fixed cyclic dependencies

lib/defs.ml

+open File_formats
+open Bistro.Std
+
+type parsed_input_tree
+
+type output_parse_input_tree =
+  | Nodes_H0
+  | Nodes_Ha
+  | Tree4detect
+  | Tree4simu
+  | Tree_diffsel
+
+type raw_dataset = {
+  input_tree: nhx workflow ;
+  fna: nucleotide_fasta workflow ;
+  }
+
+type ready_dataset = {
+  input_tree: nhx workflow ;
+  tree_dataset : [`tree_dataset] directory workflow ;
+  fna: nucleotide_fasta workflow ;
+  faa: aminoacid_fasta workflow ;
+  }
+
+type ('a,'b) w_dataset =
+  | Raw_dataset of 'a
+  | Ready_dataset of 'b
+
+
+type dataset = {
+  model_prefix: string ;
+  tree_prefix : string ;
+  ready_dataset : ready_dataset
+  }
+
+
+type det_meth =
+  | Pcoc
+  | Pcoc_gamma
+  | Diffsel
+
+let string_of_det_meth = function
+  | Pcoc -> "pcoc"
+  | Pcoc_gamma -> "pcoc_gamma"
+  | Diffsel -> "diffsel"
+
+type 'a w_det_meth =
+  | Pcoc_w of 'a
+  | Pcoc_gamma_w of 'a
+  | Diffsel of 'a
+
+type det_result = {
+  dataset : dataset ;
+  det_meth : det_meth ;
+  det_result : Convergence_detection.det_out ;
+  }
+
+type dataset_res = {
+  res_by_tools: det_result list ;
+  merged_results : string
+  }
+

lib/file_formats.ml

@@ -26,63 +26,3 @@ class type nucleotide_phylip = object
   method format : [`Nucleotide]
 end
 
-
-type parsed_input_tree
-
-type output_parse_input_tree =
-  | Nodes_H0
-  | Nodes_Ha
-  | Tree4detect
-  | Tree4simu
-  | Tree_diffsel
-
-type raw_dataset = {
-  input_tree: nhx workflow ;
-  fna: nucleotide_fasta workflow ;
-  }
-
-type ready_dataset = {
-  input_tree: nhx workflow ;
-  tree_dataset : [`tree_dataset] directory workflow ;
-  fna: nucleotide_fasta workflow ;
-  faa: aminoacid_fasta workflow ;
-  }
-
-type ('a,'b) w_dataset =
-  | Raw_dataset of 'a
-  | Ready_dataset of 'b
-
-
-type dataset = {
-  model_prefix: string ;
-  tree_prefix : string ;
-  ready_dataset : ready_dataset
-  }
-
-
-type det_meth =
-  | Pcoc
-  | Pcoc_gamma
-  | Diffsel
-
-let string_of_det_meth = function
-  | Pcoc -> "pcoc"
-  | Pcoc_gamma -> "pcoc_gamma"
-  | Diffsel -> "diffsel"
-
-type 'a w_det_meth =
-  | Pcoc_w of 'a
-  | Pcoc_gamma_w of 'a
-  | Diffsel of 'a
-
-type det_result = {
-  dataset : dataset ;
-  det_meth : det_meth ;
-  det_result : Convergence_detection.det_out ;
-  }
-
-type dataset_res = {
-  res_by_tools: det_result list ;
-  merged_results : string
-  }
-

lib/pipeline.ml

@@ -3,6 +3,7 @@ open Bistro_utils
 open Bistro.EDSL
 open Bistro.Std
 open File_formats
+open Defs
 
 let ready_dataset_of_raw_dataset raw_dataset =
     let input_tree = raw_dataset.input_tree in