Removing Core

ocaml/Atom.ml

@@ -1,4 +1,4 @@
-open Core
+open Sexplib.Std
 
 exception AtomError of string
 
@@ -11,20 +11,20 @@ type t =
 (** Read xyz coordinates of the atom *)
 let of_string ~units s =
   let buffer = s
-  |> String.split ~on:' '
+  |> String_ext.split ~on:' '
-  |> List.filter ~f:(fun x -> x <> "")
+  |> List.filter (fun x -> x <> "")
   in
   match buffer with
   | [ name; charge; x; y; z ] ->
     { element = Element.of_string name ;
       charge  = Charge.of_string  charge ;
-      coord   = Point3d.of_string ~units (String.concat [x; y; z] ~sep:" ")
+      coord   = Point3d.of_string ~units (String.concat " " [x; y; z] )
     }
   | [ name; x; y; z ] ->
     let e = Element.of_string name in
     { element = e ;
       charge  = Element.to_charge e;
-      coord   = Point3d.of_string ~units (String.concat [x; y; z] ~sep:" ")
+      coord   = Point3d.of_string ~units (String.concat " " [x; y; z])
     }
   | _ -> raise (AtomError s)
 
@@ -33,7 +33,7 @@ let to_string ~units a =
   [ Element.to_string a.element ;
     Charge.to_string  a.charge ;
     Point3d.to_string ~units a.coord ]
-  |> String.concat ~sep:"   "
+  |> String.concat "   "
 
 
 let to_xyz a =

ocaml/Bit.ml

@@ -1,4 +1,4 @@
-open Core;;
+open Sexplib.Std
 
 (*
 Type for bits
@@ -16,31 +16,31 @@ type t      =
 let to_string = function
   | Zero -> "0"
   | One  -> "1"
-;;
+
 
 let and_operator a b =
   match a, b with
   | Zero, _ -> Zero
   | _, Zero -> Zero
   | _, _ -> One
-;;
+
 
 let or_operator a b =
   match a, b with
   | One, _ -> One
   | _, One -> One
   | _, _ -> Zero
-;;
+
 
 let xor_operator a b =
   match a, b with
   | One, Zero -> One
   | Zero, One -> One
   | _, _ -> Zero
-;;
+
 
 let not_operator = function
   | One -> Zero
   | Zero -> One
-;;
+
 

ocaml/Bitlist.ml

@@ -1,5 +1,4 @@
 open Qptypes
-open Core
 
 (*
 Type for bits strings
@@ -22,15 +21,15 @@ let to_string b =
 
 
 let of_string ?(zero='0') ?(one='1') s =
-  String.to_list s
+  List.init (String.length s) (String.get s)
-  |> List.rev_map ~f:( fun c ->
+  |> List.rev_map ( fun c ->
      if (c = zero) then Bit.Zero
      else if (c = one) then Bit.One
      else (failwith ("Error in bitstring ") ) )
 
 let of_string_mp s =
-  String.to_list s
+  List.init (String.length s) (String.get s)
-  |> List.rev_map ~f:(function
+  |> List.rev_map (function
     | '-' -> Bit.Zero
     | '+' -> Bit.One
     | _   -> failwith ("Error in bitstring ") )
@@ -44,7 +43,7 @@ let of_int64 i =
   | 1L -> Bit.One  :: accu |> List.rev
   | i  ->
     let b =
-      match (Int64.bit_and i 1L ) with
+      match (Int64.logand i 1L ) with
       | 0L -> Bit.Zero
       | 1L -> Bit.One
       | _ -> raise (Failure "i land 1 not in (0,1)")
@@ -70,18 +69,18 @@ let to_int64 l =
   let rec do_work accu = function
     | [] -> accu
     | Bit.Zero::tail -> do_work Int64.(shift_left accu 1) tail
-    | Bit.One::tail  -> do_work Int64.(bit_or one (shift_left accu 1)) tail
+    | Bit.One::tail  -> do_work Int64.(logor one (shift_left accu 1)) tail
   in do_work Int64.zero (List.rev l)
 
