removed app/diffseldsparse_benchmark

app/diffseldsparse_benchmark.ml

-open Core
-open Codepi
-
-let main ~n_h0 ~n_ha ~seed:i () =
-  let open Simulation_dataset in
-  let sim =
-    bppseqgen_mixed
-      ~tree:(NHX (Bistro.Workflow.input "example/trees_analyses/cyp_coding.Chrysithr_root.nhx"))
-      ~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
-      ~n_h0 ~n_ha ~ne_s:4. ~seed:i ()
-  in
-  let w = benchmark sim in
-  Bistro_engine.Scheduler.simple_eval_exn ~np:4 ~mem:(`GB 4) (Bistro.Workflow.path w)
-  |> print_endline
-
-let command =
-  let open Command.Let_syntax in
-  Command.basic
-    ~summary:"Run diffseldsparse bench"
-    [%map_open
-      let n_ha =
-        flag "--n-ha" (required int) ~doc:"INT Number of Ha sites"
-      and n_h0 =
-        flag "--n-h0" (required int) ~doc:"INT Number of H0 sites"
-      and seed =
-        flag "--seed" (required int) ~doc:"INT Global seed"
-      in
-      main ~n_ha ~n_h0 ~seed
-    ]
-
-let () = Command.run command

app/dune

@@ -6,14 +6,6 @@
  (preprocess
   (pps ppx_jane)))
 
-(executable
- (name diffseldsparse_benchmark)
- (public_name diffseldsparse_benchmark)
- (modules diffseldsparse_benchmark)
- (libraries codepi)
- (preprocess
-  (pps ppx_jane)))
-
 (executable
  (name orthomam_app)
  (public_name orthomam_convergence)

app/lmm_benchmark.ml

@@ -3,6 +3,8 @@ open Bistro
 open Codepi
 open Codepi.File_formats
 
+module Pipeline = Simulation_pipeline.Mutsel
+
 type dataset = {
   label : string ;
   tree : nhx file ;
@@ -49,7 +51,7 @@ let orthomam_echolocation = {
 }
 
 type detection_method = {
-  result : Simulation_dataset.t -> text file ;
+  result : Pipeline.query -> text file ;
   col : int ;
   label : string ;
   requires_rooted_tree : bool ;
@@ -58,7 +60,7 @@ type detection_method = {
 let meth ?(col = 1) ?(requires_rooted_tree = false) result label =
   { result ; col ; label ; requires_rooted_tree }
 
-let methods = Simulation_dataset.[
+let methods = Pipeline.[
   meth tdg09 "tdg09" ;
   meth pcoc ~col:3 "pcoc" ;
   (* meth pcoc_v2 ~col:3 "pcoc v2" ; *)
@@ -68,65 +70,28 @@ let methods = Simulation_dataset.[
   meth topological "topological" ~requires_rooted_tree:true ;
 ]
 
-let benchmark { tree = t ; rooted ; ne_s ; branch_scale ; _ } =
-  let open Simulation_dataset in
-  let sim =
-    convdet_simulation ~seed:42 ~tree:(NHX t) ~branch_scale ~ne_s
-      ~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
-      ~n_h0:900 ~n_ha:100 ()
-  in
-  let results, labels =
-    List.filter_map methods ~f:(fun m ->
-        if not m.requires_rooted_tree || rooted then
-          Some ((m.result sim, m.col), m.label)
-        else None
-      )
-    |> List.unzip
-  in
-  Utils.average_precision_plot ~oracle:(oracle sim) ~labels ~results
-
 let benchmark_rds ?(seed = 42) { tree = t ; rooted ; ne_s ; branch_scale ; _ } =
-  let open Simulation_dataset in
-  let param =
-    Convdet_simulation_param.make ~seed ~tree:(NHX t) ~branch_scale ~ne_s
+  let q =
+    Pipeline.query ~seed ~tree:(NHX t) ~branch_scale ~ne_s
       ~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
       ~n_h0:900 ~n_ha:100 ()
   in
-  let sim = convdet_simulation_of_param param in
-  let simulation = Convdet_simulation_param.simulation param in
+  let simulation = Pipeline.simulation q in
   let results, labels =
     List.filter_map methods ~f:(fun m ->
         if not m.requires_rooted_tree || rooted then
-          Some ((m.result sim, m.col), m.label)
+          Some ((m.result q, m.col), m.label)
         else None
       )
     |> List.unzip
   in
-  benchmark_statistics simulation ~labels ~results
-
-let report =
-  let module H = Bistro_utils.Html_report in
-  H.make ~title:"Codepi benchmark" [
-    H.section "Besnard 2009 dataset" ;
-    H.pdf (benchmark besnard2009) ;
-
-    H.section "Rubisco dataset" ;
-    H.pdf (benchmark rubisco) ;
-
-    H.section "Rodent dataset" ;
-    H.pdf (benchmark oneline_rodent) ;
-
-    H.section "Orthomam/echolocation dataset" ;
-    H.pdf (benchmark orthomam_echolocation) ;
-  ]
-  |> H.render
+  Pipeline.benchmark_statistics simulation ~labels ~results
 
 let () =
   let open Bistro_utils.Repo in
   let datasets = [ besnard2009 ; rubisco ; oneline_rodent ; orthomam_echolocation ] in
   let repo =
-    item ["report.html"] report
-    :: List.map datasets ~f:(fun d ->
+    List.map datasets ~f:(fun d ->
         item [d.label ^ ".rds"] (benchmark_rds d)
       )
   in