLevels)
 {
@@ -1186,3 +1188,5 @@ ConstraintTree::split (
   }
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/ConstraintTree.h b/packages/CLPBN/horus/ConstraintTree.h
index c2970aeff..42700f9df 100644
--- a/packages/CLPBN/horus/ConstraintTree.h
+++ b/packages/CLPBN/horus/ConstraintTree.h
@@ -12,6 +12,8 @@
 #include "LiftedUtils.h"
 
 
+namespace horus {
+
 class CTNode;
 class ConstraintTree;
 
@@ -242,5 +244,7 @@ ConstraintTree::nrLogVars (void) const
   assert (LogVarSet (logVars_) == logVarSet_);
 }
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_CONSTRAINTTREE_H_
 
diff --git a/packages/CLPBN/horus/CountingBp.cpp b/packages/CLPBN/horus/CountingBp.cpp
index 88064a2ec..84a5c8f20 100644
--- a/packages/CLPBN/horus/CountingBp.cpp
+++ b/packages/CLPBN/horus/CountingBp.cpp
@@ -7,6 +7,8 @@
 #include "WeightedBp.h"
 
 
+namespace horus {
+
 bool CountingBp::fif_ = true;
 
 
@@ -427,3 +429,5 @@ CountingBp::printGroups (
   }
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/CountingBp.h b/packages/CLPBN/horus/CountingBp.h
index 64da217f0..6a2aa9456 100644
--- a/packages/CLPBN/horus/CountingBp.h
+++ b/packages/CLPBN/horus/CountingBp.h
@@ -9,6 +9,8 @@
 #include "Horus.h"
 
 
+namespace horus {
+
 class VarCluster;
 class FacCluster;
 class WeightedBp;
@@ -36,6 +38,8 @@ inline size_t hash_combine (size_t seed, const T& v)
   return seed ^ (std::hash<T>()(v) + 0x9e3779b9 + (seed << 6) + (seed >> 2));
 }
 
+}  // namespace horus
+
 
 namespace std {
 
@@ -43,7 +47,7 @@ template <typename T1, typename T2> struct hash<std::pair<T1,T2>>
 {
   size_t operator() (const std::pair<T1,T2>& p) const
   {
-    return hash_combine (std::hash<T1>()(p.first), p.second);
+    return horus::hash_combine (std::hash<T1>()(p.first), p.second);
   }
 };
 
@@ -55,15 +59,17 @@ template <typename T> struct hash<std::vector<T>>
     typename std::vector<T>::const_iterator first = vec.begin();
     typename std::vector<T>::const_iterator last  = vec.end();
     for (; first != last; ++first) {
-      h = hash_combine (h, *first);
+      h = horus::hash_combine (h, *first);
     }
     return h;
   }
 };
 
-}
+}  // namespace std
 
 
+namespace horus {
+
 class VarCluster
 {
   public:
@@ -214,5 +220,7 @@ CountingBp::setColor (const FacNode* fn, Color  c)
   facColors_[fn->getIndex()] = c;
 }
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_COUNTINGBP_H_
 
diff --git a/packages/CLPBN/horus/ElimGraph.cpp b/packages/CLPBN/horus/ElimGraph.cpp
index 2f637d85e..a6adb2546 100644
--- a/packages/CLPBN/horus/ElimGraph.cpp
+++ b/packages/CLPBN/horus/ElimGraph.cpp
@@ -3,6 +3,9 @@
 
 #include "ElimGraph.h"
 
+
+namespace horus {
+
 ElimHeuristic ElimGraph::elimHeuristic_ = MIN_NEIGHBORS;
 
 
@@ -238,3 +241,5 @@ ElimGraph::connectAllNeighbors (const EgNode* n)
   }
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/ElimGraph.h b/packages/CLPBN/horus/ElimGraph.h
index 1c97205fd..a5a1c40da 100644
--- a/packages/CLPBN/horus/ElimGraph.h
+++ b/packages/CLPBN/horus/ElimGraph.h
@@ -11,6 +11,8 @@
 #include "Horus.h"
 
 
+namespace horus {
+
 class EgNode;
 
 typedef TinySet<EgNode*> EGNeighs;
@@ -171,5 +173,7 @@ ElimGraph::neighbors (EgNode* n1, EgNode* n2) const
   return n1->isNeighbor (n2);
 }
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_ELIMGRAPH_H_
 
diff --git a/packages/CLPBN/horus/Factor.cpp b/packages/CLPBN/horus/Factor.cpp
index 381ad74a7..8626c1d56 100644
--- a/packages/CLPBN/horus/Factor.cpp
+++ b/packages/CLPBN/horus/Factor.cpp
@@ -8,6 +8,8 @@
 #include "Var.h"
 
