Merge branch 'develop' into feature/Hybrid

biocham_jupyter/guinbextension/src/config/workflows/commands.py

@@ -34,6 +34,7 @@ commands = [
     "compile_from_expression",
     "compile_from_pivp",
     "compile_program",
+    "compile_program_file",
     "compile_transfer_function",
     "compile_wgpac",
     "continue",

conservation_laws.plt

@@ -49,7 +49,7 @@ test(
       setup(set_some_conservations),
       cleanup(clear_model),
       true(Conservations ==
-        '[0] a-a+2*a\n[1] b-b+2*b\n[2] c-c+2*c\n')
+        '[0] \'a-a\'+2*a\n[1] \'b-b\'+2*b\n[2] \'c-c\'+2*c\n')
    ]
 ) :-
   with_output_to(atom(Conservations), command(list_conservations)).

influence_editor.pl

@@ -174,7 +174,7 @@ list_model_influences :-
   ).
 
 
-prolog:error_message(not_an_influence_model) -->
+prolog:message(error(not_an_influence_model)) -->
   ['Not an influence model'].
 
 
@@ -278,7 +278,7 @@ print_influence(_Id, Item) :-
   (
     Item = (Force for BasicInfluence)
   ->
-    format('~w for ', [Force])
+    format('~p for ', [Force])
   ;
     BasicInfluence = Item
   ),
@@ -294,15 +294,15 @@ print_influence(_Id, Item) :-
   (
     Inputs = (PositiveInputs / NegativeInputs)
   ->
-    format('~w / ~w', [PositiveInputs, NegativeInputs])
+    format('~p / ~p', [PositiveInputs, NegativeInputs])
   ;
     Inputs = (/ NegativeInputs)
   ->
-    format('/ ~w', [NegativeInputs])
+    format('/ ~p', [NegativeInputs])
   ;
     write(Inputs)
   ),
-  format(' ~w ~w', [Arrow, Output]).
+  format(' ~w ~p', [Arrow, Output]).
 
 
 substract_list([], Difference, Difference).

models.pl

@@ -498,10 +498,22 @@ print_item(Id) :-
   ->
     G
   ;
-    write(Item)
+    print(Item)
   ).
 
 
+% make it so that print/1 does not quote things that look like a variable
+user:portray(Thing) :-
+  atom(Thing),
+  catch(
+    read_term_from_atom(Thing, Term, []),
+    _,
+    fail
+  ),
+  \+ compound(Term),
+  !,
+  write(Thing).
+
 :- dynamic(deleting/1).
 
 
@@ -635,34 +647,20 @@ inherits(Id, AncestorId) :-
   ).
 
 
-prolog:error_message(cannot_inherit_from_itself) -->
-  [
-    'Cannot inherit from itself.'
-  ].
+prolog:message(error(cannot_inherit_from_itself)) -->
+  ['Cannot inherit from itself.'].
 
 
-prolog:error_message(already_inherits) -->
-  [
-    'There is already such an inheritance relation.'
-  ].
+prolog:message(error(already_inherits)) -->
+  ['There is already such an inheritance relation.'].
 
 
-prolog:error_message(cannot_inherit_from_descendant) -->
-  [
-    'Cannot inherit from descendant.'
-  ].
-
-prolog:error_message(
-  kind_mismatch(Ident, Kind, NeededKind)
-) -->
-  {
-    format(
-      atom(Message),
-      'There is a mismatch between the uses of ~a: ~a and ~a.',
-      [Ident, Kind, NeededKind]
-    )
-  },
-  [Message].
+prolog:message(error(cannot_inherit_from_descendant)) -->
+  ['Cannot inherit from descendant.'].
+
+prolog:message(error(kind_mismatch(Ident, Kind, NeededKind))) -->
+  ['There is a mismatch between the uses of ~a: ~a and ~a.'-[Ident,
+    Kind, NeededKind]].
 
 
 inherits_from(Id, AncestorId) :-

namespace.pl

@@ -50,17 +50,10 @@ check_identifier_kind(Ident, NeededKind) :-
   ).
 
 
-prolog:error_message(
-  already_defined_with_another_kind(Ident, Kind, NeededKind)
+prolog:message(
+  error(already_defined_with_another_kind(Ident, Kind, NeededKind))
 ) -->
-  {
-    format(
-      atom(Message),
-      '~a cannot be ~a because it is already used as ~a.',
-      [Ident, NeededKind, Kind]
-    )
-  },
-  [Message].
+  ['~a cannot be ~a because it is already used as ~a.'-[Ident, NeededKind, Kind]].
 
 
 
@@ -76,29 +69,24 @@ check_no_free_identifiers :-
   ->
     true
   ;
-    throw(error(not_defined(FreeIdents), check_no_free_identifiers))
+    throw(error(not_defined(FreeIdents)))
   ).
 
 
-prolog:error_message(not_defined(FreeIdents)) -->
+prolog:message(error(not_defined(FreeIdents))) -->
   {
-    with_output_to(
-      atom(Message),
-      (
-        FreeIdents = [FreeIdent]
-      ->
-        format('~a is not defined.', [FreeIdent])
-      ;
-        write_successes(
-          member(FreeIdent, FreeIdents),
-          write(', '),
-          write(FreeIdent)
-        ),
-        write(' are not defined.')
-      )
-    )
+    findall('~a', member(_, FreeIdents), As),
+    atomic_list_concat(As, ', ', Format),
+    (
+      FreeIdents = [_]
+    ->
+      Verb = 'is'
+    ;
+      Verb = 'are'
+    ),
+    atomic_list_concat([Format, Verb, 'not defined'], ' ', FullFormat)
   },
-  [Message].
+  [FullFormat-FreeIdents].
 
 
 update_identifier_kinds(ModelId) :-

reaction_editor.pl

@@ -179,7 +179,7 @@ list_model_reactions :-
   ).
 
 
-prolog:error_message(not_a_reaction_model) -->
+prolog:message(error(not_a_reaction_model)) -->
   ['Not a reaction model'].