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Makefile

@@ -10,8 +10,8 @@ biocham: $(MODULES) toc.org Makefile
 	@echo $(MODULES)
 	swipl -o biocham --goal=start --toplevel=toplevel -c $(MODULES)
 
-biocham_debug: $(MODULES) toc.org Makefile
-	swipl -o biocham_debug --goal=initialize -c $(MODULES)
+biocham_debug: $(MODULES) $(TEST_MODULES) toc.org Makefile
+	swipl -o biocham_debug --goal=initialize -c $(MODULES) $(TEST_MODULES)
 
 tests: biocham_tests
 	./biocham_tests

aliases.pl

@@ -29,7 +29,9 @@ add_equivalence_class_list(EquivalenceClassList) :-
     true
   ;
     list_to_equals(EquivalenceClassList, EquivalenceClass),
-    add_item(alias, EquivalenceClassList, alias(EquivalenceClass)),
+    add_item([
+      kind: alias, key: EquivalenceClassList, item: alias(EquivalenceClass)
+    ]),
     simplify_all_reactions
   ).
 
@@ -81,7 +83,7 @@ canonical(Object, Canonical) :-
 list_aliases :-
   biocham_command,
   doc('shows the values of all known aliases.'),
-  list_items([model: current_model, kind: alias]).
+  list_items([kind: alias]).
 
 
 delete_alias(Object) :-

aliases.plt

@@ -6,6 +6,6 @@ test('alias', [true(Reactions == [2 * a => c])]) :-
   clear_model,
   add_reaction(a + b => c),
   command(alias(a = b)),
-  all_items([model: current_model, kind: reaction], Reactions).
+  all_items([kind: reaction], Reactions).
 
 :- end_tests(aliases).

conservation_laws.pl

@@ -31,7 +31,7 @@ add_conservation(Conservation) :-
     a warning.'
   ),
   solution_to_conservation(Conservation, C),
-  add_item(conservation, [], Conservation, Id),
+  add_item([kind: conservation, item: Conservation, id: Id]),
   set_annotation(Id, conservation_list, C).
 
 

conservation_laws.plt

@@ -7,14 +7,14 @@
 test(
    'add_conservation adds a conservation',
    [
-      setup(models:clear_model),
-      cleanup(models:clear_model),
+      setup(clear_model),
+      cleanup(clear_model),
       forall(member(Input, ['a-a' + 2*'a', 'b', 'a' + 'b'])),
       true(Conservations == [Input])
    ]
 ) :-
    command(add_conservation(Input)),
-   all_items([model: current_model, kind: conservation], Conservations).
+   all_items([kind: conservation], Conservations).
 
 %%% FIXME should test that conservations are properly used for numerical
 %%% integration
@@ -23,31 +23,31 @@ test(
    'delete_conservation deletes the correct conservation',
    [
       setup(set_some_conservations),
-      cleanup(models:clear_model),
+      cleanup(clear_model),
       true(Conservations == ['a-a'+2*a,'c-c'+2*c])
    ]
 ) :-
    command(delete_conservation(b-b + 2*b)),
-   all_items([model: current_model, kind: conservation], Conservations).
+   all_items([kind: conservation], Conservations).
 
 
 test(
    'delete_conservations deletes all conservations',
    [
       setup(set_some_conservations),
-      cleanup(models:clear_model),
+      cleanup(clear_model),
       true(Conservations == [])
    ]
 ) :-
    command(delete_conservations),
-   all_items([model: current_model, kind: conservation], Conservations).
+   all_items([kind: conservation], Conservations).
 