 
+namespace horus {
+
 Factor::Factor (const Factor& g)
 {
   clone (g);
@@ -233,3 +235,5 @@ Factor::clone (const Factor& g)
   distId_  = g.distId();
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/Factor.h b/packages/CLPBN/horus/Factor.h
index 5d81e5ac1..23c1e0465 100644
--- a/packages/CLPBN/horus/Factor.h
+++ b/packages/CLPBN/horus/Factor.h
@@ -9,6 +9,9 @@
 #include "Indexer.h"
 #include "Util.h"
 
+
+namespace horus {
+
 template <typename T>
 class TFactor
 {
@@ -363,5 +366,7 @@ class Factor : public TFactor<VarId>
     DISALLOW_ASSIGN (Factor);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_FACTOR_H_
 
diff --git a/packages/CLPBN/horus/FactorGraph.cpp b/packages/CLPBN/horus/FactorGraph.cpp
index 7ab9a305e..201be12a9 100644
--- a/packages/CLPBN/horus/FactorGraph.cpp
+++ b/packages/CLPBN/horus/FactorGraph.cpp
@@ -8,6 +8,8 @@
 #include "Util.h"
 
 
+namespace horus {
+
 bool FactorGraph::exportLd_  = false;
 bool FactorGraph::exportUai_ = false;
 bool FactorGraph::exportGv_  = false;
@@ -480,3 +482,5 @@ FactorGraph::containsCycle (
   return false; // no cycle detected in this component
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/FactorGraph.h b/packages/CLPBN/horus/FactorGraph.h
index f829ecd1e..5a2a38256 100644
--- a/packages/CLPBN/horus/FactorGraph.h
+++ b/packages/CLPBN/horus/FactorGraph.h
@@ -10,6 +10,9 @@
 #include "BayesBallGraph.h"
 #include "Horus.h"
 
+
+namespace horus {
+
 class FacNode;
 
 
@@ -179,6 +182,7 @@ struct sortByVarId
   }
 };
 
+}  // namespace horus
 
 #endif // YAP_PACKAGES_CLPBN_HORUS_FACTORGRAPH_H_
 
diff --git a/packages/CLPBN/horus/GroundSolver.cpp b/packages/CLPBN/horus/GroundSolver.cpp
index e7538fc33..562193762 100644
--- a/packages/CLPBN/horus/GroundSolver.cpp
+++ b/packages/CLPBN/horus/GroundSolver.cpp
@@ -11,6 +11,8 @@
 #include "Util.h"
 
 
+namespace horus {
+
 void
 GroundSolver::printAnswer (const VarIds& vids)
 {
@@ -112,3 +114,5 @@ GroundSolver::getJointByConditioning (
   return prevBeliefs;
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/GroundSolver.h b/packages/CLPBN/horus/GroundSolver.h
index dfccb3eb1..23ae27afc 100644
--- a/packages/CLPBN/horus/GroundSolver.h
+++ b/packages/CLPBN/horus/GroundSolver.h
@@ -5,6 +5,8 @@
 #include "Horus.h"
 
 
+namespace horus {
+
 class GroundSolver
 {
   public:
@@ -30,5 +32,7 @@ class GroundSolver
     DISALLOW_COPY_AND_ASSIGN (GroundSolver);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_GROUNDSOLVER_H_
 
diff --git a/packages/CLPBN/horus/Histogram.cpp b/packages/CLPBN/horus/Histogram.cpp
index 23540a68c..021414825 100644
--- a/packages/CLPBN/horus/Histogram.cpp
+++ b/packages/CLPBN/horus/Histogram.cpp
@@ -7,6 +7,8 @@
 #include "Util.h"
 
 
+namespace horus {
+
 HistogramSet::HistogramSet (unsigned size, unsigned range)
 {
   size_ = size;
@@ -145,3 +147,5 @@ operator<< (std::ostream& os, const HistogramSet& hs)
   return os;
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/Histogram.h b/packages/CLPBN/horus/Histogram.h
index 2129fcdbb..1c8761c00 100644
--- a/packages/CLPBN/horus/Histogram.h
+++ b/packages/CLPBN/horus/Histogram.h
@@ -9,6 +9,8 @@
 typedef std::vector<unsigned> Histogram;
 
 
+namespace horus {
+
 class HistogramSet
 {
   public:
@@ -44,5 +46,7 @@ class HistogramSet
     DISALLOW_COPY_AND_ASSIGN (HistogramSet);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_HISTOGRAM_H_
 
diff --git a/packages/CLPBN/horus/Horus.h b/packages/CLPBN/horus/Horus.h
index 5ddb118b4..b1c23467f 100644
--- a/packages/CLPBN/horus/Horus.h
+++ b/packages/CLPBN/horus/Horus.h
@@ -14,6 +14,9 @@
 #include <vector>
 #include <string>
 
