more doc stuff

C/attvar.c

@@ -8,10 +8,8 @@
  *									 *
  **************************************************************************
  *									 *
- * File:		attvar.c						 *
+ * File:		attvar.c * Last rev:
- * Last rev:								 *
+ ** mods: * comments:	YAP support for attributed vars *
- * mods:									 *
- * comments:	YAP support for attributed vars				 *
  *									 *
  *************************************************************************/
 #ifdef SCCS
@@ -22,26 +20,27 @@ static char SccsId[] = "%W% %G%";
  * @file   attvar.c
  * @author VITOR SANTOS COSTA <vsc@VITORs-MBP-2.lan>
  * @date   Mon Apr 30 09:31:59 2018
- * 
+ *
  * @brief  attributed variables
  * @namespace prolog
- * 
+ *
  */
 #include "Yap.h"
 
-#include "Yatom.h"
 #include "YapHeap.h"
-#include "heapgc.h"
+#include "Yatom.h"
 #include "attvar.h"
+#include "heapgc.h"
 #ifndef NULL
 #define NULL (void *)0
 #endif
 
 /**
-    @defgroup AttributedVariables_Builtins Low-level support for Attributed Variables
+    @defgroup AttributedVariables_Builtins Low-level support for Attributed
-    
+   Variables
+
      @brief Implementation of Attribute Declarations
-    @ingroup attributes
+    @ingroup AttributedVariables
     @{
 */
 
@@ -211,7 +210,7 @@ static void WakeAttVar(CELL *pt1, CELL reg2 USES_REGS) {
 
 void Yap_WakeUp(CELL *pt0) {
   CACHE_REGS
-    CELL d0 = *pt0;
+  CELL d0 = *pt0;
   RESET_VARIABLE(pt0);
   WakeAttVar(pt0, d0 PASS_REGS);
 }
@@ -684,7 +683,6 @@ static Int free_att(USES_REGS1) {
   }
 }
 
-
 static Int get_atts(USES_REGS1) {
   /* receive a variable in ARG1 */
   Term inp = Deref(ARG1);
@@ -896,7 +894,7 @@ static Term AllAttVars(USES_REGS1) {
 
   while (pt < myH) {
     switch (*pt) {
-    case (CELL) FunctorAttVar:
+    case (CELL)FunctorAttVar:
       if (IsUnboundVar(pt + 1)) {
         if (ASP - myH < 1024) {
           LOCAL_Error_Size = (ASP - HR) * sizeof(CELL);
@@ -910,24 +908,23 @@ static Term AllAttVars(USES_REGS1) {
       }
       pt += (1 + ATT_RECORD_ARITY);
       break;
-    case (CELL) FunctorDouble:
+    case (CELL)FunctorDouble:
 #if SIZEOF_DOUBLE == 2 * SIZEOF_INT_P
       pt += 4;
 #else
       pt += 3;
 #endif
       break;
-    case (CELL) FunctorString:
+    case (CELL)FunctorString:
       pt += 3 + pt[1];
       break;
-    case (CELL) FunctorBigInt: {
+    case (CELL)FunctorBigInt: {
-      Int sz = 3 +
+      Int sz = 3 + (sizeof(MP_INT) +
-	(sizeof(MP_INT) +
+                    (((MP_INT *)(pt + 2))->_mp_alloc * sizeof(mp_limb_t))) /
-	 (((MP_INT *)(pt + 2))->_mp_alloc * sizeof(mp_limb_t))) /
+                       sizeof(CELL);
-	sizeof(CELL);
       pt += sz;
     } break;
-    case (CELL) FunctorLongInt:
+    case (CELL)FunctorLongInt:
       pt += 3;
       break;
     default:
@@ -976,7 +973,7 @@ static Int is_attvar(USES_REGS1) {
 static Int attvar_bound(USES_REGS1) {
   Term t = Deref(ARG1);
   return IsVarTerm(t) && IsAttachedTerm(t) &&
-    !IsUnboundVar(&(RepAttVar(VarOfTerm(t))->Done));
+         !IsUnboundVar(&(RepAttVar(VarOfTerm(t))->Done));
 }
 
 static Int void_term(USES_REGS1) { return Yap_unify(ARG1, TermVoidAtt); }
@@ -1016,7 +1013,7 @@ static Int attvar_bound(USES_REGS1) { return FALSE; }
 
 void Yap_InitAttVarPreds(void) {
   CACHE_REGS
-    Term OldCurrentModule = CurrentModule;
+  Term OldCurrentModule = CurrentModule;
   CurrentModule = ATTRIBUTES_MODULE;
 #ifdef COROUTINING
   GLOBAL_attas[attvars_ext].bind_op = WakeAttVar;
@@ -1038,8 +1035,7 @@ void Yap_InitAttVarPreds(void) {
   Yap_InitCPred("rm_att", 4, rm_att, 0);
   Yap_InitCPred("bind_attvar", 1, bind_attvar, SafePredFlag);
   Yap_InitCPred("unbind_attvar", 1, unbind_attvar, SafePredFlag);
-  Yap_InitCPred("modules_with_attributes", 2, modules_with_atts,
+  Yap_InitCPred("modules_with_attributes", 2, modules_with_atts, SafePredFlag);
-                SafePredFlag);
   Yap_InitCPred("void_term", 1, void_term, SafePredFlag);
   Yap_InitCPred("free_term", 1, free_term, SafePredFlag);
   Yap_InitCPred("fast_unify_attributed", 2, fast_unify, 0);