 
 (* Create a bit list from a list of int64 *)
 let of_int64_list l =
-  List.map ~f:of_int64 l
+  List.map of_int64 l
   |> List.concat
 
 (* Create a bit list from an array of int64 *)
 let of_int64_array l =
-  Array.map ~f:of_int64 l
+  Array.map of_int64 l
   |> Array.to_list
   |> List.concat
 
@@ -116,7 +115,7 @@ let to_int64_list l =
   in
   let l = do_work [] [] 1 l
   in
-  List.rev_map ~f:to_int64 l
+  List.rev_map to_int64 l
 
 (* Create an array of int64 from a bit list *)
 let to_int64_array l =
@@ -127,8 +126,8 @@ let to_int64_array l =
 let of_mo_number_list n_int l =
   let n_int = N_int_number.to_int n_int in
   let length = n_int*64 in
-  let a = Array.create length (Bit.Zero) in
+  let a = Array.make length (Bit.Zero) in
-  List.iter ~f:(fun i-> a.((MO_number.to_int i)-1) <- Bit.One) l;
+  List.iter (fun i-> a.((MO_number.to_int i)-1) <- Bit.One) l;
   Array.to_list a
 
 
@@ -183,10 +182,10 @@ let not_operator   b = logical_operator1 Bit.not_operator   b
 
 
 let popcnt b =
-  List.fold_left b ~init:0 ~f:(fun accu -> function
+  List.fold_left (fun accu -> function
     | Bit.One -> accu+1
     | Bit.Zero -> accu
-  )
+  ) 0 b
 
 
 

ocaml/Charge.ml

@@ -1,14 +1,14 @@
-open Core
+open Sexplib.Std
 
 type t = float [@@deriving sexp]
 
 let of_float x  = x
-let of_int   i = Float.of_int i
+let of_int   i  = float_of_int i
-let of_string s = Float.of_string s
+let of_string s = float_of_string s
 
 
 let to_float x  = x
-let to_int   x = Float.to_int x
+let to_int   x  = int_of_float x
 let to_string x =
   if x >= 0. then
     Printf.sprintf "+%f" x

ocaml/Excitation.ml

@@ -1,4 +1,3 @@
-open Core
 open Qptypes
 
 module Hole = struct
@@ -56,7 +55,7 @@ let to_string = function
         "," ;
         (MO_class.to_string (Particle.to_mo_class p));
         "]"]
-      |> String.concat ~sep:" "
+      |> String.concat " "
   | Double (h1,p1,h2,p2) ->
       [ "Double Exc. : [" ;
         (MO_class.to_string (Hole.to_mo_class h1));
@@ -67,6 +66,6 @@ let to_string = function
         "," ;
         (MO_class.to_string (Particle.to_mo_class p2));
         "]"]
-      |> String.concat ~sep:" "
+      |> String.concat " "
 
 

ocaml/GaussianPrimitive.ml

@@ -1,5 +1,5 @@
 open Qptypes
-open Core
+open Sexplib.Std
 
 type t =
   { sym  : Symmetry.t ;

ocaml/Generic_input_of_rst.ml

@@ -1,5 +1,6 @@
-open Core;;
+open Sexplib
-open Qptypes;;
+open Sexplib.Std
+open Qptypes
 
