First pass at native NDArray support.

See

- linkml/linkml#895
- linkml/linkml-arrays#5

linkml_model/model/schema/array.yaml

@@ -63,6 +63,8 @@ classes:
     slots:
       - axis
       - array
+    see_also:
+      - https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html
 
   GroupingByArrayOrder:
     mixin: true

linkml_model/model/schema/meta.yaml

@@ -1420,6 +1420,34 @@ slots:
       - BasicSubset
       - ObjectOrientedProfile
 
+  array_shape:
+    domain: slot_definition
+    range: array_shape_expression
+    inherited: true
+    description: coerces the value of the slot into an array and defines the dimensions of that array
+
+  array_axes:
+    description: definitions of each axis in the array
+    domain: array_shape_expression
+    range: array_axis_expression
+    multivalued: true
+    inlined: true
+
+  minimum_dimensions:
+    description: minimum number of dimensions in the array
+    domain: array_shape_expression
+    range: integer
+
+  maximum_dimensions:
+    description: maximum number of dimensions in the array
+    domain: array_shape_expression
+    range: integer
+
+  exact_dimensions:
+    description: exact number of dimensions in the array
+    domain: array_shape_expression
+    range: integer
+
   inherited:
     domain: slot_definition
     range: boolean
@@ -1521,6 +1549,14 @@ slots:
     in_subset:
       - SpecificationSubset
 
+  exact_cardinality:
+    is_a: list_value_specification_constant
+    range: integer
+    inherited: true
+    description: the exact number of entries for a multivalued slot
+    in_subset:
+      - SpecificationSubset
+
   minimum_cardinality:
     is_a: list_value_specification_constant
     range: integer
@@ -2715,6 +2751,7 @@ classes:
       - equals_string_in
       - equals_number
       - equals_expression
+      - exact_cardinality
       - minimum_cardinality
       - maximum_cardinality
       - has_member
@@ -2759,6 +2796,7 @@ classes:
       - domain
       - slot_uri
       - multivalued
+      - array_shape
       - inherited
       - readonly
       - ifabsent
@@ -2917,6 +2955,33 @@ classes:
     in_subset:
       - SpecificationSubset
 
+  array_shape_expression:
+    description: defines the dimensions of an array
+    mixins:
+      - extensible
+      - annotatable
+      - common_metadata
+    slots:
+      - exact_dimensions
+      - minimum_dimensions
+      - maximum_dimensions
+      - array_axes
+
+  array_axis_expression:
+    description: defines one of the dimensions of an array
+    mixins:
+      - extensible
+      - annotatable
+      - common_metadata
+    slots:
+      - name
+      - rank
+      - equals_expression
+      - alias
+      - maximum_cardinality
+      - minimum_cardinality
+      - exact_cardinality
+
   pattern_expression:
     description: a regular expression pattern used to evaluate conformance of a string
     mixins:

tests/input/examples/schema_definition-array-2.yaml

@@ -26,7 +26,7 @@ classes:
     implements:
       - linkml:NDArray
     annotations:
-      dimensions: 1
+      dimensions: "1"
     # TODO abstract from children
 
   IrregularlySampledTimestampSeries:
@@ -47,7 +47,7 @@ classes:
         unit:
           ucum_code: s
     annotations:
-      dimensions: 1
+      dimensions: "1"
 
   RegularlySampledTimestampSeries:
     is_a: TimestampSeries
@@ -82,7 +82,7 @@ classes:
         unit:
           ucum_code: s
     annotations:
-      dimensions: 1
+      dimensions: "1"
 
   Electrode:
     attributes:
@@ -106,7 +106,7 @@ classes:
         implements:
           - linkml:elements
     annotations:
-      dimensions: 1
+      dimensions: "1"
 
   ElectricalDataMatrix:
     description: >-

tests/input/examples/schema_definition-native-array-1.yaml

@@ -0,0 +1,70 @@
+id: https://example.org/arrays
+name: arrays-temperature-example
+title: Array Temperature Example
+description: |-
+  Example LinkML schema to demonstrate a 3D DataArray of temperature values with labeled axes
+license: MIT
+
+prefixes:
+  linkml: https://w3id.org/linkml/
+  wgs84: http://www.w3.org/2003/01/geo/wgs84_pos#
+  example: https://example.org/
+
+default_prefix: example
+
+imports:
+  - linkml:types
+
+classes:
+
+  TemperatureDataset:
+    tree_root: true
+    attributes:
+      name:
+        identifier: true
+        range: string
+      latitude_in_deg:
+        required: true
+        range: float
+        multivalued: true
+        unit:
+          ucum_code: deg
+        array_shape:
+          exact_dimensions: 1
+      longitude_in_deg:
+        required: true
+        range: float
+        multivalued: true
+        unit:
+          ucum_code: deg
+        array_shape:
+          exact_dimensions: 1
+      time_in_d:
+        range: float
+        multivalued: true
+        implements:
+          - linkml:elements
+        required: true
+        unit:
+          ucum_code: d
+        array_shape:
+          exact_dimensions: 1
+      temperatures_in_K:
+        range: float
+        multivalued: true
+        required: true
+        unit:
+          ucum_code: K
+        array_shape:
+          exact_dimensions: 3
+          array_axes:
+            x:
+              rank: 0
+              alias: latitude_in_deg
+            y:
+              rank: 1
+              alias: longitude_in_deg
+            t:
+              rank: 2
+              alias: time_in_d
+

tests/input/examples/schema_definition-native-array-rgb.yaml

@@ -0,0 +1,37 @@
+id: https://example.org/arrays
+name: arrays-temperature-example
+title: Array Temperature Example
+description: |-
+  Example LinkML schema to demonstrate a 3D DataArray of temperature values with labeled axes
+license: MIT
+
+prefixes:
+  linkml: https://w3id.org/linkml/
+  wgs84: http://www.w3.org/2003/01/geo/wgs84_pos#
+  example: https://example.org/
+
+default_prefix: example
+
+imports:
+  - linkml:types
+
+classes:
+
+  RGBImage:
+    attributes:
+      x:
+        range: integer
+      y:
+        range: integer
+
+    rgb:
+      range: float
+      array_shape:
+        exact_dimensions: 3
+        array_axes:
+          x:
+          y:
+          rgb:
+            exact_cardinality: 3
+            description: r, g, b values
+