Derive files that were not derived for schema version 11.2.0

[eecavanna]

When I "released" the schema (version 11.2.0) yesterday, I forgot that there are some manual steps involved in creating a release. Instead, I went straight to creating a new GitHub Release. (See issue #1960 about eliminating the manual steps from this process.)

As a result, when I tried to update the submission schema to use nmdc-schema version 11.2.0, I ran into an error involving the nmdc_materialized_patterns.yaml file that the submission schema build code fetches from this repo (as opposed to from a PyPI package).

🪗 Show/hide failing submission schema make target and associated stack trace

poetry run gen-project   \
        --exclude graphql \
        --exclude jsonld \
        --exclude jsonldcontext \
        --exclude markdown \
        --exclude prefixmap \
        --exclude proto \
        --exclude shacl \
        --exclude shex \
        --exclude excel \
        --include jsonschema \
        --exclude owl \
        --include python \
        --include sqlddl \
        --generator-arguments '{jsonschema: {not_closed: false}, sqlddl: {output: local/submission_schema.sql}}' \
        -d project src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml && mv project/*.py src/nmdc_submission_schema/datamodel
Traceback (most recent call last):
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/bin/gen-project", line 8, in <module>
    sys.exit(cli())
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/linkml/generators/projectgen.py", line 259, in cli
    gen.generate(yamlfile, project_config)
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/linkml/generators/projectgen.py", line 140, in generate
    gen = gen_cls(local_path, **all_gen_args)
  File "<string>", line 29, in __init__
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/linkml/generators/pythongen.py", line 77, in __post_init__
    super().__post_init__()
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/linkml/utils/generator.py", line 206, in __post_init__
    self._initialize_using_schemaloader(schema)
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/linkml/utils/generator.py", line 253, in _initialize_using_schemaloader
    loader.resolve()
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/linkml/utils/schemaloader.py", line 238, in resolve
    self.raise_value_error(f"slot: {slot.name} - unrecognized range ({slot.range})", slot.range)
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/linkml/utils/schemaloader.py", line 941, in raise_value_error
    SchemaLoader.raise_value_errors(error, loc_str)
  File "/root/.cache/pypoetry/virtualenvs/nmdc-submission-schema-aBGqxekb-py3.9/lib/python3.9/site-packages/linkml/utils/schemaloader.py", line 949, in raise_value_errors
    raise ValueError(f'{TypedNode.yaml_loc(loc_str, suffix="")} {error}')
ValueError: File "nmdc_submission_schema.yaml", line 56977, col 16 slot: ontologyRelation__subject - unrecognized range (OntologyClass)
make: *** [Makefile:105: gen-project] Error 1

The process documented in the release instructions in infra-admin (private) says to run $ make squeaky-clean all test. I did not do that (i.e. did not look at those instructions) when releasing nmdc-schema version 11.2.0.

The task here is to follow those instructions and make a new release. I'll do this today/now. CC: @turbomam