Add unit tests for ArrayMetadata module.

This also improves the correctness of serializing/deserializing the
ArrayMetadata type. it also removes unnecessary functions exposed in
the module signature.

lib/codecs/array_to_array.ml

@@ -1,9 +1,10 @@
 module Ndarray = Owl.Dense.Ndarray.Generic
 
-type dimension_order = int array
+type dimension_order = int array [@@deriving show]
 
 type array_to_array =
   | Transpose of dimension_order
+  [@@deriving show]
 
 type error =
   [ `Invalid_transpose_order of dimension_order * string ]

lib/codecs/array_to_array.mli

@@ -8,6 +8,9 @@ type array_to_array =
 type error =
   [ `Invalid_transpose_order of dimension_order * string ]
 
+val pp_array_to_array : Format.formatter -> array_to_array -> unit
+val show_array_to_array : array_to_array -> string
+
 module ArrayToArray : sig 
   val parse
     : ('a, 'b) Util.array_repr ->

lib/codecs/array_to_bytes.ml

@@ -4,25 +4,32 @@ open Util.Result_syntax
 
 module Ndarray = Owl.Dense.Ndarray.Generic
 
-type endianness = Little | Big
+type endianness =
+  | Little
+  | Big
+  [@@deriving show]
 
-type loc = Start | End
+type loc =
+  | Start
+  | End
+  [@@deriving show]
 
 type array_to_bytes =
   | Bytes of endianness
   | ShardingIndexed of shard_config
+  [@@deriving show]
 
 and shard_config =
   {chunk_shape : int array
   ;codecs : chain
   ;index_codecs : chain
   ;index_location : loc}
 
-and chain = {
-  a2a: array_to_array list;
-  a2b: array_to_bytes;
-  b2b: bytes_to_bytes list;
-}
+and chain =
+  {a2a: array_to_array list
+  ;a2b: array_to_bytes
+  ;b2b: bytes_to_bytes list}
+  [@@deriving show]
 
 type error =
   [ `Bytes_encode_error of string

lib/codecs/array_to_bytes.mli

@@ -20,6 +20,9 @@ and chain = {
   b2b: Bytes_to_bytes.bytes_to_bytes list;
 }
 
+val pp_chain : Format.formatter -> chain -> unit
+val show_chain : chain -> string
+
 type error =
   [ `Bytes_encode_error of string
   | `Bytes_decode_error of string

lib/codecs/bytes_to_bytes.ml

@@ -2,10 +2,12 @@ module Ndarray = Owl.Dense.Ndarray.Generic
 
 type compression_level =
   | L0 | L1 | L2 | L3 | L4 | L5 | L6 | L7 | L8 | L9
+  [@@deriving show]
 
 type bytes_to_bytes =
   | Crc32c
   | Gzip of compression_level
+  [@@deriving show]
 
 type error = 
   [ `Gzip of Ezgzip.error ]

lib/codecs/bytes_to_bytes.mli

@@ -10,6 +10,9 @@ type bytes_to_bytes =
 type error = 
   [ `Gzip of Ezgzip.error ]
 
+val pp_bytes_to_bytes : Format.formatter -> bytes_to_bytes -> unit
+val show_bytes_to_bytes : bytes_to_bytes -> string
+
 module BytesToBytes : sig
   val compute_encoded_size : int -> bytes_to_bytes -> int
   val encode : bytes_to_bytes -> string -> (string, [> error]) result

lib/codecs/codecs.ml

@@ -8,6 +8,10 @@ module Ndarray = Owl.Dense.Ndarray.Generic
 module Chain = struct
   type t = chain
 
+  let pp = pp_chain
+
+  let show = show_chain
+
   let create repr {a2a; a2b; b2b} =
     List.fold_left
       (fun acc c ->

lib/codecs/codecs.mli

@@ -58,4 +58,8 @@ module Chain : sig
   val of_yojson : Yojson.Safe.t -> (t, string) result
 
   val to_yojson : t -> Yojson.Safe.t
+
+  val pp : Format.formatter -> t -> unit
+
+  val show : t -> string
 end

lib/metadata.ml

@@ -15,6 +15,8 @@ module FillValue = struct
     | BFComplex of Complex.t
     | BBComplex of Complex.t
 
