perturbation -> intervention

CHANGES.md

@@ -116,11 +116,13 @@ is:
 [LHS] <-> [RHS] @ [binary rate] {unary rate}, [reverse rate]
 ```
 
-### every modification (perturbation action) ends by a semicolon
+### Kappa speaks about intervention instead of perturbation
 
-Perturbations used to take a semi-colon separated list of modification
+### every modification (intervention action) ends by a semicolon
+
+Interventions used to take a semi-colon separated list of modification
 as body. Now, every modification ends by a semi-colon. Said
-diferrently even the last (or only) modification of a perturbation
+diferrently even the last (or only) modification of a intervention
 ends by `;`.
 
 ```
@@ -134,7 +136,7 @@ ends by `;`.
     $ADD 10 A();
 ```
 
-### Repetitive perturbation syntax has changed
+### Repetitive intervention syntax has changed
 Usage is now if _precondition_ do _modification(s)_ and repeat as long
 as _condition_.
 
@@ -225,9 +227,9 @@ filename.
 
 ## Ctrl-c does not kill the simulator
 
-Ctrl-c now pauses the simulation and launches a toplevel environment in
-which you can do modifications and perturbations interactively, and
-then (optionally) continue the simulation.
+Ctrl-c now pauses the simulation and launches a toplevel environment
+in which you can do modifications interactively, and then (optionally)
+continue the simulation.
 
 You can use `-mode batch` to get a Ctrl-c that does kill the simulator
 (and more generally to get a KaSim that never asks questions and assumes

api/api.mli

@@ -74,8 +74,8 @@ class type manager_simulation = object
 
   method simulation_pause : unit result Lwt.t
 
-  method simulation_perturbation :
-    Api_types_t.simulation_perturbation -> string result Lwt.t
+  method simulation_intervention :
+    Api_types_t.simulation_intervention -> string result Lwt.t
 
   method simulation_continue : string -> unit result Lwt.t
 

api/api_types.atd

@@ -65,7 +65,7 @@ type simulation_parameter = {
   store_trace : bool ;
 } <ocaml field_prefix="simulation_">
 
-type simulation_perturbation = { perturbation_code : string }
+type simulation_intervention = { intervention_code : string }
 
 type plot_limit = { plot_limit_offset <json name="offset"> : int nullable ;
                     plot_limit_points <json name="nb_points"> : int nullable ; }

api/kappa_facade.ml

@@ -10,8 +10,8 @@ let msg_process_not_paused =
   "process not paused"
 let msg_observables_less_than_zero =
   "Plot observables must be greater than zero"
-let msg_missing_perturbation_context =
-  "Invalid runtime state missing missing perturbation context"
+let msg_missing_intervention_context =
+  "Invalid runtime state: missing intervention context"
 
 (**  System process
 
@@ -473,11 +473,11 @@ let stop
 let perturbation
     ~(system_process : system_process)
     ~(t : t)
-    ~(perturbation:Api_types_t.simulation_perturbation)
+    ~(perturbation:Api_types_t.simulation_intervention)
   : (string, Api_types_t.errors) Result.result Lwt.t =
   let () = ignore(system_process) in
   let lexbuf =
-    Lexing.from_string perturbation.Api_types_t.perturbation_code
+    Lexing.from_string perturbation.Api_types_t.intervention_code
   in
   Lwt.catch
     (fun () ->

api/kappa_facade.mli

@@ -21,39 +21,39 @@ val parse :
   system_process:system_process ->
   kappa_files:Api_types_t.file list ->
   overwrites:(string * Nbr.t) list ->
-  (t, Api_types_j.errors) Result.result Lwt.t
+  (t, Api_types_t.errors) Result.result Lwt.t
 
 val start :
   system_process:system_process ->
-  parameter:Api_types_j.simulation_parameter ->
+  parameter:Api_types_t.simulation_parameter ->
   t:t ->
-  (unit, Api_types_j.errors) Result.result Lwt.t
+  (unit, Api_types_t.errors) Result.result Lwt.t
 
 val pause :
   system_process:system_process ->
-  t:t -> (unit, Api_types_j.errors) Result.result Lwt.t
+  t:t -> (unit, Api_types_t.errors) Result.result Lwt.t
 
 val stop :
   system_process:system_process ->
-  t:t -> (unit, Api_types_j.errors) Result.result Lwt.t
+  t:t -> (unit, Api_types_t.errors) Result.result Lwt.t
 
 val perturbation :
   system_process:system_process ->
   t:t ->