 
 let fail_msg str (ex,range) =
@@ -15,25 +16,25 @@ let fail_msg str (ex,range) =
     let start_pos = range.start_pos.offset
     and end_pos = range.end_pos.offset
     in
-    let pre  = String.sub ~pos:0 ~len:start_pos str
+    let pre  = String.sub str 0 start_pos 
-    and mid  = String.sub ~pos:start_pos ~len:(end_pos-start_pos) str
+    and mid  = String.sub str start_pos (end_pos-start_pos) 
-    and post = String.sub ~pos:(end_pos)
+    and post = String.sub str (end_pos)
-      ~len:((String.length str)-(end_pos)) str
+      ((String.length str)-(end_pos)) 
     in
     let str = Printf.sprintf "%s ## %s ## %s" pre mid post
     in
-    let str = String.tr str ~target:'(' ~replacement:' '
+    let str = String_ext.tr str ~target:'(' ~replacement:' '
-      |> String.split ~on:')'
+      |> String_ext.split ~on:')'
-      |> List.map ~f:String.strip
+      |> List.map String_ext.strip
-      |> List.filter ~f:(fun x ->
+      |> List.filter (fun x ->
-          match String.substr_index x ~pos:0 ~pattern:"##" with
+          match String_ext.substr_index ~pos:0 ~pattern:"##" x with
           | None -> false
           | Some _ -> true
          )
-      |> String.concat ~sep:"\n"
+      |> String.concat "\n"
     in
-    Printf.eprintf "Error:  (%s)\n\n  %s\n\n" msg str;
+    Printf.eprintf "Error:  (%s)\n\n  %s\n\n" msg str
-;;
+
 
 
 let evaluate_sexp t_of_sexp s =
@@ -41,20 +42,19 @@ let evaluate_sexp t_of_sexp s =
   match ( Sexp.of_string_conv sexp t_of_sexp ) with
   | `Result r -> Some r
   | `Error ex -> ( fail_msg sexp ex; None)
-;;
+
 
 let of_rst t_of_sexp s =
   Rst_string.to_string s
-  |> String.split ~on:'\n'
+  |> String_ext.split ~on:'\n'
-  |> List.filter ~f:(fun line ->
+  |> List.filter (fun line -> String.contains line '=')
-      String.contains line '=')
+  |> List.map (fun line ->
-  |> List.map ~f:(fun line ->
       "("^(
-      String.tr line ~target:'=' ~replacement:' '
+      String_ext.tr ~target:'=' ~replacement:' ' line
       )^")" )
-  |> String.concat
+  |> String.concat ""
   |> evaluate_sexp t_of_sexp
-;;
+
 
 
 

ocaml/Message.ml

@@ -1,4 +1,4 @@
-open Core
+open Sexplib.Std
 open Qptypes
 
 (** New job : Request to create a new multi-tasked job *)
@@ -161,7 +161,7 @@ end = struct
   }
   let create ~state ~tasks = { state = State.of_string state ; tasks }
   let to_string x =
-    Printf.sprintf "add_task %s %s" (State.to_string x.state) (String.concat ~sep:"|" x.tasks)
+    Printf.sprintf "add_task %s %s" (State.to_string x.state) (String.concat "|" x.tasks)
 end
 
 
@@ -193,12 +193,12 @@ end = struct
   }
   let create ~state ~task_ids =
     { state = State.of_string state ;
-      task_ids = List.map ~f:Id.Task.of_int task_ids
+      task_ids = List.map Id.Task.of_int task_ids
     }
   let to_string x =
     Printf.sprintf "del_task %s %s"
       (State.to_string x.state)
-      (String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
+      (String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
 end
 
 
@@ -219,7 +219,7 @@ end = struct
       else "done"
     in
     Printf.sprintf "del_task_reply %s %s"
-     more (String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
+     more (String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
 end
 
 
@@ -303,11 +303,11 @@ end = struct
      "get_tasks_reply ok"
   let to_string_list x =
      "get_tasks_reply ok" :: (
-     List.map x ~f:(fun (task_id, task) ->
+     List.map (fun (task_id, task) ->
        match task_id with
        | Some task_id -> Printf.sprintf "%d %s" (Id.Task.to_int task_id) task
        | None -> Printf.sprintf "0 terminate"
-     ) )
+     ) x )
 
 end
 
@@ -408,14 +408,14 @@ end = struct
   let create ~state ~client_id ~task_ids =
     { client_id = Id.Client.of_int client_id ;
       state = State.of_string state ;
-      task_ids  = List.map ~f:Id.Task.of_int task_ids;
+      task_ids  = List.map Id.Task.of_int task_ids;
     }
 
   let to_string x =
     Printf.sprintf "task_done %s %d %s"
       (State.to_string x.state)
       (Id.Client.to_int x.client_id)
-      (String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
+      (String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
 end
 