C/flags.c

@@ -16,23 +16,29 @@
 *************************************************************************/
 
 /** @file C/flags.c
-
+    
-    @{
+    @brief  Prolog parameter setting,
-    @defgroup YAPFlags_Impl C-code to handle Prolog flags.
-    @ingroup YAPFlags
-
-@brief Low-level code to support flags. Flags can be:
-  = thread-local or global
-  = module-based or module-independent.
-  = read-only or read-write
-  = System or User Defined.
-  = Have type boolean, number, atom constant or may be a general term.
-
 */
 
 /*
  * @namespace prolog
- * /
+ */
+
+/**
+    @{
+    @defgroup YAPFlags_Impl C-code to handle Prolog flags.
+    @ingroup YAPFlags
+
+@brief Low-level code to support flags.
+
+Prolog Flags can be:
+= thread-local or global
+= module-based or module-independent.
+= read-only or read-write
+= System or User Defined.
+= Have type boolean, number, atom constant or may be a general term.
+
+*/
 
 // this is where  we define flags
 #define INIT_FLAGS 1
@@ -78,21 +84,22 @@ static Int set_prolog_flag(USES_REGS1);
 #include "YapEval.h"
 #include "yapio.h"
 
-#define YAP_FLAG(ID, NAME, WRITABLE, DEF, INIT, HELPER)                        \
+#define YAP_FLAG(ID, NAME, WRITABLE, DEF, INIT, HELPER)    { NAME, WRITABLE, DEF, INIT, HELPER }
-  { NAME, WRITABLE, DEF, INIT, HELPER }
+
+#define START_LOCAL_FLAGS static flag_info local_flags_setup[] = {
+#define END_LOCAL_FLAGS     LZERO_FLAG};
+
+#define START_GLOBAL_FLAGS static flag_info global_flags_setup[] = {
+#define END_GLOBAL_FLAGS     GZERO_FLAG};
+
+
+#define GZERO_FLAG       { NULL, false, NULL, NULL, NULL }
+#define LZERO_FLAG       { NULL, false, NULL, NULL, NULL }
 
-#define GZERO_FLAG                                                             \
-  { NULL, false, NULL, NULL, NULL }
-#define LZERO_FLAG                                                             \
-  { NULL, false, NULL, NULL, NULL }
 
-static flag_info global_flags_setup[] = {
 #include "YapGFlagInfo.h"
-    GZERO_FLAG};
 
-static flag_info local_flags_setup[] = {
 #include "YapLFlagInfo.h"
-    LZERO_FLAG};
 
 static Term indexer(Term inp) {
   if (inp == TermOff || inp == TermSingle || inp == TermCompact ||

C/modules.c

@@ -14,6 +14,8 @@
 * comments:	module support						 *
 *									 *
 *************************************************************************/
+
+
 #ifdef SCCSLookupSystemModule
 static char SccsId[] = "%W% %G%";
 #endif

H/YapFlags.h

@@ -239,7 +239,10 @@ Set or read system properties for  _Param_:
 
 
 #define YAP_FLAG(ITEM, NAME, WRITABLE, DEF, INIT, HELPER) ITEM
-
+#define START_LOCAL_FLAGS  enum {
+#define END_LOCAL_FLAGS };
+#define START_GLOBAL_FLAGS  enum {
+#define END_GLOBAL_FLAGS };
 
 /*  */  
 #include "YapGFlagInfo.h"
@@ -249,6 +252,10 @@ Set or read system properties for  _Param_:
   
 
 #undef YAP_FLAG
+#undef START_LOCAL_FLAGS
+#undef END_LOCAL_FLAGS
+#undef START_GLOBAL_FLAGS
+#undef END_GLOBAL_FLAGS
 
 bool setYapFlag(Term tflag, Term t2);
 Term getYapFlag(Term tflag);