-  perturbation:Api_types_j.simulation_perturbation ->
-  (string, Api_types_j.errors) Result.result Lwt.t
+  perturbation:Api_types_t.simulation_intervention ->
+  (string, Api_types_t.errors) Result.result Lwt.t
 
 val continue :
   system_process:system_process -> t:t -> pause_condition:string ->
-  (unit, Api_types_j.errors) Result.result Lwt.t
+  (unit, Api_types_t.errors) Result.result Lwt.t
 
 val progress :
   system_process:system_process -> t:t ->
-  (Api_types_t.simulation_progress, Api_types_j.errors) Result.result Lwt.t
+  (Api_types_t.simulation_progress, Api_types_t.errors) Result.result Lwt.t
 
 val outputs :
   system_process:system_process -> t:t ->
-  (Api_data.simulation_detail_output, Api_types_j.errors) Result.result Lwt.t
+  (Api_data.simulation_detail_output, Api_types_t.errors) Result.result Lwt.t
 
 val efficiency : t -> Counter.Efficiency.t
 

api/manager_simulation.ml

@@ -307,8 +307,8 @@ class manager_simulation
            )
         )
 
-    method simulation_perturbation
-        (simulation_perturbation : Api_types_j.simulation_perturbation) :
+    method simulation_intervention
+        (simulation_perturbation : Api_types_j.simulation_intervention) :
       string Api.result Lwt.t =
       Model_storage.bind_simulation
         project

api/mpi_api.ml

@@ -88,9 +88,9 @@ let on_message
   | `SimulationPause ->
     manager#simulation_pause >>=
     (handler (fun () -> `SimulationPause))
-  | `SimulationPerturbation simulation_perturbation ->
-    (manager#simulation_perturbation simulation_perturbation) >>=
-    (handler (fun s -> `SimulationPerturbation s))
+  | `SimulationIntervention simulation_intervention ->
+    (manager#simulation_intervention simulation_intervention) >>=
+    (handler (fun s -> `SimulationIntervention s))
   | `SimulationStart simulation_parameter ->
     (manager#simulation_start simulation_parameter) >>=
     (handler (fun result -> `SimulationStart result))
@@ -368,13 +368,13 @@ class virtual  manager_base () : manager_base_type =
                 (Api_common.result_error_exception
                    (BadResponse response)))
 
-    method simulation_perturbation
-      (simulation_perturbation : Api_types_j.simulation_perturbation) :
+    method simulation_intervention
+      (simulation_intervention : Api_types_j.simulation_intervention) :
       string Api.result Lwt.t =
-      self#message (`SimulationPerturbation simulation_perturbation) >>=
+      self#message (`SimulationIntervention simulation_intervention) >>=
       Api_common.result_bind_lwt
         ~ok:(function
-            | `SimulationPerturbation s ->
+            | `SimulationIntervention s ->
               Lwt.return (Api_common.result_ok s)
             | response ->
               Lwt.return

api/mpi_message.atd

@@ -25,7 +25,7 @@ type project_parse <ocaml from="Api_types"> = abstract
 type project_parameter <ocaml from="Api_types"> = abstract
 
 type simulation_parameter <ocaml from="Api_types"> = abstract
-type simulation_perturbation  <ocaml from="Api_types"> = abstract
+type simulation_intervention  <ocaml from="Api_types"> = abstract
 type simulation_info <ocaml from="Api_types"> = abstract
 type simulation_efficiency <ocaml module="Counter.Efficiency" t="t"> = abstract
 type file_line  <ocaml from="Api_types"> = abstract
@@ -70,7 +70,7 @@ type request = [
 	       | SimulationTrace
 	       | SimulationParameter
                | SimulationPause
-               | SimulationPerturbation of simulation_perturbation
+               | SimulationIntervention of simulation_intervention
                | SimulationStart of simulation_parameter
                ]
 
@@ -104,7 +104,7 @@ type response_content = [
    | SimulationContinue
    | SimulationDelete
    | SimulationPause
-   | SimulationPerturbation of string
+   | SimulationIntervention of string
    | SimulationStart of simulation_artifact
 ]
 

dataStructures/operator.ml

@@ -14,7 +14,7 @@ type bin_bool_op = AND | OR
 type un_bool_op = NOT
 type compare_op = GREATER | SMALLER | EQUAL | DIFF
 
-type rev_dep = ALG of int | RULE of int | PERT of int
+type rev_dep = ALG of int | RULE of int | MODIF of int
 
