doc changes

docs/doxsmall.rc

@@ -367,7 +367,7 @@ SUBGROUPING = YES
 # SEPARATE_MEMBER_PAGES.
 # The default value is: NO.
 
-INLINE_GROUPED_CLASSES = NO
+INLINE_GROUPED_CLASSES = YES
 
 # When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
 # with only public data fields or simple typedef fields will be shown inline in
@@ -551,7 +551,7 @@ SORT_MEMBER_DOCS = YES
 # this will also influence the order of the classes in the class list.
 # The default value is: NO.
 
-SORT_BRIEF_DOCS = NO
+SORT_BRIEF_DOCS = YES
 
 # If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
 # (brief and detailed) documentation of class members so that constructors and
@@ -563,7 +563,7 @@ SORT_BRIEF_DOCS = NO
 # detailed member documentation.
 # The default value is: NO.
 
-SORT_MEMBERS_CTORS_1ST = NO
+SORT_MEMBERS_CTORS_1ST = yes
 
 # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
 # of group names into alphabetical order. If set to NO the group names will
@@ -655,7 +655,7 @@ SHOW_FILES = YES
 # Folder Tree View (if specified).
 # The default value is: YES.
 
-SHOW_NAMESPACES = NO
+SHOW_NAMESPACES = YES
 
 # The FILE_VERSION_FILTER tag can be used to specify a program or script that
 # doxygen should invoke to get the current version for each file (typically from
@@ -771,7 +771,6 @@ WARN_LOGFILE =
 
 INPUT = foreigns.yap docs/yap.md pl swi C H include os packages library CXX OPTYap
 
-
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
 # libiconv (or the iconv built into libc) for the transcoding. See the libiconv
@@ -1602,7 +1601,7 @@ MAKEINDEX_CMD_NAME = makeindex
 # The default value is: NO.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-COMPACT_LATEX = NO
+COMPACT_LATEX = YES
 
 # The PAPER_TYPE tag can be used to set the paper type that is used by the
 # printer.
@@ -1723,7 +1722,9 @@ GENERATE_RTF = NO
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
 # it.
 # The default directory is: rtf.
-# This tag requires that the tag GENERATE_RTF is set to YES.
+# This tag requires that the tag GENERATE_RTb
+
+F is set to YES.
 
 RTF_OUTPUT = rtf
 

packages/ProbLog/problog.yap

@@ -252,7 +252,7 @@ You can also use the CUDD interface package in YAP. You will need to
 
 2. If a Mac user, there is a ports package.  
 
-3 Otherwise, you can obtain the version at . This version compiles under WIN32.
+3. Otherwise, you can obtain the version at . This version compiles under WIN32.
 
 Last, when you configure YAP you need to add the options --with-cidd --enable-bddlib. Binary distributed versions already have the interface.
 
@@ -291,8 +291,10 @@ Instead of probabilities every fact has a t( ) prefix. The t stands for tunable
 ~~~~
 t(0.5)::heads(_).
 ~~~~
+*/
 
-### ProbLog Predicates
+/** @defgroup ProbLogPredicates ProbLog Predicates
+@ingroup ProbLog1
 
 This chapter describes the predicates defined by ProbLog for evaluating the probability of queries.
 
@@ -347,8 +349,12 @@ This predicate returns the lower and upper bound of the probability of achieving
 This predicate returns the lower bound of the probability of achieving the goal G obtained by cutting the sld tree at the given probability for each branch.
 */
 
+%% @}
+
 /**
-### ProbLog Parameter Learning Predicates
+@defgroup ProbLogParameterLearning ProbLog Parameter Learning Predicates
+@ingroup ProbLog1
+@{
 */
 
 /**
@@ -371,7 +377,7 @@ Test examples are ignored during learning but are used afterwards to check the p
  * @pred do_learning(+N).
  *
 Starts the learning algorithm with N iterations.
-paragraph{}
+
 */
 
 /**
@@ -381,7 +387,15 @@ The output is created in the output subfolder of the current folder where YAP wa
 
 Starts the learning algorithm. The learning will stop after N iterations or if the difference of the Mean Squared Error (MSE) between two iterations gets smaller than Epsilon - depending on what happens first.
 
