Strating to remove Core

ocaml/Address.ml

@@ -1,4 +1,3 @@
-open Core
 
 module Tcp : sig
   type t 
@@ -8,7 +7,7 @@ module Tcp : sig
 end = struct
   type t = string
   let of_string x =
-    if not (String.is_prefix ~prefix:"tcp://" x) then
+    if not (String_ext.is_prefix ~prefix:"tcp://" x) then
       invalid_arg "Address Invalid"
     ;
     x
@@ -26,7 +25,7 @@ module Ipc : sig
 end = struct
   type t = string
   let of_string x =
-    assert (String.is_prefix ~prefix:"ipc://" x);
+    assert (String_ext.is_prefix ~prefix:"ipc://" x);
     x
   let create name =
     Printf.sprintf "ipc://%s" name
@@ -41,7 +40,7 @@ module Inproc : sig
 end = struct
   type t = string
   let of_string x =
-    assert (String.is_prefix ~prefix:"inproc://" x);
+    assert (String_ext.is_prefix ~prefix:"inproc://" x);
     x
   let create name =
     Printf.sprintf "inproc://%s" name

ocaml/Basis.ml

@@ -1,4 +1,4 @@
-open Core
+open Sexplib.Std
 open Qptypes
 
 type t = (Gto.t * Nucl_number.t) list [@@deriving sexp]
@@ -16,7 +16,7 @@ let read in_channel at_number =
 
 (** Find an element in the basis set file *)
 let find in_channel element =
-  In_channel.seek in_channel 0L;
+  seek_in in_channel 0;
   let element_read = ref Element.X in
   while !element_read <> element
   do
@@ -56,13 +56,13 @@ let to_string_general ~fmt ~atom_sep ?ele_array b =
     do_work ((Gto.to_string ~fmt g)::accu) n tail
   in
   do_work [new_nucleus 1] 1 b
-  |> String.concat ~sep:"\n"
+  |> String.concat "\n"
 
 let to_string_gamess ?ele_array =
     to_string_general ?ele_array ~fmt:Gto.Gamess ~atom_sep:""
 
 let to_string_gaussian ?ele_array b =
-  String.concat ~sep:"\n"
+  String.concat "\n"
   [ to_string_general ?ele_array ~fmt:Gto.Gaussian ~atom_sep:"****" b ; "****" ]
 
 let to_string ?(fmt=Gto.Gamess) =

ocaml/Determinant.ml

@@ -1,5 +1,5 @@
-open Core;;
+open Qptypes
-open Qptypes;;
+open Sexplib.Std
 
 type t = int64 array [@@deriving sexp]
 
@@ -9,8 +9,8 @@ let to_int64_array (x:t) = (x:int64 array)
 let to_alpha_beta x = 
   let x = to_int64_array x in
   let n_int = (Array.length x)/2 in
-  ( Array.init n_int ~f:(fun i -> x.(i)) ,
+  ( Array.init n_int (fun i -> x.(i)) ,
-    Array.init n_int ~f:(fun i -> x.(i+n_int)) )
+    Array.init n_int (fun i -> x.(i+n_int)) )
 
 
 let to_bitlist_couple x =
@@ -28,12 +28,14 @@ let bitlist_to_string ~mo_tot_num x =
   let len = 
     MO_number.to_int mo_tot_num
   in
-  List.map x ~f:(function
+  let s = 
-      | Bit.Zero -> "-"
+    List.map (function
-      | Bit.One  -> "+" 
+        | Bit.Zero -> "-"
-  )
+        | Bit.One  -> "+" 
-  |> String.concat
+    ) x
-  |> String.sub ~pos:0 ~len 
+    |> String.concat ""
+  in
+  String.sub s 0 len 
 
 
 
@@ -77,6 +79,6 @@ let to_string ~mo_tot_num x =
   let (xa,xb) = to_bitlist_couple x in
   [ "  " ; bitlist_to_string ~mo_tot_num xa ; "\n" ;
     "  " ; bitlist_to_string ~mo_tot_num xb ]
-  |> String.concat 
+  |> String.concat ""
 