H/YapLFlagInfo.h

@@ -24,12 +24,12 @@
 @{
 
 
-@enum local_flags flag:
+@enum local_flags_setup thread-local flag:
 */
 
-typedef enum local_flags_enum {
+START_LOCAL_FLAGS
-  
+
-/** + `autoload`: set the system to look for undefined procedures */
+  /** + `autoload`: set the system to look for undefined procedures */
 YAP_FLAG(  AUTOLOAD_FLAG, "autoload", true, booleanFlag, "false" , NULL ),
 /** + `read-only flag, that tells if Prolog is in an inner top-level */
 YAP_FLAG(  BREAK_LEVEL_FLAG, "break_level", true, nat, "0" , NULL ),
@@ -128,7 +128,6 @@ automatically redirects the user_error alias to the original
 YAP_FLAG(  USER_INPUT_FLAG, "user_input", true, stream, "user_input" , set_input_stream ),
   YAP_FLAG(  USER_OUTPUT_FLAG, "user_output", true, stream, "user_output" , set_output_stream ),
 
-
+END_LOCAL_FLAGS
-} local_flag_t;
 
 /// @}

docs/md/attributes.md

@@ -1,8 +1,9 @@
-Attributed Variables and Co-Routining   {#AttributedVariables}
+
-====================================
+@defgroup AttributedVariables Attributed Variables and Co-Routining
 
 @ingroup extensions
 
+@{
 
 YAP supports attributed variables, originally developed at OFAI by
 Christian Holzbaur. Attributes are a means of declaring that an
@@ -27,9 +28,8 @@ work with. Most packages included in YAP that use attributed
 variables, such as CHR, CLP(FD), and CLP(QR), rely on the SWI-Prolog
 awi interface.
 
-[TOC]
+@defgroup SICS_attributes SICStus Style attribute declarations.
 
-##  SICStus Style attribute declarations.              {#SICS_attributes}
 
 The YAP library `atts` implements attribute variables in the style of
 SICStus Prolog. Attributed variables work as follows:
@@ -82,9 +82,10 @@ mechanism is used for this purpose.
 
 The  attribute manipulation predicates always work as follows:
 
-+ The first argument is the unbound variable associated with
+  + The first argument is the unbound variable associated with
 attributes,
-+ The second argument is a list of attributes. Each attribute will
+
+  + The second argument is a list of attributes. Each attribute will
 be a Prolog term or a constant, prefixed with the <tt>+</tt> and <tt>-</tt> unary
 operators. The prefix <tt>+</tt> may be dropped for convenience.
 
@@ -99,9 +100,9 @@ attempting to unify an attributed variable which might have attributes
 in some  _Module_.
 
 
-Attributes are usually presented as goals. The following routines are
+At execution conclusion, attributes still unsatisfied are presented as
-used by built-in predicates such as call_residue/2 and by the
+goals. The following routines are used by built-in predicates such as
-Prolog top-level to display attributes:
+call_residue/2 and by the Prolog top-level to display attributes:
 
 
 Constraint solvers must be able to project a set of constraints to a set
@@ -269,12 +270,11 @@ variables only.  More complicated interactions are likely to be found
 in more sophisticated solvers.  The corresponding
 verify_attributes/3 predicates would typically refer to the
 attributes from other known solvers/modules via the module prefix in
-Module:get_atts/2`.
+Module:get_atts/2.
 
-@}
 
-@{
+hProlog and SWI-Prolog style Attribute Declarations              {#New_Style_Attribute_Declarations}
-####  hProlog and SWI-Prolog style Attribute Declarations              {#New_Style_Attribute_Declarations}
+------------------------------------------------
 
   The following documentation is taken from the SWI-Prolog manual.
 
@@ -286,24 +286,28 @@ Module:get_atts/2`.
   executed in this module.  The example below realises a very simple and
   incomplete finite domain reasoner.
 
-  ~~~~~
+~~~~~
-  :- module(domain,
+:- module(domain,
-  [ domain/2            % Var, ?Domain %
+[ domain/2            % Var, ?Domain %
-  ]).
+]).
-  :- use_module(library(ordsets)).
+:- use_module(library(ordsets)).
+	
+domain(X, Dom) :-
+    var(Dom), !,
+	get_attr(X, domain, Dom).
+	domain(X, List) :-
+	list_to_ord_set(List, Domain),
+	put_attr(Y, domain, Domain),
+	X = Y.
 
-  domain(X, Dom) :-
+~~~~~
-  var(Dom), !,
-  get_attr(X, domain, Dom).
-  domain(X, List) :-
-  list_to_ord_set(List, Domain),
-v  put_attr(Y, domain, Domain),
-  X = Y.
 
-                                %    An attributed variable with attribute value Domain has been %
+The next predicate is called *after* _X_, the attributed variable with attribute value _Domain_ has been
-                                %    assigned the value Y %
+assigned the value Y.
 
-  attr_unify_hook(Domain, Y) :-
+
+~~~~~
+attr_unify_hook(Domain, Y) :-
   (   get_attr(Y, domain, Dom2)
   ->  ord_intersection(Domain, Dom2, NewDomain),
   (   NewDomain == []
@@ -316,15 +320,17 @@ v  put_attr(Y, domain, Domain),
   ->  put_attr( Y, domain, Domain )
   ;   ord_memberchk(Y, Domain)
   ).
+~~~~~
 
-                                %    Translate attributes from this module to residual goals %
+The user defined attribute_goals/1 attributes from this module to residual goals 
 
-  attribute_goals(X) -->
+~~~~~
+attribute_goals(X) -->
   { get_attr(X, domain, List) },
   [domain(X, List)].
-  ~~~~~
+~~~~~
 