+
+namespace horus {
+
 class Var;
 class Factor;
 class VarNode;
@@ -57,7 +60,7 @@ extern unsigned verbosity;
 extern LiftedSolverType liftedSolver;
 extern GroundSolverType groundSolver;
 
-};
+}
 
 
 namespace Constants {
@@ -70,7 +73,9 @@ const int NO_EVIDENCE = -1;
 // number of digits to show when printing a parameter
 const unsigned PRECISION = 6;
 
-};
+}
+
+}  // namespace horus
 
 #endif // YAP_PACKAGES_CLPBN_HORUS_HORUS_H_
 
diff --git a/packages/CLPBN/horus/HorusCli.cpp b/packages/CLPBN/horus/HorusCli.cpp
index 7b3312071..ecf425c0b 100644
--- a/packages/CLPBN/horus/HorusCli.cpp
+++ b/packages/CLPBN/horus/HorusCli.cpp
@@ -11,11 +11,12 @@
 
 int readHorusFlags (int, const char* []);
 
-void readFactorGraph (FactorGraph&, const char*);
+void readFactorGraph (horus::FactorGraph&, const char*);
 
-VarIds readQueryAndEvidence (FactorGraph&, int, const char* [], int);
+horus::VarIds readQueryAndEvidence (
+    horus::FactorGraph&, int, const char* [], int);
 
-void runSolver (const FactorGraph&, const VarIds&);
+void runSolver (const horus::FactorGraph&, const horus::VarIds&);
 
 const std::string USAGE = "usage: ./hcli [solver=hve|bp|cbp] \
 [<OPTION>=<VALUE>]... <FILE> [<VAR>|<VAR>=<EVIDENCE>]... " ;
@@ -26,27 +27,27 @@ main (int argc, const char* argv[])
 {
   if (argc <= 1) {
     std::cerr << "Error: no probabilistic graphical model was given." ;
-    std::cerr << std::endl;
-    std::cerr << USAGE << std::endl;
+    std::cerr << std::endl << USAGE << std::endl;
     exit (EXIT_FAILURE);
   }
   int idx = readHorusFlags (argc, argv);
-  FactorGraph fg;
+  horus::FactorGraph fg;
   readFactorGraph (fg, argv[idx]);
-  VarIds queryIds = readQueryAndEvidence (fg, argc, argv, idx + 1);
-  if (FactorGraph::exportToLibDai()) {
+  horus::VarIds queryIds
+      = readQueryAndEvidence (fg, argc, argv, idx + 1);
+  if (horus::FactorGraph::exportToLibDai()) {
     fg.exportToLibDai ("model.fg");
   }
-  if (FactorGraph::exportToUai()) {
+  if (horus::FactorGraph::exportToUai()) {
     fg.exportToUai ("model.uai");
   }
-  if (FactorGraph::exportGraphViz()) {
+  if (horus::FactorGraph::exportGraphViz()) {
     fg.exportToGraphViz ("model.dot");
   }
-  if (FactorGraph::printFactorGraph()) {
+  if (horus::FactorGraph::printFactorGraph()) {
     fg.print();
   }
-  if (Globals::verbosity > 0) {
+  if (horus::Globals::verbosity > 0) {
     std::cout << "factor graph contains " ;
     std::cout << fg.nrVarNodes() << " variables and " ;
     std::cout << fg.nrFacNodes() << " factors " << std::endl;
@@ -79,7 +80,7 @@ readHorusFlags (int argc, const char* argv[])
       std::cerr << USAGE << std::endl;
       exit (EXIT_FAILURE);
     }
-    Util::setHorusFlag (leftArg, rightArg);
+    horus::Util::setHorusFlag (leftArg, rightArg);
   }
   return i + 1;
 }
@@ -87,7 +88,7 @@ readHorusFlags (int argc, const char* argv[])
 
 
 void
-readFactorGraph (FactorGraph& fg, const char* s)
+readFactorGraph (horus::FactorGraph& fg, const char* s)
 {
   std::string fileName (s);
   std::string extension = fileName.substr (fileName.find_last_of ('.') + 1);
@@ -104,25 +105,25 @@ readFactorGraph (FactorGraph& fg, const char* s)
 
 
 
