Performance of referencing library vs deprecated jsonschema.RefResolver is very bad when there are a lot of references in schema

Hello!

I have a library that formats scientific data into a JSON schema called the Allotrope Standard Model (ASM)

The validation schemas are fairly large and complicated compared to other schemas I've seen in discussion boards, and are very modular, meaning there are a lot of references. In allotropy we store the ASM schemas directly, and remove all remote references, replacing them with local references under $defs.

We are finding that validating against the schemas using jsonschema version 4.18.0 takes ~20x longer than 4.17.0.

As a concrete example:

Validating this data: https://raw.githubusercontent.com/Benchling-Open-Source/allotropy/refs/heads/main/tests/parsers/moldev_softmax_pro/testdata/MD_SMP_luminescence_endpoint_example08.json

Against this schema: https://github.com/Benchling-Open-Source/allotropy/blob/main/src/allotropy/allotrope/schemas/adm/plate-reader/REC/2024/06/plate-reader.schema.json

takes ~3.5s on 4.17.0 and ~55s on 4.18.0

This translates to a runtime for all 26 tests in tests/parsers/moldev_softmax_pro of ~30s in 4.17.0 to ~6m in 4.18.0

Reproduce the reported validation case using the linked test data and plate-reader schema, comparing jsonschema 4.17.0 with 4.18.0. Start with tests/parsers/moldev_softmax_pro and its 26-test runtime, then trace the referencing and validation path to identify the regression. Done means the cause is isolated and the large-reference schema no longer shows the reported slowdown.