-  Before explaining the code we give some example queries:
+  Before explaining the code in detail we give some example queries:
 
   The predicate `domain/2` fetches (first clause) or assigns
   (second clause) the variable a <em>domain</em>, a set of values it can
@@ -342,11 +348,8 @@ v  put_attr(Y, domain, Domain),
   remaining attributes to user-readable goals that, when executed, reinstate
   these attributes.
 
-@}
+Co-routining              {#CohYroutining}
-
+------------
-
-@{
-####  Co-routining              {#CohYroutining}
 
 Prolog uses a simple left-to-right flow of control. It is sometimes
 convenient to change this control so that goals will only execute when
@@ -359,31 +362,27 @@ attributed variables to implement co-routining.
 
 Two declarations are supported:
 
-+ block/1
+	+ block/1
-The argument to `block/1` is a condition on a goal or a conjunction
+   The argument to `block/1` is a condition on a goal or a conjunction
-of conditions, with each element separated by commas. Each condition is
+   of conditions, with each element separated by commas. Each condition is
-of the form `predname( _C1_,..., _CN_)`, where  _N_ is the
+   of the form `predname( _C1_,..., _CN_)`, where  _N_ is the
-arity of the goal, and each  _CI_ is of the form `-`, if the
+   arity of the goal, and each  _CI_ is of the form `-`, if the
-argument must suspend until the first such variable is bound, or
+   argument must suspend until the first such variable is bound, or
-`?`, otherwise.
+   `?`, otherwise.
 
-+ wait/1
+	+ wait/1
-The argument to `wait/1` is a predicate descriptor or a conjunction
+   The argument to `wait/1` is a predicate descriptor or a conjunction
-of these predicates. These predicates will suspend until their first
+   of these predicates. These predicates will suspend until their first
-argument is bound.
+   argument is bound.
 
 
 The following primitives can be used:
 
-- freeze/2
+	- freeze/2
 
-- dif/2
+	- dif/2
 
-- when/2
+	- when/2
 
-- frozen/2
+	- frozen/2
 
-
-@}
-
-@}

docs/md/builtins.md

@@ -6,57 +6,15 @@ Prolog programs, provide fundamental functionality such as termm manipulation or
 resources,
 
 Many of the predicates described here have been standardised by the International Standard Organization.
- The corresponding standartised subset of Prolog also known as ISO-Prolog.                                                                                             
+ The corresponding standartised subset of Prolog also known as ISO-Prolog.    
+
 In the description of the arguments of predicates the following
 notation will be used:
 
-+ a preceding plus sign will denote an argument as an "input
+	+ a preceding plus sign will denote an argument as an "input
-argument" - the argument is read, not written, and it cannot be a free variable at the time of the call;
+	argument" - the argument is read, not written, and it cannot
-+ a preceding minus sign will denote an "output argument";
+	be a free variable at the time of the call;
-+ an argument with no preceding symbol can be used in both ways.
 
-+ @ref AbsoluteFileName
+	+ a preceding minus sign will denote an "output argument";
-+ @ref CompilerAnalysis
-+ @ref New_Style_Attribute_Declarations
-+ @ref YAPControl
-+ @ref Profiling
-+ @ref Call_Counting
-+ @ref YAPConsulting
-+ @ref YAPReadFiles
-+ @ref ModPreds 
-+ @ref Conditional_Compilation
-+ @ref YAPBigLoad
-+ @ref Deb_Interaction
-+ @ref DepthLimited
-+ @ref Dialects
-+ @ref Directives
-+ @ref EAM
-+ @ref SWI-error
-+ @ref YAPErrorHandler
-+ @ref CompiledExpression
-+ @ref YAPFlags
-+ @ref Grammars
-+ @ref Hacks
-+ @ref Listing
-+ @ref LoadForeign
-+ @ref Messages
-+ @ref YAPMetaPredicates
-+ @ref ModuleBuiltins
-+ @ref YAPOS
-+ @ref pathconf
-+ @ref YAPPredDecls
-+ @ref Database
-+ @ref The_Count_Profiler
-+ @ref QLY
-+ @ref Sets
-+ @ref Deb_Preds
-+ @ref Statistics
-+ @ref Tabling
-+ @ref Threads
-+ @ref TopLevel
-+ @ref Undefined_Procedures
-+ @ref MixBag
-+ @ref InputOutput
-+ @ref IO_Sockets
-+ @ref ypp
 
+	+ an argument with no preceding symbol can be used in both ways.

docs/md/extensions.md

@@ -4,18 +4,31 @@ Extensions to core Prolog.			{#extensions}
 YAP includes a number of extensions over the original Prolog
 language. Next, we discuss how to use the most important ones.
 
