feat: implement LinkML exporter

[ahmdmhd]

This PR is based on #168 and implements LinkML exporter.

s2dm export linkml \
  --schema /path/to/schema \
  --output output.yaml \
  --id schema_id \
  --name schema_name \
  --default-prefix default_prefix \
  --default-prefix-url default_prefix_url

[jdacoello]

Following remarks:

• Fields that resolve to built-in ID scalar must have identifier: true

type SomeTypeName {
  id: ID!
  ...
}

# Current
SomeTypeName:
  attributes:
    id:
      range: string
      required: true

# Should be
SomeTypeName:
  attributes:
    id:
      range: string
      required: true
      identifier: true

• Exclude Query and input types

type Query {
  vehicle: Vehicle
}

input KeyValue {
  key: String!
  value: String!
}

  # Currently present
  Query:
    attributes:
      vehicle:
        range: Vehicle

  KeyValue:
    description: Key-value pair for storing metadata.
    attributes:
      key:
        range: string
        required: true
      value:
        range: string
        required: true

• All top-level concepts should be declared as tree_root: true

type Vehicle {
  ...
}

Vehicle:
  tree_root: true
    ...

Same for other top level concepts. I think we have already a function that returns the top level concepts (i.e., all roots) from a GraphQL schema.

• Fix handling of units

Right now, the units are passed as seen.

ambientAirTemperature(unit: TemperatureUnitEnum = DEGREE_CELSIUS): Float

enum TemperatureUnitEnum {
  DEGREE_CELSIUS
  DEGREE_FAHRENHEIT
}

temperature:
  range: float
  unit:
    symbol: DEGREE_CELSIUS    # ← enum value name used as-is, no URIs

It seems that the linkml tools expect compatible ones because some tools complain, eg.,:

linkml generate doc <spec-in-linkml.yaml> -d <directory>
TypeError: unhashable type: 'UnitOfMeasure'

• If custom unit is used, the linkml tools should be able to run (e.g., doc)

When annotation of reference is given, then reflect it, such as:

enum TemperatureUnit @reference(uri: "http://qudt.org/vocab/quantitykind/Temperature") {
  DEG_C @reference(uri: "http://qudt.org/vocab/unit/DEG_C")
  DEG_F @reference(uri: "http://qudt.org/vocab/unit/DEG_F")
}

type SomeType {
  ambientAirTemperature(unit: TemperatureUnit = DEG_C): Float
}

...
TemperatureUnitEnum:
  description: Units for "temperature"
  permissible_values:
    DEG_C:
      meaning: http://qudt.org/vocab/unit/DEG_C
    DEG_F:
      meaning: http://qudt.org/vocab/unit/DEG_F

...
# every attribute that uses unit
ambientAirTemperature:
  range: float
  unit:
    symbol: DEG_C
    exact_mappings:
      - http://qudt.org/vocab/unit/DEG_C