Webapp: more renaming

gui/JsSim.ml

@@ -15,19 +15,19 @@ let onload (_ : 'a) : bool Js.t =
   let () = Dom.appendChild main (Panel_tabs.navtabs ()) in
   let () = Dom.appendChild main (Panel_tabs.navcontents ()) in
   let () =
-    Dom.appendChild main (Tyxml_js.To_dom.of_div (Panel_settings.content ()))
+    Dom.appendChild main (Tyxml_js.To_dom.of_div (Panel_preferences.content ()))
   in
 
   let () = Panel_projects.onload () in
   let () = Panel_tabs.onload () in
-  let () = Panel_settings.onload () in
+  let () = Panel_preferences.onload () in
 
   let _ =
     Dom_html.window##.onresize :=
       Dom_html.handler (fun _ ->
           let () = Panel_projects.onresize () in
           let () = Panel_tabs.onresize () in
-          let () = Panel_settings.onresize () in
+          let () = Panel_preferences.onresize () in
           Js._true)
   in
   Js._true

gui/state/README.md

@@ -0,0 +1,13 @@
+Files in `state` manages state logic from different app part, similar to a `model` in a Control/Model/View architecture.
+
+`state_error.ml` manages errors at the webapp level
+
+`state_ui.ml` call _init_ and _sync_ for `state_*` files
+
+`state_file.ml` mainly manages editor & kasa stuff, but is accessed too from settings, state_ui
+
+`state_perturbation.ml` manages simulation perturbations, only used from panel preferences
+
+`state_runtime.ml` defines worker runtime, used from other `states_*` + preferences + projects controller
+
+`state_simulation.ml` sets simulation controls and functions to interact with simulation data

gui/state/state_ui.ml

@@ -9,12 +9,12 @@
 open Lwt.Infix
 
 let sync () : unit Lwt.t =
-  State_settings.sync () >>= State_runtime.sync >>= State_project.sync
+  State_preferences.sync () >>= State_runtime.sync >>= State_project.sync
   >>= fun _ ->
   State_file.sync () >>= fun _ -> Lwt.return_unit
 
 let init () : unit Lwt.t =
-  Lwt.return_unit >>= State_settings.init >>= State_runtime.init
+  Lwt.return_unit >>= State_preferences.init >>= State_runtime.init
   >>= State_project.init >>= State_file.init >>= State_simulation.init >>= sync
 
 let onload () : unit = Common.async __LOC__ (fun () -> Lwt.return_unit >>= init)

gui/ui/panel_settings.ml → gui/ui/panel_preferences.ml

@@ -23,7 +23,7 @@ let visible_on_states ?(a_class = [])
            a_class @ hidden_class))
 
 module FormPerturbation : Ui_common.Div = struct
-  let id = "panel_settings_perturbation"
+  let id = "panel_preferences_perturbation"
 
   let input =
     Html.input
@@ -71,7 +71,7 @@ module FormPerturbation : Ui_common.Div = struct
     let () =
       form_dom##.onsubmit :=
         Dom.handler (fun _ ->
-            let () = Panel_settings_controller.intervene_simulation () in
+            let () = Panel_preferences_controller.intervene_simulation () in
             Js._false)
     in
     let () = input_dom##.onchange := Dom.handler handler in
@@ -85,7 +85,7 @@ let signal_change input_dom signal_handler =
         Js._true)
 
 module InputPauseCondition : Ui_common.Div = struct
-  let id = "panel_settings_pause_condition"
+  let id = "panel_preferences_pause_condition"
 
   let input =
     Html.input
@@ -121,7 +121,7 @@ module InputPauseCondition : Ui_common.Div = struct
 end
 
 module InputPlotPeriod : Ui_common.Div = struct
-  let id = "panel_settings_plot_period"
+  let id = "panel_preferences_plot_period"
 
   let format_float_string value =
     let n = string_of_float value in
@@ -175,9 +175,9 @@ end
 