+  let equal x y = x = y
+
   let of_kind
   : type a b. (a, b) Bigarray.kind -> a -> t
   = fun kind a ->
@@ -109,14 +111,16 @@ module ArrayMetadata = struct
     ;fill_value : FillValue.t
     ;chunk_grid : Extensions.RegularGrid.t
     ;chunk_key_encoding : Extensions.ChunkKeyEncoding.t
-    ;attributes : Yojson.Safe.t option [@yojson.option]
-    ;dimension_names : string option list option [@yojson.option]
-    ;storage_transformers : Yojson.Safe.t Util.ext_point list option [@yojson.option]}
-  [@@deriving yojson]
+    ;attributes : Yojson.Safe.t [@default `Null]
+    ;dimension_names : string option list [@default []]
+    ;storage_transformers : Yojson.Safe.t Util.ExtPoint.t list [@default []]}
+  [@@deriving yojson, eq]
 
   let create
     ?(sep=Extensions.Slash)
     ?(codecs=Codecs.Chain.default)
+    ?(dimension_names=[])
+    ?(attributes=`Null)
     ~shape
     kind
     fv
@@ -130,23 +134,23 @@ module ArrayMetadata = struct
     ;chunk_key_encoding = Extensions.ChunkKeyEncoding.create sep
     ;zarr_format = 3
     ;node_type = "array"
-    ;storage_transformers = None
-    ;dimension_names = None
-    ;attributes = None}
+    ;attributes
+    ;dimension_names
+    ;storage_transformers = []}
 
   let shape t = t.shape
 
   let codecs t = t.codecs
 
-  let dtype t = t.data_type
-
-  let fill_value t = t.fill_value
+  let data_type t =
+    Yojson.Safe.to_string @@
+    Extensions.Datatype.to_yojson t.data_type
 
   let ndim t = Array.length @@ shape t
 
   let dimension_names t = t.dimension_names
 
-  let attributes t : Yojson.Safe.t option = t.attributes
+  let attributes t = t.attributes
 
   let chunk_shape t =
     Extensions.RegularGrid.chunk_shape t.chunk_grid
@@ -171,8 +175,8 @@ module ArrayMetadata = struct
     of_yojson @@ Yojson.Safe.from_string b >>? fun s ->
     `Json_decode_error s
 
-  let update_attributes attrs t =
-    {t with attributes = Some attrs}
+  let update_attributes t attrs =
+    {t with attributes = attrs}
 
   let update_shape t shape = {t with shape}
 

lib/metadata.mli

@@ -35,7 +35,9 @@ module ArrayMetadata : sig
 
   val create :
     ?sep:Extensions.separator ->
-    ?codecs:Codecs.Chain.t  ->
+    ?codecs:Codecs.Chain.t ->
+    ?dimension_names:string option list ->
+    ?attributes:Yojson.Safe.t ->
     shape:int array ->
     ('a, 'b) Bigarray.kind ->
     'a ->
@@ -50,40 +52,36 @@ module ArrayMetadata : sig
 
   val decode : string -> (t, [> error]) result
   (** [decode s] decodes a bytes string [s] into a {!ArrayMetadata.t}
-      type, and returns an {!error} error if the decoding process fails. *)
+      type, and returns an error if the decoding process fails. *)
 
   val shape : t -> int array
   (** [shape t] returns the shape of the zarr array represented by metadata type [t]. *)
 
-  val fill_value : t -> FillValue.t
-  (** [fill_value t] returns the fill value of the zarra array represented by [t]. *)
-
   val ndim : t -> int
   (** [ndim t] returns the number of dimension in a Zarr array. *)
 
   val chunk_shape : t -> int array
   (** [chunk_shape t] returns the shape a chunk in this zarr array. *)
 
-  val dtype : t -> Extensions.Datatype.t
-  (** [dtype t] returns the data type as specified in the array metadata. *)
+  val data_type : t -> string
+  (** [data_type t] returns the data type as specified in the array metadata.*)
 
   val is_valid_kind : t -> ('a, 'b) Bigarray.kind -> bool
-  (** [is_valid_kind t kind] checks if [kind] is a valid {!Bigarray.kind} that
+  (** [is_valid_kind t kind] checks if [kind] is a valid Bigarray kind that
       matches the data type of the zarr array represented by this metadata type. *)
 
   val fillvalue_of_kind : t -> ('a, 'b) Bigarray.kind -> 'a
   (** [fillvalue_of_kind t kind] returns the fill value of uninitialized
-      chunks in this zarr array  given [kind].
-
-      @raises [Failure] if the kind is not compatible with this array's fill value. *)
+      chunks in this zarr array  given [kind]. Raises Failure if the kind
+      is not compatible with this array's fill value. *)
 
-  val attributes : t -> Yojson.Safe.t option
+  val attributes : t -> Yojson.Safe.t
   (** [attributes t] Returns a Yojson type containing user attributes assigned
       to the zarr array represented by [t]. *)
 