-VarIds
+horus::VarIds
 readQueryAndEvidence (
-    FactorGraph& fg,
+    horus::FactorGraph& fg,
     int argc,
     const char* argv[],
     int start)
 {
-  VarIds queryIds;
+  horus::VarIds queryIds;
   for (int i = start; i < argc; i++) {
     const std::string& arg = argv[i];
     if (arg.find ('=') == std::string::npos) {
-      if (Util::isInteger (arg) == false) {
+      if (horus::Util::isInteger (arg) == false) {
         std::cerr << "Error: `" << arg << "' " ;
         std::cerr << "is not a variable id." ;
         std::cerr << std::endl;
         exit (EXIT_FAILURE);
       }
-      VarId vid = Util::stringToUnsigned (arg);
-      VarNode* queryVar = fg.getVarNode (vid);
+      horus::VarId vid = horus::Util::stringToUnsigned (arg);
+      horus::VarNode* queryVar = fg.getVarNode (vid);
       if (queryVar == false) {
         std::cerr << "Error: unknow variable with id " ;
         std::cerr << "`" << vid << "'."  << std::endl;
@@ -138,13 +139,13 @@ readQueryAndEvidence (
         std::cerr << USAGE << std::endl;
         exit (EXIT_FAILURE);
       }
-      if (Util::isInteger (leftArg) == false) {
+      if (horus::Util::isInteger (leftArg) == false) {
         std::cerr << "Error: `" << leftArg << "' " ;
         std::cerr << "is not a variable id." << std::endl;
         exit (EXIT_FAILURE);
       }
-      VarId vid = Util::stringToUnsigned (leftArg);
-      VarNode* observedVar = fg.getVarNode (vid);
+      horus::VarId vid = horus::Util::stringToUnsigned (leftArg);
+      horus::VarNode* observedVar = fg.getVarNode (vid);
       if (observedVar == false) {
         std::cerr << "Error: unknow variable with id " ;
         std::cerr << "`" << vid << "'."  << std::endl;
@@ -155,12 +156,12 @@ readQueryAndEvidence (
         std::cerr << USAGE << std::endl;
         exit (EXIT_FAILURE);
       }
-      if (Util::isInteger (rightArg) == false) {
+      if (horus::Util::isInteger (rightArg) == false) {
         std::cerr << "Error: `" << rightArg << "' " ;
         std::cerr << "is not a state index." << std::endl;
         exit (EXIT_FAILURE);
       }
-      unsigned stateIdx = Util::stringToUnsigned (rightArg);
+      unsigned stateIdx = horus::Util::stringToUnsigned (rightArg);
       if (observedVar->isValidState (stateIdx) == false) {
         std::cerr << "Error: `" << stateIdx << "' " ;
         std::cerr << "is not a valid state index for variable with id " ;
@@ -176,23 +177,25 @@ readQueryAndEvidence (
 
 
 void
-runSolver (const FactorGraph& fg, const VarIds& queryIds)
+runSolver (
+    const horus::FactorGraph& fg,
+    const horus::VarIds& queryIds)
 {
-  GroundSolver* solver = 0;
-  switch (Globals::groundSolver) {
-    case GroundSolverType::VE:
-      solver = new VarElim (fg);
+  horus::GroundSolver* solver = 0;
+  switch (horus::Globals::groundSolver) {
+    case horus::GroundSolverType::VE:
+      solver = new horus::VarElim (fg);
       break;
-    case GroundSolverType::BP:
-      solver = new BeliefProp (fg);
+    case horus::GroundSolverType::BP:
+      solver = new horus::BeliefProp (fg);
       break;
-    case GroundSolverType::CBP:
-      solver = new CountingBp (fg);
+    case horus::GroundSolverType::CBP:
+      solver = new horus::CountingBp (fg);
       break;
     default:
       assert (false);
   }
-  if (Globals::verbosity > 0) {
+  if (horus::Globals::verbosity > 0) {
     solver->printSolverFlags();
     std::cout << std::endl;
   }
diff --git a/packages/CLPBN/horus/HorusYap.cpp b/packages/CLPBN/horus/HorusYap.cpp
index 9143d05f7..e1afa082b 100644
--- a/packages/CLPBN/horus/HorusYap.cpp
+++ b/packages/CLPBN/horus/HorusYap.cpp
@@ -20,6 +20,7 @@
 #include "ElimGraph.h"
 #include "BayesBall.h"
 
+namespace horus {
 
 typedef std::pair<ParfactorList*, ObservedFormulas*> LiftedNetwork;
 
@@ -581,3 +582,5 @@ init_predicates (void)
      freeGroundNetwork, 1);
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/Indexer.h b/packages/CLPBN/horus/Indexer.h
index 7f2e82c70..0db6ba470 100644
--- a/packages/CLPBN/horus/Indexer.h
+++ b/packages/CLPBN/horus/Indexer.h
@@ -10,6 +10,8 @@
 #include "Util.h"
 
 
+namespace horus {
+
 class Indexer
 {
   public:
@@ -361,5 +363,7 @@ operator<< (std::ostream &os, const MapIndexer& indexer)
   return os;
 }
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_INDEXER_H_
 
diff --git a/packages/CLPBN/horus/LiftedBp.cpp b/packages/CLPBN/horus/LiftedBp.cpp
index a701a834a..3eb3d8649 100644
--- a/packages/CLPBN/horus/LiftedBp.cpp
+++ b/packages/CLPBN/horus/LiftedBp.cpp
@@ -8,6 +8,8 @@
 #include "FactorGraph.h"
 