 let bin_alg_op_to_string = function
   | MULT -> "*"
@@ -134,17 +134,17 @@ let print_rev_dep f = function
   | ALG id ->
     Format.fprintf f "algebraic variable [%i]" id
   (*"variable '%a'" (Model.print_alg env) id*)
-  | PERT id -> Format.fprintf f "perturbation [%i]" id
+  | MODIF id -> Format.fprintf f "intervention [%i]" id
 
 let rev_dep_to_yojson = function
   | RULE id -> `List [ `String "RULE"; `Int id ]
   | ALG id -> `List [ `String "ALG"; `Int id ]
-  | PERT id -> `List [ `String "PERT"; `Int id ]
+  | MODIF id -> `List [ `String "MODIF"; `Int id ]
 
 let rev_dep_of_yojson = function
   | `List [ `String "RULE"; `Int id ] -> RULE id
   | `List [ `String "ALG"; `Int id ] -> ALG id
-  | `List [ `String "PERT"; `Int id ] -> PERT id
+  | `List [ `String "MODIF"; `Int id ] -> MODIF id
   | x -> raise (Yojson.Basic.Util.Type_error ("Uncorrect rev_dep",x))
 
 module DepSetMap = SetMap.Make (struct type t = rev_dep

dataStructures/operator.mli

@@ -42,7 +42,7 @@ val compare_op_of_json : Yojson.Basic.json -> compare_op
 
 (** {6 Dependencies management} *)
 
-type rev_dep = ALG of int | RULE of int | PERT of int
+type rev_dep = ALG of int | RULE of int | MODIF of int
 module DepSet : SetMap.Set with type elt = rev_dep
 val print_rev_dep : Format.formatter -> rev_dep -> unit
 val rev_dep_to_yojson : rev_dep -> Yojson.Basic.json

grammar/eval.ml

@@ -244,7 +244,7 @@ let effects_of_modif
       | _ ->
         raise
           (ExceptionDefn.Malformed_Decl
-             ("Ambiguous rule in perturbation is impossible",pos)) in
+             ("Ambiguous rule in modifition is impossible",pos)) in
     (domain'',
      (Primitives.ITER_RULE (alg_pos, elem_rule))::rev_effects)
   | UPDATE ((i, _), alg_expr) ->
@@ -316,9 +316,9 @@ let effects_of_modifs
   domain',List.rev rev_effects
 
 let compile_modifications_no_track =
-  effects_of_modifs [] [] (Operator.PERT (-1))
+  effects_of_modifs [] [] (Operator.MODIF (-1))
 
-(* perturbations without pre and post, but with alarm are not applied
+(* interventions without pre and post, but with alarm are not applied
 at initialisation *)
 let pert_not_init = function
   | (Some _, None, None) ->
@@ -343,7 +343,7 @@ let pert_of_result
                raise (ExceptionDefn.Malformed_Decl
                         ("alarm has to be strictly greater than 0.0", pos)) else ()
           | None -> () in
-        let origin = Operator.PERT p_id in
+        let origin = Operator.MODIF p_id in
         let pre_expr' = pert_not_init (alarm,pre_expr,opt_post) in
         let (domain',pre) =
           compile_bool ?bwd_bisim ~compileModeOn ~origin contact_map domain pre_expr' in
@@ -537,7 +537,7 @@ let compile ~outputs ~pause ~return ~max_sharing ?bwd_bisim ~compileModeOn ?over
   let rule_nd = Array.of_list compiled_rules in
 
   pause @@ fun () ->
-  outputs (Data.Log "\t -perturbations");
+  outputs (Data.Log "\t -interventions");
   let (preenv,alg_deps'',pert,has_tracking) =
     pert_of_result
       result.variables result.rules alg_deps' ?bwd_bisim ~compileModeOn

grammar/kparser4.mly

@@ -565,7 +565,7 @@ effect:
        pend,p) }
   | INTRO annot error
     { raise (ExceptionDefn.Syntax_Error
-               (add_pos 3 "Malformed perturbation instruction, I was expecting \
+               (add_pos 3 "Malformed intervention instruction, I was expecting \
 '$ADD alg_expression kappa_expression'")) }
   | DELETE annot alg_expr pattern
     { let (m,pend,p) = $4 in
@@ -581,7 +581,7 @@ effect:
        pend,p) }
   | DELETE annot error
            { raise (ExceptionDefn.Syntax_Error
-                      (add_pos 3 "Malformed perturbation instruction, I was \
+                      (add_pos 3 "Malformed intervention instruction, I was \
 expecting '$DEL alg_expression kappa_expression'")) }
   | SNAPSHOT print_expr { let (s,pend,p) = $2 in (Ast.SNAPSHOT s,pend,p) }
   | STOP print_expr { let (s,pend,p) = $2 in (Ast.STOP s,pend,p) }

grammar/snip.ml

@@ -519,7 +519,7 @@ let rec complete_with_creation
       (Primitives.Transformation.Agent place::added) links_transf actions [] 0
 
 let incr_origin = function
-  | ( Operator.ALG _ | Operator.PERT _  as x) -> x