 

ocaml/Gto.ml

@@ -1,5 +1,5 @@
-open Core
 open Qptypes
+open Sexplib.Std
 
 exception GTO_Read_Failure of string
 exception End_Of_Basis
@@ -15,7 +15,7 @@ type t =
 
 
 let of_prim_coef_list pc =
-  let (p,c) = List.hd_exn pc in
+  let (p,c) = List.hd pc in
   let sym = p.GaussianPrimitive.sym in
   let rec check = function
   | [] -> `OK
@@ -37,12 +37,12 @@ let of_prim_coef_list pc =
 let read_one in_channel =
   (* Fetch number of lines to read on first line *)
   let buffer = input_line in_channel in
-  if ( (String.strip buffer) = "" ) then
+  if ( (String_ext.strip buffer) = "" ) then
      raise End_Of_Basis;
   let sym_str = String.sub buffer 0 2 in
   let   n_str = String.sub buffer 2 ((String.length buffer)-2) in
-  let sym = Symmetry.of_string (String.strip sym_str) in
+  let sym = Symmetry.of_string (String_ext.strip sym_str) in
-  let n = Int.of_string (String.strip n_str) in
+  let n = int_of_string (String_ext.strip n_str) in
   (* Read all the primitives *)
   let rec read_lines result = function
   | 0 -> result
@@ -50,18 +50,19 @@ let read_one in_channel =
     begin
       let line_buffer = input_line in_channel in
       let buffer = line_buffer 
-      |> String.split ~on:' ' 
+      |> String_ext.split ~on:' ' 
-      |> List.filter ~f:(fun x -> x <> "")
+      |> List.filter (fun x -> x <> "")
       in
       match buffer with
       | [ j ; expo ; coef ] ->
         begin
-          let coef = String.tr ~target:'D' ~replacement:'e' coef
+          let coef =
+            Str.global_replace (Str.regexp "D") "e" coef
           in
           let p =
             GaussianPrimitive.of_sym_expo sym 
-              (AO_expo.of_float (Float.of_string expo) )
+              (AO_expo.of_float (float_of_string expo) )
-          and c = AO_coef.of_float (Float.of_string coef) in
+          and c = AO_coef.of_float (float_of_string coef) in
           read_lines ( (p,c)::result) (i-1)
         end
       | _ -> raise (GTO_Read_Failure line_buffer)
@@ -89,7 +90,7 @@ let to_string_gamess { sym = sym ; lc = lc } =
     do_work (result::accu) (i+1) tail
   in
   (do_work [result] 1 lc)
-  |> String.concat ~sep:"\n"
+  |> String.concat "\n"
 
 
 (** Write the GTO in Gaussian format *)
@@ -109,7 +110,7 @@ let to_string_gaussian { sym = sym ; lc = lc } =
     do_work (result::accu) (i+1) tail
   in
   (do_work [result] 1 lc)
-  |> String.concat ~sep:"\n"
+  |> String.concat "\n"
 
 
 (** Transform the gto to a string *)

ocaml/Long_basis.ml

@@ -1,5 +1,5 @@
-open Core;;
+open Qptypes
-open Qptypes;;
+open Sexplib.Std
 
 type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list [@@deriving sexp]
 
@@ -10,14 +10,14 @@ let of_basis b =
         begin
           let new_accu = 
             Symmetry.Xyz.of_symmetry g.Gto.sym 
-            |> List.rev_map ~f:(fun x-> (x,g,n)) 
+            |> List.rev_map (fun x-> (x,g,n)) 
           in
           do_work (new_accu@accu) tail
         end
   in
   do_work [] b
   |> List.rev
-;;
+
 
 let to_basis b =
   let rec do_work accu = function
@@ -25,7 +25,7 @@ let to_basis b =
   | (s,g,n)::tail -> 
     let first_sym = 
       Symmetry.Xyz.of_symmetry g.Gto.sym
-      |> List.hd_exn
+      |> List.hd
     in
     let new_accu = 
       if ( s = first_sym ) then
@@ -36,19 +36,19 @@ let to_basis b =
     do_work new_accu tail
   in
   do_work [] b 
-;;
+
 
 let to_string b =
-  let middle = List.map ~f:(fun (x,y,z) -> 
+  let middle = List.map (fun (x,y,z) -> 
-     "( "^((Int.to_string (Nucl_number.to_int z)))^", "^
+     "( "^((string_of_int (Nucl_number.to_int z)))^", "^
      (Symmetry.Xyz.to_string x)^", "^(Gto.to_string y)
      ^" )"
   ) b
-  |> String.concat ~sep:",\n"
+  |> String.concat ",\n"
   in "("^middle^")"
-;;
 