 
 test(
    'list_conservations lists all conservations',
    [
       setup(set_some_conservations),
-      cleanup(models:clear_model),
+      cleanup(clear_model),
       true(Conservations ==
         '[0] a-a+2*a\n[1] b-b+2*b\n[2] c-c+2*c\n')
    ]
@@ -58,8 +58,8 @@ test(
 test(
   'check_conservations is ok with trivial P-invariants',
   [
-    setup((models:clear_model, set_prolog_flag(verbose, silent))),
-    cleanup((models:clear_model, set_prolog_flag(verbose, normal)))
+    setup((clear_model, set_prolog_flag(verbose, silent))),
+    cleanup((clear_model, set_prolog_flag(verbose, normal)))
   ]
 ) :-
   command(add_reaction(a => b)),
@@ -71,8 +71,8 @@ test(
 test(
   'check_conservations is ok with kinetically conserved moieties',
   [
-    setup((models:clear_model, set_prolog_flag(verbose, silent))),
-    cleanup((models:clear_model, set_prolog_flag(verbose, normal)))
+    setup((clear_model, set_prolog_flag(verbose, silent))),
+    cleanup((clear_model, set_prolog_flag(verbose, normal)))
   ]
 ) :-
   command(add_reaction(k*[a] for a => b)),
@@ -84,8 +84,8 @@ test(
 test(
   'check_conservations is unhappy with non-conserved moieties',
   [
-    setup((models:clear_model, set_prolog_flag(verbose, silent))),
-    cleanup((models:clear_model, set_prolog_flag(verbose, normal))),
+    setup((clear_model, set_prolog_flag(verbose, silent))),
+    cleanup((clear_model, set_prolog_flag(verbose, normal))),
     true(Warnings == 1)
   ]
 ) :-
@@ -101,7 +101,7 @@ test(
 
 
 set_some_conservations :-
-  models:clear_model,
+  clear_model,
   command(add_conservation(a-a + 2*a)),
   command(add_conservation(b-b + 2*b)),
   command(add_conservation(c-c + 2*c)).

doc.pl

@@ -36,7 +36,7 @@ biocham_silent(_).
 
 
 generate_doc :-
-  set_plot_driver(plot_png),
+  set_plot_driver(gnu_plot_png),
   set_counter(plot_png, 0),
   generate_doc(doc),
   generate_doc(devdoc).
@@ -839,6 +839,10 @@ write_command(begin, enumerate, Stream) :-
   nb_setval(opened_li, false),
   write(Stream, '</div>\n<ol>\n').
 
+write_command(begin, example, Stream) :-
+  !,
+  write(Stream, '</div><div class="example"><div><strong>Example.</strong> ').
+
 write_command(item, Argument, Stream) :-
   !,
   close_opened_li(Stream),
@@ -856,18 +860,17 @@ write_command(end, enumerate, Stream) :-
   close_opened_li(Stream),
   write(Stream, '</ol>\n<div>').
 
-write_command(example, Argument, Stream) :-
+write_command(end, example, Doc) :-
   !,
-  write(Stream, '</div>\n<div><strong>Example.</strong> '),
-  write_doc(Stream, Argument).
+  write(Doc, '</div></div><div>').
 
 write_command(section, Argument, Stream) :-
   !,
   nb_getval(current_counters, Counters),
-  length(Counnters, CounterCount),
+  length(Counters, CounterCount),
   SectionLevel is CounterCount + 2,
   format(Stream, '</div>\n<h~d>', [SectionLevel]),
-  write_doc(Stream, Argument)
+  write_doc(Stream, Argument),
   format(Stream, '</h~d>\n<div>', [SectionLevel]).
 
