renaming

lib/simulator.ml → lib/mutsel_simulator.ml

@@ -22,7 +22,7 @@ let simulation ?branch_scale ?seed ~n_h0 ~n_ha ~ne_s:(ne_s0, ne_s1) ~gBGC:(gBGC0
         |> to_fitness
         |> Array.map ~f: Amino_acid.Vector.of_array_exn
       ) in
-    Codepitk.Simulator.Site_independent_mutsel.simulation
+    Codepitk.Mutsel_simulator.Site_independent.simulation
       ?branch_scale ?seed ~n_h0 ~n_ha ~gBGC:(gBGC0, gBGC1)
       ~ne_s:(ne_s0, ne_s1) ~tree ~fitness_profiles ()
   in
@@ -30,7 +30,7 @@ let simulation ?branch_scale ?seed ~n_h0 ~n_ha ~ne_s:(ne_s0, ne_s1) ~gBGC:(gBGC0
 
 let alignment_of_simulation sim =
   let f = fun%workflow dest ->
-    let sim : Codepitk.Simulator.Site_independent_mutsel.simulation =
+    let sim : Codepitk.Mutsel_simulator.Site_independent.simulation =
       [%eval sim]
     in
     let species_name = Phylogenetics.Tree.leaves sim.tree in
@@ -45,7 +45,7 @@ let alignment_of_simulation sim =
 let fitness_histogram sim =
   let f = fun%workflow dest ->
     let open Phylogenetics in
-    let sim : Codepitk.Simulator.Site_independent_mutsel.simulation =
+    let sim : Codepitk.Mutsel_simulator.Site_independent.simulation =
       [%eval sim]
     in
     let params = Array.append sim.h0_params sim.ha_params in

lib/simulator.mli → lib/mutsel_simulator.mli

@@ -12,14 +12,14 @@ val simulation :
   tree:nhx file ->
   fitness_profiles:#text file ->
   unit ->
-  Simulator.Site_independent_mutsel.simulation workflow
+  Mutsel_simulator.Site_independent.simulation workflow
 
 val alignment_of_simulation :
-  Simulator.Site_independent_mutsel.simulation workflow ->
+  Mutsel_simulator.Site_independent.simulation workflow ->
   nucleotide_fasta file
 
 val fitness_histogram :
-  Simulator.Site_independent_mutsel.simulation workflow ->
+  Mutsel_simulator.Site_independent.simulation workflow ->
   pdf file
 
 val pair_tree :

lib/simulation_pipeline.ml

@@ -29,7 +29,7 @@ let tree_workflow = function
   | Pair_tree { branch_length1 ;
                 branch_length2 ;
                 npairs } ->
-    Simulator.pair_tree ~branch_length1 ~branch_length2 ~npairs
+    Mutsel_simulator.pair_tree ~branch_length1 ~branch_length2 ~npairs
 
 module Make(Q : Detection_pipeline.Query) = struct
   include Detection_pipeline.Make(Q)
@@ -68,11 +68,11 @@ module Mutsel_query = struct
   let simulation { n_h0 ; n_ha ; profiles ; ne_s ; gBGC ; branch_scale ; seed ; tree ; _ } =
     let tree = tree_workflow tree in
     let fitness_profiles = Workflow.input profiles in
-    Simulator.simulation ~branch_scale ~n_ha ~n_h0 ~ne_s ~gBGC ~tree ~seed ~fitness_profiles ()
+    Mutsel_simulator.simulation ~branch_scale ~n_ha ~n_h0 ~ne_s ~gBGC ~tree ~seed ~fitness_profiles ()
 
   let nucleotide_alignment p =
     simulation p
-    |> Simulator.alignment_of_simulation
+    |> Mutsel_simulator.alignment_of_simulation
 
   let tree ~branch_length_unit:_ { tree ; _ } = tree_workflow tree
 end
@@ -103,7 +103,7 @@ module Mutsel = struct
     let f = fun%workflow () ->
       let open Phylogenetics in
       let open Codepitk in
-      let open Codepitk.Simulator.Site_independent_mutsel in
+      let open Codepitk.Mutsel_simulator.Site_independent in
       let module Codon = Codon.Universal_genetic_code.NS in
       let sim : simulation = [%eval simulation q] in
       let result_paths = [%eval Bistro.Workflow.path_list (List.map methods ~f:(fun f -> f q))] in

lib/simulation_pipeline.mli

@@ -34,7 +34,7 @@ module Mutsel : sig
 
   val simulation :
     query ->
-    Codepitk.Simulator.Site_independent_mutsel.simulation workflow
+    Codepitk.Mutsel_simulator.Site_independent.simulation workflow
 
 
   type benchmark = {

lib/tk/simulator.ml → lib/tk/mutsel_simulator.ml

@@ -8,7 +8,7 @@ let tree_rescale_branch_length t ~scale =
       { bi with length = bi.length *. scale }
     )
 
-module Site_independent_mutsel = struct
+module Site_independent = struct
   include Simulator.Make(Mutsel.NSCodon)(Mutsel)(Branch_info)
 
   let alignment tree ~root param =

lib/tk/simulator.mli → lib/tk/mutsel_simulator.mli

 open Phylogenetics
 
-module Site_independent_mutsel : sig
+module Site_independent : sig
   type simulation = {
     sequences : Dna.t list ;
     fitness_profiles : Amino_acid.vector array ;