Merge branch 'release/4.3.10'

about.pl

@@ -8,7 +8,7 @@
     about/0
   ]).
 
-version('4.3.9').
+version('4.3.10').
 
 copyright(
   'Copyright (C) 2003-2020 Inria, EPI Lifeware, Saclay-Île de France, France'

biocham_jupyter/guinbextension/package.json

 {
   "name": "gui",
-  "version": "4.3.9",
+  "version": "4.3.10",
   "description": "biocham gui in jupyter notebook",
   "main": "src/index.js",
   "scripts": {

biocham_jupyter/kernel/biocham_kernel/__init__.py

 """Example magic"""
-__version__ = '4.3.9'
+__version__ = '4.3.10'

foltl.pl

@@ -524,6 +524,9 @@ expand_expression(Expression, ExpandedExpression) :-
   !,
   expand_expression(NewBody, ExpandedExpression).
 
+expand_expression(Parameter, Value) :-
+  parameter_value(Parameter, Value),
+  !.
 
 expand_expression(Expression, ExpandedExpression) :-
   grammar_map(

install.sh

@@ -162,6 +162,7 @@ else
 fi
 echo "installing python packages ($packages)…"
 python3 -m pip install -U $packages
+jupyter nbextension enable --py widgetsnbextension
 
 ### trust all our notebooks but make them read-only
 find . -name '*.ipynb' -print0 | xargs -0 jupyter trust

numerical_simulation.pl

@@ -370,20 +370,19 @@ solve :-
   add_table('numerical_simulation', Table).
 
 
-gather_fields(Events, Fields) :-
+gather_fields(Events, ['Time':t|Fields_tail]) :-
   findall(
     Field,
     (
-      Field = 'Time': t
-    ;
       enumerate_variables(Field)
     ;
       enumerate_nonconstant_parameters(Events, Field)
     ;
       enumerate_nonparametric_functions(Field)
     ),
-    Fields
-  ).
+    Fields_unsorted
+  ),
+  sort(Fields_unsorted, Fields_tail).
 
 
 enumerate_variables(Header: x(VariableIndex)) :-

plot.pl

@@ -34,7 +34,10 @@ axes(xy).
 :- initial(option(show: {})).
 :- initial(option(logscale: '')).
 :- initial(option(against: 'Time')).
-
+:- initial(option(xmin:42)).
+:- initial(option(ymin:42)).
+:- initial(option(xmax:42)).
+:- initial(option(ymax:42)).
 
 plot :-
   biocham_command,
@@ -51,6 +54,22 @@ plot :-
     against, object, Against,
     'Selects the X axis for the plot, defaulting to Time.'
   ),
+  option(
+    xmin, number, _Xmin,
+    'Select the axes for the current plot (42 is overwrite to *)'
+  ),
+  option(
+    ymin, number, _Ymin,
+    'Select the axes for the current plot (42 is overwrite to *)'
+  ),
+  option(
+    xmax, number, _Xmax,
+    'Select the axes for the current plot (42 is overwrite to *)'
+  ),
+  option(
+    ymax, number, _Ymax,
+    'Select the axes for the current plot (42 is overwrite to *)'
+  ),
   doc('
     plots the current trace. After a simulation, the trace is composed of molecular concentrations and user-defined functions over time.
     \\begin{example}'
@@ -216,6 +235,8 @@ set format "%.5g"
 set style data lines
 set datafile separator ","
 '),
+  get_axes(Xmin, Xmax, Ymin, Ymax),
+  format(Stream, "set xrange [~w:~w]~nset yrange [~w:~w]~n", [Xmin, Xmax, Ymin, Ymax]),
   logscale(Axes),
   (
     Axes == ''
@@ -276,5 +297,26 @@ handle_show(Show) :-
   ).
 
 
+%! get_axes(-Xmin, -Xmax, -Ymin, -Ymax)
+%
+% retrieve the option values for the axes of gnuplot
+
+get_axes(Xmin, Xmax, Ymin, Ymax) :-
+  get_one_axe(xmin, Xmin),
+  get_one_axe(xmax, Xmax),
+  get_one_axe(ymin, Ymin),
+  get_one_axe(ymax, Ymax).
+
+get_one_axe(Name, Value) :-
+  get_option(Name, RawV),
+  (
+    RawV = 42
+  ->
+    Value = '*'
+  ;
+    Value = RawV
+  ).
+
+
 unquoted_term_to_atom(T, A) :-
   with_output_to(atom(A), write(T)).

