Improve clarity of code in kappa compiler and counter compiler

core/KaSa_rep/abstract_domains/mvbdu/dune

@@ -1,10 +1,17 @@
 (library
-  (name kappa_mvbdu)
-  (libraries kappa_kasa_kastor_toolset kappa-library.generic)
-  (flags (:standard -w @a
-    -open Kappa_parameters
-    -open Kappa_errors
-    -open Kappa_logging
-    -open Kappa_kasa_kastor_toolset
-    -open Kappa_generic_toolset
-    )))
+ (name kappa_mvbdu)
+ (libraries kappa_kasa_kastor_toolset kappa-library.generic)
+ (flags
+  (:standard
+   -w
+   @a
+   -open
+   Kappa_parameters
+   -open
+   Kappa_errors
+   -open
+   Kappa_logging
+   -open
+   Kappa_kasa_kastor_toolset
+   -open
+   Kappa_generic_toolset)))

core/KaSa_rep/abstract_domains/numerical_domains/dune

@@ -1,11 +1,19 @@
 (library
-  (name kappa_numerical_domains)
-  (libraries kappa_kasa_frontend)
-  (flags (:standard -w @a
-    -open Kappa_parameters
-    -open Kappa_errors
-    -open Kappa_logging
-    -open Kappa_kasa_kastor_toolset
-    -open Kappa_generic_toolset
-    -open Kappa_kasa_frontend
-    )))
+ (name kappa_numerical_domains)
+ (libraries kappa_kasa_frontend)
+ (flags
+  (:standard
+   -w
+   @a
+   -open
+   Kappa_parameters
+   -open
+   Kappa_errors
+   -open
+   Kappa_logging
+   -open
+   Kappa_kasa_kastor_toolset
+   -open
+   Kappa_generic_toolset
+   -open
+   Kappa_kasa_frontend)))

core/KaSa_rep/backend/dune

@@ -1,14 +1,29 @@
 (library
-  (name kappa_kasa_backend)
-  (libraries yojson kappa_kasa_frontend kappa_kasa_remanent_state kappa_kasa_site_graphs)
-  (flags (:standard -w @a
-    -open Kappa_kasa_frontend
-    -open Kappa_kasa_kastor_toolset
-    -open Kappa_parameters
-    -open Kappa_errors
-    -open Kappa_logging
-    -open Kappa_generic_toolset
-    -open Kappa_kasa_remanent_state
-    -open Kappa_kasa_site_graphs
-    -open Kappa_kasa_type_interface
-     )))
+ (name kappa_kasa_backend)
+ (libraries
+  yojson
+  kappa_kasa_frontend
+  kappa_kasa_remanent_state
+  kappa_kasa_site_graphs)
+ (flags
+  (:standard
+   -w
+   @a
+   -open
+   Kappa_kasa_frontend
+   -open
+   Kappa_kasa_kastor_toolset
+   -open
+   Kappa_parameters
+   -open
+   Kappa_errors
+   -open
+   Kappa_logging
+   -open
+   Kappa_generic_toolset
+   -open
+   Kappa_kasa_remanent_state
+   -open
+   Kappa_kasa_site_graphs
+   -open
+   Kappa_kasa_type_interface)))

core/KaSa_rep/counting_enumerating_species/dune

@@ -1,12 +1,19 @@
 (library
-  (name kappa_species_count_enumeration)
-  (libraries num kappa_kasa_remanent_state kappa-library.generic)
-  (flags (:standard)
-    -open Kappa_parameters
-    -open Kappa_errors
-    -open Kappa_kasa_remanent_state
-    -open Kappa_kasa_frontend
-    -open Kappa_logging
-    -open Kappa_generic_toolset
-    -open Kappa_kasa_kastor_toolset
-))
+ (name kappa_species_count_enumeration)
+ (libraries num kappa_kasa_remanent_state kappa-library.generic)
+ (flags
+  (:standard)
+  -open
+  Kappa_parameters
+  -open
+  Kappa_errors
+  -open
+  Kappa_kasa_remanent_state
+  -open
+  Kappa_kasa_frontend
+  -open
+  Kappa_logging
+  -open
+  Kappa_generic_toolset
+  -open
+  Kappa_kasa_kastor_toolset))

