TD1 et TD2, doc de plot et odefunction

Makefile

@@ -112,7 +112,7 @@ unit_tests: biocham_debug
 
 # slow tests too
 test: biocham_debug
-	echo "flag(slow_test, _, true), run_tests_and_halt." | ./biocham_debug
+	echo "flag(slow_test, _, false), run_tests_and_halt." | ./biocham_debug
 	$(MAKE) jupyter_tests
 
 jupyter_tests: install_kernel
@@ -120,7 +120,7 @@ jupyter_tests: install_kernel
 
 # runs test unit %
 test_%: biocham_debug
-	echo "flag(slow_test, _, true), run_tests_and_halt('$*')." | ./biocham_debug
+	echo "flag(slow_test, _, false), run_tests_and_halt('$*')." | ./biocham_debug
 
 install_kernel: biocham $(KERNEL_DIR)/commands.js $(KERNEL_DIR)/commands.py $(WORKFLOWS_DIR)/workflows.js
 	- pip3 install --user $(JUPYTER_DIR)/kernel || pip install --user $(JUPYTER_DIR)/kernel

odefunction.pl

@@ -407,30 +407,11 @@ add_function(FunctionList) :-
   import_reactions_from_ode_system(OdeSystem),
   delete_item(OdeSystem).
 
-%% compile_program_file(+InputFile:input_file) is det
-%
-%   Compile the high-level language program from file.
-%   Transform the terms in a file into internal list format of 'add_function'.
-compile_program_file( InputFile ) :-
-  biocham_command,
-  type( InputFile, input_file ),
-  option( 'simplify_variable_init', yesno, _,
-          'set if the variable initialization in program need to be simplified to \\emph{present} command' ),
-  option( 'zero_ultra_mm', yesno, _,
-          'set the kinetics of zero-order ultrasensitivity to Michaelis-Menten kinetics' ),
-  devdoc( "Transform the terms in a file into internal list format of 'add_function'." ),
-
-  doc( "Compile the high-level language program from file." ),
-  access_file( InputFile, read ),
-  !,
-  open( InputFile, read, File ),
-  compile( File ),
-  close( File ).
 
 %% compile_program(+InputFile:atom) is det
 %
-%   Compile the high-level language program from atom.
-%   Transform the terms in an atom into internal list format of 'add_function'.
+%   Compiles a high-level imperative program from a string.
+%   Transform the terms in the string into an internal list format for 'add_function'.
 compile_program( Program ) :-
   biocham_command,
   type( Program, atom ),
@@ -450,9 +431,9 @@ compile_program( Program ) :-
   biocham( numerical_simulation( time: 20 ) ),
   biocham( plot( show:{ x_p, x_n, y_p, y_n, z_p, z_n } ) ),
 
-  doc( "Here is an example shows the compilation result of euclid division: "),
-  biocham_silent( clear_model ),
-  biocham( compile_program( 'a := 7, b := 3. while( a >= b ). t1 := a - b, t2 := q + 1. a := t1, q := t2. endwhile. r := a.', simplify_variable_init: yes, zero_ultra_mm: yes ) ),
+%  doc( "Here is an example shows the compilation result of euclid division: "),
+%  biocham_silent( clear_model ),
+%  biocham( compile_program( 'a := 7, b := 3. while( a >= b ). t1 := a - b, t2 := q + 1. a := t1, q := t2. endwhile. r := a.', simplify_variable_init: yes, zero_ultra_mm: yes ) ),
   % FIXME tooooooo slow
   % biocham( numerical_simulation( time: 200 ) ),
   % biocham( plot( show:{ a_p, a_n, b_p, b_n, q_p, q_n, r_p, r_n } ) ),
@@ -464,6 +445,27 @@ compile_program( Program ) :-
   compile( Stream ),
   close( Stream ).
 
+%% compile_program_file(+InputFile:input_file) is det
+%
+%   Compiles a high-level imperative program file.
+%   Transforms the terms in the file into an internal list format for 'add_function'.
+compile_program_file( InputFile ) :-
+  biocham_command,
+  type( InputFile, input_file ),
+  option( 'simplify_variable_init', yesno, _,
+          'set if the variable initialization in program need to be simplified to \\emph{present} command' ),
+  option( 'zero_ultra_mm', yesno, _,
+          'set the kinetics of zero-order ultrasensitivity to Michaelis-Menten kinetics' ),
+  devdoc( "Transform the terms in a file into internal list format of 'add_function'." ),
+
+  doc( "Compile the high-level language program from file." ),
+  access_file( InputFile, read ),
+  !,
+  open( InputFile, read, File ),
+  compile( File ),
+  close( File ).
+
+
 %% create_ode(+FunctionList:list, +OdeSystem:'ode system') is det
 %
 %   Compile the _FunctionList_ into PIVP.

plot.pl

@@ -40,7 +40,7 @@ plot :-
   ),
   option(
     show, {object}, Show,
-    'Restricts the plot to the given set of objects; everything will be
+    'Restricts the plot to the given set of objects and functions; everything will be
     plotted if the set is empty'
   ),
   option(
@@ -48,7 +48,7 @@ plot :-
     'Selects the X axis for the plot, defaulting to Time.'
   ),
   doc('
-    plots the current trace.
+    plots the current trace. After a simulation, the trace is composed of molecular concentrations and user-defined functions over time.
     \\begin{example}'
   ),
   handle_show(Show),