simplified multi-scripts shell steps

lib/convergence_detection.ml

@@ -124,24 +124,15 @@ let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~t
     | Some _ -> None
     | None -> Some default_t
   in
-  let package_diffsel_script_utils = tmp // "diffsel_script_utils.py" in
-  let package_plot_data = tmp // "plot_data.py" in
-  let script_plot_convergent_sites = tmp // "plot_convergent_sites.py" in
   let out = dest // "results.svg" in
   let inner =
     Workflow.shell ~descr:"convergence_detection.plot_results" [
       within_container img (
         and_list [
-          mkdir_p tmp ;
-        mkdir_p dest ;
-          cd tmp ;
-
-          cmd "cp" [ file_dump (string Scripts.diffsel_script_utils) ; package_diffsel_script_utils ] ;
-          cmd "cp" [ file_dump (string Scripts.plot_data) ; package_plot_data] ;
-          cmd "cp" [ file_dump (string Scripts.plot_convergent_sites); script_plot_convergent_sites ] ;
+          mkdir_p dest ;
 
           cmd "python" [
-            string "plot_convergent_sites.py" ;
+            Utils.script_dump Scripts.[ diffsel_script_utils ; plot_data ; plot_convergent_sites ] ;
             opt "-msa" dep faa ;
             opt "-tsv" dep tsv ;
             opt "-tree" dep tree ;

lib/scripts/plot_convergent_sites.py

@@ -28,9 +28,6 @@
 # its terms.
 
 from ete3 import Tree, NodeStyle, TreeStyle, TextFace
-from diffsel_script_utils import *
-from plot_data import *
-
 import pandas as pd
 from Bio import AlignIO, SeqIO, Seq, SeqRecord
 

lib/utils.ml

@@ -14,3 +14,5 @@ let bash_script args code =
   in
   seq ~sep:"\n" [ prelude ; string code ]
 
+let script_dump xs =
+  file_dump (string (String.concat ~sep:"\n" xs))