-### Miscelaneous
+*/
+
+%% @}
+
+
+/** @defgroup ProbLogMiscellaneous ProbLog Miscellaneous Predicates
+@ingroup ProbLog1
+@{
+
 
 Both the learning and the inference module have various parameters, or flags, that can be adjusted by the user.
 The following predicates are defined by ProbLog to access and set these flags.
@@ -395,11 +409,9 @@ This predicate lists all the flags name, value, domain and description.
 */
 
 
-/**
+/**  @pred problog_flag(+Name, -Value)
- * @pred problog_flag(+Name, -Value)
- *
-This predicate gives the value of the flag with the specified name. The supported flags are:
 
+This predicate gives the value of the flag with the specified name. The supported flags are:
 
 + use_db_trie
 
@@ -461,7 +473,7 @@ The possible values for this flag are true or false.
     Flag that sets the representation of the ancestor list.
 The possible values for this flag are list or integer
 
-+ max\cccccccccccc_depth
++ max_depth
 
     Sets the maximum proof depth.
 The possible values for this flag are any integer.
@@ -478,8 +490,7 @@ The possible values for this flag are any integer greater than zero.
 
 + min_mc_samples
 
-    Flag related to Monte Carlo Sampling that sets the minimum number of samples before convergence.
+    Flag related to Monte Carlo Sampling that sets the minimum number of samples before convergence. The possible values for this flag are any integer greater than or equal to zero.
-The possible values for this flag are any integer greater than or equal to zero.
 
 + max_mc_samples
 
@@ -591,6 +602,8 @@ The possible values for this flag are true or false.
     Flag telling the location of the output files directory.
 The possible values for this flag are any valid directory name.
 
+*/
+
 /** @pred set_problog_flag(+Name, +Value)
 
 the predicate sets the value of the given flag. The supported flags are the ones listed in above
@@ -601,7 +614,7 @@ the predicate sets the value of the given flag. The supported flags are the ones
 the predicate sets the value of the given flag. The supported flags are the ones listed in above
 */
 
-/** @pred learning_flag(+Name, -Value)}
+/** @pred learning_flag(+Name, -Value)
 
 This predicate gives the value of the learning flag with the specified name. The supported flags are:
 

packages/myddas/pl/myddas.ypp

@@ -146,10 +146,11 @@ statistics from the MYDDAS system;
     This option is only available in MySQL.  It enables the option to interact with the MySQL server in
 two different ways. As if we were on the MySQL Client Shell, and as if
 we were using Datalog. 
-@}
 
 */
 
+%% @}
+
 /** @defgroup MYDDAS_Architecture MYDDAS Architecture
 @ingroup MYDDAS
 @{
@@ -202,15 +203,18 @@ FROM 'phonebook' A
 WHERE A.Name = 'John Doe';
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-@}
-
-
 */
 
+%% @}
+
+
 /** @defgroup View_Level_Interface View Level Interface
 @ingroup MYDDAS
 @{
 
+*/
+
+/**
  @pred db view(+,+,+). 
 
 
@@ -302,16 +306,17 @@ FROM Edge A WHERE A.attr1 = 10;
 To know how to use db `view/3`, please refer to Draxler's Prolog to
 SQL Compiler Manual. 
 
-@}
-
-
 */
 
+%% @}
+
 /** @defgroup Accessing_Tables_in_Data_Sources_Using_SQL Accessing Tables in Data Sources Using SQL 
 @ingroup MYDDAS
 @{
 
- @pred db_sql(+,+,?).  
+*/
+
+/** @pred db_sql(+,+,?).  
 