 module DivErrorMessage : Ui_common.Div = struct
   let id = "configuration_error_div"
-  let message_nav_inc_id = "panel_settings_message_nav_inc_id"
-  let message_nav_dec_id = "panel_settings_message_nav_dec_id"
-  let message_file_label_id = "panel_settings_message_file_label"
+  let message_nav_inc_id = "panel_preferences_message_nav_inc_id"
+  let message_nav_dec_id = "panel_preferences_message_nav_dec_id"
+  let message_file_label_id = "panel_preferences_message_file_label"
   let error_index, error_index_set = Hooked.S.create ~debug:"error_index" None
 
   let () =
@@ -303,7 +303,7 @@ module DivErrorMessage : Ui_common.Div = struct
         Dom.handler (fun _ ->
             let () =
               Common.debug ~loc:__LOC__
-                (Js.string "[Panel_settings] clicked file_click_handler")
+                (Js.string "[Panel_preferences] clicked file_click_handler")
             in
             let message : Api_types_t.message option =
               get_message
@@ -317,7 +317,7 @@ module DivErrorMessage : Ui_common.Div = struct
             in
             let () =
               match range with
-              | Some range -> Panel_settings_controller.focus_range range
+              | Some range -> Panel_preferences_controller.focus_range range
               | None -> ()
             in
             Js._true)
@@ -330,7 +330,7 @@ module DivErrorMessage : Ui_common.Div = struct
         Dom.handler (fun _ ->
             let () =
               Common.debug ~loc:__LOC__
-                (Js.string "[Panel_settings] clicked index_click_handler")
+                (Js.string "[Panel_preferences] clicked index_click_handler")
             in
             let index : int option =
               sanitize_index
@@ -364,7 +364,7 @@ module DivErrorMessage : Ui_common.Div = struct
 end
 
 module ButtonStart : Ui_common.Div = struct
-  let id = "panel_settings_start_button"
+  let id = "panel_preferences_start_button"
 
   let button =
     Html.button
@@ -393,15 +393,15 @@ module ButtonStart : Ui_common.Div = struct
     let () =
       start_button_dom##.onclick :=
         Dom.handler (fun _ ->
-            let () = Panel_settings_controller.start_simulation () in
+            let () = Panel_preferences_controller.start_simulation () in
             Js._true)
     in
 
     ()
 end
 
 module ButtonClear : Ui_common.Div = struct
-  let id = "panel_settings_clear_button"
+  let id = "panel_preferences_clear_button"
 
   let button =
     Html.button
@@ -420,14 +420,14 @@ module ButtonClear : Ui_common.Div = struct
     let () =
       dom##.onclick :=
         Dom.handler (fun _ ->
-            let () = Panel_settings_controller.stop_simulation () in
+            let () = Panel_preferences_controller.stop_simulation () in
             Js._true)
     in
     ()
 end
 
 module ButtonPause : Ui_common.Div = struct
-  let id = "panel_settings_pause_button"
+  let id = "panel_preferences_pause_button"
 
   let button =
     Html.button
@@ -446,14 +446,14 @@ module ButtonPause : Ui_common.Div = struct
     let () =
       button_dom##.onclick :=
         Dom.handler (fun _ ->
-            let () = Panel_settings_controller.pause_simulation () in
+            let () = Panel_preferences_controller.pause_simulation () in
             Js._true)
     in
     ()
 end
 
 module ButtonTrace : Ui_common.Div = struct
-  let id = "panel_settings_get_trace_button"
+  let id = "panel_preferences_get_trace_button"
 
   let button =
     Html.button
@@ -483,14 +483,14 @@ module ButtonTrace : Ui_common.Div = struct
     let () =
       button_dom##.onclick :=
         Dom.handler (fun _ ->
-            let () = Panel_settings_controller.simulation_trace () in
+            let () = Panel_preferences_controller.simulation_trace () in
             Js._true)
     in
     ()
 end
 
 module ButtonOutputs : Ui_common.Div = struct
-  let id = "panel_settings_outputs_button"
+  let id = "panel_preferences_outputs_button"
 