core/KaSa_rep/export/dune

@@ -1,25 +1,50 @@
 (library
-  (name kappa_kasa_export)
-  (libraries kappa_flow_analysis kappa_reachability kappa_influence_map kappa_polymers_analysis  kappa_symmetries)
-  (flags (:standard)
-    -open Kappa_kasa_frontend
-    -open Kappa_kasa_remanent_state
-    -open Kappa_grammar
-    -open Kappa_terms
-    -open Kappa_logging
-    -open Kappa_generic_toolset
-    -open Kappa_errors
-    -open Kappa_reachability
-    -open Kappa_flow_analysis
-    -open Kappa_parameters
-    -open Kappa_kasa_kastor_toolset
-    -open Kappa_cli
-    -open Kappa_profiling
-    -open Kappa_mixtures
-    -open Kappa_influence_map
-    -open Kappa_polymers_analysis
-    -open Kappa_kasa_site_graphs
-    -open Kappa_kasa_backend
-    -open Kappa_symmetries
-    -open Kappa_kasa_type_interface
-))
+ (name kappa_kasa_export)
+ (libraries
+  kappa_flow_analysis
+  kappa_reachability
+  kappa_influence_map
+  kappa_polymers_analysis
+  kappa_symmetries)
+ (flags
+  (:standard)
+  -open
+  Kappa_kasa_frontend
+  -open
+  Kappa_kasa_remanent_state
+  -open
+  Kappa_grammar
+  -open
+  Kappa_terms
+  -open
+  Kappa_logging
+  -open
+  Kappa_generic_toolset
+  -open
+  Kappa_errors
+  -open
+  Kappa_reachability
+  -open
+  Kappa_flow_analysis
+  -open
+  Kappa_parameters
+  -open
+  Kappa_kasa_kastor_toolset
+  -open
+  Kappa_cli
+  -open
+  Kappa_profiling
+  -open
+  Kappa_mixtures
+  -open
+  Kappa_influence_map
+  -open
+  Kappa_polymers_analysis
+  -open
+  Kappa_kasa_site_graphs
+  -open
+  Kappa_kasa_backend
+  -open
+  Kappa_symmetries
+  -open
+  Kappa_kasa_type_interface))

core/KaSa_rep/export/export.ml

@@ -221,17 +221,21 @@ functor
         in
         let () = cli.Run_cli_args.syntaxVersion <- syntax_version in
         let () = cli.Run_cli_args.inputKappaFileNames <- files in
-        let (_, env, contactmap, _, _, _, _, init), _ =
+        let compilation_result : Cli_init.compilation_result =
           Cli_init.get_compilation
             ~warning:(fun ~pos:_ _msg -> ())
-            ~debugMode:false cli
+            ~debug_mode:false cli
         in
         let state =
-          Remanent_state.set_init_state init
-            (Remanent_state.set_env (Some env)
-               (Remanent_state.set_contact_map_int (Some contactmap) state))
+          Remanent_state.set_init_state compilation_result.init_l
+            (Remanent_state.set_env (Some compilation_result.env)
+               (Remanent_state.set_contact_map_int
+                  (Some compilation_result.contact_map) state))
         in
-        state, Some (env : Model.t), Some init, Some contactmap
+        ( state,
+          Some (compilation_result.env : Model.t),
+          Some compilation_result.init_l,
+          Some compilation_result.contact_map )
 
     let compute_env show_title state =
       let state, env, _, _ = compute_env_init show_title state in
@@ -1713,27 +1717,38 @@ functor
                               (Ckappa_sig.site_name_of_int y)
                           in
                           ( state,
-                            (Locality.dummy_annot sx, Locality.dummy_annot sy)
+                            (Loc.annot_with_dummy sx, Loc.annot_with_dummy sy)
                             :: list ))
                         (state, []) rev_binding
                     in
                     let states' =
                       NamedDecls.create
                         (Tools.array_map_of_list
-                           (fun i -> Locality.dummy_annot i, ())
+                           (fun i -> Loc.annot_with_dummy i, ())
                            states)
                     in
                     ( state,
-                      (Locality.dummy_annot x, (states', binding', None)) :: acc
-                    ))
+                      ( Loc.annot_with_dummy x,
+                        {
+                          Signature.internal_state = states';
+                          links = Some binding';
+                          counters_info = None;
+                        } )
+                      :: acc ))
                   (state, []) interface
               in
               ( state,
-                (Locality.dummy_annot a, NamedDecls.create (Array.of_list acc))
+                (Loc.annot_with_dummy a, NamedDecls.create_from_list acc)
                 :: list ))
           (state, []) l.(0)
       in
-      let signature = Signature.create ~counters:[] true l in
+
+      let agent_sigs =
+        LKappa_compiler.agent_sigs_of_agent_sigs_with_links_as_lists
+          ~build_contact_map:true
+          (NamedDecls.create_from_list l)
+      in
+      let signature = Signature.create ~counters_per_agent:[] agent_sigs in
       Remanent_state.set_signature signature state, signature
 
     let get_signature = get_gen Remanent_state.get_signature compute_signature
@@ -1907,7 +1922,7 @@ functor
         let cache = LKappa_auto.init_cache () in
         let cc_cache = Pattern.PreEnv.of_env (Model.domain env) in
         let _cc_cache, chemical_species =
-          Symmetry_interface.species_of_initial_state_env ~debugMode:false env
+          Symmetry_interface.species_of_initial_state_env ~debug_mode:false env
             contact_map_int cc_cache init
         in
         let state, contact_map = get_contact_map ~accuracy_level state in

