Skip to content

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Added

  • Release CI: Publish WASM module to Wasmer Registry as eddiethedean/ontologos (WASMER_TOKEN, .github/scripts/publish-wasmer.sh)
  • CI: Manual Publish Wasmer workflow (workflow_dispatch) to build and publish WASM without a full release
  • Docs: Wasmer badge and install links for eddiethedean/ontologos across README and docs
  • Release CI: Publish npm packages ontologos (multi-platform N-API) and @ontologos/wasm (NPM_TOKEN)
  • CI: Manual Publish npm workflow (workflow_dispatch) for on-demand npm publishes
  • Docs: npm install channels and badges for Node/WASM
  • npm: Published ontologos@1.1.4 and @ontologos/wasm@1.1.4; fix WASM pack to ship pkg/ (remove wasm-pack pkg/.gitignore before publish)

1.1.4 - 2026-07-13

Fixed

  • Conformance nightly: Soft-skip deferred WG cases under cargo test -- --ignored; convert Consistent-but-all-unsat regressions into active honesty tests; Keys-002 sample for guard/full agreement nightly
  • Catalog: Honor deferred_wg_ids.txt across activate-from-disk so HermiT catalog drift stays green
  • CI: Retry flaky corpus downloads (curl exit 35); bump check-1.0-release-gates.sh workspace pin to 1.1.4

Changed

  • Drop-in patch over v1.1.3 — bump all ontologos-* pins together

1.1.3 - 2026-07-12

Fixed

  • Conformance: Remove weak consistent_but_all_unsat IRI-shape entailment guard; defer Consistent-but-all-unsat (status=deferred) until DL proves named-class ⊥
  • Tests: Replace tautological / floor-only assertions (facade, contract, profile, EL, Python) with oracle-backed expectations
  • Docs: Track shared benchmarks/data/semantic-fixtures.json for cross-language binding parity

Changed

  • Tests: Demote dump-only DL triage tests behind #[ignore]; add EL negative subsumption, contract MUST-NOT, parser mapping oracle, catalog honesty, and maintainer oracle policy

1.1.2 - 2026-07-06

Fixed

  • Docs: Restore v1.0.x-to-v1.1.0 migration guide links broken in the v1.1.1 version bump (MkDocs strict build)
  • Includes all v1.1.1 fixes when upgrading from v1.1.0 (parser, DL, SWRL, RL, bindings) — see 1.1.1 below

1.1.1 - 2026-07-06

Fixed

  • Parser: Lenient import merge skips supplement axioms after non-punnable entity kind conflicts (#21)
  • Parser: validate_loaded_ontology_light rejects dangling DL class/data expression references (#23)
  • DL: Malformed XSD numeric literals no longer silently coerce to 0.0 (#25)
  • SWRL: Forward chaining propagates EL classify failures when rule bodies need class-variable subsumption; classify_for_swrl ignores SWRL rules for EL profile checks (#28)
  • DL store: from_json_with_limits validates via validate_with_limits (#29)
  • RL: MaterializationReport records sameAs/differentFrom clashes (#27)
  • Parser: Partial intersection decomposition fix (#20)
  • Bindings: Python/JS query() calls rewrite_query; QL handles owl:Nothing/unsat (#19)
  • EL: Profile::Auto incremental classification routes through EL engine (#17)

1.1.0 - 2026-07-04

Added

  • ontologos-ffi: shared stable C ABI for native language bindings (ontology, builder, reasoner, error handling)
  • Java bindings: JNI cdylib (ontologos-jni) + Maven project (dev.ontologos:ontologos)
  • .NET bindings: P/Invoke cdylib (ontologos-dotnet) + C# API with DllImportResolver
  • C/C++ bindings: ontologos-c cdylib with ontologos.h / ontologos.hpp, CMake smoke tests
  • CI: scripts/ci-bindings.sh (Java, .NET, C/C++ + ontologos-js), scripts/ci-node.sh (Node + WASM); consolidated GitHub Actions bindings job
  • Docs: guides for Java, .NET, C/C++; security sections for new bindings

Changed

  • Workspace and binding package versions bump to 1.1.0
  • Node, WASM, Java, .NET, and C bindings delegate through ontologos-js (same architecture as Python)
  • WASM classify() JSON round-trip returns plain JS objects (matches Node/Python semantics)
  • Local CI (run-ci-local.sh) includes bindings and node jobs

Fixed

  • Clippy: FFI pointer-deref lint, const thread-local in ontologos-ffi, test mut cleanup

1.0.1 - 2026-07-03

SUPERSEDED: Patch release notes retained for history; 1.1.0 is the current workspace target.