 
 
@@ -336,12 +341,17 @@ Example:
 LA = ['D','John Doe',123456789] ?
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-@section Insertion_of_Rows Insertion of Rows 
+*/
 
- @pred db_assert(+,+).  
+%% @}
 
+/** @defgroup Insertion_of_Rows Insertion of Rows
+@ingroup MYDDAS
+@{
 
+*/
 
+/** @pred db_assert(+,+).  
  @pred db_assert(+).
 
 
@@ -385,10 +395,9 @@ yes
 Would insert the row: `A,null value,31` into the relation
 `Hello World`, assuming that the second row allows null values.
 
- @pred db insert(+,+,+).  
+*/
-
-
 
+/** @pred db insert(+,+,+).  
  @pred db insert(+,+).  
 
 
@@ -412,15 +421,17 @@ yes
 yes
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-@}
-
 */
 
+%% @}
+
 /** @defgroup  Types_of_Attributes Types of AttributesL 
 @ingroup MYDDAS
 @{
 
- @pred db_get_attributes_types(+,+,?). 
+*/
+
+/** @pred db_get_attributes_types(+,+,?). 
 
 
 
@@ -448,20 +459,18 @@ yes
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 where <tt>Hello World</tt> is the name of the relation and <tt>myddas</tt> is the
 connection identifier. 
-
-
-@}
-
 */
 
+%% @}
+
+
 /** @defgroup  Number_of_Fields Number of Fields 
 @ingroup MYDDAS
 @{
 
- @pred db_number_of_fields(+,?). 
+*/
-
-
 
+/** @pred db_number_of_fields(+,?). 
  @pred db_number_of_fields(+,+,?).
 
 
@@ -486,18 +495,18 @@ where `Hello World` is the name of the
 relation and `myddas` is the connection identifier.
 
 
-@}
-
 */
 
+%% @}
+
+
 /** @defgroup  Describing_a_Relation Describing a Relation
 @ingroup MYDDAS
 @{
 
- @pred db_datalog_describe(+,+). 
+*/
-
-
 
+/** @pred db_datalog_describe(+,+). 
  @pred db_datalog_describe(+).
 
 
@@ -518,7 +527,9 @@ command, the same way as `DESCRIBE` in the MySQL prompt would.
 yes
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
- @pred db_describe(+,+). 
+*/
+
+/** @pred db_describe(+,+). 
 
 
 
@@ -538,15 +549,17 @@ no
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 
-@}
-
 */
+%% @}
+
 
 /** @defgroup Enumerating_Relations Enumeration Relations Describing_a_Relation Describing a Relation
 @ingroup MYDDAS
 @{
 
- @pred db_datalog_show_tables(+).
+*/
+
+/** @pred db_datalog_show_tables(+).
  @pred db_datalog_show_tables
 
 
@@ -565,7 +578,9 @@ it does not returns any value, but instead prints to the screen the result of th
 yes
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
- @pred db_show_tables(+, ?). 
+*/
+
+/** @pred db_show_tables(+, ?). 
 
 
 
@@ -584,19 +599,19 @@ Table = table('Hello World') ? ;
 no
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-@}
-
 */
 
+%%@}
+
+
 /** @defgroup  The_MYDDAS_MySQL_Top_Level The MYDDAS MySQL Top Level
 @ingroup MYDDAS
 @{
 
+*/
 
+/**
  @pred db_top_level(+,+,+,+,+).  
-
-
-
  @pred db_top_level(+,+,+,+).
 
 
@@ -644,18 +659,19 @@ Bye
 yes
 ?- 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-@}
-
 */
 
+%%@}
+
+
 /** @defgroup   Other_MYDDAS_Properties Other MYDDAS Properties 
 @ingroup MYDDAS
 @{
 
+*/
 
-
+/**
 @pred db_verbose(+). 
- @pred db_top_level(+,+,+,+).
 