rosenbrock.pl

@@ -62,7 +62,7 @@ rosenbrock_init(Epsilon_abs) :-
 % Start of the ode solver, cf numerical_simulation.pl for Options
 
 ode_solver([
-    fields: _,
+    fields: Fields,
     equations: Equations,
     initial_values: InitialState,
     initial_parameter_values: InitialParameters,
@@ -102,8 +102,9 @@ ode_solver([
           ),
     nb_getval(variable_list,VariableList),
     initialize_functions_list,
-    add_functions_names(VariableList, Var_Func_List),
-    assertz(saved_row(['#''Time'|Var_Func_List])), %initialize the label of the numerical table
+    % add_functions_names(VariableList, Var_Func_List),
+    initialize_names(Fields, Names),
+    assertz(saved_row(Names)), %initialize the label of the numerical table
     eval_state(InitialState,InitialParameters,TrueInitialState),
     split_events(Events, RegularEvents, TimeEvents),
     nb_setval(events_list,RegularEvents),
@@ -114,11 +115,11 @@ ode_solver([
     add_functions_values(TrueInitialState, InitialTime, FullState),
     SecondRow =.. [row,InitialTime|FullState],
     nb_setval(last_row, SecondRow),
-    assertz(saved_row([InitialTime|FullState])),
+    log_current_row(InitialTime, FullState, Fields),
     TrueInitialTime is InitialTime
   ),
   rosenbrock_init(Epsilon_abs),
-  rosenbrock(Equations,TrueInitialTime,Duration,MaxStSz,MinStSz,Jacobian),
+  rosenbrock(Equations,TrueInitialTime,Duration,MaxStSz,MinStSz,Jacobian,Fields),
   retractall(k_fail).
 
 
@@ -187,6 +188,37 @@ add_functions_names(VarName, VarFuncName) :-
 give_function_name(function(Name, _Expr), Name).
 
 
+%! initialize_names(+Fields, -Names)
+%
+% Extract the name of the different fields to be plotted
+
+initialize_names_int([], []).
+
+initialize_names_int([Name:_|FTail], [Name|NTail]) :-
+  initialize_names_int(FTail, NTail).
+
+initialize_names([Name:_|FTail], [NName|NTail]) :-
+  atom_concat('# ', Name, NName),
+  initialize_names_int(FTail, NTail).
+
+
+%! log_current_row(+Time, +State, +Fields)
+
+log_current_row(Time, State, Fields) :-
+  prepare_row(Time, State, Fields, ToSave),
+  assertz(saved_row(ToSave)).
+
+prepare_row(_Time, _State, [], []) :- !.
+
+prepare_row(Time, State, [_N:t|FTail], [Time|VTail]) :-
+  !,
+  prepare_row(Time, State, FTail, VTail).
+
+prepare_row(Time, State, [_N:x(N)|FTail], [Val|VTail]) :-
+  nth0(N, State, Val),
+  prepare_row(Time, State, FTail, VTail).
+
+
 %! add_functions_values(+State, +Time, -FullState)
 %
 % Add the value of all functions to construct the FullState list
@@ -350,13 +382,13 @@ get_last_row(Time,CurrentState):-
 /* Rosenbrock method */
 /*********************/
 
-%! rosenbrock(+Equations, +InitialTime, +Duration, +Jacobian)
+%! rosenbrock(+Equations, +InitialTime, +Duration, +Max, +Min, +Jacobian, +Fields)
 %
 % Parameters are stored within the global variable parameters_list
 % The current state of the simulation if obtained in the final row of the global
 % variable numerical_table
 
-rosenbrock(Equations, InitialTime, Duration, MaxStSz, MinStSz, Jacobian) :-
+rosenbrock(Equations, InitialTime, Duration, MaxStSz, MinStSz, Jacobian, Fields) :-
   FinalTime is InitialTime + Duration,
   StepSizeMax is Duration*MaxStSz,
   StepSizeMin is Duration*MinStSz,
@@ -402,7 +434,8 @@ rosenbrock(Equations, InitialTime, Duration, MaxStSz, MinStSz, Jacobian) :-
     add_functions_values(Next_state, Time2, Next_state_full),
     NewLine =.. [row,Time2|Next_state_full],
     nb_setval(last_row, NewLine),
-    assertz(saved_row([Time2|Next_state_full])),
+    log_current_row(Time2, Next_state_full, Fields),
+    % assertz(saved_row([Time2|Next_state_full])),
     nb_setval(last_time,Time2),
   Time2 >= FinalTime,!,
   %Collect the data for numerical table

rosenbrock.plt

@@ -8,7 +8,7 @@ check_integration_1([], _Epsilon) :- !.
 check_integration_1([Head|Tail], Epsilon) :-
   Head = row(T,A,B),
   Sum is A+B, near(1.0, Sum, Epsilon),
-  Value is exp(-T), near(B, Value, Epsilon),
+  Value is exp(-T), near(A, Value, Epsilon),
   check_integration_1(Tail, Epsilon).
 