 
+namespace horus {
+
 LiftedBp::LiftedBp (const ParfactorList& parfactorList)
     : LiftedSolver (parfactorList)
 {
@@ -235,3 +237,5 @@ LiftedBp::getJointByConditioning (
   return prevBeliefs;
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/LiftedBp.h b/packages/CLPBN/horus/LiftedBp.h
index ff470dac1..92020d139 100644
--- a/packages/CLPBN/horus/LiftedBp.h
+++ b/packages/CLPBN/horus/LiftedBp.h
@@ -7,6 +7,8 @@
 #include "ParfactorList.h"
 
 
+namespace horus {
+
 class FactorGraph;
 class WeightedBp;
 
@@ -43,5 +45,7 @@ class LiftedBp : public LiftedSolver
     DISALLOW_COPY_AND_ASSIGN (LiftedBp);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_LIFTEDBP_H_
 
diff --git a/packages/CLPBN/horus/LiftedKc.cpp b/packages/CLPBN/horus/LiftedKc.cpp
index b655189bc..74536152e 100644
--- a/packages/CLPBN/horus/LiftedKc.cpp
+++ b/packages/CLPBN/horus/LiftedKc.cpp
@@ -7,6 +7,8 @@
 #include "Indexer.h"
 
 
+namespace horus {
+
 OrNode::~OrNode (void)
 {
   delete leftBranch_;
@@ -1316,3 +1318,5 @@ LiftedKc::printSolverFlags (void) const
   std::cout << ss.str() << std::endl;
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/LiftedKc.h b/packages/CLPBN/horus/LiftedKc.h
index def739d65..788ec4e65 100644
--- a/packages/CLPBN/horus/LiftedKc.h
+++ b/packages/CLPBN/horus/LiftedKc.h
@@ -11,6 +11,8 @@
 #include "ParfactorList.h"
 
 
+namespace horus {
+
 enum CircuitNodeType {
   OR_NODE,
   AND_NODE,
@@ -303,5 +305,7 @@ class LiftedKc : public LiftedSolver
     DISALLOW_COPY_AND_ASSIGN (LiftedKc);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_LIFTEDKC_H_
 
diff --git a/packages/CLPBN/horus/LiftedOperations.cpp b/packages/CLPBN/horus/LiftedOperations.cpp
index dcf5aa64c..0c2220f89 100644
--- a/packages/CLPBN/horus/LiftedOperations.cpp
+++ b/packages/CLPBN/horus/LiftedOperations.cpp
@@ -5,6 +5,8 @@
 #include "LiftedOperations.h"
 
 
+namespace horus {
+
 void
 LiftedOperations::shatterAgainstQuery (
     ParfactorList& pfList,
@@ -273,3 +275,5 @@ LiftedOperations::absorve (
   return absorvedPfs;
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/LiftedOperations.h b/packages/CLPBN/horus/LiftedOperations.h
index fd2006d21..7917f648d 100644
--- a/packages/CLPBN/horus/LiftedOperations.h
+++ b/packages/CLPBN/horus/LiftedOperations.h
@@ -3,6 +3,9 @@
 
 #include "ParfactorList.h"
 
+
+namespace horus {
+
 class LiftedOperations
 {
   public:
@@ -25,5 +28,7 @@ class LiftedOperations
     DISALLOW_COPY_AND_ASSIGN (LiftedOperations);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_LIFTEDOPERATIONS_H_
 
diff --git a/packages/CLPBN/horus/LiftedSolver.h b/packages/CLPBN/horus/LiftedSolver.h
index ad352dc09..319cbd0fc 100644
--- a/packages/CLPBN/horus/LiftedSolver.h
+++ b/packages/CLPBN/horus/LiftedSolver.h
@@ -4,6 +4,8 @@
 #include "ParfactorList.h"
 
 
+namespace horus {
+
 class LiftedSolver
 {
   public:
@@ -23,5 +25,7 @@ class LiftedSolver
     DISALLOW_COPY_AND_ASSIGN (LiftedSolver);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_LIFTEDSOLVER_H_
 
diff --git a/packages/CLPBN/horus/LiftedUtils.cpp b/packages/CLPBN/horus/LiftedUtils.cpp
index 6b839055c..507e04156 100644
--- a/packages/CLPBN/horus/LiftedUtils.cpp
+++ b/packages/CLPBN/horus/LiftedUtils.cpp
@@ -5,6 +5,8 @@
 #include "LiftedUtils.h"
 