-  + @ref Rational_Trees
+	+ @ref Rational_Trees
 
-  + @ref AttributedVariables
+	+ @ref AttributedVariables
 
-  + @ref  DepthLimited
+	+ @ref  DepthLimited
 
-  + @ref  Tabling
+	+ @ref  Tabling
 
-  + @ref Threads
+	+ @ref Threads
 
-  + @ref Profiling
+	+ @ref Profiling
+
+	+ @ref YAPArrays
+
+	+ @ref Parallelism
+
+In the description of the arguments of predicates the following
+notation will be used:
+	
+	+ a preceding plus sign will denote an argument as an "input
+argument": the argument is read, not written, and it cannot be a free
+variable at the time of the call.
+	
+	+ a preceding minus sign will denote an "output argument";
+
+	+ an argument with no preceding symbol can be used in both ways.
 
-  + @ref YAPArrays
 
-  + @ref Parallelism

docs/md/library.md

@@ -1,61 +1,27 @@
 
-YAP Prolog Library                       {#library}
+YAP Prolog Library                       {#LibraryPage}
 ===================
 
 
- the library_directory path (set by the
+YAP provides a collection of Prolog utilities, that extend core Prolog
-  `LIBDIR` variable in the Makefile for YAP). Several files in the
+with data-structures such as balanced trees and hash tables, extend
-  library are originally from the public-domain Edinburgh Prolog library.
+Input Output, or use the `C`-interface to interact with the
+Operating System or to implement arrays.
+  
+These programs are stored at the library_directory path (set by the
+`LIBDIR` variable in the Makefile for YAP). 
 
-@tableofcontents
+The files have different sources. Many were part of the public-domain
+Edinburgh Prolog library. Other Prolog systems such as SWI-Prolog
+were kind enough to allow using files from their distributions.
+	
+
+@copydoc library
 
 
-+ @ref apply_stub
+@{
-+ @ref apply_macros
+
-+ @ref args
+@defgroup library The YAP Library
-+ @ref Association_Lists
+
-+ @ref sicsatts
+@}
-+ @ref avl
+
-+ @ref bhash
-+ @ref block_diagram
-+ @ref c_alarms
-+ @ref charsio
-+ @ref clauses
-+ @ref cleanup
-+ @ref dbqueues
-+ @ref dbusage
-+ @ref dgraphs
-+ @ref exo_interval
-+ @ref flags
-+ @ref gensym
-+ @ref yap_hacks
-+ @ref heaps
-+ @ref lam_mpi
-+ @ref line_utils
-+ @ref Log2MD
-+ @ref mapargs
-+ @ref maplist
-+ @ref matlab
-+ @ref matrix
-+ @ref nb
-+ @ref ordsets
-+ @ref parameters
-+ @ref queues
-+ @ref random
-+ @ref Pseudo_Random
-+ @ref rbtrees
-+ @ref readutil
-+ @ref regexp
-+ @ref rltrees
-+ @ref Splay_Trees
-+ @ref operating_system_support
-+ @ref Terms
-+ @ref timeout
-+ @ref trees
-+ @ref tries
-+ @ref ugraphs
-+ @ref undgraphs
-+ @ref varnumbers
-+ @ref wdgraphs
-+ @ref wgraphs
-+ @ref wundgraphs

docs/md/load_files.md

@@ -6,7 +6,7 @@ Loading and Organising YAP Programs    {#load_files}
 
   + @ref YAPConsulting
 
-  - @page modules
+  + @page modules
 
   + @ref YAPBigLoad
 

docs/md/modules.md

@@ -40,7 +40,8 @@ the type-in module permanently by using the built-in `module/1`.
 
 [TOC]
 
-## Explicit Naming                                    {#ExplicitNaming}
+Explicit Naming                                    {#ExplicitNaming}
++++++++++++++++
 
 The module system allows one to _explicitly_ specify the source mode for
 a clause by prefixing a clause with its module, say:
@@ -228,7 +229,8 @@ X = 2 ? ;
 
 The state of  the module system after this error is undefined.
 
-## BuiltIn predicates                                     {#ModuleBuiltins)
+BuiltIn predicates                                     {#ModuleBuiltins)
+++++++++++++++++++
 
 @\pred module(+ M:atom,+ L:list ) is directive
   the current file defines module _M_ with exports _L_. The list may include
@@ -298,7 +300,7 @@ the graphs library is implemented on top of the red-black trees library, and som
 Unfortunately it is still not possible to change argument order.
 