 write_command(Command, _Argument, _Stream) :-

graph_editor.pl

+:- module(
+  graph_editor,
+  [
+    new_graph/0,
+    delete_graph/1,
+    set_graph_name/1,
+    list_graphs/0,
+    select_graph/1,
+    draw_graph/0,
+    export_graph/1,
+    add_vertex/1,
+    delete_vertex/1,
+    add_attribute/2,
+    delete_attribute/2,
+    list_attributes/1,
+    edge/1,
+    add_edge/1,
+    delete_edge/1,
+    list_edges/0,
+    get_current_graph/1
+  ]
+).
+
+
+:- devdoc('\\section{Commands}').
+
+
+new_graph :-
+  biocham_command,
+  doc('Creates a new graph.'),
+  add_item([kind: graph, key: new_graph, id: Id]),
+  set_current_graph(Id).
+
+
+delete_graph(Name) :-
+  biocham_command,
+  type(Name, name),
+  doc('Deletes a graph.'),
+  delete_items([kind: graph, key: Name]).
+
+
+set_graph_name(Name) :-
+  biocham_command,
+  type(Name, name),
+  doc('Sets the name of the current graph.'),
+  get_current_graph(Id),
+  replace_item(Id, graph, Name, Name).
+
+
+list_graphs :-
+  biocham_command,
+  doc('Lists the graph of the current model.'),
+  list_items([kind: graph]).
+
+
+select_graph(Name) :-
+  biocham_command,
+  type(Name, name),
+  doc('Selects a graph'),
+  find_item([kind: graph, key: Name, id: Id]),
+  set_current_graph(Id).
+
+
+draw_graph :-
+  biocham_command,
+  doc('').
+
+
+export_graph(Argument) :-
+  biocham_command,
+  type(Argument, type),
+  doc('').
+
+
+add_vertex(Name) :-
+  biocham_command,
+  type(Name, name),
+  doc('Adds a vertex to the current graph.'),
+  get_current_graph(GraphId),
+  add_item([parent: GraphId, kind: vertex, key: Name]).
+
+
+delete_vertex(Name) :-
+  biocham_command,
+  type(Name, name),
+  doc('Removes a vertex from the current graph.'),
+  get_current_graph(GraphId),
+  delete_item([parent: GraphId, kind: vertex, key: Name]).
+
+
+add_attribute(Name, Attribute) :-
+  biocham_command,
+  type(Name, name),
+  type(Attribute, name),
+  doc('Adds an attribute to a vertex.'),
+  find_vertex(Name, Id),
+  (
+    find_item([parent: Id, kind: attribute, key: Attribute])
+  ->
+    true
+  ;
+    add_item([parent: Id, kind: attribute, key: Attribute])
+  ).
+
+
+delete_attribute(Name, Attribute) :-
+  biocham_command,
+  type(Name, name),
+  type(Abbribute, name),
+  doc('Removes an attribute from a vertex.'),
+  find_vertex(Name, Id),
+  delete_item([parent: Id, kind: attribute, key: Attribute]).
+
+
+list_attributes(Name) :-
+  biocham_command,
+  type(Name, name),
+  doc('List the attributes of a vertex.'),
+  find_vertex(Name, Id),
+  list_items([parent: Id, kind: attribute]).
+
+
+:- grammar(edge).
+
+
+edge(From -> To) :-
+  name(From),
+  name(To).
+
+
+add_edge(Edge) :-
+  biocham_command,
+  type(Edge, edge),
+  doc('Adds an edge'),
+  Edge = (From -> To),
+  find_vertex(From, FromId),
+  find_vertex(To, ToId),
+  get_current_graph(GraphId),
+  add_item([parent: GraphId, kind: edge, key: Edge, id: Id]),
+  add_dependency(Id, FromId),
+  add_dependency(Id, ToId).
+
+
+delete_edge(Edge) :-
+  biocham_command,
+  type(Edge, edge),
+  doc('Deletes an edge'),
+  get_current_graph(GraphId),
+  delete_item([parent: GraphId, kind: edge, key: Edge]).
+
+
+list_edges :-
+  biocham_command,
+  doc('Lists the edges of the current graph'),
+  get_current_graph(GraphId),
+  list_items([parent: GraphId, kind: edge]).
+
+
+:- devdoc('\\section{End of commands}').
+
+
+find_vertex(Name, Id) :-
+  get_current_graph(GraphId),
+  find_item([parent: GraphId, kind: vertex, key: Name, id: Id]).
+
+
+deselect_graph :-
+  \+ (
+    item([kind: Graph, id: Id]),
+    \+ (
+      (
+        delete_annotation(Id, selected)
+      ->
+        true
+      ;
+        true
+      )
+    )
+  ).
+
+
+set_current_graph(Id) :-
+  deselect_graph,
+  set_annotation(Id, selected, selected).
+
+
+get_current_graph(Id) :-
+  (
+    item([kind: Graph, id: Id]),
+    get_annotation(Id, selected, selected)
+  ->
+    true
+  ;
+    throw(error(no_graph_selected))
+  ).