-  val dimension_names : t -> string option list option
-  (** [dimension_name t] returns a list of dimension names, if any are
-      defined in the array's JSON metadata document. *)
+  val dimension_names : t -> string option list
+  (** [dimension_name t] returns a list of dimension names. If none are
+      defined then an empty list is returned. *)
 
   val codecs : t -> Codecs.Chain.t
   (** [codecs t] Returns a type representing the chain of codecs applied
@@ -105,20 +103,25 @@ module ArrayMetadata : sig
   val chunk_key : t -> int array -> string
   (** [chunk_key t idx] returns a key encoding of a the chunk index [idx]. *)
 
-  val update_attributes : Yojson.Safe.t -> t -> t
-  (** [update_attributes json t] returns a new metadata type with an updated
+  val update_attributes : t -> Yojson.Safe.t -> t
+  (** [update_attributes t json] returns a new metadata type with an updated
       attribute field containing contents in [json] *)
 
   val update_shape : t -> int array -> t
   (** [update_shape t new_shp] returns a new metadata type containing
       shape [new_shp]. *)
 
+  val equal : t -> t -> bool
+  (** [equal a b] returns true if [a] [b] are equal array metadata documents
+      and false otherwise. *)
+
   val of_yojson : Yojson.Safe.t -> (t, string) result
-  (** [of_yojson json] converts a {!Yojson.Safe.t} object into a {!ArrayMetadata.t}
+  (** [of_yojson json] converts a [Yojson.Safe.t] object into a {!ArrayMetadata.t}
      and returns an error message upon failure. *)
 
   val to_yojson : t -> Yojson.Safe.t
-  (** [to_yojson t] serializes an array metadata type into a {!Yojson.Safe.t} object. *)
+  (** [to_yojson t] serializes an array metadata type into a [Yojson.Safe.t]
+      object. *)
 end
 
 module GroupMetadata : sig
@@ -135,19 +138,19 @@ module GroupMetadata : sig
   (** [encode t] returns a byte string representing a JSON Zarr group metadata. *)
 
   val decode : string -> (t, [> error]) result
-  (** [decode s] decodes a bytes string [s] into a {!GroupMetadata.t}
-      type, and returns an {!Metadata.error} error if the decoding process fails. *)
+  (** [decode s] decodes a bytes string [s] into a {!t} type, and returns
+      an error if the decoding process fails. *)
 
   val update_attributes : t -> Yojson.Safe.t -> t
   (** [update_attributes t json] returns a new metadata type with an updated
       attribute field containing contents in [json]. *)
 
   val of_yojson : Yojson.Safe.t -> (t, string) result
-  (** [of_yojson json] converts a {!Yojson.Safe.t} object into a {!GroupMetadata.t}
+  (** [of_yojson json] converts a [Yojson.Safe.t] object into a {!GroupMetadata.t}
      and returns an error message upon failure. *)
 
   val to_yojson : t -> Yojson.Safe.t
-  (** [to_yojson t] serializes a group metadata type into a {!Yojson.Safe.t} object. *)
+  (** [to_yojson t] serializes a group metadata type into a [Yojson.Safe.t] object. *)
 
   val show : t -> string
   (** [show t] pretty-prints the contents of the group metadata type t. *)

lib/storage/interface.ml

@@ -38,6 +38,8 @@ module type S = sig
 
   val create_array
     : ?sep:Extensions.separator ->
+      ?dimension_names:string option list ->
+      ?attributes:Yojson.Safe.t ->
       ?codecs:Codecs.chain ->
       shape:int array ->
       chunks:int array ->
@@ -100,19 +102,27 @@ module Make (M : STORE) : S with type t = M.t = struct
       | Error _ -> create_group t n) @@ Node.ancestors node
 
   let create_array
-    ?(sep=Extensions.Slash) ?codecs ~shape ~chunks kind fill_value node t =
+    ?(sep=Extensions.Slash)
+    ?(dimension_names=[])
+    ?(attributes=`Null)
+    ?codecs
+    ~shape
+    ~chunks
+    kind
+    fill_value
+    node
+    t
+    =
     let open Util in
-    let repr =
-      {kind
-      ;fill_value
-      ;shape = chunks}
-    in
+    let repr = {kind; fill_value; shape = chunks} in
     (match codecs with
     | Some c -> Codecs.Chain.create repr c
     | None -> Ok Codecs.Chain.default)
-    >>= fun codecs' ->
+    >>= fun codecs ->
     let meta =
-      AM.create ~sep ~codecs:codecs' ~shape kind fill_value chunks in
+      AM.create
+        ~sep ~codecs ~dimension_names ~attributes ~shape kind fill_value chunks
+    in
     set t (Node.to_metakey node) (AM.encode meta);
     Ok (make_implicit_groups_explicit t node)
 

test/dune

@@ -1,3 +1,7 @@
 (test
  (name test_zarr)
- (libraries ounit2 zarr))
+ (libraries
+   zarr
+   ounit2)
+ (preprocess
+   (pps ppx_deriving.show)))