   let button =
     Html.button
@@ -509,14 +509,14 @@ module ButtonOutputs : Ui_common.Div = struct
     let () =
       button_dom##.onclick :=
         Dom.handler (fun _ ->
-            let () = Panel_settings_controller.simulation_outputs () in
+            let () = Panel_preferences_controller.simulation_outputs () in
             Js._true)
     in
     ()
 end
 
 module ButtonContinue : Ui_common.Div = struct
-  let id = "panel_settings_continue_button"
+  let id = "panel_preferences_continue_button"
 
   let button =
     Html.button
@@ -535,7 +535,7 @@ module ButtonContinue : Ui_common.Div = struct
     let () =
       button_dom##.onclick :=
         Dom.handler (fun _ ->
-            let () = Panel_settings_controller.continue_simulation () in
+            let () = Panel_preferences_controller.continue_simulation () in
             Js._true)
     in
     ()

gui/ui/modal_preferences.ml → gui/ui/panel_preferences_modal.ml

@@ -205,7 +205,7 @@ let set_action () =
 
 let set_and_save_action () =
   set_action ();
-  State_settings.set_parameters_as_default ();
+  State_preferences.set_parameters_as_default ();
   State_project.set_parameters_as_default ()
 
 let onload () =
@@ -252,12 +252,12 @@ let onload () =
 
          Js._false);
 
-  let () = State_settings.updateFontSize ~delta:0. in
+  let () = State_preferences.updateFontSize ~delta:0. in
   (Tyxml_js.To_dom.of_button increase_font)##.onclick
   := Dom_html.handler (fun _ ->
-         let () = State_settings.updateFontSize ~delta:0.2 in
+         let () = State_preferences.updateFontSize ~delta:0.2 in
          Js._false);
   (Tyxml_js.To_dom.of_button decrease_font)##.onclick
   := Dom_html.handler (fun _ ->
-         let () = State_settings.updateFontSize ~delta:(-0.2) in
+         let () = State_preferences.updateFontSize ~delta:(-0.2) in
          Js._false)

gui/ui/panel_projects.ml

@@ -22,7 +22,7 @@ let project_id_input =
     ()
 
 let li_new = Html.li [ Html.a [ Html.cdata "New project" ] ]
-let li_prefs = Html.li (Modal_preferences.content ())
+let li_prefs = Html.li (Panel_preferences_modal.content ())
 let project_id_input_dom = Tyxml_js.To_dom.of_input project_id_input
 
 let content () =
@@ -121,7 +121,7 @@ let content () =
     ]
 
 let onload () =
-  let () = Modal_preferences.onload () in
+  let () = Panel_preferences_modal.onload () in
   let () =
     Common.jquery_on
       ("#" ^ project_id_modal_id)

gui/ui/tabs/tab_din.ml → gui/ui/panel_tabs/tab_din.ml

@@ -179,7 +179,7 @@ let content () : [> Html_types.div ] Html.elt list =
   ]
 
 let navli () : [> `PCDATA | `Span ] Html.elt ReactiveData.RList.t =
-  Ui_react_sim_status.badge (fun state ->
+  Ui_track_sim_status.badge (fun state ->
       match state with
       | None -> 0
       | Some state ->

gui/ui/tabs/tab_editor/subtab_constraints.ml → gui/ui/panel_tabs/tab_editor/subtab_constraints.ml

@@ -40,32 +40,32 @@ let content () =
                           let list =
                             match conclusion with
                             | [ site_graph ] ->
-                              Utility.print_site_graph site_graph
-                                (Utility.print_newline list)
+                              Html_utility.print_site_graph site_graph
+                                (Html_utility.print_newline list)
                             | _ :: _ | [] ->
-                              let list = Utility.print_newline list in
-                              let list = Utility.print_string " ]" list in
+                              let list = Html_utility.print_newline list in
+                              let list = Html_utility.print_string " ]" list in
                               let list =
                                 snd
                                   (List.fold_left
                                      (fun (bool, list) a ->
                                        let list =
                                          if bool then
-                                           Utility.print_string " v " list
+                                           Html_utility.print_string " v " list
                                          else
                                            list
                                        in
                                        let list =
-                                         Utility.print_site_graph a list
+                                         Html_utility.print_site_graph a list
                                        in
                                        true, list)
                                      (false, list) (List.rev conclusion))
                               in
-                              let list = Utility.print_string "[ " list in
+                              let list = Html_utility.print_string "[ " list in
                               list
                           in
-                          let list = Utility.print_string "  =>  " list in
-                          let list = Utility.print_site_graph hyp list in
+                          let list = Html_utility.print_string "  =>  " list in
+                          let list = Html_utility.print_site_graph hyp list in
                           list)
                         [] (List.rev b)
                     in