 (** Terminate *)
@@ -460,7 +460,7 @@ end = struct
   type t = string
   let create x = x
   let to_string x =
-     String.concat ~sep:" "  [ "error" ; x ]
+     String.concat " "  [ "error" ; x ]
 end
 
 

ocaml/Molecule.ml

@@ -207,7 +207,7 @@ let distance_matrix molecule =
 
 
 
-open Core ;;
+
 include To_md5
 let to_md5 = to_md5 sexp_of_t
 

ocaml/Multiplicity.ml

@@ -1,10 +1,11 @@
-open Core;;
+open Qptypes 
-open Qptypes ;;
+open Sexplib.Std
 
 type t = Strictly_positive_int.t [@@deriving sexp]
 
-let of_int = Strictly_positive_int.of_int ;;
+let of_int = Strictly_positive_int.of_int 
-let to_int = Strictly_positive_int.to_int ;;
+
+let to_int = Strictly_positive_int.to_int
 
 let to_string m =
   match (to_int m) with
@@ -18,7 +19,7 @@ let to_string m =
   | 8 -> "Octet"
   | 9 -> "Nonet"
   | i -> Printf.sprintf "%d-et" i
-;;
+
 
 let of_alpha_beta a b =
   let a = Elec_alpha_number.to_int a
@@ -26,11 +27,11 @@ let of_alpha_beta a b =
   in
   assert (a >= b);
   of_int (1 + a - b)
-;;
+
 
 let to_alpha_beta ne m =
   let ne = Elec_number.to_int ne in
   let nb = (ne-(to_int m)+1)/2 in
   let na = ne - nb in
   (Elec_alpha_number.of_int na, Elec_beta_number.of_int nb)
-;;
+

ocaml/Progress_bar.ml

@@ -1,5 +1,3 @@
-open Core
-
 type t =
 {
   title: string;
@@ -7,14 +5,14 @@ type t =
   cur_value  : float;
   end_value  : float;
   bar_length : int;
-  init_time  : Time.t;
+  init_time  : float;
   dirty      : bool;
-  next       : Time.t;
+  next       : float;
 }
 
 let init ?(bar_length=20) ?(start_value=0.) ?(end_value=1.) ~title =
   { title ; start_value ; end_value ; bar_length ; cur_value=start_value ;
-    init_time= Time.now () ; dirty = false ; next = Time.now () }
+    init_time= Unix.time () ; dirty = false ; next = Unix.time () }
 
 let update ~cur_value bar =
   { bar with cur_value ; dirty=true }
@@ -40,23 +38,23 @@ let display_tty bar =
       |> Float.to_int
     in
     let hashes =
-      String.init bar.bar_length ~f:(fun i ->
+      String.init bar.bar_length (fun i ->
         if (i < n_hashes) then '#'
         else ' '
       )
     in
     let now =
-      Time.now ()
+      Unix.time ()
     in
     let running_time =
-      Time.abs_diff now bar.init_time
+      now -. bar.init_time
     in
-    Printf.eprintf "%s : [%s] %4.1f%% | %10s\r%!"
+    Printf.eprintf "%s : [%s] %4.1f%% | %8.0f s\r%!"
       bar.title
       hashes
       percent
-      (Time.Span.to_string running_time);
+      running_time;
-    { bar with dirty = false ; next = Time.add now (Time.Span.of_sec 0.1) }
+    { bar with dirty = false ; next = now +. 0.1 }
 
 
 let display_file bar =
@@ -65,19 +63,19 @@ let display_file bar =
               (bar.end_value -. bar.start_value)
     in
     let running_time =
-      Time.abs_diff (Time.now ()) bar.init_time
+      (Unix.time ()) -. bar.init_time
     in
-    Printf.eprintf "%5.2f %%  in  %20s \n%!"
+    Printf.eprintf "%5.2f %%  in  %20.0f seconds \n%!"
       percent
-      (Time.Span.to_string running_time);
+      running_time;
-    { bar with dirty = false ; next = Time.add (Time.now ()) (Time.Span.of_sec 10.) }
+    { bar with dirty = false ; next = (Unix.time ()) +. 10. }
 
