Add support for Zstd bytes->bytes Codec.

.github/workflows/build-and-test.yml

@@ -44,6 +44,7 @@ jobs:
       - name: setup
         run: |
           opam install --deps-only --with-test --with-doc --yes zarr
+          opam install bytesrw conf-zlib conf-zstd --yes
           opam install lwt --yes
           opam exec -- dune build zarr zarr-sync zarr-lwt
 

README.md

@@ -92,7 +92,7 @@ assert (Ndarray.equal x' y);;
 ```ocaml
 let config =
   {chunk_shape = [|5; 3; 5|]
-  ;codecs = [`Transpose [|2; 0; 1|]; `Bytes LE; `Gzip L5]
+  ;codecs = [`Transpose [|2; 0; 1|]; `Bytes LE; `Zstd (0, true)]
   ;index_codecs = [`Bytes BE; `Crc32c]
   ;index_location = Start};;
 

dune-project

@@ -29,7 +29,6 @@
    (ocaml
      (and (>= 4.14.0)))
    (yojson (>= 1.6.0))
-   (ezgzip (>= 0.2.0))
    (stdint (>= 0.7.2))
    (checkseum (>= 0.4.0))
    (odoc :with-doc)

zarr-sync/test/test_sync.ml

@@ -45,7 +45,7 @@ let test_storage
     {chunk_shape = [|2; 5; 5|]
     ;index_location = End
     ;index_codecs = [`Bytes LE; `Crc32c]
-    ;codecs = [`Transpose [|2; 0; 1|]; `Bytes BE; `Gzip L5]} in
+    ;codecs = [`Transpose [|2; 0; 1|]; `Bytes BE; `Zstd (0, false)]} in
   let cfg2 =
     {chunk_shape = [|2; 5; 5|]
     ;index_location = Start

zarr.opam

@@ -17,7 +17,6 @@ depends: [
   "dune" {>= "3.15"}
   "ocaml" {>= "4.14.0"}
   "yojson" {>= "1.6.0"}
-  "ezgzip" {>= "0.2.0"}
   "stdint" {>= "0.7.2"}
   "checkseum" {>= "0.4.0"}
   "odoc" {with-doc}
@@ -40,3 +39,6 @@ build: [
   ]
 ]
 dev-repo: "git+https://github.com/zoj613/zarr-ml.git"
+pin-depends: [
+  ["bytesrw.dev" "git+https://erratique.ch/repos/bytesrw.git"]
+]

zarr.opam.template

@@ -0,0 +1,3 @@
+pin-depends: [
+  ["bytesrw.dev" "git+https://erratique.ch/repos/bytesrw.git"]
+]

zarr/src/codecs/array_to_bytes.ml

@@ -375,7 +375,7 @@ end = struct
         let* l = acc in
         match c with
         | `Crc32c -> Ok (`Crc32c :: l)
-        | `Gzip _ -> Error msg) ic.b2b (Ok [])
+        | `Gzip _ | `Zstd _ -> Error msg) ic.b2b (Ok [])
     in
     let+ a2b = match ic.a2b with
       | `Bytes e -> Ok (`Bytes e)

zarr/src/codecs/bytes_to_bytes.ml

@@ -1,4 +1,5 @@
 open Codecs_intf
+open Bytesrw
 
 (* https://zarr-specs.readthedocs.io/en/latest/v3/codecs/gzip/v1.0.html *)
 module GzipCodec = struct
@@ -13,10 +14,13 @@ module GzipCodec = struct
       Error (Printf.sprintf "Invalid Gzip level %d" i)
 
   let encode l x =
-    Ezgzip.compress ~level:(to_int l) x
+    Bytes.Reader.to_string @@
+    Bytesrw_zlib.Gzip.compress_reads ~level:(to_int l) () @@
+    Bytes.Reader.of_string x
 
   let decode x =
-    Result.get_ok @@ Ezgzip.decompress x
+    Bytes.Reader.to_string @@
+    Bytesrw_zlib.Gzip.decompress_reads () @@ Bytes.Reader.of_string x
 
   let to_yojson l =
     `Assoc
@@ -52,27 +56,68 @@ module Crc32cCodec = struct
       Ok `Crc32c
 end
 
+(* https://github.com/zarr-developers/zarr-specs/pull/256 *)
+module ZstdCodec = struct
+  let min_clevel = -131072 and max_clevel = 22
+
+  let parse_clevel l =
+    if l < min_clevel || max_clevel < l then (raise Invalid_zstd_level)
+
+  let encode clevel checksum x =
+    let params = Bytesrw_zstd.Cctx_params.make ~checksum ~clevel () in
+    Bytes.Reader.to_string @@
+    Bytesrw_zstd.compress_reads ~params () @@ Bytes.Reader.of_string x
+
+  let decompress_params = Bytesrw_zstd.Dctx_params.default
+
+  let decode x =
+    Bytes.Reader.to_string @@
+    Bytesrw_zstd.decompress_reads ~params:decompress_params () @@
+    Bytes.Reader.of_string x
+
+  let to_yojson l c =
+    `Assoc
+    [("name", `String "zstd")
+    ;("configuration", `Assoc [("level", `Int l); ("checksum", `Bool c)])]
+
+  let of_yojson x =
+    match Yojson.Safe.Util.(member "configuration" x) with
+    | `Assoc [("level", `Int l); ("checksum", `Bool c)] ->
+      begin match parse_clevel l with
+      | exception Invalid_zstd_level -> Error "Invalid_zstd_level"
+      | () -> Result.ok @@ `Zstd (l, c) end
+    | _ -> Error "Invalid Zstd configuration."