 
 When we ask a question to YAP, using a predicate asserted by
@@ -670,8 +686,16 @@ yes
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 If we want to
 disable this feature, we must call the `db_verbose/1` predicate with the value 0.
+\
+*/
 
- @pred db_module(?).  
+/**
+ @pred db_top_level(+,+,+,+).
+
+
+*/
+
+/** @pred db_module(?).  
 
 
 
@@ -707,11 +731,9 @@ yes
  ?-
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
- @pred db_my_result_set(?). 
+*/
-
-
-
 
+/** @pred db_my_result_set(?). 
 
 The MySQL C API permits two modes for transferring the data generated by
 a query to the client, in our case YAP. The first mode, and the default
@@ -736,7 +758,9 @@ After this command, all
 of the database predicates will use use result by default. We can change
 this by doing again `db_my_result_set(store_result)`.  
 
- @pred db_my_sql_mode(+Conn,?SQL_Mode). 
+*/
+
+/** @pred db_my_sql_mode(+Conn,?SQL_Mode). 
 
 
 
@@ -758,6 +782,8 @@ You can see the available SQL Modes at the MySQL homepage at
 
 */
 
+%% @}
+
 #ifdef MYDDAS_TOP_LEVEL
 :- use_module(myddas_top_level,[
 				db_top_level/4,

pl/boot.yap

@@ -24,25 +24,8 @@
 */
 
 
-/** @pred   :_P_ , :_Q_   is iso 
-
-
-Conjunction of goals (and).
-
-Example:
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- p(X) :- q(X), r(X).
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-should be read as "p( _X_) if q( _X_) and r( _X_)".
-
- 
-*/
 
 /** @pred   :_P_ ; :_Q_  is iso
-
-
 Disjunction of goals (or).
 
 Example:
@@ -56,7 +39,7 @@ should be read as "p( _X_) if q( _X_) or r( _X_)".
 */
 
 /** @pred  \+ :_P_  is iso
-
+Negation by failure.
 
 Goal  _P_ is not provable. The execution of this predicate fails if
 and only if the goal  _P_ finitely succeeds. It is not a true logical
@@ -65,12 +48,19 @@ negation, which is impossible in standard Prolog, but
 
 This predicate might be defined as:
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~
  \+(P) :- P, !, fail.
  \+(_).
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~
 if  _P_ did not include "cuts".
 
+If _P_ includes cuts, the cuts are defined to be scoped by _P_: they canno cut over the calling prredicate.
+
+ ~~~~~~~~~~~~
+  go(P).
+          :- \+ P, !, fail.
+  \+(_).
+ ~~~~~~~~~~~~
 
 */
 
@@ -89,7 +79,7 @@ versions of YAP. Uses of not/1 should be replaced by
 
 
 
-/** @pred   :_P_ -> :_Q_ is iso 
+/** @pred   :_Condition__ -> :_Action_  is iso
 
 
 Read as "if-then-else" or "commit". This operator is similar to the
@@ -137,13 +127,18 @@ arguments.
 
 */
 
-/** @pred    :_Condition_ *-> :_Action_  
+/** @pred    :_Condition_ *-> :_Action_ is iso
 
 This construct implements the so-called <em>soft-cut</em>. The control is
-defined as follows: If  _Condition_ succeeds at least once, the
+defined as follows:
-semantics is the same as ( _Condition_,  _Action_). If
+  + If  _Condition_ succeeds at least once, the
+semantics is the same as ( _Condition_,  _Action_).
+
+  + If
  _Condition_ does not succeed, the semantics is that of (\\+
- _Condition_,  _Else_). In other words, If  _Condition_
+ _Condition_,  _Else_).
+
+ In other words, if  _Condition_
 succeeds at least once, simply behave as the conjunction of
  _Condition_ and  _Action_, otherwise execute  _Else_.
 