 
+namespace horus {
+
 namespace LiftedUtils {
 
 std::unordered_map<std::string, unsigned> symbolDict;
@@ -130,3 +132,5 @@ operator<< (std::ostream& os, const Substitution& theta)
   return os;
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/LiftedUtils.h b/packages/CLPBN/horus/LiftedUtils.h
index 02c9cdf72..8ec4e915c 100644
--- a/packages/CLPBN/horus/LiftedUtils.h
+++ b/packages/CLPBN/horus/LiftedUtils.h
@@ -10,6 +10,8 @@
 #include "Util.h"
 
 
+namespace horus {
+
 class Symbol
 {
   public:
@@ -67,25 +69,28 @@ LogVar::valid (void) const
   return id_ != Util::maxUnsigned();
 }
 
+}  // namespace horus
 
 
 namespace std {
 
-template <> struct hash<Symbol> {
-  size_t operator() (const Symbol& s) const {
+template <> struct hash<horus::Symbol> {
+  size_t operator() (const horus::Symbol& s) const {
     return std::hash<unsigned>() (s);
   }
 };
 
-template <> struct hash<LogVar> {
-  size_t operator() (const LogVar& X) const {
+template <> struct hash<horus::LogVar> {
+  size_t operator() (const horus::LogVar& X) const {
     return std::hash<unsigned>() (X);
   }
 };
 
-};
+}  // namespace std
 
 
+namespace horus {
+
 typedef std::vector<Symbol>  Symbols;
 typedef std::vector<Symbol>  Tuple;
 typedef std::vector<Tuple>   Tuples;
@@ -205,5 +210,7 @@ Substitution::nrReplacements (void) const
   return subs_.size();
 }
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_LIFTEDUTILS_H_
 
diff --git a/packages/CLPBN/horus/LiftedVe.cpp b/packages/CLPBN/horus/LiftedVe.cpp
index 6565920be..5c004b291 100644
--- a/packages/CLPBN/horus/LiftedVe.cpp
+++ b/packages/CLPBN/horus/LiftedVe.cpp
@@ -12,6 +12,8 @@
 #include "Util.h"
 
 
+namespace horus {
+
 std::vector<LiftedOperator*>
 LiftedOperator::getValidOps (
     ParfactorList& pfList,
@@ -732,3 +734,5 @@ LiftedVe::getBestOperation (const Grounds& query)
   return bestOp;
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/LiftedVe.h b/packages/CLPBN/horus/LiftedVe.h
index a8b84735b..35455183d 100644
--- a/packages/CLPBN/horus/LiftedVe.h
+++ b/packages/CLPBN/horus/LiftedVe.h
@@ -8,6 +8,8 @@
 #include "ParfactorList.h"
 
 
+namespace horus {
+
 class LiftedOperator
 {
   public:
@@ -167,5 +169,7 @@ class LiftedVe : public LiftedSolver
     DISALLOW_COPY_AND_ASSIGN (LiftedVe);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_LIFTEDVE_H_
 
diff --git a/packages/CLPBN/horus/LiftedWCNF.cpp b/packages/CLPBN/horus/LiftedWCNF.cpp
index 73f7eca8f..fdd4c4057 100644
--- a/packages/CLPBN/horus/LiftedWCNF.cpp
+++ b/packages/CLPBN/horus/LiftedWCNF.cpp
@@ -8,6 +8,8 @@
 #include "Indexer.h"
 
 
+namespace horus {
+
 bool
 Literal::isGround (ConstraintTree constr, LogVarSet ipgLogVars) const
 {
@@ -660,3 +662,5 @@ LiftedWCNF::printClauses (void) const
   Clause::printClauses (clauses_);
 }
 
+}
+
diff --git a/packages/CLPBN/horus/LiftedWCNF.h b/packages/CLPBN/horus/LiftedWCNF.h
index d0da678d8..99599f0f2 100644
--- a/packages/CLPBN/horus/LiftedWCNF.h
+++ b/packages/CLPBN/horus/LiftedWCNF.h
@@ -9,6 +9,8 @@
 #include "ParfactorList.h"
 
 
+namespace horus {
+
 class ConstraintTree;
 
 enum LogVarType
@@ -241,5 +243,7 @@ class LiftedWCNF
     DISALLOW_COPY_AND_ASSIGN (LiftedWCNF);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_LIFTEDWCNF_H_
 
diff --git a/packages/CLPBN/horus/Parfactor.cpp b/packages/CLPBN/horus/Parfactor.cpp
index 2bcf1f28f..f71bc119d 100644
--- a/packages/CLPBN/horus/Parfactor.cpp
+++ b/packages/CLPBN/horus/Parfactor.cpp
@@ -10,6 +10,8 @@
 #include "Horus.h"
 