 
-\pred module(+ M:atom,+ L:list ) is directive
+@pred module(+ M:atom,+ L:list ) is directive
   the current file defines module _M_ with exports _L_. The list may include
 
   + predicate indicators

docs/md/syntax.md

@@ -1,6 +1,6 @@
-YAP Syntax                                  {#YAPSyntax}
+@defgroup YAPSyntax YAP Syntax
-============
 
+@{
 	@ingroup YAPProgrammming
 
 We will describe the syntax of YAP at two levels. We first will
@@ -9,6 +9,7 @@ the  tokens from which Prolog  terms are
 built.
 
 @defgroup Formal_Syntax Syntax of Terms
+@{
 @ingroup YAPSyntax
 
 Below, we describe the syntax of YAP terms from the different
@@ -82,19 +83,22 @@ paragraph). When a name consisting of a single dot could be taken for
 the end of term marker, the ambiguity should be avoided by surrounding the
 dot with single quotes.
 
+@}
+@defgroup Tokens Prolog Tokens
 
-
+@{
-# @defgroup Tokens Prolog Tokens
 @ingroup YAPSyntax
 
 Prolog tokens are grouped into the following categories:
 
-## @defgroup Numbers Numbers
+@defgroup Numbers Numbers
+@{
 @ingroup Tokens
 
 Numbers can be further subdivided into integer and floating-point numbers.
 
-### @defgroup  Integers Integers
+@defgroup  Integers Integers
+@{
 @ingroup Numbers
 
 Integer numbers
@@ -141,8 +145,10 @@ YAP (version 6.3.4) supports integers that can fit
 the word size of the machine. This is 32 bits in most current machines,
 but 64 in some others, such as the Alpha running Linux or Digital
 Unix. The scanner will read larger or smaller integers erroneously.
+@}
 
-### @defgroup  Floats Floats
+@defgroup  Floats Floats
+@}
 @ingroup Numbers
 
 Floating-point numbers are described by:
@@ -167,7 +173,10 @@ Examples:
 Floating-point numbers are represented as a double in the target
 machine. This is usually a 64-bit number.
 
-## Strings @defgroup  Strings Character Strings
+@}
+@}
+@defgroup  Strings Character Strings
+@{
 
 Strings are described by the following rules:
 
@@ -218,7 +227,7 @@ Escape sequences can be used to include the non-printable characters
 `f` (form feed), `t` (horizontal tabulation), `n` (new
 line), and `v` (vertical tabulation). Escape sequences also be
 include the meta-characters `\\`, `"`, `'`, and
-```. Last, one can use escape sequences to include the characters
+`''`. Last, one can use escape sequences to include the characters
 either as an octal or hexadecimal number.
 
 The next examples demonstrates the use of escape sequences in YAP:
@@ -237,7 +246,12 @@ versions of YAP up to 4.2.0. Escape sequences can be disabled by using:
 :- yap_flag(character_escapes,false).
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-## @addgroup Atoms Atoms
+@}
+
+@addtogroup Atoms Atoms
+
+@}
+
 @ingroup Tokens
 
 Atoms are defined by one of the following rules:
@@ -278,7 +292,10 @@ Version `4.2.0` of YAP removed the previous limit of 256
 characters on an atom. Size of an atom is now only limited by the space
 available in the system.
 
-## @addgroup Variables Variables
+@}
+
+ @addtogroup Variables Variables
+@{
 @ingroup Tokens
 
 Variables are described by:
@@ -299,7 +316,9 @@ variables are known as anonymous variables. Note that different
 occurrences of `_` on the same term represent <em>different</em>
 anonymous variables.
 
-## @addgroup Punctuation_Tokens Punctuation Tokens
+@}
+@addtogroup Punctuation_Tokens Punctuation Tokens
+@{
 @ingroup Tokens
 Punctuation tokens consist of one of the following characters:
 
@@ -309,7 +328,10 @@ Punctuation tokens consist of one of the following characters:
 
 These characters are used to group terms.
 
-@subsection LayoutComents Character Layout
+@}
+@defgroup LayoutComents Character Layout
+@{
+	@ingroup Tokens
 Any characters with ASCII code less than or equal to 32 appearing before
 a token are ignored.
 
@@ -321,8 +343,11 @@ layout characters, the YAP parser behaves as if it had found a
 single blank character. The end of a file also counts as a blank
 character for this purpose.
 
-## @addgroup WideChars Encoding Wide Character Support
+@}
-@ingroup YAPSyntax
+@}
+@addtogroup WideChars Encoding Wide Character Support
+@{
+	@ingroup YAPSyntax
 
 
 YAP now implements a SWI-Prolog compatible interface to wide
@@ -353,7 +378,8 @@ other software components using the foreign language interface. In this
 section we only deal with I/O through streams, which includes file I/O
 as well as I/O through network sockets.
 
-== @addtogroup Stream_Encoding Wide character encodings on streams
+@addtogroup Stream_Encoding Wide character encodings on streams
+@{
 @ingroup WideChars
 
 The UCS standard describes all possible characters (or code points, as they include
@@ -460,9 +486,10 @@ errors can be controlled using `open/4` or `set_stream/2` (not
 implemented). Initially the terminal stream write the characters using
 Prolog escape sequences while other streams generate an I/O exception.
 