core/KaSa_rep/flow/dune

@@ -1,11 +1,15 @@
 (library
-  (name kappa_flow_analysis)
-  (libraries kappa_kasa_frontend)
-  (flags (:standard)
-    -open Kappa_kasa_frontend
-    -open Kappa_generic_toolset
-    -open Kappa_parameters
-    -open Kappa_logging
-    -open Kappa_errors
-
-))
+ (name kappa_flow_analysis)
+ (libraries kappa_kasa_frontend)
+ (flags
+  (:standard)
+  -open
+  Kappa_kasa_frontend
+  -open
+  Kappa_generic_toolset
+  -open
+  Kappa_parameters
+  -open
+  Kappa_logging
+  -open
+  Kappa_errors))

core/KaSa_rep/frontend/build_graph.ml

@@ -29,7 +29,7 @@ let add_agent parameters error handler cckappa_only agent_id agent_type mixture
       Cckappa_sig.agent_kasim_id = agent_id;
       Cckappa_sig.agent_name = agent_type;
       Cckappa_sig.agent_interface = Ckappa_sig.Site_map_and_set.Map.empty;
-      Cckappa_sig.agent_position = Locality.dummy;
+      Cckappa_sig.agent_position = Loc.dummy;
       Cckappa_sig.is_created = false;
     }
   in
@@ -45,7 +45,7 @@ let add_agent parameters error handler cckappa_only agent_id agent_type mixture
 let empty_port =
   {
     Cckappa_sig.site_name = Ckappa_sig.dummy_site_name;
-    Cckappa_sig.site_position = Locality.dummy;
+    Cckappa_sig.site_position = Loc.dummy;
     Cckappa_sig.site_free = None;
     Cckappa_sig.site_state =
       {
@@ -81,7 +81,7 @@ let add_site parameters error handler cckappa_only agent_id site_name mixture =
     let site =
       {
         Cckappa_sig.site_name;
-        Cckappa_sig.site_position = Locality.dummy;
+        Cckappa_sig.site_position = Loc.dummy;
         Cckappa_sig.site_free = None;
         Cckappa_sig.site_state =
           {
@@ -330,7 +330,7 @@ let add_link parameters error agent_id site_name agent_id' site_name'
     in_progress =
   let handler = in_progress.kappa_handler in
   let lnk_id = in_progress.fresh_bond_id in
-  let fresh_bond_id = Ckappa_sig.next_lnk_value in_progress.fresh_bond_id in
+  let fresh_bond_id = Ckappa_sig.next_link_value in_progress.fresh_bond_id in
   let error, mixture =
     add_link parameters error handler in_progress.cckappa_only agent_id
       site_name agent_id' site_name' lnk_id in_progress.mixture

core/KaSa_rep/frontend/cckappa_sig.ml

@@ -26,7 +26,7 @@ type kappa_handler = {
   nagents: Ckappa_sig.c_agent_name;
   agents_dic: Ckappa_sig.agent_dic;
   agents_annotation:
-    (string * Locality.t list)
+    (string * Loc.t list)
     Ckappa_sig.Agent_type_nearly_Inf_Int_storage_Imperatif.t;
   interface_constraints:
     Ckappa_sig.agent_specification
@@ -201,8 +201,7 @@ type compil = {
   rules: enriched_rule Ckappa_sig.Rule_nearly_Inf_Int_storage_Imperatif.t;
   (*rules (possibly named)*)
   observables:
-    (mixture, string) Alg_expr.e Locality.annot
-    Int_storage.Nearly_inf_Imperatif.t;
+    (mixture, string) Alg_expr.e Loc.annoted Int_storage.Nearly_inf_Imperatif.t;
   (*list of patterns to plot*)
   init: enriched_init Int_storage.Nearly_inf_Imperatif.t;
   (*initial graph declaration*)
@@ -615,7 +614,7 @@ let empty_port site =
       site_name = site;
       site_free = None;
       site_state = empty_interval;
-      site_position = Locality.dummy;
+      site_position = Loc.dummy;
     }
   in
   empty_port

core/KaSa_rep/frontend/cckappa_sig.mli

@@ -26,7 +26,7 @@ type kappa_handler = {
   nagents: Ckappa_sig.c_agent_name;
   agents_dic: Ckappa_sig.agent_dic;
   agents_annotation:
-    (string * Locality.t list)
+    (string * Loc.t list)
     Ckappa_sig.Agent_type_nearly_Inf_Int_storage_Imperatif.t;
   interface_constraints:
     Ckappa_sig.agent_specification
@@ -194,8 +194,7 @@ type compil = {
   rules: enriched_rule Ckappa_sig.Rule_nearly_Inf_Int_storage_Imperatif.t;
   (*rules (possibly named)*)
   observables:
-    (mixture, string) Alg_expr.e Locality.annot
-    Int_storage.Nearly_inf_Imperatif.t;
+    (mixture, string) Alg_expr.e Loc.annoted Int_storage.Nearly_inf_Imperatif.t;
   (*list of patterns to plot*)
   init: enriched_init Int_storage.Nearly_inf_Imperatif.t;
   (*initial graph declaration*)