Graph editor

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).
@@ -835,6 +835,10 @@ write_command(begin, enumerate, Doc) :-
   nb_setval(opened_li, false),
   write(Doc, '<ol>').
 
+write_command(begin, example, Doc) :-
+  !,
+  write(Doc, '</div><div class="example"><div><strong>Example.</strong> ').
+
 write_command(item, Argument, Doc) :-
   !,
   close_opened_li(Doc),
@@ -852,11 +856,9 @@ write_command(end, enumerate, Doc) :-
   close_opened_li(Doc),
   write(Doc, '</ol>').
 
-write_command(example, Argument, Doc) :-
+write_command(end, example, Doc) :-
   !,
-  write(Doc, '</div><div><strong>Example.</strong> '),
-  atom_chars(Argument, ArgumentChars),
-  write_doc_chars(ArgumentChars, Doc).
+  write(Doc, '</div></div><div>').
 
 write_command(Command, _Argument, _Doc) :-
   throw(error(unknown_command(Command))).

graph_editor.pl

+:- module(
+  graph_editor,
+  [
+    new_graph/0,
+    delete_graph/1,
+    set_graph_name/1,
+    list_graphs/0,
+    select_graph/1,
+    dot/0,
+    export_dot/1,
+    add_vertex/1,
+    delete_vertex/1,
+    add_attribute/2,
+    delete_attribute/2,
+    add_edge/1,
+    delete_edge/1,
+    list_edges/2
+  ]
+).
+
+:- devdoc('').

install-macos.sh

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

numerical_simulation.pl

@@ -9,14 +9,18 @@
 
 numerical_simulation :-
   biocham_command,
-  doc('performs a numerical simulation up to 20s.'),
+  doc('
+    performs a numerical simulation up to 20s.
+    \\begin{example}
+  '),
   biocham_silent(clear_model),
   biocham(a => b),
   biocham(present(a)),
-  biocham(list_reactions),
-  biocham(list_ODE),
   biocham(numerical_simulation),
   biocham(plot),
+  doc('
+    \\end{example}
+  '),
   numerical_simulation(20).
 
 

ode.pl

@@ -12,7 +12,16 @@ list_ODE :-
   biocham_command,
   doc('
     returns the set of ordinary differential equations
-    and initial concentrations (one line per molecule).'),
+    and initial concentrations (one line per molecule).
+    \\begin{example}
+  '),
+  biocham_silent(clear_model),
+  biocham(a => b),
+  biocham(present(a)),
+  biocham(list_ODE),
+  doc('
+    \\end{example}
+  '),
   compute_ode,
   print_ode.
 

plot.pl

@@ -4,7 +4,7 @@
     plot/0,
     set_plot_driver/1,
     gnu_plot/0,
-    plot_png/0,
+    gnu_plot_png/0,
     export_plot/1,
     export_plot_to_png/1
   ]
@@ -13,7 +13,6 @@
 plot :-
   biocham_command,
   doc('plots the current trace.'),
-  doc('\\example'),
   get_plot_driver(Driver),
   Driver.
 
@@ -31,7 +30,7 @@ gnu_plot :-
   execute_plot(['-persist', 'plot.plot']).
 
 
-plot_png :-
+gnu_plot_png :-
   count(plot_png, Index),
   format(atom(Filename), 'plot~d.png', [Index]),
   export_plot_to_png(Filename),