-@{
+@}
 
 @addtogroup BOM BOM: Byte Order Mark
+@{
 @ingroup WideChars
 
 From Stream Encoding, you may have got the impression that
@@ -483,11 +510,10 @@ writing, writing a BOM can be requested using the option
 UTF-32; otherwise the default is not to write a BOM. BOMs are not avaliable for ASCII and
 ISO-LATIN-1.
 
-@{
+@}
-
-
 @}
  @addgroup Operators Summary of YAP Predefined Operators
+ @{
 @ingroup YapSyntax
 
 The Prolog syntax caters for operators of three main kinds:
@@ -567,3 +593,4 @@ The following is the list of the declarations of the predefined operators:
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 @}
+@}

docs/md/yap.md

@@ -60,43 +60,6 @@ Jan Wielemaker. We would also like to gratefully
 acknowledge the contributions from Ashwin Srinivasian.
 
 
-@page Library YAP Library
-
-
- the library_directory path (set by the
-  `LIBDIR` variable in the Makefile for YAP). Several files in the
-  library are originally from the public-domain Edinburgh Prolog library.
-
- 
-
-@page Extensions  YAP Extensions
-
-YAP includes a number of extensions over the original Prolog
-language.
-
-  + @subpage attributes.md
-
-  + @ref Rational_Trees
-  
-  + @ref CohYroutining
-
-  + @ref  DepthLimited
-
-  + @ref  Tabling
-
-  + @ref Threads
-
-  + @ref Profiling
-
-  + @ref YAPArrays
-
-  + @ref Parallelism
-
-
-@page YAPProgramming Programming in YAP
-
-
-@page packages Packages for YAP
 
 
   

library/lists.yap

@@ -48,7 +48,8 @@
 /**  
  * @{
  *
- * @addtogroup library The Prolog Library
+ * @addtogroup lists List Predicates in the Prolog Library
+ * @ingroup library  
  *
  * @brief  List Manipulation Predicates
  *

pl/consult.yap

@@ -91,7 +91,7 @@
 /**
 
   @defgroup YAPConsulting Loading files into YAP
-  @ingroup consult
+  @ingroup load_files
 
   @{
 
@@ -1322,7 +1322,7 @@ account the following observations:
   + In order to obtain efficient execution, YAP compiles
   dependencies between re-exported predicates. In practice, this means
   that changing a `reexport` declaration and then *just* recompiling
-  the file may result in incorrect execution. 
+  the file may result in incorrect execution.
 
 */
 '$reexport'( TOpts, File, Reexport, Imports, OldF ) :-

pl/corout.yap

@@ -41,14 +41,11 @@
 
 
 /**
- *  @defgroup attscorouts Implementing Attributed Variables and Co-Routining
+ *  @ingroup AttributedVariables_Builtins
- *
- *  @ingroup attributes
  *  @{
- *  @brief  Support for co-routining
+ *
-	*
+ *
-	*
+ */
-””	*/
 
 
 /** @pred attr_unify_hook(+ _AttValue_,+ _VarValue_)

pl/debug.yap

@@ -245,7 +245,9 @@ be lost.
 
 
  /**
-   *  ### Implementation
+   * @defgroup DebImplementation Implementation of the Debugger
+   * @{
+   * @brief Prolog code to do debugging.
    *
    * The debugger is an interpreter. with main predicates:
    * - $trace: this is the API
@@ -256,7 +258,7 @@ be lost.
    *    + asking Prolog to do it (system_library-builtins)
    *
    *	|flag	        | description	| initial | possible values
-   *       ----------------------------------------------------------------
+   *    |   ----------------------------------------------------------------
    *	| spy_gn	| last goal number 	| 1	| 1...
    *	| spy_trace	| trace	 		| 0	| 0, 1
    *	| spy_status	| step	 	 	| creep	| creep,leap,skip
@@ -395,7 +397,7 @@ be lost.
 %% @pred '$trace_query'( +G, +M, +CP, +Expanded)
 %
 % debug a complex query
-% 
+%
 '$trace_query'(V, M, CP, _, '$trace'([M|V],CP)) :-
 	var(V), !.
 '$trace_query'(!, _, CP, _, '$$cut_by'(CP)) :-
@@ -496,13 +498,13 @@ be lost.
 
 /**
  * @pred '$enter_trace'(+L, 0:G, +Module, +Info)
- * 
+ *
  * call goal: prelims
- *  
+ *
- * @parameter _Module_:_G_ 
+ * @parameter _Module_:_G_
  * @parameter _L_ is the list of active goals
  * @parameter _Info_ describes the goal
- * 
+ *
  */
 '$enter_trace'(L, G, Module, Info) :-
         /* get goal no.	*/
@@ -533,16 +535,16 @@ be lost.
 
