Merge /home/vsc/yap

.configure-custom.sh

@@ -12,11 +12,15 @@ WITH_VARS="swig|yes|WITH_SWIG \
    mpi|yes|WITH_MPI \
    gecode|yes|WITH_GECODE \
    docs|yes|WITH_DOCS \
-   r|yes|WITH_REAL \
+   r|yes|WITH_R \
+   myddas|yes|WITH_MYDDAS \
    cudd|yes|WITH_CUDD \
    xml2|yes|WITH_XML2 \
    raptor|yes|WITH_RAPTOR \
    python|yes|WITH_PYTHON \
    openssl|yes|WITH_OPENSSL\
+   java|yes|WITH_JAVA
+   lbfgs|yes|WITH_LBFGS
+   extensions|yes|WITH_EXTENSIONS
    readline|yes|WITH_READLINE \
    gmp|yes|WITH_GMP" 

C/c_interface.c

@@ -1811,27 +1811,6 @@ X_API bool YAP_RetryGoal(YAP_dogoalinfo *dgi) {
   return out;
 }
 
-static void completeInnerCall(bool on_cut, yamop *old_CP, yamop *old_P) {
-  if (on_cut) {
-    P = old_P;
-    ENV = (CELL *)ENV[E_E];
-    CP = old_CP;
-    LOCAL_AllowRestart = TRUE;
-    // we are back to user code again, need slots */
-  } else {
-    P = old_P;
-    ENV = B->cp_env;
-    ENV = (CELL *)ENV[E_E];
-    CP = old_CP;
-    HR = B->cp_h;
-    TR = B->cp_tr;
-    B = B->cp_b;
-    LOCAL_AllowRestart = FALSE;
-    SET_ASP(ENV, E_CB * sizeof(CELL));
-    // make sure the slots are ok.
-  }
-}
-
 X_API bool YAP_LeaveGoal(bool successful, YAP_dogoalinfo *dgi) {
   CACHE_REGS
   choiceptr myB, handler;

C/dbase.c

@@ -25,7 +25,7 @@ static char SccsId[] = "%W% %G%";
  * 
  * @brief  record and other forms of storing terms.
  *
- * /
+ */
 
 
 /** @defgroup Internal_Database Internal Data Base

C/text.c

@@ -59,54 +59,6 @@ typedef struct TextBuffer_manager {
 } text_buffer_t;
 
 int AllocLevel(void) { return LOCAL_TextBuffer->lvl; }
-int push_text_stack__(USES_REGS1) {
-  int i = LOCAL_TextBuffer->lvl;
-  i++;
-  LOCAL_TextBuffer->lvl = i;
-
-  return i;
-}
-
-int pop_text_stack__(int i) {
-  int lvl = LOCAL_TextBuffer->lvl;
-  while (lvl >= i) {
-    struct mblock *p = LOCAL_TextBuffer->first[lvl];
-    while (p) {
-      struct mblock *np = p->next;
-      free(p);
-      p = np;
-    }
-    LOCAL_TextBuffer->first[lvl] = NULL;
-    LOCAL_TextBuffer->last[lvl] = NULL;
-    lvl--;
-  }
-  LOCAL_TextBuffer->lvl = lvl;
-  return lvl;
-}
-
-void *pop_output_text_stack__(int i, const void *export) {
-  int lvl = LOCAL_TextBuffer->lvl;
-  while (lvl >= i) {
-    struct mblock *p = LOCAL_TextBuffer->first[lvl];
-    while (p) {
-      struct mblock *np = p->next;
-      if (p + 1 == export) {
-        size_t sz = p->sz - sizeof(struct mblock);
-        memmove(p, p + 1, sz);
-        export = p;
-      } else {
-        free(p);
-      }
-      p = np;
-    }
-    LOCAL_TextBuffer->first[lvl] = NULL;
-    LOCAL_TextBuffer->last[lvl] = NULL;
-    lvl--;
-  }
-  LOCAL_TextBuffer->lvl = lvl;
-  return (void *)export;
-}
-
 //	void pop_text_stack(int i) { LOCAL_TextBuffer->lvl = i; }
 void insert_block(struct mblock *o) {
   int lvl = o->lvl;
@@ -138,6 +90,68 @@ void release_block(struct mblock *o) {
     o->next->prev = o->prev;
 }
 