 
 
 let display bar =
   if (not bar.dirty) then
      bar
-  else if (Time.now () < bar.next) then
+  else if (Unix.time () < bar.next) then
      bar
   else
     begin

ocaml/Pseudo.ml

@@ -1,4 +1,4 @@
-open Core
+open Sexplib.Std
 open Qptypes
 
 
@@ -81,12 +81,12 @@ let to_string_local = function
 | t  ->
   "Local component:" ::
   ( Printf.sprintf "%20s %8s %20s" "Coeff." "r^n" "Exp." ) ::
-  ( List.map t ~f:(fun (l,c) -> Printf.sprintf "%20f %8d %20f"
+  ( List.map (fun (l,c) -> Printf.sprintf "%20f %8d %20f"
       (AO_coef.to_float c)
       (R_power.to_int   l.GaussianPrimitive_local.r_power)
       (AO_expo.to_float l.GaussianPrimitive_local.expo)
-  ) )
+  ) t )
-  |> String.concat ~sep:"\n"
+  |> String.concat "\n"
 
 
 (** Transform the non-local component of the pseudopotential to a string *)
@@ -95,7 +95,7 @@ let to_string_non_local = function
 | t  ->
   "Non-local component:" ::
   ( Printf.sprintf "%20s %8s %20s %8s" "Coeff." "r^n" "Exp." "Proj") ::
-  ( List.map t ~f:(fun (l,c) ->
+  ( List.map (fun (l,c) ->
       let p =
         Positive_int.to_int l.GaussianPrimitive_non_local.proj
       in
@@ -104,8 +104,8 @@ let to_string_non_local = function
       (R_power.to_int   l.GaussianPrimitive_non_local.r_power)
       (AO_expo.to_float l.GaussianPrimitive_non_local.expo)
       p p
-  ) )
+  ) t )
-  |> String.concat ~sep:"\n"
+  |> String.concat "\n"
 
 (** Transform the Pseudopotential to a string *)
 let to_string t =
@@ -116,29 +116,30 @@ let to_string t =
   :: to_string_local t.local
   :: to_string_non_local t.non_local
   :: []
-  |> List.filter ~f:(fun x -> x <> "")
+  |> List.filter (fun x -> x <> "")
-  |> String.concat ~sep:"\n"
+  |> String.concat "\n"
 
 
 (** Find an element in the file *)
 let find in_channel element =
-  In_channel.seek in_channel 0L;
+  seek_in in_channel 0;
 
   let loop, element_read, old_pos =
      ref true,
      ref None,
-     ref (In_channel.pos in_channel)
+     ref (pos_in in_channel)
   in
 
   while !loop
   do
     try
       let buffer =
-        old_pos := In_channel.pos in_channel;
+        old_pos := pos_in in_channel;
-        match In_channel.input_line in_channel with
+        try 
-        | Some line -> String.split ~on:' ' line
+          input_line in_channel
-          |> List.hd_exn
+          |> String_ext.split ~on:' ' 
-        | None -> raise End_of_file
+          |> List.hd
+        with _ -> raise End_of_file 
       in
       element_read := Some (Element.of_string buffer);
       loop := !element_read <> (Some element)
@@ -146,7 +147,7 @@ let find in_channel element =
     | Element.ElementError _ -> ()
     | End_of_file -> loop := false
   done ;
-  In_channel.seek in_channel !old_pos;
+  seek_in in_channel !old_pos;
   !element_read
 
