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 el caso de validación reportado usando los datos de prueba y el esquema de plate-reader enlazados, comparando jsonschema 4.17.0 con 4.18.0. Comienza con tests/parsers/moldev_softmax_pro y su tiempo de ejecución de 26 pruebas; después, sigue la ruta de referenciación y validación para identificar la regresión. Se considera terminado cuando la causa está aislada y el esquema con referencias grandes ya no muestra la ralentización reportada.