+int push_text_stack__(USES_REGS1) {
+  int i = LOCAL_TextBuffer->lvl;
+  i++;
+  LOCAL_TextBuffer->lvl = i;
+
+  return i;
+}
+
+int pop_text_stack__(int i) {
+  int lvl = LOCAL_TextBuffer->lvl;
+  while (lvl >= i) {
+    struct mblock *p = LOCAL_TextBuffer->first[lvl];
+    while (p) {
+      struct mblock *np = p->next;
+      free(p);
+      p = np;
+    }
+    LOCAL_TextBuffer->first[lvl] = NULL;
+    LOCAL_TextBuffer->last[lvl] = NULL;
+    lvl--;
+  }
+  LOCAL_TextBuffer->lvl = lvl;
+  return lvl;
+}
+
+void *pop_output_text_stack__(int i, const void *export) {
+  int lvl = LOCAL_TextBuffer->lvl;
+  bool found = false;
+  while (lvl >= i) {
+    struct mblock *p = LOCAL_TextBuffer->first[lvl];
+    while (p) {
+      struct mblock *np = p->next;
+      if (p + 1 == export) {
+	found = true;
+      } else {
+        free(p);
+      }
+      p = np;
+    }
+    LOCAL_TextBuffer->first[lvl] = NULL;
+    LOCAL_TextBuffer->last[lvl] = NULL;
+    lvl--;
+  }
+  LOCAL_TextBuffer->lvl = lvl;
+  if (found) {
+  if (lvl) {
+    struct mblock *o = (struct mblock *)export-1;
+    o->lvl = lvl;
+    o->prev = o->next = 0;
+    insert_block(o);
+
+  } else {
+        struct mblock *p = (struct mblock *)export-1;
+	size_t sz = p->sz - sizeof(struct mblock);
+        memmove(p, p + 1, sz);
+        export = p;
+    
+  }
+  }
+  return (void *)export;
+}
+
 void *Malloc(size_t sz USES_REGS) {
   int lvl = LOCAL_TextBuffer->lvl;
   if (sz == 0)
@@ -1027,10 +1041,11 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
   void **bufv;
   unsigned char *buf;
   int i, j;
-  // int lvl = push_text_stack();
+
+  int lvl = push_text_stack();
   bufv = Malloc(tot * sizeof(unsigned char *));
   if (!bufv) {
-    // pop_text_stack(lvl);
+     pop_text_stack(lvl);
     return NULL;
   }
   for (i = 0, j = 0; i < tot; i++) {
@@ -1038,7 +1053,7 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
     unsigned char *nbuf = Yap_readText(inp + i PASS_REGS);
 
     if (!nbuf) {
-      // pop_text_stack(lvl);
+       pop_text_stack(lvl);
       return NULL;
     }
     //      if (!nbuf[0])
@@ -1054,7 +1069,7 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
     buf = concat(tot, bufv PASS_REGS);
   }
   bool rc = write_Text(buf, out PASS_REGS);
-  // pop_text_stack( lvl );
+   pop_text_stack( lvl );
 
   return rc;
 }

configure

@@ -165,7 +165,7 @@ print_help() {
   --mandir=DIR            man documentation [DATAROOTDIR/man]
   --docdir=DIR            documentation root [DATAROOTDIR/doc/PROJECT_NAME]
 
-  --generator=Generator	  Specify the tool used to send callss
+  --generator=GENERATOR	  Specify the tool used to send callss
 EOF
 
     first=y
@@ -220,6 +220,8 @@ EOF
     exit 0
 }
 
+
+
 while [ $# != 0 ]; do
     case "$1" in
         "--cmake="*)
@@ -291,10 +293,10 @@ while [ $# != 0 ]; do
         "--docdir")
             CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_INSTALL_DOCDIR=$(quote "$2")"; shift;;
 
-        "-G="|"--generator="*)
+        "--generator="*)
-            CMAKE_ARGS+="-G"${1#*=};;
+            CMAKE_ARGS="$CMAKE_ARGS -G ${1#*=}";;
-        "-G"|"--generator")
+        "-G")
-            CMAKE_ARGS+="-G$"$2; shift;;
+            CMAKE_ARGS="$CMAKE_ARGS -G $2"; shift;;
 
         "CC="*)
             CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_C_COMPILER=$(quote "${1#*=}")";;

os/sysbits.c

@@ -769,11 +769,11 @@ static Int real_path(USES_REGS1) {
   int lvl = push_text_stack();
   rc0 = myrealpath(cmd PASS_REGS);
   if (!rc0) {
+    pop_text_stack(lvl);
     PlIOError(SYSTEM_ERROR_OPERATING_SYSTEM, ARG1, NULL);
   }
   bool out = Yap_unify(MkAtomTerm(Yap_LookupAtom(rc0)), ARG2);
-  pop_output_text_stack(lvl, rc0);
+  pop_text_stack(lvl);
-
   return out;
 }
 

packages/ProbLog/problog_lbdd.yap

@@ -24,6 +24,7 @@ problog_low_lbdd(_, _, Prob, ok, bdd(Dir, Tree, MapList)) :-
 	bind_maplist(MapList, BoundVars),
 	bdd_tree(BDD, bdd(Dir, Tree, _Vars)),
 	bdd_to_probability_sum_product(BDD, BoundVars, Prob),
+	bdd_close(BDD),
 	(problog_flag(verbose, true)->
 	 problog_statistics
 	;
@@ -37,7 +38,8 @@ problog_low_lbdd(_, _, Prob, ok, bdd(Dir, Tree, MapList)) :-
 problog_kbest_bdd(Goal, K, Prob, ok) :-
 	problog_kbest_to_bdd(Goal, K, BDD, MapList),
 	bind_maplist(MapList, BoundVars),
-	bdd_to_probability_sum_product(BDD, BoundVars, Prob).
+	bdd_to_probability_sum_product(BDD, BoundVars, Prob),
+bdd_close(BDD).
 
 problog_kbest_as_bdd(Goal, K, bdd(Dir, Tree, MapList)) :-
 	problog_kbest_to_bdd(Goal, K, BDD, MapList),
@@ -70,6 +72,7 @@ problog_fl_bdd(_,Prob) :-
 	bind_maplist(MapList, BoundVars),
 	bdd_to_probability_sum_product(BDD, BoundVars, Prob),
 	(problog_flag(retain_tables, true) -> retain_tabling; true),
+	bdd_close(BDD),
 	clear_tabling.
 