+end
+
 module BytesToBytes = struct
   let encoded_size :
     int -> fixed_bytestobytes -> int
     = fun input_size -> function
     | `Crc32c -> Crc32cCodec.encoded_size input_size
 
+  let parse = function
+    | `Gzip _ | `Crc32c -> ()
+    | `Zstd (l, _) -> ZstdCodec.parse_clevel l
+
   let encode x = function
     | `Gzip l -> GzipCodec.encode l x
     | `Crc32c -> Crc32cCodec.encode x
+    | `Zstd (l, c) -> ZstdCodec.encode l c x
 
   let decode t x = match t with
     | `Gzip _ -> GzipCodec.decode x
     | `Crc32c -> Crc32cCodec.decode x
+    | `Zstd _ -> ZstdCodec.decode x
 
   let to_yojson = function
     | `Gzip l -> GzipCodec.to_yojson l
     | `Crc32c -> Crc32cCodec.to_yojson 
+    | `Zstd (l, c) -> ZstdCodec.to_yojson l c
 
   let of_yojson x =
     match Util.get_name x with
     | "gzip" -> GzipCodec.of_yojson x
     | "crc32c" -> Crc32cCodec.of_yojson x
+    | "zstd" -> ZstdCodec.of_yojson x
     | s -> Error (Printf.sprintf "codec %s is not supported." s)
 end

zarr/src/codecs/bytes_to_bytes.mli

@@ -1,6 +1,7 @@
 open Codecs_intf
 
 module BytesToBytes : sig
+  val parse : bytestobytes -> unit
   val encoded_size : int -> fixed_bytestobytes -> int
   val encode : string -> bytestobytes -> string
   val decode : bytestobytes -> string -> string

zarr/src/codecs/codecs.ml

@@ -76,6 +76,7 @@ module Chain = struct
     | x :: _ as xs -> 
       ArrayToArray.parse x shape;
       List.fold_left ArrayToArray.encoded_repr shape xs);
+    List.iter BytesToBytes.parse b2b;
     {a2a; a2b; b2b}
 
   let encode t x =

zarr/src/codecs/codecs.mli

@@ -19,6 +19,8 @@ module Chain : sig
         if [c] contains more than one bytes->bytes codec.
       @raise Invalid_transpose_order
         if [c] contains a transpose codec with invalid order array.
+      @raise Invalid_zstd_level
+        if [c] contains a Zstd codec whose compression level is invalid.