Fixed

  • Parser: map self-inverse RDF properties (P owl:inverseOf P) to SymmetricObjectProperty so IYOUIT agent.owl loads under strict parse
  • ALC role queries: merge asserted RBox SubObjectPropertyOf edges into getSubObjectProperties (OWLLink Bob knows 20 / 101)
  • DL bounded cancel is per-operation so one timed-out case no longer poisons concurrent conformance scans
  • Promoted WG hygiene scan uses modest parallelism (4 threads) so 30s budgets are not starved on CI
  • Conformance guard unit tests: consistent_but_all_unsat and complex_concept assert production paths; serialize tableau env mutations
  • Optional profile-corpora tests skip cleanly when galen.owl / go-subset.owl are absent (nightly --ignored)
  • Tier C HermiT JAR cross-check: disable incomplete pizza.owl DL taxonomy check (tracked as post-1.0 work)

Changed

  • Workspace and PyPI package bump to 1.0.1

1.0.0 - 2026-07-02

Added

  • HermiT conformance: auto-promotion pipeline (promote_catalog, promoted_axiom_ids.txt, promote-hermit-catalog.sh)
  • DL engine: datatype-aware profile detection, ⊤/⊥ seeding in clausification, consistency-only axiom checks
  • RL/RDFS: inverse-functional and irreflexive property characteristics; bottom object property chain detection
  • Metrics: DL OFN pass-rate report; conformance coverage by catalog status
  • Production DL integration guide: budget_secs, check_consistency, conformance env warnings
  • Security docs: max_literal_bytes, horned-owl parser mutex contract, conformance harness env vars
  • #[non_exhaustive] on ClassifyOutcome for forward-compatible facade matches
  • Python: ontologos.types TypedDict exports; profile-aware Reasoner stubs; Pyright CI on python + tests

Changed

  • Workspace and PyPI package bump to 1.0.0
  • Active HermiT conformance tests: 1048 (100% catalog parity; 0 generated catalog ignores)
  • JSON snapshot format version 3 (readers accept v2/v3)
  • Tier C strict HermiT identity gate (compare-tier-c-strict-family.sh) permanently informational — 26 extra subsumptions on family.owl waived until 2.0
  • Doc/code alignment: entailment cap 192 named classes; ParseLimits::merge_imports default false
  • SECURITY.md supported versions updated for 1.0.x
  • Removed workspace crates: ontologos-rdfs, ontologos-abox, ontologos-query (empty shims — use ontologos-rl / ontologos-ql); ontologos-watch (unused orphan)
  • Python: __init__.py raises on missing native extension instead of exporting None placeholders

Fixed

  • 32 verified bugs across ALC, facade, SWRL, parser, bridge, Python, and CLI (B-01–B-32)
  • Removed stale ignored dl650_and_dl910_should_be_inconsistent triage test (covered by phase4_remaining_consistency_cases_fast)

Documentation

  • Release status and install pins updated for 1.0.0
  • Documentation adoption audit: facade-first examples, evaluator scope page, query/QL reference rewrite, channel banners, parity metric reconciliation, doc snippet CI
  • Reconciled conformance metrics (1048 active / 1 ignored; 0 generated catalog ignores) in release status and evaluator scope
  • Updated removed-crate references (ontologos-rdfs, ontologos-abox) in choosing-an-api, dependency-first ADR, and tests README
  • Documented reasonable sameAs/differentFrom clash reporting gap in reasonable-limits reference