 problog_full_bdd(Goal,_K,  _) :-
@@ -86,6 +89,7 @@ problog_full_bdd(_,Prob) :-
 	tabled_trie_to_bdd(Trie_Completed_Proofs, BDD, MapList),
 	bind_maplist(MapList, BoundVars),
 	bdd_to_probability_sum_product(BDD, BoundVars, Prob),
+	bdd_close(BDD),
 	(problog_flag(retain_tables, true) -> retain_tabling; true),
 	clear_tabling.
 

packages/ProbLog/problog_lbfgs.yap

@@ -431,7 +431,7 @@ do_learning_intern(Iterations,Epsilon) :-
 	 true
 	),
 
-%	update_values,
+	update_values,
 
 	(
 	 last_mse(Last_MSE)
@@ -450,15 +450,11 @@ do_learning_intern(Iterations,Epsilon) :-
 	),
 
 	(
-	 (problog_flag(rebuild_bdds,BDDFreq),BDDFreq>0,0 =:= CurrentIteration mod BDDFreq)
-	->
-	 (
 	  retractall(values_correct),
 	  retractall(query_is_similar(_,_)),
 	  retractall(query_md5(_,_,_)),
 	  empty_bdd_directory,
 	  init_queries
-	 ); true
 	),
 
 
@@ -491,11 +487,48 @@ init_learning :-
 init_learning :-
 	check_examples,
 
+	retractall(current_iteration(_)),
+	assert(current_iteration(0)),
 %	empty_output_directory,
 	logger_write_header,
-
 	format_learning(1,'Initializing everything~n',[]),
 	
+	succeeds_n_times(user:test_example(_,_,_,_),TestExampleCount),
+	format_learning(3,'~q test examples~n',[TestExampleCount]),
+
+	succeeds_n_times(user:example(_,_,_,_),TrainingExampleCount),
+	assertz(example_count(TrainingExampleCount)),
+	format_learning(3,'~q training examples~n',[TrainingExampleCount]),
+
+
+
+	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	% build BDD script for every example
+        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	once(init_queries),
+
+	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	% done
+        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	assertz(current_iteration(-1)),
+	assertz(learning_initialized),
+
+	format_learning(1,'~n',[]).
+
+%========================================================================
+%= Updates all values of query_probability/2 and query_gradient/4
+%= should be called always before these predicates are accessed
+%= if the old values are still valid, nothing happens
+%========================================================================
+
+update_values :-
+	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	% delete old values
+	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	retractall(query_probability_intern(_,_)),
+	retractall(query_gradient_intern(_,_,_,_)).	
+
+
 
 
         %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -503,7 +536,7 @@ init_learning :-
 	% if yes, switch to problog_exact
         % continuous facts are not supported yet.
         %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
-	set_default_gradient_method,
+set_default_gradient_method :-
 	(	problog_flag(continuous_facts, true )
 	->
 	 problog_flag(init_method,(_,_,_,_,OldCall)),
@@ -527,31 +560,11 @@ init_learning :-
 	   set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile)))
 	  );
 	  true
-	 ),
+	 ).
-
-	succeeds_n_times(user:test_example(_,_,_,_),TestExampleCount),
-	format_learning(3,'~q test examples~n',[TestExampleCount]),
-
-	succeeds_n_times(user:example(_,_,_,_),TrainingExampleCount),
-	assertz(example_count(TrainingExampleCount)),
-	format_learning(3,'~q training examples~n',[TrainingExampleCount]),
   
 
 
-	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+empty_bdd_directory :-
-	% build BDD script for every example
-        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-	once(init_queries),
-
-	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-	% done
-        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-	assertz(current_iteration(0)),
-	assertz(learning_initialized),
-
-	format_learning(1,'~n',[]).
-
- empty_bdd_directory :-
 	current_key(_,I),
 	integer(I),
 	recorded(I,bdd(_,_,_),R),
@@ -560,21 +573,6 @@ init_learning :-
 empty_bdd_directory.
 
 
-set_default_gradient_method :-
-    problog_flag(continuous_facts, true),
-    !,
-    % problog_flag(init_method,OldMethod),
-    format_learning(2,'Theory uses continuous facts.~nWill use problog_exact/3 as initalization method.~2n',[]),
-    set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile))).
-set_default_gradient_method :-
-    problog_tabled(_), problog_flag(fast_proofs,false),
-    !,
-    format_learning(2,'Theory uses tabling.~nWill use problog_exact/3 as initalization method.~2n',[]),
-    set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile))).
-%set_default_gradient_method :-
-%    problog_flag(init_method,(gene(X,Y),N,Bdd,graph2bdd(X,Y,N,Bdd))),
-%    !.
-set_default_gradient_method.
 
