chore(main): release biotope 0.10.0

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0.10.0 (2026-09-28)

⚠ BREAKING CHANGES

• graph: project validation callbacks and per-capability states are gone; structural checks are not equivalent, and review-time independent reads replace them. interpretation no longer travels inside the graph; concept and property descriptions in schema_config.yaml, run.json policies and scope, and graph/ASSUMPTIONS.md replace the query context, so graph/build/ must travel with the graph. biotope graph quality prints its results instead of writing graph/reports/quality.json; biotope graph metagraph writes graph/metagraph.html by default. schemas are never re-rendered. Generated and 0.9 schemas no longer follow manifest changes; each change surfaces as source.drift for review. Authored types are not compared with Croissant dataType or nullability. new scaffolds bind fields through @ids scoped under their RecordSet; other ids produce source.unscoped_field, while an existing field_refs mapping still binds them. a new package's name depends on the directories that already exist, so it can differ from a from-scratch generation. removed keywords such as SourceContract(generated=) and Pipeline(query_context=) fail with ordinary TypeErrors; run.json and definition reports are schema_version 2 (replacement and --report accept 1 and 2). See docs/migration.md for the 0.9 migration steps.
• graph: builds no longer write topology.json, ontology.ttl, query_context.json, provenance.jsonl or BiotopeQueryContext rows. Provenance is reached through each object's biotope_provenance_id in provenance.json. biotope graph build defaults to /build and replaces the previous generated build instead of requiring a new --out directory; --out still chooses another location. Export is headless and labels drop the namespace (for example Gene rather than CvdGene), so Entity is no longer reserved.

Features

• graph: generate complete source inventories and check drift, retire validation and query context (957b2ce)
• graph: integrate authored source contracts, staged builds and a provenance catalog (4686916)

Bug Fixes

• add: register byte-identical files once (90a2838)
• add: register byte-identical files that Baker parses once (160e2ae)
• add: skip byte-identical copies before Baker parses them (287bef0)
• graph: check exported objects in a write that no build context checked (924c06c)
• graph: end a failed run with its error and log phases without a terminal (845a229)
• graph: end a failed run with its finding code and log one line per phase (907792e)
• graph: keep descriptions of node properties named source or target (bea90ae)
• graph: record the libraries graph code imports and warn when they are undeclared (789da09)
• graph: refuse unexportable values when a mapping emits them (7b4bdf1)
• graph: size the Neo4j read buffer to the export's longest line (c2f6757)
• graph: state the oversized-value threshold in characters and document the read buffer (e2b5e82)

Performance Improvements

• graph: validate each value once per step and drop repeated work (1fc51b7)

Documentation

• document the 0.10 graph project shape and how to migrate to it (31ee718)
• skills: describe structured files Baker cannot parse as record sets (d70ae3d)
• skills: install reader libraries from graph/pyproject.toml (683efbb)
• skills: rework biotope-croissant around the generated source inventory (a1d8c92)
• skills: say that aliases and missing-value tokens are declarations only (5a7ffce)

Build System

• release: release breaking changes before 1.0 as a minor version and describe the package (df3fa17)

Refactoring

• graph: raise value problems in one helper and share the item loop (3c4e7dc)

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🤖 Created releases:

• biotope-v0.10.0

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