diff --git a/C/dbase.c b/C/dbase.c
index 9bbc370fa..57e52a05f 100644
--- a/C/dbase.c
+++ b/C/dbase.c
@@ -33,8 +33,9 @@ static char SccsId[] = "%W% %G%";
 
 
 /** @defgroup Internal_Database Internal Data Base
-@ingroup builtins
-@{
+
+    @ingroup builtins
+    @{
 
 Some programs need global information for, e.g. counting or collecting
 data obtained by backtracking. As a rule, to keep this information, the
diff --git a/os/iopreds.c b/os/iopreds.c
index f526e122b..01e2406f8 100644
--- a/os/iopreds.c
+++ b/os/iopreds.c
@@ -1237,10 +1237,11 @@ static Int do_open(Term file_name, Term t2, Term tlist USES_REGS) {
   encoding_t encoding;
   Term tenc;
   char io_mode[8];
-  file_name = Deref( file_name);
-      if (IsVarTerm(file_name)) {
-      Yap_ThrowError(INSTANTIATION_ERROR, file_name, "while opening a list of options");
-    }
+  file_name = Deref(file_name);
+  if (IsVarTerm(file_name)) {
+    Yap_ThrowError(INSTANTIATION_ERROR, file_name,
+                   "while opening a list of options");
+  }
   // open mode
   if (IsVarTerm(t2)) {
     Yap_Error(INSTANTIATION_ERROR, t2, "open/3");
@@ -1583,18 +1584,19 @@ int Yap_OpenStream(Term tin, const char *io_mode, Term user_name,
         vfsp->open(vfsp, fname, io_mode, sno)) {
       // read, write, append
       user_name = st->user_name;
+      st->vfs = vfsp;
       UNLOCK(st->streamlock);
     } else {
       st->file = fopen(fname, io_mode);
       if (st->file == NULL) {
-	UNLOCK(st->streamlock);
-	if (errno == ENOENT && !strchr(io_mode, 'r')) {
-	  PlIOError(EXISTENCE_ERROR_SOURCE_SINK, tin, "%s: %s", fname,
-		    strerror(errno));
-	} else {
-	  PlIOError(PERMISSION_ERROR_OPEN_SOURCE_SINK, tin, "%s: %s", fname,
-                  strerror(errno));
-	}
+        UNLOCK(st->streamlock);
+        if (errno == ENOENT && !strchr(io_mode, 'r')) {
+          PlIOError(EXISTENCE_ERROR_SOURCE_SINK, tin, "%s: %s", fname,
+                    strerror(errno));
+        } else {
+          PlIOError(PERMISSION_ERROR_OPEN_SOURCE_SINK, tin, "%s: %s", fname,
+                    strerror(errno));
+        }
       }
       st->vfs = NULL;
     }
@@ -1644,9 +1646,9 @@ int Yap_OpenStream(Term tin, const char *io_mode, Term user_name,
       Yap_ThrowError(DOMAIN_ERROR_SOURCE_SINK, tin, "open");
     }
   }
-    if (!strchr(io_mode, 'b') && binary_file(fname)) {
-      flags |= Binary_Stream_f;
-    }
+  if (!strchr(io_mode, 'b') && binary_file(fname)) {
+    flags |= Binary_Stream_f;
+  }
   Yap_initStream(sno, st->file, fname, io_mode, user_name, LOCAL_encoding,
                  flags, vfsp);
   __android_log_print(ANDROID_LOG_INFO, "YAPDroid", "exists %s <%d>", fname,
@@ -1761,8 +1763,8 @@ int Yap_CheckTextStream__(const char *file, const char *f, int line, Term arg,
   return sno;
 }
 
-int Yap_CheckTextWriteStream__(const char *file, const char *f, int line, Term arg,
-   const char *msg) {
+int Yap_CheckTextWriteStream__(const char *file, const char *f, int line,
+                               Term arg, const char *msg) {
   int sno, kind = Output_Stream_f;
   if ((sno = CheckStream__(file, f, line, arg, kind, msg)) < 0)
     return -1;
@@ -1779,8 +1781,8 @@ int Yap_CheckTextWriteStream__(const char *file, const char *f, int line, Term a
   return sno;
 }
 
-int Yap_CheckTextReadStream__(const char *file, const char *f, int line, Term arg,
-    const char *msg) {
+int Yap_CheckTextReadStream__(const char *file, const char *f, int line,
+                              Term arg, const char *msg) {
   int sno, kind = Input_Stream_f;
   if ((sno = CheckStream__(file, f, line, arg, kind, msg)) < 0)
     return -1;
diff --git a/packages/python/pyio.c b/packages/python/pyio.c
index b7c1950d0..28cf54a04 100644
--- a/packages/python/pyio.c
+++ b/packages/python/pyio.c
@@ -10,9 +10,8 @@ YAP_Term TermErrStream, TermOutStream;
 
 static unsigned char *outbuf, *errbuf;
 