 
@@ -156,13 +157,13 @@ let read_element in_channel element =
   | Some e when e = element ->
     begin
       let rec read result =
-        match In_channel.input_line in_channel with
+        try 
-        | None -> result
+          let line = input_line in_channel in
-        | Some line ->
+          if (String.trim line = "") then
-          if (String.strip line = "") then
             result
           else
             read (line::result)
+        with _ -> result
       in
 
       let data =
@@ -171,20 +172,20 @@ let read_element in_channel element =
       in
 
       let debug_data =
-        String.concat ~sep:"\n" data
+        String.concat "\n" data
       in
 
       let decode_first_line = function
       | first_line :: rest ->
         begin
           let first_line_split =
-            String.split first_line ~on:' '
+            String_ext.split first_line ~on:' '
-            |> List.filter ~f:(fun x -> (String.strip x) <> "")
+            |> List.filter (fun x -> (String.trim x) <> "")
           in
           match first_line_split with
           | e :: "GEN" :: n :: p ->
             {  element = Element.of_string e ;
-              n_elec  = Int.of_string n |> Positive_int.of_int ;
+              n_elec  = int_of_string n |> Positive_int.of_int ;
               local = [] ;
               non_local = []
             }, rest
@@ -200,18 +201,18 @@ let read_element in_channel element =
       | (n,line::rest) ->
         begin
           match
-            String.split line ~on:' '
+            String_ext.split line ~on:' '
-            |> List.filter ~f:(fun x -> String.strip x <> "")
+            |> List.filter (fun x -> String.trim x <> "")
           with
           | c :: i :: e :: [] ->
             let i =
-              Int.of_string i
+              int_of_string i
             in
             let elem =
               ( create_primitive
-                (Float.of_string e |> AO_expo.of_float)
+                (float_of_string e |> AO_expo.of_float)
                 (i-2 |> R_power.of_int),
-                Float.of_string c |> AO_coef.of_float
+                float_of_string c |> AO_coef.of_float
               )
             in
             loop create_primitive (elem::accu) (n-1, rest)
@@ -230,8 +231,8 @@ let read_element in_channel element =
         match data with
         | n :: rest ->
             let n =
-              String.strip n
+              String.trim n
-              |> Int.of_string
+              |> int_of_string
               |> Positive_int.of_int
             in
             decode_local_n n rest
@@ -250,8 +251,8 @@ let read_element in_channel element =
           match data with
           | n :: rest ->
               let n =
-                String.strip n
+                String.trim  n
-                |> Int.of_string
+                |> int_of_string
                 |> Positive_int.of_int
               in
               let result =

ocaml/Qpackage.ml

@@ -1,45 +1,45 @@
-open Core;;
+open Qptypes
-open Qptypes;;
+open Qputils
-open Qputils;;
 
 (** Variables related to the quantum package installation *)
 
 let root =
-  match (Sys.getenv "QP_ROOT") with
+  match (Sys.getenv_opt "QP_ROOT") with
   | None -> failwith "QP_ROOT environment variable is not set.
 Please source the quantum_package.rc file."
   | Some x -> x
-;;
+
 
 let bit_kind_size = lazy (
   let filename = root^"/src/bitmask/bitmasks_module.f90" in
-  if not (Sys.file_exists_exn filename) then
+  if not (Sys.file_exists filename) then
      raise (Failure ("File "^filename^" not found"));
 
-  let in_channel = In_channel.create filename in
+  let in_channel = open_in filename in
-  let lines = In_channel.input_lines in_channel in
+  let lines = input_lines in_channel in
-  In_channel.close in_channel;
+  close_in in_channel;
 
   let rec get_data = function
   | [] -> raise (Failure ("bit_kind_size not found in "^filename))
   | line::tail ->
       let line =
-     begin match String.split ~on:'!' line |> List.hd with
+        try
-     | Some x -> x
+          String_ext.split ~on:'!' line
-     | None -> ""
+          |> List.hd 
-     end in
+        with _ -> line
-     begin match (String.rsplit2 ~on:':' line) with
+      in
+      begin match (String_ext.rsplit2 ~on:':' line) with
       | Some (_ ,buffer) ->
-       begin match (String.split ~on:'=' buffer |> List.map ~f:String.strip) with
+        begin match (String_ext.split ~on:'=' buffer |> List.map String.trim) with
         | ["bit_kind_size"; x] -> 
-         Int.of_string x |> Bit_kind_size.of_int
+          int_of_string x |> Bit_kind_size.of_int
         | _  -> get_data tail
         end
       | _ -> get_data tail
       end
   in
   get_data lines )
-;;
+
 