 
+namespace horus {
+
 Parfactor::Parfactor (
     const ProbFormulas& formulas,
     const Params& params,
@@ -946,3 +948,5 @@ Parfactor::alignLogicalVars (Parfactor* g1, Parfactor* g2)
   g2->applySubstitution (theta2);
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/Parfactor.h b/packages/CLPBN/horus/Parfactor.h
index eabb7729d..cbf75aafd 100644
--- a/packages/CLPBN/horus/Parfactor.h
+++ b/packages/CLPBN/horus/Parfactor.h
@@ -11,6 +11,8 @@
 #include "Horus.h"
 
 
+namespace horus {
+
 class Parfactor : public TFactor<ProbFormula>
 {
   public:
@@ -120,5 +122,7 @@ class Parfactor : public TFactor<ProbFormula>
 
 typedef std::vector<Parfactor*> Parfactors;
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_PARFACTOR_H_
 
diff --git a/packages/CLPBN/horus/ParfactorList.cpp b/packages/CLPBN/horus/ParfactorList.cpp
index be484f98a..8a810384c 100644
--- a/packages/CLPBN/horus/ParfactorList.cpp
+++ b/packages/CLPBN/horus/ParfactorList.cpp
@@ -7,6 +7,8 @@
 #include "ParfactorList.h"
 
 
+namespace horus {
+
 ParfactorList::ParfactorList (const ParfactorList& pfList)
 {
   ParfactorList::const_iterator it = pfList.begin();
@@ -644,3 +646,5 @@ ParfactorList::disjoint (
   return (ts1 & ts2).empty();
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/ParfactorList.h b/packages/CLPBN/horus/ParfactorList.h
index d60bedbec..a471a8fcc 100644
--- a/packages/CLPBN/horus/ParfactorList.h
+++ b/packages/CLPBN/horus/ParfactorList.h
@@ -6,6 +6,9 @@
 #include "Parfactor.h"
 #include "ProbFormula.h"
 
+
+namespace horus {
+
 class Parfactor;
 
 
@@ -117,5 +120,7 @@ class ParfactorList
     std::list<Parfactor*> pfList_;
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_PARFACTORLIST_H_
 
diff --git a/packages/CLPBN/horus/ProbFormula.cpp b/packages/CLPBN/horus/ProbFormula.cpp
index 76fa9a36f..290f72d76 100644
--- a/packages/CLPBN/horus/ProbFormula.cpp
+++ b/packages/CLPBN/horus/ProbFormula.cpp
@@ -5,6 +5,9 @@
 #include "ProbFormula.h"
 
 
+
+namespace horus {
+
 PrvGroup ProbFormula::freeGroup_ = 0;
 
 
@@ -162,3 +165,5 @@ operator<< (std::ostream& os, const ObservedFormula& of)
   return os;
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/ProbFormula.h b/packages/CLPBN/horus/ProbFormula.h
index f595537d6..f978f67fe 100644
--- a/packages/CLPBN/horus/ProbFormula.h
+++ b/packages/CLPBN/horus/ProbFormula.h
@@ -9,6 +9,9 @@
 #include "LiftedUtils.h"
 #include "Horus.h"
 
+
+namespace horus {
+
 typedef unsigned long PrvGroup;
 
 class ProbFormula
@@ -111,5 +114,7 @@ class ObservedFormula
 
 typedef std::vector<ObservedFormula> ObservedFormulas;
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_PROBFORMULA_H_
 
diff --git a/packages/CLPBN/horus/TinySet.h b/packages/CLPBN/horus/TinySet.h
index e21c0edeb..7e1510490 100644
--- a/packages/CLPBN/horus/TinySet.h
+++ b/packages/CLPBN/horus/TinySet.h
@@ -6,6 +6,8 @@
 #include <ostream>
 
 
+namespace horus {
+
 template <typename T, typename Compare = std::less<T>>
 class TinySet
 {
@@ -402,5 +404,7 @@ TinySet<T,C>::consistent (void) const
   return true;
 }
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_TINYSET_H_
 
diff --git a/packages/CLPBN/horus/Util.cpp b/packages/CLPBN/horus/Util.cpp
index 8eb865c53..824d4c8f2 100644
--- a/packages/CLPBN/horus/Util.cpp
+++ b/packages/CLPBN/horus/Util.cpp
@@ -4,6 +4,8 @@
 #include "BeliefProp.h"
 
 
+namespace horus {
+
 namespace Globals {
 
 bool logDomain = false;
@@ -14,7 +16,7 @@ LiftedSolverType liftedSolver = LiftedSolverType::LVE;
 
 GroundSolverType groundSolver = GroundSolverType::VE;
 
-};
+}
 
 
 
@@ -329,8 +331,7 @@ printDashedLine (std::ostream& os)
   os << std::endl;
 }
 
-
-}
+}  // namespace Util
 
 
 
@@ -426,5 +427,8 @@ pow (Params& v, double exp)
   Globals::logDomain ? v *= exp : v ^= exp;
 }
 