-static void  pyflush( StreamDesc *st)
-{
-  #if 0
+static void pyflush(StreamDesc *st) {
+#if 0
   st->u.w_irl.ptr[0] = '\0';
   fprintf(stderr,"%s\n", st->u.w_irl.buf);
   term_t tg = python_acquire_GIL();
@@ -20,12 +19,11 @@ static void  pyflush( StreamDesc *st)
     PySys_WriteStdout("%s", st->u.w_irl.buf);
   } else {
     PySys_WriteStderr("%s", st->u.w_irl.buf);
-    
+
   }
   python_release_GIL(tg);
   st->u.w_irl.ptr =   st->u.w_irl.buf;
-  #endif
-      
+#endif
 }
 
 static int py_putc(int sno, int ch) {
@@ -43,7 +41,7 @@ static int py_putc(int sno, int ch) {
      }
         return ch;
   }
-  #endif
+#endif
   char s[2];
   PyObject *err;
   s[0] = ch;
@@ -96,31 +94,27 @@ static void *py_open(VFS_t *me, const char *name, const char *io_mode,
     //  } else if (strcmp(name, "input") == 0) {
     //pystream = PyObject_Call(pystream, PyTuple_New(0), NULL);
     } else */
-  {
-    st->user_name = YAP_MkAtomTerm(st->name);
-  }
-    st->u.private_data = pystream;
+  { st->user_name = YAP_MkAtomTerm(st->name); }
+  st->u.private_data = pystream;
   st->vfs = me;
   st->file = NULL;
   python_release_GIL(ctk);
   return st;
 }
 
-
 static void py_flush(int sno) {
   StreamDesc *s = YAP_GetStreamFromId(sno);
   term_t tg = python_acquire_GIL();
   PyObject *flush = PyObject_GetAttrString(s->u.private_data, "flush");
-   pyflush(s);
+  pyflush(s);
   PyObject_CallFunction(flush, NULL);
   python_release_GIL(tg);
 }
 
-
 static bool py_close(int sno) {
   StreamDesc *st = YAP_RepStreamFromId(sno);
-  if (st->status & (Output_Stream_f|Append_Stream_f))
-  py_flush(sno);
+  if (st->status & (Output_Stream_f | Append_Stream_f))
+    py_flush(sno);
   if (strcmp(st->name, "sys.stdout") && strcmp(st->name, "sys.stderr")) {
     Py_XDECREF(st->u.private_data);
     st->u.w_irl.buf = st->u.w_irl.ptr = NULL;
@@ -137,13 +131,14 @@ static bool getLine(int inp) {
   term_t ctk = python_acquire_GIL();
   Py_ssize_t size;
   PyObject *prompt = PyUnicode_FromString("?- "),
-           *msg = PyUnicode_FromString(" **input** ");
+           *msg = PyUnicode_FromString(" **input** "),
+           *o = PyObject_GetAttrString(rl_iostream->u.private_data, "read");
   /* window of vulnerability opened */
-  myrl_line = PyUnicode_AsUTF8AndSize(PyObject_CallFunctionObjArgs(
-								   rl_instream->u.private_data, msg, prompt, NULL), &size);
+  myrl_line = PyUnicode_AsUTF8AndSize(
+      PyObject_CallFunctionObjArgs(o, msg, prompt, NULL), &size);
   python_release_GIL(ctk);
   rl_instream->u.irl.ptr = rl_instream->u.irl.buf =
-    (const unsigned char *)malloc(size);
+      (const unsigned char *)malloc(size);
   memcpy((void *)rl_instream->u.irl.buf, myrl_line, size);
   return true;
 }
diff --git a/packages/python/yap_kernel/yap_ipython/prolog/jupyter.yap b/packages/python/yap_kernel/yap_ipython/prolog/jupyter.yap
index abbf43f96..abc85b04e 100644
--- a/packages/python/yap_kernel/yap_ipython/prolog/jupyter.yap
+++ b/packages/python/yap_kernel/yap_ipython/prolog/jupyter.yap
@@ -26,13 +26,13 @@
 jupyter_query(Caller, Cell, Line ) :-
 	jupyter_cell(Caller, Cell, Line).
 