 %========================================================================
 %= This predicate goes over all training and test examples,
@@ -584,6 +582,7 @@ set_default_gradient_method.
 
 
 init_queries :-
+    empty_bdd_directory,
 	format_learning(2,'Build BDDs for examples~n',[]),
 	forall(user:test_example(ID,Query,_Prob,_),init_one_query(ID,Query,test)),
 	forall(user:example(ID,Query,_Prob,_),init_one_query(ID,Query,training)).
@@ -703,28 +702,56 @@ ground_truth_difference :-
 %= -Float
 %========================================================================
 
-mse_trainingset_only_for_linesearch(MSE, FX) :-
+mse_trainingset :-
+	current_iteration(Iteration),
+	create_training_predictions_file_name(Iteration,File_Name),
+	open(File_Name, write,Handle),
+	format_learning(2,'MSE_Training ',[]),
 	update_values,
+	findall(t(LogCurrentProb,SquaredError),
+		(user:training_example(QueryID,Query,TrueQueryProb,_Type),
+		 once(update_query(QueryID,'+',probability)),
+		 query_probability(QueryID,CurrentProb),
+ 		 format(Handle,'ex(~q,training,~q,~q,~10f,~10f).~n',[Iteration,QueryID,Query,TrueQueryProb,CurrentProb]),
 
-	example_count(Example_Count),
+		 once(update_query_cleanup(QueryID)),
+		  SquaredError is (CurrentProb-TrueQueryProb)**2,
+		 LogCurrentProb is log(CurrentProb)
+		),
+		All),
+	maplist(tuple, All, AllLogs, AllSquaredErrors),
+	sum_list( AllLogs, LLH_Training_Queries),
+        close(Handle),
 
-	bb_put(error_train_line_search,0.0),
+	length(AllSquaredErrors,Length),
-	forall(user:example(QueryID,_Query,QueryProb,Type),
+
-	       (
+	(
-		once(update_query(QueryID,'.',probability)),
+	 Length>0
-		once(update_query_cleanup(QueryID)),
+	->
-	       ),
+	 (
-	format_learning(3,' (~8f)~n',[MSE]),
+	  sum_list(AllSquaredErrors,SumAllSquaredErrors),
-	retractall(values_correct).
+	  min_list(AllSquaredErrors,MinError),
+	  max_list(AllSquaredErrors,MaxError),
+	  MSE is SumAllSquaredErrors/Length
+	 );(
+	    MSE=0.0,
+	    MinError=0.0,
+	    MaxError=0.0
+	   )
+	),
+
+	logger_set_variable(mse_trainingset,MSE),
+	logger_set_variable(mse_min_trainingset,MinError),
+	logger_set_variable(mse_max_trainingset,MaxError),
+	logger_set_variable(llh_training_queries,LLH_Training_Queries),
+	format_learning(2,' (~8f)~n',[MSE]).
+
+tuple(t(X,Y),X,Y).
 
 mse_testset :-
 	current_iteration(Iteration),
 	create_test_predictions_file_name(Iteration,File_Name),
-	open(File_Name,'write',Handle),
+  	open(File_Name, write,Handle),
-	format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
-	format(Handle,"% Iteration, train/test, QueryID, Query, GroundTruth, Prediction %~n",[]),
-	format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
-
 	format_learning(2,'MSE_Test ',[]),
 	update_values,
 	bb_put(llh_test_queries,0.0),
@@ -732,7 +759,7 @@ mse_testset :-
 		(user:test_example(QueryID,Query,TrueQueryProb,Type),
 		 once(update_query(QueryID,'+',probability)),
 		 query_probability(QueryID,CurrentProb),
-		 format(Handle,'ex(~q,test,~q,~q,~10f,~10f).~n',[Iteration,QueryID,Query,TrueQueryProb,CurrentProb]),
+ 		 format(Handle,'ex(~q,test,~q,~q,~10f,~10f).~n',[Iteration,QueryID,Query,TrueQueryProb,CurrentProb]),
 
 		 once(update_query_cleanup(QueryID)),
 		 (
@@ -808,11 +835,6 @@ save_old_probabilities :-
 gradient_descent :-
     problog_flag(sigmoid_slope,Slope),
 %	current_iteration(Iteration),
-	% create_training_predictions_file_name(Iteration,File_Name),
-	Handle = user_error,
-	format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
-	format(Handle,"% Iteration, train/test, QueryID, Query, GroundTruth, Prediction %~n",[]),
-	format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
 	findall(FactID,tunable_fact(FactID,GroundTruth),L), length(L,N),
 %	leash(0),trace,
 	lbfgs_initialize(N,X,0,Solver),
@@ -839,20 +861,20 @@ user:evaluate(LLH_Training_Queries, X,Grad,N,_,_) :-
     N1 is N-1,    
     forall(between(0,N1,I),
 	   (Grad[I] <== 0.0, S <== X[I], sigmoid(S,Slope, P), Probs[I] <== P)
-	  ), nl,
+	  ),
     forall( 
 	full_example(QueryID,QueryProb,BDD),	   
 	   compute_grad(QueryID, BDD, QueryProb,Grad, Probs, Slope,LLs)
     ),
-    LLH_Training_Queries <== sum(LLs),
+    LLH_Training_QueriesSum <== sum(LLs),
-    writeln(LLH_Training_Queries).
+LLH_Training_Queries is LLH_Training_QueriesSum/TrainingExampleCount .
 %wrap(X, Grad, GradCount).
 
 full_example(QueryID,QueryProb,BDD) :-
     user:example(QueryID,_Query,QueryProb,_),
      recorded(QueryID,BDD,_),
-         BDD = bdd(_Dir, _GradTree, MapList),
+     BDD = bdd(_Dir, _GradTree, MapList),
-         MapList = [_|_].
+     MapList = [_|_].
 
 compute_grad(QueryID,BDD,QueryProb, Grad, Probs, Slope, LLs) :-
     BDD = bdd(_Dir, _GradTree, MapList),
@@ -863,7 +885,7 @@ compute_grad(QueryID,BDD,QueryProb, Grad, Probs, Slope, LLs) :-
     LLs[QueryID] <== LL,    
 %writeln( qprobability(BDD,Slope,BDDProb) ),
     forall(
-	    member(I-_, MapList),
+	member(I-_, MapList),
 	gradientpair(I, BDD,Slope,BDDProb, QueryProb, Grad, Probs)
     ).
 