0.9.0 - 2026-06-13

Added

  • Python: Ontology and OntologyBuilder for in-memory construction (JSON v2 dict or fluent builder)
  • Python: Reasoner(path=...) or Reasoner(ontology=...); explain() proof graph dict
  • Python: multi-pass incremental mutations (add_subclass_of, remove_subclass_of, add_axiom_json)
  • Python: optional subsumptions_to_pandas / subsumptions_to_polars export helpers
  • CI: Pizza EL golden pytest; macOS Python job; corpora download before Python tests

Documentation

Changed

  • Workspace and PyPI package bump to 0.9.0
  • Python guide documents explain trace limits and full v0.9 API

0.8.0 - 2026-06-13

Added

  • Core: axiom-level dirty tracking (OntologyRevision, DirtySet), remove_axiom, ReasonerSession slot on Reasoner
  • Core: asserted vs inferred axiom provenance (add_inferred_axiom, strip_inferred_axioms) for correct RL/RDFS removal rematerialization
  • EL: incremental classification via partition overdelete-rederive on CompletionGraph (ElSession, ReasonerConfig::incremental)
  • RL/RDFS: ReasonableSession wrapper over reasonable incremental reason() / set_base_triples
  • ontologos-watch: library file-watch + ontology reload hook for Ontocode (not published)
  • CLI / Python: --incremental flag and Reasoner(..., incremental=True) (library multi-pass workflows)
  • Benchmarks: incremental edit suite, incremental_correctness tests, optional bench-el-incremental.sh perf gate
  • Tests: bridge reasonable_session, RL/RDFS incremental removal, ontologos-watch integration tests

Changed

  • Workspace and published crates bump to 0.8.0
  • Incremental engines validate session revision, restore sessions on merge failure, and skip no-op passes when ontology is clean

Fixed

  • RL/RDFS: stale inferred axioms after remove_axiom — strip inferred set before rematerialize
  • RL/RDFS: removal path uses cold ReasonableReasoner reset with correct full_rebuild flag
  • EL: overdelete_signature rebuilds domains and clears traces; revision mismatch forces full classify
  • Bridge: empty incremental delta clears dirty state; ReasonableSession stores RL vs RDFS profile
  • Perf gate: bench-el-incremental.sh runs with --ignored; bench uses unique deltas per iteration

0.7.0 - 2026-06-13

Changed

  • Semver: release 0.7.0 aligns crate versions with ROADMAP v0.7 (dependency-first adapters); no public API changes from 0.6.1
  • Documentation and install examples updated to 0.7.0

Fixed

  • EL validation: validate_el_profile uses el_classification_forbidden_in (complex TBox constructs the completion engine cannot handle)
  • EL completion: multiple ObjectPropertyDomain axioms per property are all applied
  • Parser: horned-owl panics on malformed RDF/XML (e.g. duplicate rdf:ID) converted to Error::Parse
  • CLI: materialization reports include clashes in text and JSON output
  • Conformance: sub_and_super_roles uses direct subproperty assertion; manifest marks reasonable upstream gaps as ignored
  • Bridge: optional MergeLimits::max_axioms cap during RL/RDFS merge
  • Security: expanded security_regressions tests for JSON limits documented in docs/security.md

0.6.1 - 2026-06-13

Changed

  • EL engine: restore in-house ELK-style completion in ontologos-el; remove git whelk dependency
  • ontologos-bridge: horned-owl/oxrdf/reasonable adapters only (no whelk)
  • Pizza EL golden baseline regenerated from in-house EL (84 direct subsumptions)
  • All library crates publishable to crates.io again (full publish order restored)

Fixed

  • ontologos-query: removed ontologos-el dev-dependency so the crate publishes cleanly
  • ontologos-explain: ProofGraph::is_acyclic uses the same validator as build_proof_graph

0.6.0 - 2026-06-12

Note: The v0.6.0 tag shipped a brief whelk EL delegation experiment and partial crates.io publish (core, parser, profile, query only). v0.6.1 is the corrected public release: in-house EL restored, full library publish. See 0.6.1 below.