 let bit_kind = lazy (
   Lazy.force bit_kind_size
@@ -47,23 +47,26 @@ let bit_kind = lazy (
   |> fun x -> x / 8
   |> Bit_kind.of_int
   )
-;;
+
 
 let executables = lazy (
-  let filename = root^"/data/executables"
+  let filename = root^"/data/executables" in
-  and func in_channel =
+  let lines = 
-    In_channel.input_lines in_channel
+    let in_channel = open_in filename in
-     |> List.map ~f:(fun x ->
+    let result = input_lines in_channel in
-         let e = String.split ~on:' ' x
+    close_in in_channel;
-           |> List.filter ~f:(fun x -> x <> "")
+    result
+  in
+  lines
+  |> List.map (fun x ->
+         let e = String_ext.split ~on:' ' x
+           |> List.filter (fun x -> x <> "")
          in
          match e with
-         | [a;b] -> (a,String.substr_replace_all ~pattern:"$QP_ROOT" ~with_:root b)
+         | [a;b] -> (a,String_ext.substr_replace_all ~pattern:"$QP_ROOT" ~with_:root b)
          | _ -> ("","")
      )
-  in
+  |> List.sort (fun (x,_) (y,_) ->
-  In_channel.with_file filename ~f:func
-  |> List.sort ~compare:(fun (x,_) (y,_) ->
       if x < y then -1
       else if x > y then 1
       else 0)
@@ -72,33 +75,37 @@ let executables = lazy (
 
 
 let get_ezfio_default_in_file ~directory ~data ~filename =
-  let lines = In_channel.with_file filename ~f:(fun in_channel ->
+  let lines = 
-    In_channel.input_lines in_channel) in
+    let in_channel = open_in filename in
+    let result = input_lines in_channel in
+    close_in in_channel;
+    result
+  in
   let rec find_dir = function
     | line :: rest ->
-        if ((String.strip line) = directory) then
+        if ((String.trim line) = directory) then
           rest
         else
           find_dir rest
-    | [] -> raise Caml.Not_found
+    | [] -> raise Not_found
   in
   let rec find_data = function
     | line :: rest ->
         if (line = "") then
-          raise Caml.Not_found
+          raise Not_found
         else if (line.[0] <> ' ') then
-          raise Caml.Not_found
+          raise Not_found
         else
           begin
-            match (String.lsplit2 ~on:' ' (String.strip line)) with
+            match (String_ext.lsplit2 ~on:' ' (String.trim line)) with
               | Some (l,r) ->
                 if (l = data) then
-                  String.strip r
+                  String.trim r
                 else
                   find_data rest
-              | None -> raise Caml.Not_found
+              | None -> raise Not_found
           end
-    | [] -> raise Caml.Not_found
+    | [] -> raise Not_found
   in
   find_dir lines
     |> find_data ;
@@ -111,7 +118,7 @@ let get_ezfio_default directory data =
   | []           ->
       begin
         Printf.printf "%s/%s not found\n%!" directory data;
-        raise Caml.Not_found
+        raise Not_found
       end
   | filename :: tail ->
     let filename =
@@ -120,7 +127,7 @@ let get_ezfio_default directory data =
     try
       get_ezfio_default_in_file ~directory ~data ~filename
     with
-    | Caml.Not_found -> aux tail
+    | Not_found -> aux tail
   in
   Sys.readdir dirname
   |> Array.to_list
@@ -131,10 +138,7 @@ let ezfio_work ezfio_file =
   let result =
     Filename.concat ezfio_file  "work"
   in
-  begin
+  if not (Sys.file_exists result) then
-    match Sys.is_directory result with
+      ( Ezfio.set_file ezfio_file ; Ezfio.set_work_empty false);
-    | `Yes -> ()
-    | _ -> ( Ezfio.set_file ezfio_file ; Ezfio.set_work_empty false)
-  end;
   result
 ;;

ocaml/Qputils.ml

@@ -42,3 +42,11 @@ let rmdir dirname =
 
 
 