-include To_md5;;
+
+include To_md5
 let to_md5 = to_md5 sexp_of_t
-;;
+
 

ocaml/Qputils.ml

@@ -1,4 +1,4 @@
-open Core
+open Sexplib
 
 (*
 let rec transpose = function
@@ -14,12 +14,12 @@ let rec transpose = function
 
 let input_to_sexp s =
     let result = 
-      String.split_lines s 
+      String_ext.split ~on:'\n' s 
-      |> List.filter ~f:(fun x->
+      |> List.filter (fun x-> (String_ext.strip x) <> "")
-         (String.strip x) <> "")
+      |> List.map (fun x-> "("^ 
-      |> List.map ~f:(fun x->
+        (Str.global_replace (Str.regexp "=") " " x)
-         "("^(String.tr '=' ' ' x)^")")
+        ^")")
-      |> String.concat 
+      |> String.concat ""
     in
     print_endline ("("^result^")");
     "("^result^")"
@@ -29,10 +29,10 @@ let rmdir dirname =
   let rec remove_one dir =
     Sys.chdir dir;
     Sys.readdir "."
-    |> Array.iter ~f:(fun x ->
+    |> Array.iter (fun x ->
-      match (Sys.is_directory x, Sys.is_file x) with
+      match (Sys.is_directory x, Sys.file_exists x) with
-      | (`Yes, _) -> remove_one x
+      | (true, _) -> remove_one x
-      | (_, `Yes) -> Sys.remove x
+      | (_, true) -> Sys.remove x
       | _ -> failwith ("Unable to remove file "^x^".")
     );
     Sys.chdir "..";

ocaml/Range.ml

@@ -1,4 +1,4 @@
-open Core;;
+open Sexplib.Std
 
 (* A range is a string of the type:
  * 
@@ -12,14 +12,14 @@ open Core;;
 *)
 
 
-type t = int list [@@deriving sexp]
+type t = int list [@@deriving sexp] 
 
 let expand_range r =
-  match String.lsplit2 ~on:'-' r with
+  match String_ext.lsplit2 ~on:'-' r with
   | Some (s, f) ->
       begin
-        let start = Int.of_string s
+        let start = int_of_string s
-        and finish =  Int.of_string f
+        and finish =  int_of_string f
         in
         assert (start <= finish) ;
         let rec do_work = function
@@ -31,9 +31,9 @@ let expand_range r =
       begin
         match r with
           | "" -> []
-          | _  -> [Int.of_string r] 
+          | _  -> [int_of_string r] 
       end
-;;
+
 
 let of_string s =
   match s.[0] with
@@ -43,36 +43,37 @@ let of_string s =
     assert (s.[0] = '[') ;
     assert (s.[(String.length s)-1] = ']') ;
     let s = String.sub s 1 ((String.length s) - 2) in
-    let l = String.split ~on:',' s in
+    let l = String_ext.split ~on:',' s in
-    let l = List.map ~f:expand_range l in
+    let l = List.map expand_range l in
-  List.concat l |> List.dedup ~compare:Int.compare |> List.sort ~cmp:Int.compare
+  List.concat l
-;;
+  |> List.sort_uniq compare 
+
 
 let to_string l =
   let rec do_work buf symbol = function
     | [] -> buf
     | a::([] as t) -> 
-          do_work (buf^symbol^(Int.to_string a)) "" t
+          do_work (buf^symbol^(string_of_int a)) "" t
     | a::(b::q as t) ->
         if (b-a = 1) then
           do_work buf "-" t
         else
-          do_work (buf^symbol^(Int.to_string a)^","^(Int.to_string b)) "" t
+          do_work (buf^symbol^(string_of_int a)^","^(string_of_int b)) "" t
   in
   let result = 
     match l with
     | [] ->
         "[]"
     | h::t  ->
-        do_work ("["^(Int.to_string h)) "" l in
+        do_work ("["^(string_of_int h)) "" l in
   (String.sub result 0 ((String.length result)))^"]"
-;;
+
 
 let test_module () =
   let s = "[72-107,36-53,126-131]" in
   let l = of_string s in
-  print_string s ; Out_channel.newline stdout ;
+  print_string s ; print_newline () ;
-  List.iter ~f:(fun x -> Printf.printf "%d, " x) l ; Out_channel.newline stdout ;
+  List.iter (fun x -> Printf.printf "%d, " x) l ; print_newline () ;
-  to_string l |> print_string ;  Out_channel.newline stdout
+  to_string l |> print_string ;  print_newline ();
-;;
+
 

ocaml/Range.mli

@@ -1,4 +1,4 @@
-type t = int list [@@deriving sexp]
+type t = int list [@@deriving sexp] 
 