Added

  • ontologos-explain: ProofGraph, build_proof_graph, explain_with_profile, explain_rdfs/explain_rl/explain_el
  • ontologos-bridge: core ↔ horned-owl/oxrdf/whelk/reasonable adapters (workspace-only until whelk is on crates.io)
  • InferenceTrace / TraceStep in ontologos-core for engine-agnostic explanation traces
  • Query APIs: explain_subsumption, explain_unsatisfiable with EL-first HST pruning
  • Human-readable render_text formatter for proof graphs
  • CLI ontologos explain --profile auto|el|rl|rdfs (JSON + text output)
  • Conformance: explain_benchmarks.rs; Pizza EL golden vs in-house EL (compare-pizza-el-golden.sh); Family RL triple closure vs reasonable (compare-reasonable.sh)
  • petgraph taxonomy views in ontologos-query and proof-graph acyclic checks in ontologos-explain
  • RDFS MaterializationReport::clashes forwarded from reasonable diagnostics

Changed

  • Dependency-first adapters: ontologos-el → whelk; ontologos-rdfs / ontologos-rl → reasonable; parsing remains horned-owl
  • Custom in-tree EL completion, RDFS/RL rule engines, and RL TripleIndex removed; public facade crate names unchanged
  • RDFS/RL MaterializationReport.traces renamed to .trace (InferenceTrace)
  • ReasonerConfig::explanations honored on classify routes (traces empty until upstream exposes rule diagnostics)
  • Pizza EL golden baseline regenerated from whelk; HermiT RL/RDFS tests document reasonable upstream gaps via #[ignore]

Fixed

  • Bridge merge: owl:sameAs, owl:disjointWith, and owl:differentFrom no longer mis-map as property assertions
  • Bridge merge: existential blank-node IDs include filler; restriction triples reconstruct SubClassOfExistential
  • Bridge export: DisjointClasses and DifferentIndividuals mapped to horned-owl (no longer silently dropped)
  • Reflexive sameAs triples from reasonable skipped on merge (avoids invalid SameIndividual axioms)
  • RL report previously dropped RDFS inference traces during saturation (pre-adapter)

Documentation

Breaking

  • Per-rule MaterializationReport::inferred_by_rule counts are empty when using the reasonable adapter (upstream does not expose rule-level diagnostics yet)
  • EL classification returns Taxonomy without mutating the ontology; RL/RDFS saturation merges inferred axioms into core

0.5.0 - 2026-06-12

Added

  • ontologos-el: OWL EL completion classifier (ElClassifier, classify_reasoner, classify_with_profile)
  • ontologos-query: taxonomy query API (direct_subclasses, is_subsumed, equivalent_classes, unsatisfiable_classes)
  • Taxonomy type in ontologos-core (subsumptions, equivalences, unsatisfiable)
  • CLI --profile el|rl|rdfs|auto on classify; taxonomy JSON/text output for EL
  • Python profile="el" / "auto"; classify() returns taxonomy or materialization dict
  • Parser: decompose SubClassOf(C, ObjectIntersectionOf(...)) into EL axioms
  • HermiT ClassificationTest pizza harness with vendored fixtures (benchmarks/data/hermit/)
  • Pizza EL golden conformance (pizza-el-golden.json, compare-pizza-el-golden.sh in CI)
  • Vendored go-subset.owl EL performance gate (< 10s)

Changed

  • Breaking: CLI classify defaults to --profile auto (EL/RL routing), not RDFS-only — use materialize or --profile rdfs for RDFS
  • Python package version aligned to 0.5.0

Fixed

  • RL soundness: replace unsound upward existential subClassOf propagation with downward scm-spo1
  • RL existential subsumption: compare asserted existentials only (avoids spurious inferences from property weakening)
  • EL completion graph: seed EquivalentObjectProperties at graph build time