-}
+}  // namespace LogAware
+
+}  // namespace horus
+
 
diff --git a/packages/CLPBN/horus/Util.h b/packages/CLPBN/horus/Util.h
index cce3601f0..839e8cc13 100644
--- a/packages/CLPBN/horus/Util.h
+++ b/packages/CLPBN/horus/Util.h
@@ -16,12 +16,13 @@
 
 #include "Horus.h"
 
+namespace horus {
 
 namespace {
 
 const double NEG_INF = -std::numeric_limits<double>::infinity();
 
-};
+}
 
 
 namespace Util {
@@ -100,7 +101,7 @@ void printAsteriskLine (std::ostream& os = std::cout);
 
 void printDashedLine (std::ostream& os = std::cout);
 
-};
+}  // namespace Util
 
 
 
@@ -289,7 +290,7 @@ void pow (Params&, unsigned);
 
 void pow (Params&, double);
 
-};
+}  // namespace LogAware
 
 
 
@@ -430,7 +431,9 @@ struct abs_diff_exp : public std::binary_function<T, T, T>
   }
 };
 
-}
+}  // namespace FuncObject
+
+}  // namespace horus
 
 #endif // YAP_PACKAGES_CLPBN_HORUS_UTIL_H_
 
diff --git a/packages/CLPBN/horus/Var.cpp b/packages/CLPBN/horus/Var.cpp
index af81159b0..cb3031007 100644
--- a/packages/CLPBN/horus/Var.cpp
+++ b/packages/CLPBN/horus/Var.cpp
@@ -3,6 +3,8 @@
 #include "Var.h"
 
 
+namespace horus {
+
 std::unordered_map<VarId, VarInfo> Var::varsInfo_;
 
 
@@ -108,3 +110,5 @@ Var::clearVarsInfo (void)
   varsInfo_.clear();
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/Var.h b/packages/CLPBN/horus/Var.h
index adfc42f9f..f20820a53 100644
--- a/packages/CLPBN/horus/Var.h
+++ b/packages/CLPBN/horus/Var.h
@@ -10,6 +10,8 @@
 #include "Horus.h"
 
 
+namespace horus {
+
 struct VarInfo
 {
   VarInfo (std::string l, const States& sts)
@@ -105,5 +107,7 @@ Var::operator!= (const Var& var) const
   return !(*this == var);
 }
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_VAR_H_
 
diff --git a/packages/CLPBN/horus/VarElim.cpp b/packages/CLPBN/horus/VarElim.cpp
index 5ce16ad85..cbfc01f4c 100644
--- a/packages/CLPBN/horus/VarElim.cpp
+++ b/packages/CLPBN/horus/VarElim.cpp
@@ -8,6 +8,8 @@
 #include "Util.h"
 
 
+namespace horus {
+
 Params
 VarElim::solveQuery (VarIds queryVids)
 {
@@ -198,3 +200,5 @@ VarElim::printActiveFactors (void)
   }
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/VarElim.h b/packages/CLPBN/horus/VarElim.h
index 9ac9ef6d9..3389176be 100644
--- a/packages/CLPBN/horus/VarElim.h
+++ b/packages/CLPBN/horus/VarElim.h
@@ -9,6 +9,8 @@
 #include "Horus.h"
 
 
+namespace horus {
+
 class VarElim : public GroundSolver
 {
   public:
@@ -39,5 +41,7 @@ class VarElim : public GroundSolver
     DISALLOW_COPY_AND_ASSIGN (VarElim);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_VARELIM_H_
 
diff --git a/packages/CLPBN/horus/WeightedBp.cpp b/packages/CLPBN/horus/WeightedBp.cpp
index c6c21fca3..107f829c1 100644
--- a/packages/CLPBN/horus/WeightedBp.cpp
+++ b/packages/CLPBN/horus/WeightedBp.cpp
@@ -4,6 +4,7 @@
 
 #include "WeightedBp.h"
 
+namespace horus {
 
 WeightedBp::~WeightedBp (void)
 {
@@ -304,3 +305,5 @@ WeightedBp::printLinkInformation (void) const
   }
 }
 
+}  // namespace horus
+
diff --git a/packages/CLPBN/horus/WeightedBp.h b/packages/CLPBN/horus/WeightedBp.h
index c093a8a1e..ad66e5138 100644
--- a/packages/CLPBN/horus/WeightedBp.h
+++ b/packages/CLPBN/horus/WeightedBp.h
@@ -6,6 +6,8 @@
 #include "BeliefProp.h"
 
 
+namespace horus {
+
 class WeightedLink : public BpLink
 {
   public:
@@ -68,5 +70,7 @@ class WeightedBp : public BeliefProp
      DISALLOW_COPY_AND_ASSIGN (WeightedBp);
 };
 
+}  // namespace horus
+
 #endif // YAP_PACKAGES_CLPBN_HORUS_WEIGHTEDBP_H_