refactored assemble_rule and name_and_purify_rule

Kappa-Dev · Nov 9, 2023 · 064e776 · 064e776
1 parent d9f23e5
commit 064e776
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Showing 4 changed files with 213 additions and 125 deletions.
diff --git a/core/grammar/ast.ml b/core/grammar/ast.ml
@@ -147,7 +147,7 @@ type ('agent, 'pattern, 'mixture, 'id, 'rule) compil = {
     or kinetic rate *)
   signatures: 'agent list;  (** agent signature declaration *)
   rules: (string Locality.annoted option * 'rule Locality.annoted) list;
-      (** rules (possibly named) *)
+      (** rules (possibly named): [name_option * rule_definition] *)
   observables: ('pattern, 'id) Alg_expr.e Locality.annoted list;
       (** list of patterns to plot *)
   init: ('pattern, 'mixture, 'id) init_statment list;

diff --git a/core/grammar/counters_compiler.ml b/core/grammar/counters_compiler.ml
@@ -6,7 +6,7 @@
 (* |_|\_\ * GNU Lesser General Public License Version 3                       *)
 (******************************************************************************)
 
-type 'a rule_agent_counters = {
+type 'a with_ra_counters = {
   ra: 'a;
   ra_counters: (Ast.counter * LKappa.switching) option array;
 }

diff --git a/core/grammar/counters_compiler.mli b/core/grammar/counters_compiler.mli
@@ -6,7 +6,7 @@
 (* |_|\_\ * GNU Lesser General Public License Version 3                       *)
 (******************************************************************************)
 
-type 'a rule_agent_counters = {
+type 'a with_ra_counters = {
   ra: 'a;
   ra_counters: (Ast.counter * LKappa.switching) option array;
 }
@@ -24,8 +24,8 @@ val make_counter : int -> string -> Ast.counter
 
 val remove_counter_rule :
   Signature.s ->
-  LKappa.rule_agent rule_agent_counters list ->
-  Raw_mixture.agent rule_agent_counters list ->
+  LKappa.rule_agent with_ra_counters list ->
+  Raw_mixture.agent with_ra_counters list ->
   LKappa.rule_agent list * Raw_mixture.agent list
 
 val counters_perturbations :
@@ -45,23 +45,23 @@ val annotate_dropped_counters :
   int ->
   string ->
   (int -> unit) option ->
-  LKappa.rule_agent rule_agent_counters
+  LKappa.rule_agent with_ra_counters
 
 val annotate_edit_counters :
   Signature.s ->
   string * Locality.t ->
   Ast.counter list ->
   LKappa.rule_agent ->
   (int -> int -> int -> int -> unit) ->
-  LKappa.rule_agent rule_agent_counters
+  LKappa.rule_agent with_ra_counters
 
 val annotate_created_counters :
   Signature.s ->
   string * Locality.t ->
   Ast.counter list ->
   (int -> int -> int -> int -> unit) ->
   Raw_mixture.agent ->
-  Raw_mixture.agent rule_agent_counters
+  Raw_mixture.agent with_ra_counters
 
 val annotate_counters_with_diff :
   Signature.s ->
@@ -70,7 +70,7 @@ val annotate_counters_with_diff :
   Ast.counter list ->
   LKappa.rule_agent ->
   (int -> int -> int -> int -> unit) ->
-  LKappa.rule_agent rule_agent_counters
+  LKappa.rule_agent with_ra_counters
 
 val add_counter_to_contact_map :
   Signature.s -> (int -> int -> int -> int -> unit) -> unit