-jupyter_cell(_Caller, Cell, _) :-
+jupyter_cell(_Caller, Cell, _Line) :-
 	jupyter_consult(Cell),	%stack_dump,
 	fail.
+jupyter_cell( _Caller, _, '' ) :- !.
 jupyter_cell( _Caller, _, Line ) :-
 	blank( Line ),
 	!.
-jupyter_cell( _Caller, _, '' ) :- !.
 jupyter_cell( Caller, _, Line ) :-
 	Self := Caller.query,
 		       python_query(Self,Line).
@@ -54,19 +54,13 @@ jupyter_consult(Text) :-
 jupyter_consult(Cell) :-
 %	Name = 'Inp',
 %	stream_property(Stream, file_name(Name) ),
-	setup_call_cleanup(
+%	setup_call_cleanup(
   open_mem_read_stream( Cell, Stream),
-  load_files(user:'jupyter cell',[stream(Stream)]),
-	close(Stream)
-  ).
+  load_files(user:'jupyter cell',[stream(Stream)]).
 
 blank(Text) :-
 	atom_codes(Text, L),
-	maplist( blankc, L).
-
-blankc(' ').
-blankc('\n').
-blankc('\t').
+	maplist( code_type(space), L).
 
 :- dynamic cell_stream/1.
 
diff --git a/pl/arith.yap b/pl/arith.yap
index 533f1c2db..ab4a3f264 100644
--- a/pl/arith.yap
+++ b/pl/arith.yap
@@ -36,6 +36,7 @@
 
 /** @defgroup CompilerAnalysis Internal Clause Rewriting
     @ingroup YAPCompilerSettings
+    @{
 
   YAP supports several clause optimisation mechanisms, that
   are designed to improve execution of arithmetic
@@ -59,7 +60,6 @@
 
 */
 
-%% @{
 
 /** @pred expand_exprs(- _O_,+ _N_)
 	Control term expansion during compilation.
diff --git a/pl/arithpreds.yap b/pl/arithpreds.yap
index d06964a82..033cfdb97 100644
--- a/pl/arithpreds.yap
+++ b/pl/arithpreds.yap
@@ -15,14 +15,13 @@
 *									 *
 *************************************************************************/
 
-%% @{
 
 /**
   @file arithpreds.yap
 
   @addtogroup arithmetic_preds
 
-
+ @{
 */
 
 :- system_module(arithmetic_predicates, [
diff --git a/pl/atoms.yap b/pl/atoms.yap
index 14d21737a..1e2bc621b 100644
--- a/pl/atoms.yap
+++ b/pl/atoms.yap
@@ -26,7 +26,7 @@
 
 /**
  * @addtogroup Predicates_on_Atoms
- *
+ * @{
 */
 
 /** @pred  atom_concat(+ As, ? A)
diff --git a/pl/boot.yap b/pl/boot.yap
index 5173424ca..794583e36 100644
--- a/pl/boot.yap
+++ b/pl/boot.yap
@@ -19,11 +19,11 @@
   @file boot.yap
   @brief YAP bootstrap
 
-@{
 
   @addtogroup TopLevel Top-Level and Boot Predicates
 
   @ingroup builtins
+  @{
 
 
 */
diff --git a/pl/bootutils.yap b/pl/bootutils.yap
index ca97c0bdf..a4b3901de 100644
--- a/pl/bootutils.yap
+++ b/pl/bootutils.yap
@@ -3,6 +3,7 @@
   @short utilities
 
   @addtogroup Internal_Database
+ @{
   */
 
 /** @pred  recordaifnot(+ _K_, _T_,- _R_) 
@@ -41,3 +42,4 @@ recordzifnot(K,T,R) :-
 recordzifnot(K,T,R) :-
         recordz(K,T,R).
 
+%% @}
diff --git a/pl/builtins.yap b/pl/builtins.yap
index 23d37f050..a0fe95c07 100644
--- a/pl/builtins.yap
+++ b/pl/builtins.yap
@@ -21,8 +21,7 @@
 
   @addtogroup YAPControl Control Predicates
   @ingroup builtins
-
-@{
+  @{
 
 */
 
diff --git a/pl/callcount.yap b/pl/callcount.yap
index f3891412c..d3ba19a37 100644
--- a/pl/callcount.yap
+++ b/pl/callcount.yap
@@ -39,11 +39,11 @@ implementation.
 
  */
 
-%% @{  
-
-/** @defgroup Call_Counting Counting Calls
-@ingroup Profiling
-  
+/**
+ @defgroup Call_Counting Counting Calls
+ @ingroup Profiling
+ @{ 
+ 
 Predicates compiled with YAP's flag call_counting set to
 `on` update counters on the numbers of calls and of
 retries. Counters are actually decreasing counters, so that they can be
diff --git a/pl/checker.yap b/pl/checker.yap
index 02bb5836f..0b45d6000 100644
--- a/pl/checker.yap
+++ b/pl/checker.yap
@@ -22,12 +22,11 @@
         '$syntax_check_multiple'/2,
         '$syntax_check_single_var'/2]).
 
