Added a ReferenceValidator that performs complete normalizations.

[cmungall]

This PR implements a reference validator, which is intended to be a direct implementation of part 5 of the spec

This also performs instance normalization as defined in part 6 of the spec

The test suite performs auto-documentation, generating a markdown file as output that will serve as a reference document for validators.

The PR also introduces a temporary validation datamodel that forks the core linkml-model one, with the plan to fold these changes back in.

Note the current implementation may be incomplete.

There is a very preliminary CLI:

linkml-normalize --help
Usage: linkml-normalize [OPTIONS] INPUT

  Normalizes and validates a YAML document against a schema.

  Normalization is a mix of casting types (e.g. "5" to 5), as well as LinkML
  *collection forms*, e.g. ExpandedDict to CompactDict.

  Validations is performed using a derived schema, as per part 5 of the
  specification.

  Note that in future this will be folded into the main linkml-validate
  command.

  Currently this CLI lacks features such as the ability to customize which
  severity rules to fail on.

  :param schema: :param target: :param input: :param output: :return:

Options:
  -s, --schema TEXT      [required]
  -C, --target TEXT
  -o, --output FILENAME
  --help                 Show this message and exit.

[codecov-commenter]

Codecov Report

Merging #239 (f597921) into main (b992fe0) will increase coverage by 0.24%. The diff coverage is 45.33%.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more

@@            Coverage Diff             @@
##             main     #239      +/-   ##
==========================================
+ Coverage   63.54%   63.78%   +0.24%     
==========================================
  Files          53       53              
  Lines        6117     6188      +71     
  Branches     1650     1678      +28     
==========================================
+ Hits         3887     3947      +60     
+ Misses       1774     1762      -12     
- Partials      456      479      +23     

Impacted Files	Coverage Δ
linkml_runtime/utils/schemaview.py	82.89% <33.87%> (-3.51%)	:arrow_down:
linkml_runtime/dumpers/rdflib_dumper.py	97.91% <100.00%> (ø)
linkml_runtime/utils/namespaces.py	73.05% <100.00%> (+2.16%)	:arrow_up:
linkml_runtime/utils/yamlutils.py	78.15% <100.00%> (ø)
linkml_runtime/linkml_model/meta.py	53.93% <0.00%> (+1.14%)	:arrow_up:

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