 check_integration_2([], _Epsilon) :- !.
@@ -76,7 +76,7 @@ test(test_time_event, [setup(command(clear_model)), cleanup(command(clear_model)
   command(add_event('Time'>=4, k=1)),
   command(numerical_simulation(method:rsbk, time:5)),
   get_table_data(D),
-  last(D, row(T,_B,A)),
+  last(D, row(T,A,_B)),
   near(A, exp(2-T), 1e-5).
 
 :- end_tests(rosenbrock).

tmpnb/tmpnb_panama.sh

@@ -2,4 +2,4 @@
 
 export TOKEN=$( head -c 30 /dev/urandom | xxd -p )
 docker run -d --restart=always --net=host -e CONFIGPROXY_AUTH_TOKEN=$TOKEN --expose 8000 --name=proxy jupyterhub/configurable-http-proxy --default-target http://127.0.0.1:9999
-docker run -d --restart=always --net=host -e CONFIGPROXY_AUTH_TOKEN=$TOKEN --name=tmpnb -v /var/run/docker.sock:/docker.sock jupyter/tmpnb python orchestrate.py --image='registry.gitlab.inria.fr/lifeware/biocham:v4.1.29' --pool-size=40 --command='start.sh biocham --notebook --NotebookApp.base_url={base_path} --NotebookApp.token={token} --ip=0.0.0.0 --port {port}'
+docker run -d --restart=always --net=host -e CONFIGPROXY_AUTH_TOKEN=$TOKEN --name=tmpnb -v /var/run/docker.sock:/docker.sock jupyter/tmpnb python orchestrate.py --image='registry.gitlab.inria.fr/lifeware/biocham:v4.3.9' --pool-size=40 --command='start.sh biocham --notebook --NotebookApp.base_url={base_path} --NotebookApp.token={token} --ip=0.0.0.0 --port {port}'

tropical.pl

@@ -235,7 +235,7 @@ subst_deg_and_vars(A/N, Vars, Ai, AA - D) :-
   !,
   subst_deg_and_vars(A, Vars, Ai, AA).
 
-% Only accept division by constants
+% Only accept addition of constants
 subst_deg_and_vars(N + M, _Vars, _Ai, D) :-
   const_degree(N+M, D),
   !.
@@ -263,7 +263,7 @@ const_eval(N, N) :-
 
 const_eval(Term, D) :-
   Term =.. [Op, A, B],
-  member(Op, ['+', '*', '-', '/']),
+  member(Op, ['+', '*', '-', '^', '/']),
   const_eval(A, AA),
   const_eval(B, BB),
   TTerm =.. [Op, AA, BB],

web/index.html

@@ -32,7 +32,7 @@
 </head>
 <body>
 <h1>The Biochemical Abstract Machine BIOCHAM 4</h1>
-<h1>version 4.3.9 January 2020</h1>
+<h1>version 4.3.10 January 2020</h1>
 
 <div class="authors">
 <p>
@@ -143,8 +143,11 @@ synthesizing reaction systems for executing imperative programs or computing rea
 </l>
 <br>
   <li><span style="text-decoration: underline;">docker images:</span>&nbsp;
-    <a href="https://gitlab.inria.fr/lifeware/biocham">https://gitlab.inria.fr/lifeware/biocham/container_registry</a>. </li>
-
+    <a
+       href="https://gitlab.inria.fr/lifeware/biocham/container_registry">https://gitlab.inria.fr/lifeware/biocham/container_registry</a>.<br/>Launch
+    with <pre>docker run -p 8888:8888 registry.gitlab.inria.fr/lifeware/biocham:[tag]</pre>
+    You can add <pre>start.sh biocham --notebook --NotebookApp.token=''</pre> if you don't want
+    token-based authentication.</li>
 <br>
 <li><span>current notebook version online:</span>&nbsp;
   <a href="http://lifeware.inria.fr/biocham4/online/">biocham4 notebook</a>. </li>