Remove Rxn-INSIGHT reaction classification

[skearnes]

Summary

Reaction classification ran inside the ORM's derived stage, behind --classify_reactions and a guarded import, writing labels to derived.reaction_classes. Removing it: the model is a transformer loaded per worker, and that work belongs to a job that can be given a GPU rather than to the ingest that loads a dataset.

Changes

• Deleted ord_schema/orm/reaction_class.py and its test.
• database.py: the guarded import, _classify_reactions, classify_dataset, and the classify_reactions argument to update_derived_data.
• loading.py: the classify pass, _classify_shard, _CLASSIFY_JOBS_CAP, and the classify_reactions / classify_jobs arguments to load_datasets and derive_dataset.
• scripts/add_datasets.py: --classify_reactions and --classify_jobs.
• derived_mappers.py: the ReactionClasses mapper, which is the schema change — see Notes.
• pyproject.toml: the reaction-class extra, added one PR down the stack and now unnecessary.
• Docs: the ORM README and the orm-database-load skill.

Testing

uv run pytest -n auto — 1186 passed. All three of the suite's skips are gone with it, since every one was a test the missing extra was skipping:

SKIPPED ord_schema/orm/reaction_class_test.py:21: could not import 'rxn_insight'
SKIPPED ord_schema/orm/database_test.py:287: reaction-class extra not installed
SKIPPED ord_schema/dependencies_test.py:214: ord-schema[orm,reaction-class] is not installed here

No consumer at origin references reaction_class, classify_dataset, classify_reactions, or reaction_classes — checked against origin/main of ord-interface, ord-app, ord-infrastructure, and ord-data.

Notes

This changes the schema. The mappers are what create the tables, so a database built after this has no derived.reaction_classes. An existing one keeps the table and its rows, now unmapped and untouched by any pass here; dropping it is a separate decision, and a GPU job that writes classifications later can define its own.

Stacked on #976, which is where the reaction-class extra was added — it was a true statement about the tree as it stood, and this PR removes both the extra and what needed it. Retarget to main once #976 lands.

🤖 Generated with Claude Code

Greptile Summary

The PR removes Rxn-INSIGHT reaction classification from the ORM and its installation surface.

• Removes the classification mapper, implementation, loading pass, API parameters, and CLI flags.
• Removes the optional dependency profile and its transitive lockfile packages.
• Updates ORM documentation, operational guidance, and tests to match the reduced schema and interfaces.

Confidence Score: 5/5

The PR appears safe to merge.

No blocking failure remains.

Important Files Changed

Filename	Overview
ord_schema/orm/database.py	Removes the guarded classifier import, classification API, and classification option from derived-data updates.
ord_schema/orm/loading.py	Removes classification workers and arguments while preserving the SMILES and RDKit derivation pipeline.
ord_schema/orm/derived_mappers.py	Removes the ReactionClasses mapper so newly prepared databases no longer create that table.
ord_schema/orm/scripts/add_datasets.py	Removes the classification-related command-line options and forwarding logic.
pyproject.toml	Removes the obsolete reaction-class optional dependency profile.
uv.lock	Prunes the removed reaction-class profile and its transitive dependency graph.
ord_schema/dependencies_test.py	Removes dependency-profile coverage for the deleted classifier module and extra.
ord_schema/orm/README.md	Removes the remaining documentation for reaction-class schema data and classification controls.

_{Reviews (2): Last reviewed commit: "Merge main into agent/remove-reaction-cl..." | Re-trigger Greptile}