-%% @{
-
 /**
 
-@defgroup   YAPStyle Checker
-    @ingroup  YAPCompilerSettings
+   @defgroup   YAPStyle Checker
+   @ingroup  YAPCompilerSettings
+   @{
 
 YAP implements a style-checker thay currently verifies whether:
 
diff --git a/pl/control.yap b/pl/control.yap
index 650e81969..34616d13f 100644
--- a/pl/control.yap
+++ b/pl/control.yap
@@ -83,11 +83,9 @@
 
 @addtogroup YAPControl
 @ingroup builtins
-
+@{
 */
 
-%% @{
-
 /** @pred  forall(: _Cond_,: _Action_)
 
 
diff --git a/pl/dbload.yap b/pl/dbload.yap
index 4eb4a05e3..45a8e201e 100644
--- a/pl/dbload.yap
+++ b/pl/dbload.yap
@@ -30,10 +30,9 @@
 %%
 % @defgroup YAPBigLoad Loading Large Tables
 % @ingroup YAPConsulting
-% 
+% @{
 % @brief Fast and  Exo Loading
 %
-% @{
 
 /*!
  * @pred load_mega_clause( +Stream ) is detail
diff --git a/pl/debug.yap b/pl/debug.yap
index c90b36297..df53eec52 100644
--- a/pl/debug.yap
+++ b/pl/debug.yap
@@ -24,6 +24,7 @@
 
 /**
   @defgroup Deb_Interaction Interacting with the debugger
+@{
   @ingroup YAPProgramming
 
 Debugging with YAP is similar to debugging with C-Prolog. Both systems
@@ -237,6 +238,8 @@ be lost.
 
 */
 
+
+
 /*-----------------------------------------------------------------------------
 
 				spy
diff --git a/pl/depth_bound.yap b/pl/depth_bound.yap
index 1e4d8c96b..fb5c0b6c7 100644
--- a/pl/depth_bound.yap
+++ b/pl/depth_bound.yap
@@ -18,6 +18,7 @@
 /**
 
 @defgroup DepthLimited Depth Limited Search
+@{
 @ingroup extensions
 
 YAP implements various extensions to the default Prolog search. One of
@@ -27,9 +28,12 @@ the most iseful s restricting the maximum search depth.
  :-
 system_module( '$_depth_bound', [depth_bound_call/2], []).
 
-%depth_bound_call(A,D) :-
-%write(depth_bound_call(A,D)), nl, fail.
+%% @pred depth_bound_call(A,D)
+%
+% CallError _A_ with maximum stack_el depth_reduction _B_.
+%
 depth_bound_call(A,D) :-
 	'$execute_under_depth_limit'(A,D).
 
 
+%% @}
diff --git a/pl/eam.yap b/pl/eam.yap
index b294b9d15..e9e1cd71b 100755
--- a/pl/eam.yap
+++ b/pl/eam.yap
@@ -23,6 +23,7 @@
   * 
   * @brief  Extended Abstract Machine
   * @defgroup EAM Extended Abstract Machine
+  * @{
   * @ingroup extensions
   * 
   * 
@@ -54,3 +55,5 @@ eamconsult(File):- eam, eam,                    %fails if eam is disable
                 assert((user:term_expansion((A :- B),(A :- C)):- eamtrans(B,C))),
                 eam, ( consult(File) ; true), eam,
 		abolish(user:term_expansion,2).
+
+%% @}
diff --git a/pl/hacks.yap b/pl/hacks.yap
index f720d5b96..1ad678150 100644
--- a/pl/hacks.yap
+++ b/pl/hacks.yap
@@ -32,6 +32,7 @@
 	   code_location/3]).
 
 /**
+ * @namespace yap_hacks
  *
  * @defgroup Hacks Low-level access
  * @ingroup builtins
diff --git a/pl/listing.yap b/pl/listing.yap
index d1a33a693..49816a9d9 100644
--- a/pl/listing.yap
+++ b/pl/listing.yap
@@ -25,27 +25,27 @@
   */
 
 
-:- system_module( '$_listing', [listing/0,
+/*:- system_module( '$_listing', [listing/0,
         listing/1,
         portray_clause/1,
         portray_clause/2], []).
+*/
 
 /**
-  * @defgroup Listing  List predicates in a module
-  * @{
+  * @defgroup listingGroup  List predicates in a module
+  * 
   * @ingroup builtins
   *
+  * @{ 
 */
 
 
 :- use_system_module( '$_errors', ['$do_error'/2]).
-
-:- use_system_module( '$_preds', ['$clause'/4,
         '$current_predicate'/4]).
 
-/* listing : Listing clauses in the database
-
-*/
+/** @brief listing : Listing clauses in the database
+ *
+ */
 
 /** @pred  listing
 
@@ -347,3 +347,5 @@ portray_clause(Clause) :-
 	'$list_transform'(L,M).
 '$list_transform'([_|L],M) :-
 	'$list_transform'(L,M).
+
+%% @}