 (** A range is a sorted list of ints in an interval.
     It is created using a string :

ocaml/String_ext.ml

@@ -2,6 +2,8 @@ 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  ->
@@ -21,6 +23,7 @@ let split ?(on=' ') str =
             do_work ~accu ~left:new_left new_s
     in
     do_work str
+*)
   
 
 (** Strip blanks on the left of a string *)
@@ -101,12 +104,39 @@ let rsplit2_exn ?(on=' ') s =
     do_work length
 
 
+let lsplit2 ?(on=' ') s =
+  try
+    Some (lsplit2_exn ~on s) 
+  with
+  | Not_found -> None
+
+
+let rsplit2 ?(on=' ') s =
+  try
+    Some (rsplit2_exn ~on s) 
+  with
+  | Not_found -> None
+
+
 let to_list s =
   Array.init (String.length s) (fun i -> s.[i])
   |> Array.to_list
 
+
 let fold ~init ~f s =
     to_list s
     |> List.fold_left f init 
-  
 
+  
+let is_prefix ~prefix s =
+  let len =
+    String.length prefix
+  in
+  if len > String.length s then
+    false
+  else
+    prefix = String.sub s 0 len 
+
+
+let of_char c =
+  String.make 1 c

ocaml/Symmetry.ml

@@ -1,5 +1,5 @@
 open Qptypes
-open Core
+open Sexplib.Std
 
 type t = S|P|D|F|G|H|I|J|K|L [@@deriving sexp]
 
@@ -86,7 +86,7 @@ module Xyz = struct
     let flush state accu number =
       let n = 
         if (number = "") then 1
-        else (Int.of_string number) 
+        else (int_of_string number) 
       in
       match state with
       | X -> { x= Positive_int.(of_int ( (to_int accu.x) +n));
@@ -111,10 +111,9 @@ module Xyz = struct
     | 'Z'::rest | 'z'::rest -> 
         let new_accu = flush state accu number in 
         do_work Z new_accu "" rest
-    | c::rest -> do_work state accu (number^(String.of_char c)) rest
+    | c::rest -> do_work state accu (number^(String_ext.of_char c)) rest
     in
-    String.to_list_rev s 
+    String_ext.to_list s 
-    |> List.rev 
     |> do_work Null 
      { x=Positive_int.of_int 0 ; 
        y=Positive_int.of_int 0 ;

ocaml/To_md5.ml

@@ -1,5 +1,5 @@
-open Core;;
+open Qptypes
-open Qptypes;;
+open Sexplib
 
 let to_md5 sexp_of_t t =
   sexp_of_t t

ocaml/qptypes_generator.ml

@@ -1,4 +1,10 @@
-open Core;;
+let global_replace x = 
+  x
+  |> Str.global_replace (Str.regexp "Float.to_string") "string_of_float"
+  |> Str.global_replace (Str.regexp "Float.of_string") "float_of_string"
+  |> Str.global_replace (Str.regexp "Int.to_string") "string_of_int"
+  |> Str.global_replace (Str.regexp "Int.of_string") "int_of_string"
+  |> Str.global_replace (Str.regexp "String.\(to\|of\)_string") ""
 
 let input_data = "
 * Positive_float : float  
@@ -118,8 +124,12 @@ let input_data = "
 
 * MD5 : string
   assert ((String.length x) = 32);
-  assert (String.fold x ~init:true ~f:(fun accu x ->
+  assert (
-     accu && (x < 'g')));
+    let a =
+      Array.init (String.length x) (fun i -> x.[i])
+    in
+    Array.fold_left (fun accu x -> accu && (x < 'g')) true a
+    );
 
 * Rst_string : string
 
@@ -127,7 +137,7 @@ let input_data = "
   assert (x <> \"\") ;
 
 "
-;;
+
 
 let input_ezfio = "
 * MO_number : int
@@ -156,7 +166,7 @@ let input_ezfio = "
   More than 10 billion of determinants
 
 "
-;;
+
 
 let untouched = "
 module MO_guess : sig
@@ -206,7 +216,7 @@ end = struct
 end
 "
 
-;;
+
 
 let template = format_of_string "
 module %s : sig
@@ -222,35 +232,36 @@ end = struct
 end
 