@@ -971,7 +993,7 @@ user:progress(FX,X,_G,X_Norm,G_Norm,Step,_N,Iteration,Ls,0) :-
     NextIteration is CurrentIteration+1,
     assertz(current_iteration(NextIteration)),
     save_model,
-    set_problog_flag(mse_trainingset, FX),
+    logger_set_variable(mse_trainingset, FX),
     X0 <== X[0], sigmoid(X0,Slope,P0),
     X1 <== X[1], sigmoid(X1,Slope,P1),
     format('~d. Iteration : (x0,x1)=(~4f,~4f)  f(X)=~4f  |X|=~4f  |X\'|=~4f  Step=~4f  Ls=~4f~n',[Iteration,P0                                               ,P1,FX,X_Norm,G_Norm,Step,Ls]).

packages/bdd/cudd.c

@@ -863,6 +863,9 @@ static YAP_Bool p_cudd_print_with_names(void) {
 
 static YAP_Bool p_cudd_die(void) {
   DdManager *manager = (DdManager *)YAP_IntOfTerm(YAP_ARG1);
+  //Cudd_FreeTree(manager);
+  //cuddFreeTable(manager);
+  Cudd_CheckZeroRef(manager);
   Cudd_Quit(manager);
   return TRUE;
 }

packages/jpl/CMakeLists.txt

@@ -1,3 +1,4 @@
+
 #CHECK: JavaLibs
 
 set (JPL_SOURCES

packages/jpl/src/c/CMakeLists.txt

@@ -4,16 +4,25 @@ add_lib(jplYap  jpl.h jpl.c hacks.h)
 
 include_directories (${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2} ${JAVA_AWT_PATH} )
 
+
+
 if (APPLE)
-get_filename_component ( JAVA_AWT_DIR ${JAVA_AWT_LIBRARY} DIRECTORY)
+  set(CMAKE_MACOSX_RPATH 1)
-find_library (JLI jli ${JAVA_AWT_DIR}/jli)
+  get_filename_component ( JAVA_AWT_DIR ${JAVA_AWT_LIBRARY} DIRECTORY)
+  get_filename_component ( JAVA_JNI_DIR ${JAVA_JVM_LIBRARY} DIRECTORY)
+  find_library (JLI jli ${JAVA_AWT_DIR}/jli)
+  find_library (JAL JavaApplicationLauncher FRAMEWORK ONLY PATH /System/Library/PrivateFrameworks)
+  find_library (JL JavaLaunching FRAMEWORK ONLY PATH /System/Library/PrivateFrameworks)
+  SET(CMAKE_INSTALL_RPATH "${JAVA_AWT_DIR}/jli")
+  target_link_libraries(jplYap libYap ${JL} ${JAL} -L${JAVA_AWT_DIR}/jli -ljli )
+else()
+  target_link_libraries(jplYap  libYap ${JAVA_JVM_LIBRARY})
+
 endif()
 
-  target_link_libraries(jplYap  libYap ${JLI} ${JNI_LIBRARIES})
 
   set_target_properties(jplYap PROPERTIES
     OUTPUT_NAME jpl
-    INSTALL_RPATH_USE_LINK_PATH TRUE
     )
 
   # set(YAP_SYSTEM_OPTIONS "jpl " ${YAP_SYSTEM_OPTIONS} PARENT_SCOPE)

packages/jpl/test_jpl.pl

@@ -1,4 +1,4 @@
-:- module(test_jpl,
+f:- module(test_jpl,
 	  [ run_tests/0,
 	    run_tests/1
 	  ]).

packages/myddas/mysql/CMakeLists.txt

@@ -1,4 +1,6 @@
 
+if (WITH_MYSQL)
+
   set(MYSQL_SOURCES
           myddas_mysql.c
           myddas_util.c
@@ -51,3 +53,5 @@
           "enable the MYDDAS top-level (REPL) support for MySQL" OFF
           'USE_MYDDAS AND MYSQL_FOUND' OFF)
   #TODO:
+
+endif()

packages/myddas/odbc/CMakeLists.txt

@@ -1,39 +1,42 @@
+if (WITH_ODBC)
   
