Examples in doc

biocham.pl

@@ -38,6 +38,7 @@ initialize :-
   set_prolog_flag(allow_variable_name_as_functor, true),
   prolog_history(enable),
   set_counter(item_id, 0),
+  set_plot_driver(gnu_plot),
   new_model.
 
 

doc.pl

@@ -4,6 +4,8 @@
     doc/1,
     devdoc/1,
     grammar/1,
+    biocham/1,
+    biocham_silent/1,
     generate_doc/0
   ]
 ).
@@ -27,7 +29,15 @@ grammar(_) :-
   doc('Declares a grammar predicate to be written in the documentation.').
 
 
+biocham(_).
+
+
+biocham_silent(_).
+
+
 generate_doc :-
+  set_plot_driver(plot_png),
+  set_counter(plot_png, 0),
   generate_doc(doc),
   generate_doc(devdoc).
 
@@ -38,12 +48,14 @@ generate_doc(Type) :-
     error(existence_error(directory, _), _),
     true
   ),
-  format(atom(IndexFilename), '~a/index.html', [Type]),
+  working_directory(OldDir, Type),
+  format(atom(IndexFilename), 'index.html', [Type]),
   setup_call_cleanup(
     open(IndexFilename, write, Stream),
     generate_doc(Stream, Type),
     close(Stream)
-  ).
+  ),
+  working_directory(_OldDir, OldDir).
 
 
 generate_doc(Doc, Type) :-
@@ -222,7 +234,7 @@ filter_id([_ | Tail], Id) :-
 
 read_toc(Type) :-
   setup_call_cleanup(
-    open('toc.org', read, Stream),
+    open('../toc.org', read, Stream),
     read_toc(Stream, Type),
     close(Stream)
   ).
@@ -315,8 +327,9 @@ generate_body_item(section(Level, Title), Doc, _Type) :-
 
 
 generate_body_item(file(File), Doc, Type) :-
+  atom_concat('../', File, ParentFile),
   setup_call_cleanup(
-    open(File, read, Stream),
+    open(ParentFile, read, Stream),
     generate_body_item_stream(Stream, Doc, Type),
     close(Stream)
   ).
@@ -487,11 +500,14 @@ generate_body_item_clause(Clause, Stream, Type) :-
     format(Stream, '<h5 id="~a""><code>~a', [Id, Command]),
     write_arguments(Arguments, Stream),
     write(Stream, '.</code></h5>\n'),
+    write(Stream, '<div>'),
     \+ (
       member(DocItem, Doc),
-      write_doc_item(DocItem, Stream, Type),
-      fail
-    )
+      \+ (
+        write_doc_item(DocItem, Stream, Type)
+      )
+    ),
+    write(Stream, '</div>')
   ;
     true
   ).
@@ -650,8 +666,32 @@ write_doc_item(doc(DocBody), Stream, _Type) :-
   write_doc(Stream, DocBody).
 
 
-write_doc_item(devdoc(DocBody), Stream, devdoc) :-
-  write_doc(Stream, DocBody).
+write_doc_item(devdoc(DocBody), Stream, Type) :-
+  (
+    Type = devdoc
+  ->
+    write_doc(Stream, DocBody)
+  ;
+    true
+  ).
+
+write_doc_item(biocham_silent(Command), _Stream, _Type) :-
+  command(Command).
+
+write_doc_item(biocham(Command), Stream, _Type) :-
+  with_output_to(
+    atom(Output),
+    command(Command)
+  ),
+  prompt(Prompt),
+  format(
+    Stream,
+    '</div>
+<div><code>~a</code><kbd>~w.</kbd></div>
+<pre>~a</pre>
+<div>',
+    [Prompt, Command, Output]
+  ).
 
 
 write_doc(Doc, DocBody) :-
@@ -812,6 +852,12 @@ write_command(end, enumerate, Doc) :-
   close_opened_li(Doc),
   write(Doc, '</ol>').
 
+write_command(example, Argument, Doc) :-
+  !,
+  write(Doc, '</div><div><strong>Example.</strong> '),
+  atom_chars(Argument, ArgumentChars),
+  write_doc_chars(ArgumentChars, Doc).
+
 write_command(Command, _Argument, _Doc) :-
   throw(error(unknown_command(Command))).
 

gsl.pl

@@ -296,5 +296,6 @@ compile_c_program(ExecutableFilename) :-
 
 
 call_subprocess(ExecutableFilename, Arguments) :-
-  process_create(ExecutableFilename, Arguments, [process(Pid)]),
+  absolute_file_name(ExecutableFilename, Absolute),
+  process_create(Absolute, Arguments, [process(Pid)]),
   process_wait(Pid, exit(0)).

numerical_simulation.pl

@@ -10,6 +10,13 @@
 numerical_simulation :-
   biocham_command,
   doc('performs a numerical simulation up to 20s.'),
+  biocham_silent(clear_model),
+  biocham(a => b),
+  biocham(present(a)),
+  biocham(list_reactions),
+  biocham(list_ODE),
+  biocham(numerical_simulation),
+  biocham(plot),
   numerical_simulation(20).
 
 

plot.pl

@@ -2,6 +2,9 @@
   plot,
   [
     plot/0,
+    set_plot_driver/1,
+    gnu_plot/0,
+    plot_png/0,
     export_plot/1,
     export_plot_to_png/1
   ]
@@ -10,10 +13,31 @@
 plot :-
   biocham_command,
   doc('plots the current trace.'),
+  doc('\\example'),
+  get_plot_driver(Driver),
+  Driver.
+
+
+get_plot_driver(Driver) :-
+  nb_getval(plot_driver, Driver).
+
+
+set_plot_driver(Driver) :-
+  nb_setval(plot_driver, Driver).
+
+
+gnu_plot :-
   export_plot(plot),
   execute_plot(['-persist', 'plot.plot']).
 
 
+plot_png :-
+  count(plot_png, Index),
+  format(atom(Filename), 'plot~d.png', [Index]),
+  export_plot_to_png(Filename),
+  format('<img src="~a">', [Filename]).
+
+
 execute_plot(Options) :-
   process_create(path(gnuplot), Options, []).
 

toplevel.pl

@@ -4,7 +4,8 @@
     execute_command/1,
     toplevel/0,
     quit/0,
-    command/1
+    command/1,
+    prompt/1
   ]).
 
 

types.pl

@@ -46,6 +46,10 @@ collect_info(DocItem, _Arguments, _ArgumentTypes, _BiochamCommand, Doc) :-
     DocItem = doc(_)
   ;
     DocItem = devdoc(_)
+  ;
+    DocItem = biocham(_)
+  ;
+    DocItem = biocham_silent(_)
   ),
   !,
   Doc = [DocItem].
@@ -126,6 +130,8 @@ check_type(Grammar, Item, NewItem) :-
     clause(NewHead, NewBody),
     copy_term((NewHead, NewBody), (Head, Body)),
     check_grammar_body(Body, NewBody)
+  ->
+    true
   ;
     throw(error(expected(Grammar)))
   ).