       @raise Invalid_sharding_chunk_shape
         if [c] contains a shardingindexed codec with an
         incorrect inner chunk shape. *)

zarr/src/codecs/codecs_intf.ml

@@ -2,6 +2,7 @@ exception Array_to_bytes_invariant
 exception Invalid_transpose_order
 exception Invalid_sharding_chunk_shape
 exception Invalid_codec_ordering
+exception Invalid_zstd_level
 
 type arraytoarray =
   [ `Transpose of int array ]
@@ -13,7 +14,8 @@ type fixed_bytestobytes =
   [ `Crc32c ]
 
 type variable_bytestobytes =
-  [ `Gzip of compression_level ]
+  [ `Gzip of compression_level
+  | `Zstd of int * bool ]
 
 type bytestobytes =
   [ fixed_bytestobytes | variable_bytestobytes ]
@@ -62,6 +64,9 @@ module type Interface = sig
   (** raised when a codec chain has incorrect ordering of codecs. i.e if the
       ordering is not [arraytoarray list -> 1 arraytobytes -> bytestobytes list]. *)
 
+  exception Invalid_zstd_level
+  (** raised when a codec chain contains a Zstd codec with an incorrect compression value.*)
+
   (** The type of [array -> array] codecs. *)
   type arraytoarray =
     [ `Transpose of int array ]
@@ -78,7 +83,8 @@ module type Interface = sig
   (** A type representing [bytes -> bytes] codecs that produce
       variable sized encoded strings. *)
   type variable_bytestobytes =
-    [ `Gzip of compression_level ]
+    [ `Gzip of compression_level
+    | `Zstd of int * bool ]
 
   (** The type of [bytes -> bytes] codecs. *)
   type bytestobytes =

zarr/src/dune

@@ -3,7 +3,8 @@
  (public_name zarr)
  (libraries
    yojson
-   ezgzip
+   bytesrw.zstd
+   bytesrw.zlib
    stdint
    checkseum)
  (ocamlopt_flags

zarr/test/test_codecs.ml

@@ -238,19 +238,22 @@ let tests = [
             [{"name": "bytes", "configuration": {"endian": "big"}}]}}]|}
     ~msg:"Must be exactly one array->bytes codec.";
   (* test violation of index_codec invariant when it contains variable-sized codecs. *)
-  decode_chain
-    ~shape:[|5; 5; 5|]
-    ~str:{|[
-      {"name": "sharding_indexed",
-       "configuration":
-         {"index_location": "start",
-          "chunk_shape": [5, 5, 5],
-          "index_codecs":
-            [{"name": "bytes", "configuration": {"endian": "big"}},
-             {"name": "gzip", "configuration": {"level": 1}}],
-          "codecs":
-            [{"name": "bytes", "configuration": {"endian": "big"}}]}}]|}
-    ~msg:"Must be exactly one array->bytes codec.";
+  List.iter
+    (fun c ->
+      decode_chain
+        ~shape:[|5; 5; 5|]
+        ~str:(Format.sprintf {|[
+          {"name": "sharding_indexed",
+           "configuration":
+             {"index_location": "start",
+              "chunk_shape": [5, 5, 5],
+              "index_codecs":
+                [{"name": "bytes", "configuration": {"endian": "big"}}, %s],
+              "codecs":
+                [{"name": "bytes", "configuration": {"endian": "big"}}]}}]|} c)
+        ~msg:"Must be exactly one array->bytes codec.")
+    [{|{"name": "zstd", "configuration": {"level": 0, "checksum": false}}|}
+    ;{|{"name": "gzip", "configuration": {"level": 1}}|}];
 
   let shape = [|10; 15; 10|] in
   let kind = Ndarray.Float64 in
@@ -365,6 +368,47 @@ let tests = [
       assert_equal arr @@ Chain.decode c {shape; kind} encoded)
     [L0; L1; L2; L3; L4; L5; L6; L7; L8; L9])
 ;
+
+"test zstd codec" >:: (fun _ ->
+  (* test wrong compression level *)
+  List.iter
+    (fun l ->
+      decode_chain
+        ~shape:[||]
+        ~str:(Format.sprintf {|[{"name": "bytes", "configuration": {"endian": "little"}},
+                {"name": "zstd", "configuration": {"level": %d, "checksum": false}}]|} l)
+        ~msg:"zstd codec is unsupported or has invalid configuration.")
+    [50; -500_000];
+
+  (* test incorrect configuration *)
+  decode_chain
+    ~shape:[||]
+    ~str:{|[{"name": "bytes", "configuration": {"endian": "little"}},
+            {"name": "zstd", "configuration": {"something": -1}}]|}
+    ~msg:"zstd codec is unsupported or has invalid configuration.";
+
+  (* test correct deserialization of zstd compression level *)
+  let shape = [|10; 15; 10|] in
+  List.iter
+    (fun level ->
+      let str =
+        Format.sprintf
+        {|[{"name": "bytes", "configuration": {"endian": "little"}},
+           {"name": "zstd", "configuration": {"level": %d, "checksum": false}}]|} level 
+      in
+      let r = Chain.of_yojson shape @@ Yojson.Safe.from_string str in
+      assert_bool "Encoding this chain should not fail" @@ Result.is_ok r) [-131072; 0];
+
+  (* test encoding/decoding for various compression levels *)
+  let arr = Ndarray.create Int shape Int.max_int in
+  List.iter
+    (fun (level, checksum) ->
+      let c = Chain.create shape [`Bytes LE; `Zstd (level, checksum)] in
+      let encoded = Chain.encode c arr in
+      assert_equal arr @@ Chain.decode c {shape; kind = Ndarray.Int} encoded)
+    [(-131072, false); (-131072, true); (0, false); (0, true)])
+;
+
 "test bytes codec" >:: (fun _ ->
   let shape = [|2; 2; 2|] in
   (* test decoding of chain with invalid endianness name *)