-set( YAPODBC_SOURCES
+  set( YAPODBC_SOURCES
-  myddas_odbc.c
+    myddas_odbc.c
-)
-
-set(SO_MAJOR 1)
-set(SO_MINOR 0)
-set(SO_PATCH 0)
-
-macro_optional_find_package(ODBC ON)
-
-if (ODBC_FOUND)
-  # ODBC_INCLUDE_DIRECTORIES, where to find sql.h
-  # ODBC_LIBRARIES, the libraries to link against to use ODBC
-  # ODBC_FOUND.  If false, you cannot build anything that requires Odbc.
-add_lib(YAPodbc  ${YAPODBC_SOURCES})
-target_link_libraries(YAPodbc libYap ${ODBC_LIBRARIES})
-include_directories (${ODBC_INCLUDE_DIRECTORIES} ..)
-
-set_target_properties (YAPodbc PROPERTIES
-  POSITION_INDEPENDENT_CODE ON
-      PREFIX ""
-  )
-
-  list (APPEND MYDDAS_FLAGS -DMYDDAS_ODBC=1)
-  set (MYDDAS_FLAGS ${MYDDAS_FLAGS} ON PARENT_SCOPE)
-  set_property(GLOBAL APPEND PROPERTY COMPILE_DEFINITIONS
-          -DMYDDAS_ODBC=1)
-
-
-  install(TARGETS  YAPodbc
-          LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
-          RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
-    ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
     )
 
-else()
+  set(SO_MAJOR 1)
-  add_definitions (-DMYDDAS_ODBC=0)
+  set(SO_MINOR 0)
+  set(SO_PATCH 0)
+
+  macro_optional_find_package(ODBC ON)
+
+  if (ODBC_FOUND)
+    # ODBC_INCLUDE_DIRECTORIES, where to find sql.h
+    # ODBC_LIBRARIES, the libraries to link against to use ODBC
+    # ODBC_FOUND.  If false, you cannot build anything that requires Odbc.
+    add_lib(YAPodbc  ${YAPODBC_SOURCES})
+    target_link_libraries(YAPodbc libYap ${ODBC_LIBRARIES})
+    include_directories (${ODBC_INCLUDE_DIRECTORIES} ..)
+
+    set_target_properties (YAPodbc PROPERTIES
+      POSITION_INDEPENDENT_CODE ON
+      PREFIX ""
+      )
+
+    list (APPEND MYDDAS_FLAGS -DMYDDAS_ODBC=1)
+    set (MYDDAS_FLAGS ${MYDDAS_FLAGS} ON PARENT_SCOPE)
+    set_property(GLOBAL APPEND PROPERTY COMPILE_DEFINITIONS
+      -DMYDDAS_ODBC=1)
+
+
+    install(TARGETS  YAPodbc
+      LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
+      RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
+      ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
+      )
+
+  else()
+    add_definitions (-DMYDDAS_ODBC=0)
   endif (ODBC_FOUND)
+
+endif()

packages/myddas/postgres/CMakeLists.txt

@@ -1,35 +1,39 @@
 
-set( YAPPOSTGRES_SOURCES
+if (WITH_POSTGRES)
-  myddas_postgres.c
-)
 
-set(SO_MAJOR 1)
+  set( YAPPOSTGRES_SOURCES
-set(SO_MINOR 0)
+    myddas_postgres.c
-set(SO_PATCH 0)
-
-macro_optional_find_package(PostgreSQL ON)
-
-if (PostgreSQL_FOUND)
-#  PostgreSQL_FOUND         - Set to true when PostgreSQL is found.
-#  PostgreSQL_INCLUDE_DIRS  - Include directories for PostgreSQL
-#  PostgreSQL_LIBRARY_DIRS  - Link directories for PostgreSQL libraries
-#  PostgreSQL_LIBRARIES     - The PostgreSQL libraries.
-  add_lib(YAPpostgres  ${YAPPOSTGRES_SOURCES})
-  target_link_libraries(YAPpostgres libYap   ${PostgreSQL_LIBRARIES})
-  include_directories (${PostgreSQL_INCLUDE_DIRS} ..)
- set_target_properties (YAPpostgres PROPERTIES
-    POSITION_INDEPENDENT_CODE ON
-    PREFIX ""
-  )
-
-list (APPEND MYDDAS_FLAGS -DMYDDAS_POSTGRES=1)
-set (MYDDAS_FLAGS ${MYDDAS_FLAGS} ON PARENT_SCOPE)
-set_property(GLOBAL APPEND PROPERTY COMPILE_DEFINITIONS
-        -DMYDDAS_POSTGRES=1)
-
-install(TARGETS  YAPpostgres
-    LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
-    RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
-    ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
     )
-endif (PostgreSQL_FOUND)
+
+  set(SO_MAJOR 1)
+  set(SO_MINOR 0)
+  set(SO_PATCH 0)
+
+  macro_optional_find_package(PostgreSQL ON)
+
+  if (PostgreSQL_FOUND)
+    #  PostgreSQL_FOUND         - Set to true when PostgreSQL is found.
+    #  PostgreSQL_INCLUDE_DIRS  - Include directories for PostgreSQL
+    #  PostgreSQL_LIBRARY_DIRS  - Link directories for PostgreSQL libraries
+    #  PostgreSQL_LIBRARIES     - The PostgreSQL libraries.
+    add_lib(YAPpostgres  ${YAPPOSTGRES_SOURCES})
+    target_link_libraries(YAPpostgres libYap   ${PostgreSQL_LIBRARIES})
+    include_directories (${PostgreSQL_INCLUDE_DIRS} ..)
+    set_target_properties (YAPpostgres PROPERTIES
+      POSITION_INDEPENDENT_CODE ON
+      PREFIX ""
+      )
+
+    list (APPEND MYDDAS_FLAGS -DMYDDAS_POSTGRES=1)
+    set (MYDDAS_FLAGS ${MYDDAS_FLAGS} ON PARENT_SCOPE)
+    set_property(GLOBAL APPEND PROPERTY COMPILE_DEFINITIONS
+      -DMYDDAS_POSTGRES=1)
+
+    install(TARGETS  YAPpostgres
+      LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
+      RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
+      ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
+      )
+  endif (PostgreSQL_FOUND)
+
+endif()

packages/myddas/sqlite3/CMakeLists.txt

@@ -1,68 +1,72 @@
-message( "   * Sqlite3 Data-Base (http://www.sqlite3.org), distributed with MYDDAS" )
+if (WITH_SQLITE3)
 
