tk/Note: support for croquis

lib/detection_pipeline.ml

@@ -250,9 +250,12 @@ module Make (Q : Query) = struct
         Biotk.Fasta.from_file alignment_path
         |> Base.Result.ok_or_failwith |> snd
       in
-      CS.make ~condition tree alignment site_pos
-      |> CS.draw |> Biotk_croquis.Croquis.Layout.simple
-      |> Base.Fn.flip Biotk_croquis.Croquis.Layout.render_pdf dest
+      let layout =
+        CS.make ~condition tree alignment site_pos
+        |> CS.draw
+        |> Biotk_croquis.Croquis.Layout.simple
+      in
+      Biotk_croquis.Croquis.Layout.render `pdf layout (`File dest)
     in
     Workflow.path_plugin ~descr:"detection_pipeline.view_site" f
 

lib/orthomam.ml

@@ -466,9 +466,11 @@ let convergence_species_tree_pdf ~convergent_species db =
           Codepitk.Convergence_tree.infer_binary_condition_on_branches
             t ~convergent_leaves:convergent_species)
     in
-    render_tree tree_or_branch
-    |> Biotk_croquis.Croquis.Layout.simple
-    |> Fn.flip Biotk_croquis.Croquis.Layout.render_pdf dest
+    let layout =
+      render_tree tree_or_branch
+      |> Biotk_croquis.Croquis.Layout.simple
+    in
+    Biotk_croquis.Croquis.Layout.render `pdf layout (`File dest)
   in
   Workflow.path_plugin ~descr:"orthomam.convergence_species_tree_pdf" f
 
@@ -589,7 +591,7 @@ let draw_site q pos =
         |> Candidate_site.draw
         |> Croquis.Layout.simple
       in
-      Croquis.Layout.render_pdf picture dest
+      Croquis.Layout.render `pdf picture (`File dest)
     | Error msg -> failwith msg
   in
   Workflow.path_plugin ~descr:"orthomam." f

lib/tk/note.ml

@@ -5,7 +5,7 @@ type elt =
   | Dataframe of Dataframe.t * (string * Dataframe.html_formatter) list
   | Png of string
   | Svg of string
-  | Vg  of Vg.image
+  | Croquis of Biotk_croquis.Croquis.Picture.t
 
 type t = {
   title : string ;
@@ -21,7 +21,7 @@ let text x = Text x
 let dataframe ?(formatters = []) d = Dataframe (d, formatters)
 let png fn = Png fn
 let svg fn = Svg fn
-let vg i = Vg i
+let croquis c = Croquis c
 
 let render_picture format data buf =
   let format = match format with
@@ -39,6 +39,16 @@ let render_dataframe formatters data buf =
   Tyxml.Html.pp_elt () fmt (Dataframe.to_html ~formatters data) ;
   Format.pp_print_flush fmt ()
 
+let render_croquis croquis buf =
+  let open Biotk_croquis.Croquis in
+  let data =
+    let pic_buf = Buffer.create 253 in
+    Layout.(render `svg (simple croquis) (`Buffer pic_buf)) ;
+    Buffer.contents pic_buf
+  in
+  render_picture `svg data buf
+
+
 let header doc =
   sprintf {|---
 title: %s
@@ -55,7 +65,7 @@ let render_doc doc =
         | Png fn -> render_picture_on_disk `png fn buf
         | Svg fn -> render_picture_on_disk `svg fn buf
         | Dataframe (data, formatters) -> render_dataframe formatters data buf
-        | Vg _ -> assert false
+        | Croquis croquis -> render_croquis croquis buf
       ) ;
       Buffer.add_string buf "\n\n"
     ) ;

lib/tk/note.mli

@@ -11,7 +11,7 @@ val dataframe :
 
 val png : string -> elt
 val svg : string -> elt
-val vg : Vg.image -> elt
+val croquis : Biotk_croquis.Croquis.Picture.t -> elt
 
 val make :
   ?toc:bool ->