initial_state.pl

@@ -17,7 +17,7 @@
 
 get_initial_state(Object, State) :-
   (
-    item([model: current_model, kind: initial_state, key: Object, item: Item])
+    item([kind: initial_state, key: Object, item: Item])
   ->
     (
       Item = present(Object)
@@ -59,7 +59,7 @@ list_initial_state :-
   doc('
     lists the objects which are present (including their initial concentration)
     and absent from the initial state.'),
-  list_items([model: current_model, kind: initial_state]).
+  list_items([kind: initial_state]).
 
 
 clear_initial_state :-
@@ -67,12 +67,7 @@ clear_initial_state :-
   doc('
     makes undefined all objects possibly present or absent in the initial
     state.'),
-  \+ (
-    item([model: current_model, kind: initial_state, id: Id]),
-    \+ (
-      delete_item(Id)
-    )
-  ).
+  delete_items([kind: initial_state]).
 
 
 present(ObjectSet) :-
@@ -109,7 +104,7 @@ set_state(ObjectSet, Object, State) :-
     member(Object, ObjectSet),
     \+ (
       undefined_object(Object),
-      add_item(initial_state, Object, State)
+      add_item([kind: initial_state, key: Object, item: State])
     )
   ).
 
@@ -130,7 +125,7 @@ undefined(ObjectSet) :-
 
 undefined_object(Object) :-
   (
-    item([model: current_model, kind: initial_state, key: Object, id: Id])
+    item([kind: initial_state, key: Object, id: Id])
   ->
     delete_item(Id)
   ;
@@ -169,4 +164,4 @@ make_absent_not_present :-
 
 
 defined(Object) :-
-  once(item([model: current_model, kind: initial_state, key: Object])).
+  once(item([kind: initial_state, key: Object])).

initial_state.plt

@@ -8,7 +8,7 @@ test(
 ) :-
   clear_model,
   command(present({ a, b })),
-  all_items([model: current_model, kind: initial_state], InitialState).
+  all_items([kind: initial_state], InitialState).
 
 test(
   'absent',
@@ -16,7 +16,7 @@ test(
 ) :-
   clear_model,
   command(absent({ a, b })),
-  all_items([model: current_model, kind: initial_state], InitialState).
+  all_items([kind: initial_state], InitialState).
 
 test(
   'undefined',
@@ -26,7 +26,7 @@ test(
   command(present({ a, b, c })),
   command(absent({ b, c, e })),
   command(undefined({ c, d, e })),
-  all_items([model: current_model, kind: initial_state], InitialState).
+  all_items([kind: initial_state], InitialState).
 
 test(
   'make_absent_not_present',
@@ -36,7 +36,7 @@ test(
   add_reaction(a => b),
   command(present(a)),
   make_absent_not_present,
-  all_items([model: current_model, kind: initial_state], InitialState).
+  all_items([kind: initial_state], InitialState).
 
 test(
   'make_present_not_absent',
@@ -46,6 +46,6 @@ test(
   add_reaction(a => b),
   command(absent(a)),
   make_present_not_absent,
-  all_items([model: current_model, kind: initial_state], InitialState).
+  all_items([kind: initial_state], InitialState).
 