-set (SQLITE_EXTRA
+  message( "   * Sqlite3 Data-Base (http://www.sqlite3.org), distributed with MYDDAS" )
-  chinook.db
-  sqlitest.yap)
 
-set( YAPSQLITE3_SOURCES
+  set (SQLITE_EXTRA
-  myddas_sqlite3.c
+    chinook.db
-  src/sqlite3.h
+    sqlitest.yap)
-  src/sqlite3ext.h
+
- )
+  set( YAPSQLITE3_SOURCES
+    myddas_sqlite3.c
+    src/sqlite3.h
+    src/sqlite3ext.h
+    )
 
 
-#sqlite3 is now in the system
+  #sqlite3 is now in the system
 
-set (SQLITE3_FOUND ON CACHE PRIVATE "")
+  set (SQLITE3_FOUND ON CACHE PRIVATE "")
 
-include_directories ( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/..)
+  include_directories ( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/..)
 
-if (ANDROID)
+  if (ANDROID)
-  add_definitions(-DSQLITE_FCNTL_MMAP_SIZE=0 )
+    add_definitions(-DSQLITE_FCNTL_MMAP_SIZE=0 )
+
+  endif()
+
+  add_definitions(-DSQLITE_ENABLE_COLUMN_METADATA=1 )
+
+  add_definitions(-DSQLITE_ENABLE_JSON1=1 )
+
+  add_definitions(-DSQLITE_ENABLE_RBU=1 )
+
+  add_definitions(-DSQLITE_ENABLE_RTREE=1 )
+  add_definitions(-DSQLITE_ENABLE_FTS5=1 )
+
+  SET_PROPERTY(DIRECTORY PROPERTY COMPILE_DEFINITIONS YAP_KERNEL=1 )
+
+
+  if (ANDROID )
+    add_library(  YAPsqlite3 OBJECT
+      ${YAPSQLITE3_SOURCES} )
+
+  else()
+
+    list(APPEND YAPSQLITE3_SOURCES src/sqlite3.c)
+
+    
+    add_library(  YAPsqlite3 SHARED
+      ${YAPSQLITE3_SOURCES})
+
+    target_link_libraries(YAPsqlite3 libYap )
+
+    set_target_properties(YAPsqlite3
+      PROPERTIES
+      #  RPATH ${libdir} VERSION ${LIBYAPTAI_FULL_VERSION}
+      #  SOVERSION ${LIBYAPTAI_MAJOR_VERSION}.${LIBYAPTAI_MINOR_VERSION}
+      POSITION_INDEPENDENT_CODE ON
+      PREFIX ""
+      )
+
+    install(TARGETS YAPsqlite3
+      RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
+      ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
+      LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
+      )
+  endif()
+
+  install(FILES ${SQLITE_EXTRA}
+    DESTINATION ${libpl}
+    )
 
 endif()
-
-add_definitions(-DSQLITE_ENABLE_COLUMN_METADATA=1 )
-
-add_definitions(-DSQLITE_ENABLE_JSON1=1 )
-
-add_definitions(-DSQLITE_ENABLE_RBU=1 )
-
-add_definitions(-DSQLITE_ENABLE_RTREE=1 )
-add_definitions(-DSQLITE_ENABLE_FTS5=1 )
-
-SET_PROPERTY(DIRECTORY PROPERTY COMPILE_DEFINITIONS YAP_KERNEL=1 )
-
-
-if (ANDROID )
-add_library(  YAPsqlite3 OBJECT
-  ${YAPSQLITE3_SOURCES} )
-
-else()
-
-  list(APPEND YAPSQLITE3_SOURCES src/sqlite3.c)
-
-  
-add_library(  YAPsqlite3 SHARED
-  ${YAPSQLITE3_SOURCES})
-
-  target_link_libraries(YAPsqlite3 libYap )
-
- set_target_properties(YAPsqlite3
-  PROPERTIES
-  #  RPATH ${libdir} VERSION ${LIBYAPTAI_FULL_VERSION}
-  #  SOVERSION ${LIBYAPTAI_MAJOR_VERSION}.${LIBYAPTAI_MINOR_VERSION}
-    POSITION_INDEPENDENT_CODE ON
-    PREFIX ""
-  )
-
-install(TARGETS YAPsqlite3
-        RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
-        ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
-        LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
-        )
-endif()
-
-    install(FILES ${SQLITE_EXTRA}
-     DESTINATION ${libpl}
-        )

packages/python/pybips.c

@@ -591,7 +591,8 @@ static long get_len_of_range(long lo, long hi, long step) {
 }
 