@@ -219,11 +214,7 @@ private(_).
 %
 % boootstrap predicates.
 %
-:- system_module( '$_boot', [(*->)/2,
+:- system_module( '$_boot', [
-        (',')/2,
-        (->)/2,
-        (;)/2,
-        (\+)/1,
         bootstrap/1,
         call/1,
         catch/3,
@@ -234,8 +225,7 @@ private(_).
         (not)/1,
         repeat/0,
         throw/1,
-        true/0,
+        true/0], ['$$compile'/4,
-        ('|')/2], ['$$compile'/4,
         '$call'/4,
         '$catch'/3,
         '$check_callable'/2,
@@ -299,8 +289,9 @@ private(_).
 %
 %
 %
-/** @pred  true is iso 
 
+/** @pred true is iso
+Succeed.
 
 Succeeds once.
 
@@ -1137,6 +1128,19 @@ incore(G) :- '$execute'(G).
 	'$stop_creeping'.
 
 
+/** @pred   :_P_ , :_Q_   is iso, meta
+Conjunction of goals (and).
+
+The conjunction is a fundamental construct of Prolog. Example:
+
+~~~~~~~
+ p(X) :- q(X), r(X).
+~~~~~~~
+
+should be read as `p( _X_) if q( _X_) and r( _X_).
+
+
+*/
 ','(X,Y) :-
 	yap_hacks:env_choice_point(CP),
 	'$current_module'(M),
@@ -1576,4 +1580,3 @@ log_event( String, Args ) :-
 /**
 @}
 */
-

pl/modules.yap

@@ -1506,6 +1506,17 @@ import_module(Mod, ImportModule) :-
 import_module(Mod, EM) :-
 	'$do_error'(type_error(atom,Mod),import_module(Mod, EM)).
 
+
+/** add_import_module( + _Module_, + _ImportModule_ , +_Pos_) is det
+Add all exports in _ImportModule_ as available to _Module_.
+
+    
+All exported predicates from _ExportModule_ are made available to the 
+ source  module _ImportModule_. If _Position_ is bound to `start` the 
+ module _ImportModule_ is tried first, if _Position_ is bound to `end`, 
+ the module is consulted last.
+
+*/
 add_import_module(Mod, ImportModule, Pos) :-
 	var(Mod),
 	'$do_error'(instantiation_error,add_import_module(Mod, ImportModule, Pos)).
@@ -1526,6 +1537,14 @@ add_import_module(Mod, ImportModule, Pos) :-
 add_import_module(Mod, ImportModule, Pos) :-
 	'$do_error'(domain_error(start_end,Pos),add_import_module(Mod, ImportModule, Pos)).
 
+/** delete_import_module( + _ExportModule_, + _ImportModule_ ) is det
+Exports in _ImportModule_ are no longer available to _Module_.
+
+    
+All exported predicates from _ExportModule_ are discarded from the 
+ ones used vy the source  module _ImportModule_.
+
+*/
 delete_import_module(Mod, ImportModule) :-
 	var(Mod),
 	'$do_error'(instantiation_error,delete_import_module(Mod, ImportModule)).
@@ -1548,6 +1567,21 @@ delete_import_module(Mod, ImportModule) :-
 '$set_source_module'(Source0, SourceF) :-
 	current_module(Source0, SourceF).
 
+/** module_property( + _Module_, ? _Property_ ) is nondet
+Enumerate non-deterministically the main properties of _Module_ .
+
+Reports the following properties of _Module_:
+
+  + `class`( ?_Class_ ): whether it is a `system`, `library`, or `user` module.
+
+  + `line_count`(?_Ls_): number of lines in source file.
+
+  + `file`(?_F_): source file for _Module_.
+
+  + `exports`(-Es): list of all predicate symbols and
+   operator symbols exported or re-exported by this module.
+
+*/
 module_property(Mod, class(L)) :-
 	'$module_class'(Mod, L).
 module_property(Mod, line_count(L)) :-