 "
-;;
+
 
 let parse_input input=
-  print_string "open Core;;\nlet warning = print_string;;\n" ;
+  print_string "open Sexplib.Std\nlet warning = print_string\n" ;
   let rec parse result = function
     | [] -> result
     | ( "" , ""   )::tail -> parse result tail
     | ( t  , text )::tail -> 
         let name,typ,params,params_val = 
-          match String.split ~on:':' t with
+          match String_ext.split ~on:':' t with
           | [name;typ] -> (name,typ,"","")
           | name::typ::params::params_val -> (name,typ,params,
-            (String.concat params_val ~sep:":") )
+            (String.concat ":" params_val) )
           | _ -> assert false
         in
-        let typ  = String.strip typ
+        let typ  = String_ext.strip typ
-        and name = String.strip name in
+        and name = String_ext.strip name in
         let typ_cap = String.capitalize typ in
         let newstring = Printf.sprintf template name typ typ typ params_val typ typ 
-          typ typ params ( String.strip text ) typ_cap
+          typ typ params ( String_ext.strip text ) typ_cap
         in
         List.rev (parse (newstring::result) tail )
   in
-     String.split ~on:'*' input
+     String_ext.split ~on:'*' input
-  |> List.map ~f:(String.lsplit2_exn ~on:'\n') 
+  |> List.map (String_ext.lsplit2_exn ~on:'\n') 
   |> parse []
-  |> String.concat 
+  |> String.concat  ""
+  |> global_replace
   |> print_string
-;;
+
 
 
 let ezfio_template = format_of_string "
@@ -287,24 +298,24 @@ end = struct
     end
 end
 "
-;;
+
 
 let parse_input_ezfio input=
   let parse s = 
     match (
-      String.split s ~on:'\n'
+      String_ext.split s ~on:'\n'
-      |> List.filter ~f:(fun x -> (String.strip x) <> "")
+      |> List.filter (fun x -> (String_ext.strip x) <> "")
     ) with
     | [] -> ""
     | a :: b :: c :: d :: [] ->
       begin
-        let (name,typ) = String.lsplit2_exn ~on:':' a
+        let (name,typ) = String_ext.lsplit2_exn ~on:':' a
         and ezfio_func = b
-        and (min, max) = String.lsplit2_exn ~on:':' c
+        and (min, max) = String_ext.lsplit2_exn ~on:':' c
         and msg = d
         in 
         let (name, typ, ezfio_func, min, max, msg) = 
-        match (List.map [ name ; typ ; ezfio_func ; min ; max ; msg ] ~f:String.strip) with
+        match List.map String_ext.strip [ name ; typ ; ezfio_func ; min ; max ; msg ] with
         | [ name ; typ ; ezfio_func ; min ; max ; msg ] -> (name, typ, ezfio_func, min, max, msg)
         | _ -> assert false
         in
@@ -314,16 +325,17 @@ let parse_input_ezfio input=
       end
     | _ -> failwith "Error in input_ezfio"
   in
-     String.split ~on:'*' input
+     String_ext.split ~on:'*' input
-  |> List.map ~f:parse
+  |> List.map parse
-  |> String.concat 
+  |> String.concat ""
+  |> global_replace
   |> print_string
-;;
+
 
 let () = 
   parse_input input_data ;
   parse_input_ezfio input_ezfio;
-  print_endline untouched;
+  print_endline untouched
 
 
 

ocaml/test_symmetry.ml

@@ -1,15 +1,13 @@
-open Core
 open Qputils
 open Qptypes
 open Symmetry
 
 let () =
   "SPDFGHIJKL"
-  |> String.to_list_rev
+  |> String_ext.to_list
-  |> List.rev
+  |> List.map of_char
-  |> List.map ~f:of_char
+  |> List.map Xyz.of_symmetry
-  |> List.map ~f:Xyz.of_symmetry
+  |> List.iter (fun x -> List.iter (fun y -> Xyz.to_string y |> print_endline) x ;
-  |> List.iter ~f:(fun x -> List.iter x ~f:(fun y -> Xyz.to_string y |> print_endline) ;
      print_newline ();)
 
 

ocaml/test_task_server.ml

@@ -1,5 +1,3 @@
-open Core
-
 let () =
   TaskServer.run 12345
 

scripts/ezfio_interface/ezfio_generate_ocaml.py

@@ -170,7 +170,7 @@ class EZFIO_ocaml(object):
             else:
                 l_template += ["    {0:<30} : {1};".format(p, t.ocaml)]
 
-        l_template += ["  } with sexp",
+        l_template += ["  } [@@deriving sexp]",
                        ";;"]
 
         # ~#~#~#~#~#~ #

scripts/ezfio_interface/qp_edit_template

@@ -4,7 +4,7 @@
 
 open Qputils
 open Qptypes
-open Core.Std
+open Core
 
 (** Interactive editing of the input.