+  | ( Operator.ALG _ | Operator.MODIF _  as x) -> x
   | Operator.RULE i -> Operator.RULE (succ i)
 
 let connected_components_of_mixture created mix (env,origin) =

js/panel_settings.ml

@@ -38,7 +38,7 @@ module FormPerturbation : Ui_common.Div = struct
     Html.button
       ~a:[ Html.a_button_type `Submit
          ; Html.a_class ["btn"; "btn-default" ] ]
-      [ Html.cdata "perturbation" ]
+      [ Html.cdata "intervention" ]
   let form = Html.form ~a:
       [Tyxml_js.R.Html.a_class
          (visible_on_states
@@ -56,13 +56,13 @@ module FormPerturbation : Ui_common.Div = struct
        (fun _ ->
           let model_perturbation : string = Js.to_string input_dom##.value in
           let () =
-            State_perturbation.set_model_perturbation model_perturbation in
+            State_perturbation.set_model_intervention model_perturbation in
           Js._true)
      in
 
      let () = form_dom##.onsubmit :=
          Dom.handler (fun _ ->
-             let () = Panel_settings_controller.perturb_simulation () in
+             let () = Panel_settings_controller.intervene_simulation () in
              Js._false) in
      let () = input_dom##.onchange := Dom.handler handler in
      ()

js/panel_settings_controller.ml

@@ -58,14 +58,14 @@ let start_simulation () =
        >>= (fun _ -> Lwt.return_unit)
     )
 
-let perturb_simulation () =
+let intervene_simulation () =
   Common.async
     __LOC__
     (fun () ->
       let model_perturbation =
-        React.S.value State_perturbation.model_perturbation in
+        React.S.value State_perturbation.model_intervention in
       State_error.wrap
-        __LOC__ (State_simulation.perturb_simulation model_perturbation) >>=
+        __LOC__ (State_simulation.intervene_simulation model_perturbation) >>=
       Api_common.result_map
         ~ok:(fun _ message_text ->
             let () = State_error.add_error __LOC__ [{

js/panel_settings_controller.mli

@@ -10,6 +10,6 @@ val continue_simulation : unit -> unit
 val pause_simulation : unit -> unit
 val stop_simulation : unit -> unit
 val start_simulation : unit -> unit
-val perturb_simulation : unit -> unit
+val intervene_simulation : unit -> unit
 val simulation_trace : unit -> unit
 val focus_range : Api_types_j.range -> unit

js/rest_api.ml

@@ -278,18 +278,18 @@ class manager
         (fun result ->
            (`SimulationParameter
                         (Mpi_message_j.simulation_parameter_of_string result)))
-    | `SimulationPerturbation simulation_perturbation ->
+    | `SimulationIntervention simulation_intervention ->
       send
         ?timeout
         (Format.sprintf
-           "%s/v2/projects/%s/simulation/perturbation"
+           "%s/v2/projects/%s/simulation/intervention"
            url
            project_id)
         `PUT
-        ~data:(Api_types_j.string_of_simulation_perturbation
-                 simulation_perturbation)
+        ~data:(Api_types_j.string_of_simulation_intervention
+                 simulation_intervention)
         (fun result ->
-           `SimulationPerturbation
+           `SimulationIntervention
              (Yojson.Safe.read_string
                 (Yojson.Safe.init_lexer ()) (Lexing.from_string result)))
     | `SimulationStart simulation_parameter ->

js/state_perturbation.ml

@@ -6,4 +6,4 @@
 (* |_|\_\ * GNU Lesser General Public License Version 3                       *)
 (******************************************************************************)
 
-let model_perturbation, set_model_perturbation = React.S.create ""
+let model_intervention, set_model_intervention = React.S.create ""

js/state_perturbation.mli

@@ -5,5 +5,5 @@
 (* | . \  * This file is distributed under the terms of the                   *)
 (* |_|\_\ * GNU Lesser General Public License Version 3                       *)
 (******************************************************************************)
-val model_perturbation : string React.signal
-val set_model_perturbation : ?step:React.step -> string -> unit
+val model_intervention : string React.signal
+val set_model_intervention : ?step:React.step -> string -> unit