With this simple schema example_dynamic_term_set.yaml:

id: https://w3id.org/linkml/examples/nwb_dynamic_enums
name: nwb_dynamic_enums

prefixes:
  CL: http://purl.obolibrary.org/obo/CL_

enums:
  NeuronTypeEnum:
    reachable_from:
      source_ontology: obo:cl
      source_nodes:
        - CL:0000540  ## neuron
      include_self: false
      relationship_types:
        - rdfs:subClassOf

and this simple code test_value_set_expander.py:

from oaklib.utilities.subsets.value_set_expander import ValueSetExpander
expander = ValueSetExpander()
schema_path = "example_dynamic_term_set.yaml"
expander.expand_in_place(schema_path, ["NeuronTypeEnum"], "test.yaml")

Running with python -W error -W ignore::DeprecationWarning -W ignore:pkg_resources:UserWarning test_value_set_expander.py results in

Exception ignored in: <sqlite3.Connection object at 0x12ff5b100>
ResourceWarning: unclosed database in <sqlite3.Connection object at 0x12ff5b100>

I traced this to the sql connector and engine Engine(sqlite:////Users/rly/.data/oaklib/cl.db) not being properly closed when python execution ends and garbage collection happens. This seems to be resolved by adding:

def __del__(self):
    if self._session is not None:
        self._session.close()
    if self.engine is not None:
        self.engine.dispose()

to sql_implementation.py.