 #if PY_MAJOR_VERSION >= 3
-static PyStructSequence_Field pnull[] = {
+/*
+ static PyStructSequence_Field pnull[] = {
     {"A1", NULL},  {"A2", NULL},  {"A3", NULL},  {"A4", NULL},  {"A5", NULL},
     {"A6", NULL},  {"A7", NULL},  {"A8", NULL},  {"A9", NULL},  {"A9", NULL},
     {"A10", NULL}, {"A11", NULL}, {"A12", NULL}, {"A13", NULL}, {"A14", NULL},
@@ -600,6 +601,7 @@ static PyStructSequence_Field pnull[] = {
     {"A24", NULL}, {"A25", NULL}, {"A26", NULL}, {"A27", NULL}, {"A28", NULL},
     {"A29", NULL}, {"A29", NULL}, {"A30", NULL}, {"A31", NULL}, {"A32", NULL},
     {NULL, NULL}};
+*/
  
 static PyObject *structseq_str(PyObject *iobj) {
 
@@ -763,7 +765,7 @@ PyObject *term_to_nametuple(const char *s, arity_t arity, PyObject *tuple) {
       PyStructSequence_Desc *desc = calloc(sizeof(PyStructSequence_Desc), 1);
       desc->name = PyMem_Malloc(strlen(s) + 1);
       desc->doc = "YAPTerm";
-      desc->fields = pnull;
+      desc->fields = NULL;
       desc->n_in_sequence = arity;
       if (PyStructSequence_InitType2(typp, desc) < 0)
         return NULL;

packages/python/yap_kernel/yap_ipython/yapi.py

@@ -6,14 +6,14 @@ from traitlets import Bool
 
 
 from yap4py.yapi import *
-from yap_ipython.core.completer import Completer
+from IPython.core.completer import Completer
-# import yap_ipython.core
+# import IPython.core
 from traitlets import Instance
-from yap_ipython.core.inputsplitter import *
+from IPython.core.inputsplitter import *
-from yap_ipython.core.inputtransformer import *
+from IPython.core.inputtransformer import *
-from yap_ipython.core.interactiveshell import *
+from IPython.core.interactiveshell import *
 from ipython_genutils.py3compat import builtin_mod
-from yap_ipython.core import interactiveshell
+from IPython.core import interactiveshell
 
 from collections import namedtuple
 import traceback
@@ -198,11 +198,11 @@ class YAPInputSplitter(InputSplitter):
             self.reset()
 
     def push(self, lines):
-        """Push one or more lines of yap_ipython input.
+        """Push one or more lines of IPython input.
 
         This stores the given lines and returns a status code indicating
         whether the code forms a complete Python block or not, after processing
-        all input lines for special yap_ipython syntax.
+        all input lines for special IPython syntax.
 
         Any exceptions generated in compilation are swallowed, but if an
         exception was produced, the method returns True.
@@ -488,7 +488,7 @@ class YAPCompleter(Completer):
 
             If ``IPCompleter.debug`` is :any:`True` will yield a ``--jedi/ipython--``
             fake Completion token to distinguish completion returned by Jedi
-            and usual yap_ipython completion.
+            and usual IPython completion.
 
         .. note::
 
@@ -507,7 +507,7 @@ class YAPCompleter(Completer):
 
 
 
-class YAPRun:
+class YAPRun(InteractiveShell):
     """An enhanced, interactive shell for YAP."""
 
     def __init__(self, shell):
@@ -602,28 +602,29 @@ class YAPRun:
             return self.result
 
 
-    def _yrun_cell(self, raw_cell, store_history=True, silent=False,
-                 shell_futures=True):
-        """Run a complete IPython cell.
  
-        Parameters
+    def _yrun_cell(self, raw_cell, store_history=True, silent=False,
-                   ----------
+                  shell_futures=True):
-                   raw_cell : str
+         """Run a complete IPython cell.
-                   The code (including IPython code such as
+-
-                   %magic functions) to run.
+       Parameters
-                   store_history : bool
+                  ----------
-          If True, the raw and translated cell will be stored in IPython's
+                  raw_cell : str
-                   history. For user code calling back into
+                  The code (including IPython code such as
-                   IPython's machinery, this
+                  %magic functions) to run.
-                   should be set to False.
+                  store_history : bool
-                   silent : bool
+         If True, the raw and translated cell will be stored in IPython's
-          If True, avoid side-effects, such as implicit displayhooks and
+                  history. For user code calling back into
-                   and logging.  silent=True forces store_history=False.
+                  IPython's machinery, this
-                   shell_futures : bool
+                  should be set to False.
-          If True, the code will share future statements with the interactive
+                  silent : bool
-                   shell. It will both be affected by previous
+         If True, avoid side-effects, such as implicit displayhooks and
-                    __future__ imports, and any __future__ imports in the code
+                  and logging.  silent=True forces store_history=False.
-                     will affect the shell. If False,
+                  shell_futures : bool
+         If True, the code will share future statements with the interactive
+                  shell. It will both be affected by previous
+                  __future__ imports, and any __future__ imports in the code
+                        will affect the shell. If False,
                    __future__ imports are not shared in either direction.
 
         Returns
@@ -727,6 +728,7 @@ class YAPRun:
             self.result.result = False
         has_raised = False
         try:
+            builtin_mod.input = self.shell.sys_raw_input
             self.yapeng.mgoal(streams(True),"user", True)
             if cell.strip('\n \t'):
                 #create a Trace object, telling it what to ignore, and whether to