 :- end_tests(initial_state).

install-macos.sh

 #!/bin/sh
-brew install swi-prolog gsl libsbml
+brew install swi-prolog gsl libsbml gnuplot

macros.pl

@@ -21,7 +21,7 @@ set_macro(MacroList) :-
           replace_item(Id, macro, Macro, macro(Macro = Value))
         ),
         error(unknown_item),
-        add_item(macro, Macro, macro(Macro = Value))
+        add_item([kind: macro, key: Macro, item: macro(Macro = Value)])
       )
     )
   ).
@@ -31,9 +31,7 @@ show_macro(Macro) :-
   biocham_command,
   type(Macro, macro),
   doc('shows the expression associated to the given macro.'),
-  find_item(
-    [model: current_model, kind: macro, key: Macro, item: macro(_ = Expression)]
-  ),
+  find_item([kind: macro, key: Macro, item: macro(_ = Expression)]),
   write(Expression),
   nl.
 
@@ -41,7 +39,7 @@ show_macro(Macro) :-
 list_macros :-
   biocham_command,
   doc('lists all known macros.'),
-  list_items([model: current_model, kind: macro]).
+  list_items([kind: macro]).
 
 
 delete_macro(MacroSet) :-
@@ -51,7 +49,6 @@ delete_macro(MacroSet) :-
   \+ (
     member(Macro, MacroSet),
     \+ (
-      find_item([model: current_model, kind: macro, key: Macro, id: Id]),
-      delete_item(Id)
+      delete_item([kind: macro, key: Macro])
     )
   ).

macros.plt

@@ -9,6 +9,6 @@ test(
   clear_model,
   command(set_macro(a = 1, b = 2)),
   command(set_macro(b = 3)),
-  all_items([model: current_model, kind: macro], Macros).
+  all_items([kind: macro], Macros).
 
 :- end_tests(macros).

models.pl

@@ -2,20 +2,23 @@
   models,
   [
     load/1,
+    add/1,
     load_biocham/1,
+    add_biocham/1,
     new_model/0,
     clear_model/0,
-    get_model_name/1,
-    get_model_name/2,
-    set_model_name/1,
     list_models/0,
     list_current_models/0,
+    range/1,
+    ref/1,
     select_model/1,
+    set_model_name/1,
+    delete/1,
+    get_model_name/1,
+    get_model_name/2,
     current_models/1,
     single_model/1,
-    add_item/2,
-    add_item/3,
-    add_item/4,
+    add_item/1,
     replace_item/4,
     set_annotation/3,
     get_annotation/3,
@@ -28,14 +31,12 @@
     list_ids/1,
     delete_item/1,
     delete_items/1,
-    delete/1,
-    range/1
+    add_dependency/2
   ]
 ).
 
 
-:- dynamic(fresh/0).
-
+:- devdoc('\\section{Commands}').
 
 
 load(InputFile) :-
@@ -85,6 +86,113 @@ add_biocham(InputFile) :-
   add_all('.bc', InputFile).
 
 
+new_model :-
+  biocham_command,
+  doc('opens a new fresh model.'),
+  new_model(_Id).
+
+
+clear_model :-
+  biocham_command,
+  doc('clears the current model.'),
+  current_models(CurrentModels),
+  \+ (
+    member(Id, CurrentModels),
+    \+ (
+      delete_item(Id)
+    )
+  ).
+
+
+list_models :-
+  biocham_command,
+  doc('lists all open models'),
+  list_items([parent: top, kind: model]).
+
+
+list_current_models :-
+  biocham_command,
+  doc('lists current models'),
+  current_models(CurrentModels),
+  list_ids(CurrentModels).
+
+
+:- grammar(range).
+
+
+range(Integer0 - Integer1) :-
+  integer(Integer0),
+  integer(Integer1).
+
+range(Integer) :-
+  integer(Integer).
+
+
+:- grammar(ref).
+
+
+ref(Range) :-
+  list(range, Range).
+
+ref(Name) :-
+  name(Name).
+
+
+select_model(RefSet) :-
+  biocham_command,
+  type(RefSet, {ref}),
+  doc('selects some models.'),
+  findall(
+    Id,
+    (
+      member(Ref, RefSet),