properly deprecate eliminate functions

gtsam/inference/EliminateableFactorGraph-inst.h

@@ -78,29 +78,31 @@ namespace gtsam {
   }
 
   /* ************************************************************************* */
-  template<class FACTORGRAPH>
+  template <class FACTORGRAPH>
-  boost::shared_ptr<typename EliminateableFactorGraph<FACTORGRAPH>::BayesTreeType>
+  boost::shared_ptr<
-    EliminateableFactorGraph<FACTORGRAPH>::eliminateMultifrontal(
+      typename EliminateableFactorGraph<FACTORGRAPH>::BayesTreeType>
-    OptionalOrderingType orderingType, const Eliminate& function,
+  EliminateableFactorGraph<FACTORGRAPH>::eliminateMultifrontal(
-    OptionalVariableIndex variableIndex) const
+      OptionalOrderingType orderingType, const Eliminate& function,
-  {
+      OptionalVariableIndex variableIndex) const {
-    if(!variableIndex) {
+    if (!variableIndex) {
-      // If no VariableIndex provided, compute one and call this function again IMPORTANT: we check
+      // If no VariableIndex provided, compute one and call this function again
-      // for no variable index first so that it's always computed if we need to call COLAMD because
+      // IMPORTANT: we check for no variable index first so that it's always
-      // no Ordering is provided.  When removing optional from VariableIndex, create VariableIndex
+      // computed if we need to call COLAMD because no Ordering is provided.
-      // before creating ordering.
+      // When removing optional from VariableIndex, create VariableIndex before
+      // creating ordering.
       VariableIndex computedVariableIndex(asDerived());
-      return eliminateMultifrontal(function, computedVariableIndex, orderingType);
+      return eliminateMultifrontal(orderingType, function,
-    }
+                                   computedVariableIndex);
-    else {
+    } else {
-      // Compute an ordering and call this function again.  We are guaranteed to have a
+      // Compute an ordering and call this function again.  We are guaranteed to
-      // VariableIndex already here because we computed one if needed in the previous 'if' block.
+      // have a VariableIndex already here because we computed one if needed in
+      // the previous 'if' block.
       if (orderingType == Ordering::METIS) {
         Ordering computedOrdering = Ordering::Metis(asDerived());
-        return eliminateMultifrontal(computedOrdering, function, variableIndex, orderingType);
+        return eliminateMultifrontal(computedOrdering, function, variableIndex);
       } else {
         Ordering computedOrdering = Ordering::Colamd(*variableIndex);
-        return eliminateMultifrontal(computedOrdering, function, variableIndex, orderingType);
+        return eliminateMultifrontal(computedOrdering, function, variableIndex);
       }
     }
   }
@@ -273,7 +275,7 @@ namespace gtsam {
       else
       {
         // No ordering was provided for the unmarginalized variables, so order them with COLAMD.
-        return factorGraph->eliminateSequential(function);
+        return factorGraph->eliminateSequential(Ordering::COLAMD, function);
       }
     }
   }
@@ -340,7 +342,7 @@ namespace gtsam {
       else
       {
         // No ordering was provided for the unmarginalized variables, so order them with COLAMD.
-        return factorGraph->eliminateMultifrontal(function);
+        return factorGraph->eliminateMultifrontal(Ordering::COLAMD, function);
       }
     }
   }

gtsam/inference/EliminateableFactorGraph.h

@@ -288,6 +288,7 @@ namespace gtsam {
     FactorGraphType& asDerived() { return static_cast<FactorGraphType&>(*this); }
 
   public:
+  #ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V41
     /** \deprecated ordering and orderingType shouldn't both be specified */
     boost::shared_ptr<BayesNetType> eliminateSequential(
       const Ordering& ordering,
@@ -339,6 +340,7 @@ namespace gtsam {
       OptionalVariableIndex variableIndex = boost::none) const {
           return marginalMultifrontalBayesTree(variables, function, variableIndex);
       }
+  #endif
   };
 
 }

gtsam/linear/GaussianFactorGraph.cpp

@@ -290,10 +290,11 @@ namespace gtsam {
     return blocks;
   }
 
-  /* ************************************************************************* */
+  /* ************************************************************************ */
   VectorValues GaussianFactorGraph::optimize(const Eliminate& function) const {
     gttic(GaussianFactorGraph_optimize);
-    return BaseEliminateable::eliminateMultifrontal(function)->optimize();
+    return BaseEliminateable::eliminateMultifrontal(Ordering::COLAMD, function)
+        ->optimize();
   }
 
   /* ************************************************************************* */

gtsam/nonlinear/Marginals.cpp

@@ -80,11 +80,14 @@ Marginals::Marginals(const GaussianFactorGraph& graph, const VectorValues& solut
 
 /* ************************************************************************* */
 void Marginals::computeBayesTree() {
+  // The default ordering to use.
+  const Ordering ordering = Ordering::COLAMND;
   // Compute BayesTree
-  if(factorization_ == CHOLESKY)
+  if (factorization_ == CHOLESKY)
-    bayesTree_ = *graph_.eliminateMultifrontal(EliminatePreferCholesky);
+    bayesTree_ =
-  else if(factorization_ == QR)
+        *graph_.eliminateMultifrontal(ordering, EliminatePreferCholesky);
-    bayesTree_ = *graph_.eliminateMultifrontal(EliminateQR);
+  else if (factorization_ == QR)
+    bayesTree_ = *graph_.eliminateMultifrontal(ordering, EliminateQR);
 }
 
 /* ************************************************************************* */

gtsam/nonlinear/NonlinearOptimizer.cpp

@@ -147,11 +147,13 @@ VectorValues NonlinearOptimizer::solve(const GaussianFactorGraph& gfg,
   } else if (params.isSequential()) {
     // Sequential QR or Cholesky (decided by params.getEliminationFunction())
     if (params.ordering)
-      delta = gfg.eliminateSequential(*params.ordering, params.getEliminationFunction(),
+      delta = gfg.eliminateSequential(*params.ordering,
-                                      boost::none, params.orderingType)->optimize();
+                                      params.getEliminationFunction())
+                  ->optimize();
     else
-      delta = gfg.eliminateSequential(params.getEliminationFunction(), boost::none,
+      delta = gfg.eliminateSequential(params.orderingType,
-                                      params.orderingType)->optimize();
+                                      params.getEliminationFunction())
+                  ->optimize();
   } else if (params.isIterative()) {
     // Conjugate Gradient -> needs params.iterativeParams
     if (!params.iterativeParams)