gui/ui/tabs/tab_editor/subtab_contact_map.ml → gui/ui/panel_tabs/tab_editor/subtab_contact_map.ml

@@ -26,7 +26,7 @@ let extract_contact_map = function
   | _ -> failwith "Wrong ugly contact_map extractor"
 
 let contact_map_js : Js_contact.contact_map Js.t =
-  Js_contact.create_contact_map display_id State_settings.agent_coloring
+  Js_contact.create_contact_map display_id State_preferences.agent_coloring
 
 let contact_map_text : string React.signal =
   State_project.on_project_change_async ~on:tab_is_active None accuracy "null"

gui/ui/tabs/tab_editor/subtab_polymers.ml → gui/ui/panel_tabs/tab_editor/subtab_polymers.ml

@@ -15,7 +15,7 @@ let tab_was_active = ref false
 let site a = [ a, None, Some (Public_data.Bound_to 1), None ]
 
 let print_edge ((a, b), (c, d)) list =
-  Utility.print_newline (Utility.print_site_graph [ a, site b; c, site d ] list)
+  Html_utility.print_newline (Html_utility.print_site_graph [ a, site b; c, site d ] list)
 
 let content () =
   let scc =
@@ -29,23 +29,23 @@ let content () =
                 let scc = List.rev_map List.rev scc in
                 let output =
                   if scc = [] || scc = [ [] ] then
-                    Utility.print_string
+                    Html_utility.print_string
                       "The size of biomolecular compounds is uniformly bounded."
                       []
                   else (
                     let list =
                       List.fold_left
                         (fun list list_edges ->
-                          let list = Utility.print_newline list in
+                          let list = Html_utility.print_newline list in
                           List.fold_left
                             (fun list ((a, b), (c, d)) ->
                               print_edge ((a, b), (c, d)) list)
                             list list_edges)
                         [] scc
                     in
-                    let list = Utility.print_newline list in
+                    let list = Html_utility.print_newline list in
                     let list =
-                      Utility.print_string
+                      Html_utility.print_string
                         "The following bonds may form arbitrary long chains of \
                          agents:"
                         list

gui/ui/tabs/tab_log.ml → gui/ui/panel_tabs/tab_log.ml

@@ -20,7 +20,7 @@ let line_count state =
     state.simulation_info_output.simulation_output_log_messages
 
 let navli () =
-  Ui_react_sim_status.label_news tab_is_active (fun state -> line_count state)
+  Ui_track_sim_status.label_news tab_is_active (fun state -> line_count state)
 
 let content () =
   let state_log =

gui/ui/tabs/tab_outputs.ml → gui/ui/panel_tabs/tab_outputs.ml

@@ -27,7 +27,7 @@ let file_count state =
     state.Api_types_t.simulation_info_output
       .Api_types_t.simulation_output_file_lines
 
-let navli () = Ui_react_sim_status.badge (fun state -> file_count state)
+let navli () = Ui_track_sim_status.badge (fun state -> file_count state)
 
 let xml () =
   let select (file_line_ids : string list) : [> Html_types.select ] Html.elt =
@@ -126,7 +126,7 @@ let select_outputs () : unit =
   update_outputs fileindex
 
 let content () =
-  [ Ui_react_sim_status.toggle_element (fun t -> file_count t > 0) (xml ()) ]
+  [ Ui_track_sim_status.toggle_element (fun t -> file_count t > 0) (xml ()) ]
 
 let onload () =
   let () =