+let input_lines ic = 
+  let n = in_channel_length ic in
+  let s = Bytes.create n in
+  really_input ic s 0 n;                                                                    
+  close_in ic;
+  Bytes.to_string s
+  |> String_ext.split ~on:'\n'
+

ocaml/String_ext.ml

@@ -3,27 +3,6 @@ include String
 (** Split a string on a given character *)
 let split ?(on=' ') str =
   split_on_char on str
-(*
-    let rec do_work ?(accu=[]) ?(left="") = function
-    | "" -> List.rev (left::accu)
-    | s  ->
-        let new_s =
-            (length s) - 1
-            |> sub s 1
-        in
-        if (s.[0] = on) then
-            let new_accu =
-                left :: accu
-            in
-            do_work ~accu:new_accu new_s
-        else
-            let new_left =
-                concat "" [ left ; make 1 s.[0] ]
-            in
-            do_work ~accu ~left:new_left new_s
-    in
-    do_work str
-*)
 
 
 (** Strip blanks on the left of a string *)
@@ -101,7 +80,7 @@ let rsplit2_exn ?(on=' ') s =
         else
            do_work (i-1)
     in
-    do_work length
+    do_work (length-1)
 
 
 let lsplit2 ?(on=' ') s =
@@ -140,3 +119,23 @@ let is_prefix ~prefix s =
 
 let of_char c =
   String.make 1 c
+
+let tr ~target ~replacement s =
+  String.map (fun c -> if c = target then replacement else c) s
+
+
+let substr_index ?(pos=0) ~pattern s =
+  try
+    let regexp = 
+      Str.regexp pattern
+    in
+    Some (Str.search_forward regexp s pos)
+  with Not_found -> None
+
+
+let substr_replace_all ~pattern ~with_ s =
+  let regexp =
+    Str.regexp pattern
+  in
+  Str.global_replace regexp with_ s
+

ocaml/TaskServer.ml

@@ -33,7 +33,7 @@ type t =
 
 let debug_env =
   try
-    Sys.getenv "QP_TASK_DEBUG"; true
+    Sys.getenv "QP_TASK_DEBUG" = "1"
   with Not_found -> false
 
 

ocaml/create_git_sha1.sh

@@ -4,9 +4,8 @@ SHA1=$(git log -1  | head -1 | cut -d ' ' -f 2)
 DATE=$(git log -1  | grep Date | cut -d ':' -f 2-)
 MESSAGE=$(git log -1  | tail -1 | sed 's/"/\\"/g')
 cat << EOF > Git.ml
-open Core
+let sha1 = "$SHA1" |> String.trim
-let sha1 = "$SHA1" |> String_ext.strip
+let date = "$DATE" |> String.trim
-let date = "$DATE" |> String_ext.strip
+let message = "$MESSAGE" |> String.trim
-let message = "$MESSAGE" |> String_ext.strip
 EOF
 

ocaml/element_create_db.ml

@@ -1,4 +1,3 @@
-open Core
 open Qptypes
 open Element
 
@@ -6,9 +5,10 @@ let () =
   let indices =
     Array.init 78 (fun i -> i)
   in
-  Out_channel.with_file (Qpackage.root ^ "/data/list_element.txt")
+  let out_channel = 
-    ~f:(fun out_channel ->
+    open_out (Qpackage.root ^ "/data/list_element.txt")
-       Array.init 110 ~f:(fun i ->
+  in
+  Array.init 110 (fun i ->
       let element =
         try
           Some (of_charge (Charge.of_int i))
@@ -21,7 +21,6 @@ let () =
                     i (to_string x) (to_long_string x) (Positive_float.to_float @@ mass x )
     )
   |> Array.to_list
-        |> String.concat ~sep:""
+  |> String.concat ""
-        |> Out_channel.output_string out_channel
+  |> Printf.fprintf out_channel "%s" 
-    )