 /**
  * @pred '$enter_trace'(+L, 0:G, +Module, +Info)
- * 
+ *
  * call goal: setup the diferrent cases
  *  - zip, just run through
  *  - source, call an interpreter
  *  - compiled code: try black magic.
- *  
+ *
- * @parameter _Module_:_G_ 
+ * @parameter _Module_:_G_
  * @parameter _GoalNumber_ identifies the active goal
  * @parameter _Info_ describes the goal
- * 
+ *
  */
 '$debug'(_, G, M, _H) :-
         '__NB_getval__'('$debug_status',state(zip,_Border,_), fail),
@@ -558,16 +560,16 @@ be lost.
 
 /**
  * @pred '$trace_go'(+L, 0:G, +Module, +Info)
- * 
+ *
  * It needs to run in two separate steps:
  *    1. Select a clause;
  *    2. Debug it.
  * We use a marker to track who we are in gated_call.
- *  
+ *
- * @parameter _Module_:_G_ 
+ * @parameter _Module_:_G_
  * @parameter _GoalNumber_ identifies the active goal
  * @parameter _Info_ describes the goal
- * 
+ *
  */
 '$trace_go'(GoalNumber, G, M, Info) :-
 		X=marker(_,M,G),
@@ -1065,3 +1067,6 @@ be lost.
 '$creep'(creep) :- '$creep'.
 '$creep'(leap) :- '$creep'.
 '$creep'(zip).
+
+%% @}
+%% @}

pl/directives.yap

@@ -23,7 +23,8 @@
   * @brief  Control File Loading
   %
   % @defgroup Directives Prolog Directives
-  @ @ingroup consult
+  * @ingroup YAPConsulting
+  * @{
   *
   *
 */
@@ -279,3 +280,5 @@ user_defined_directive(Dir,Action) :-
       !.
   '$process_directive'(G, _Mode, M, _VL, _Pos) :-
       format(user_error,':- ~w:~w failed.~n',[M,G]).
+
+%% @}

pl/error.yap

@@ -26,7 +26,7 @@
 
 /**
  @defgroup SWI-error High-level error testing.
-@ingroup YAPError
+@ingroup builtins
 
 This  SWI module  provides  predicates  to  simplify  error  generation  and
 checking. Adapted to use YAP built-ins.

pl/init.yap

@@ -14,7 +14,17 @@
 * comments:	initializing the full prolog system			 *
 *									 *
 *************************************************************************/
+/**
+ * @file init.yap
+ *
+ * @brief how to boot and run the top-level.
+ *
+*/
 
+/**
+ * @insection YAPControl
+ *
+*/
 
 '$init_globals' :-
 	% set_prolog_flag(break_level, 0),

pl/load_foreign.yap

@@ -29,7 +29,7 @@
 /**
 
 @defgroup LoadForeign Access to Foreign Language Programs
-@ingroup fli_c_cx
+@ingroup fli_c_cxx
 
 @{
 

pl/metadecls.yap

@@ -4,9 +4,11 @@
   * @author VITOR SANTOS COSTA <vsc@vcosta-laptop.dcc.fc.up.pt>
   * @date   Sat Apr  7 03:08:03 2018
   *
-  * @brief  meta=declarations to run early.
+  * @brief  meta=declarations, must be run early.
   *
+  *   @addtogroup Meta-Calls The Module System versus the meta-call.
   *   @ingroup YAPMetaPredicates
+  *   @{
   *
 */
 
@@ -99,3 +101,5 @@
 			      ->(2,2,?,?),
 			      \+(2,?,?),
 			      \+( 0 )]).
+
+@}

pl/qly.yap

@@ -19,7 +19,7 @@
 
 /**
 @defgroup QLY Creating and Using a saved state
-@ingroup YAPConsulting
+@ingroup load_files
 @{
 */
 

pl/spy.yap

@@ -1,4 +1,8 @@
-:- system_module( '$_debug', [debug/0,
+/**
+ * @file spy.yap
+ * @brief debugger operation.
+ */
+  :- system_module( '$_debug', [debug/0,
         debugging/0,
         leash/1,
         nodebug/0,
@@ -27,8 +31,9 @@
 
 -----------------------------------------------------------------------------*/
 
-/** @defgroup Deb_Preds Debugging Predicates
+/**
-@ingroup builtins
+ * @defgroup DebSet Debugger Control
+ * @ingroup builtins Deb_Interaction
 
 @{
 The
@@ -39,10 +44,7 @@ programs:
 
     Switches the debugger on.
 
-+ debuggi=
++ debugging
-r
-
-g
 
 
     Outputs status information about the debugger which includes the leash
@@ -50,7 +52,6 @@ mode and the existing spy-points, when the debugger is on.
 
 + nodebug
 
-
     Switches the debugger off.