Documentation

0.4.0 - 2026-06-12

Added

  • ABox in ontologos-core: ClassAssertion, ObjectPropertyAssertion, SameIndividual, DifferentIndividuals, EquivalentObjectProperties, AsymmetricObjectProperty
  • Axiom indexes for individuals, property assertions, sameAs, and equivalent properties
  • JSON snapshot v2 round-trip for new axiom variants; OntologyBuilder ABox helpers
  • Parser mapping for named ABox axioms and AsymmetricObjectProperty / EquivalentObjectProperties
  • ontologos-rl: OWL RL forward-chaining (RlEngine::saturate) on top of RDFS materialization
  • ontologos_rl::classify_reasoner / materialize_reasoner for Profile::Rl
  • HermiT Tier-A ports: testSubsumption2 / testSubsumption3 (inlined existential encoding)
  • Family RL corpus test; optional compare-reasonable.sh harness for external diff

Changed

  • Profile detection: mapped ABox constructs are allowed under OWL RL (family corpus → RL)
  • Python profile="rl" routes through ontologos_rl::classify_reasoner
  • Reasoner::classify() with Profile::Rl returns delegate hint (use ontologos_rl)
  • CLI classify prints stderr note that it runs RDFS only; explain hidden from --help until v0.6

Documentation

  • Read the Docs site with adoption-focused guides (crates.io quick start, RDFS tutorial, capability matrix, glossary, performance, production integration)
  • FAQ and onboarding fixes; README slimmed for evaluators
  • MkDocs strict build enforced in CI

Published

0.3.1 - 2026-06-12

Changed

  • ontologos classify emits the same inference report as materialize (status: classified, axiom counts, per-rule breakdown)
  • Clarified Reasoner::classify documentation: CLI/Python use ontologos_rdfs for Profile::Rdfs

Fixed

  • Reasoner::classify() with Profile::Rdfs returns a delegate hint instead of generic NotImplemented
  • FAQ, load guide, and CLI reference updated for Pizza → DL profile detection
  • Documented OWL import non-resolution, RDFS materialization scope, and batch fixed-point engine (vs worklist)

Published

0.3.0 - 2026-06-12

Added

  • ontologos-rdfs: TBox RDFS materialization (subClassOf / subPropertyOf closure, domain/range inheritance)
  • MaterializationReport with per-rule inference counts and optional traces
  • materialize_reasoner(&mut Reasoner) and classify_reasoner(&mut Reasoner) for Profile::Rdfs
  • Reasoner::ontology_mut() for in-place materialization
  • OntologyBuilder::property_domain / property_range helpers
  • RDFS unit tests (including long transitive chains) and Family/Pizza corpus conformance tests
  • ontologos materialize CLI with text and JSON report output
  • DL profile diagnostics explaining mapped constructs that rule out EL/RL
  • Python Reasoner(path, profile="rdfs") for RDFS materialization via classify()
  • ontologos-conformance workspace harness with HermiT Tier-A RDFS test ports (tests/hermit/)
  • HermiT replacement strategy doc (docs/internal/research/hermit-replacement.md)

Changed

  • RdfsEngine::materialize now takes &mut Ontology and returns a structured report
  • Reasoner::classify now takes &mut self (delegates to ontologos-rdfs from CLI/Python for Profile::Rdfs)
  • ontologos classify runs RDFS materialization (OWL EL/RL classification remains v0.5)
  • Workspace version bumped to 0.3.0

Fixed

  • Parser path sandbox: reject prefix-bypass paths (uploads_base vs uploads_base_evil)
  • Parser mapping: allow axioms at entity limit; DeclareDatatype no longer blocks class with same IRI
  • RDFS inference traces now record premise axiom ids
  • Profile detection docs and Pizza corpus expectations aligned with DL classification (658 mapped axioms)

Published

0.2.0 - 2026-06-11

Added

  • ontologos-parser: OWL/XML, RDF/XML, OWL Functional Syntax, and Turtle loading via horned-owl; ParseLimits; ParseMeta on loaded ontologies
  • ontologos-profile: EL / RL / QL / DL profile detection with diagnostics
  • New axiom variants: SubClassOfExistential, SymmetricObjectProperty, ReflexiveObjectProperty, FunctionalObjectProperty
  • Parser fixtures and manifest-driven integration tests (Pizza, Family)
  • benchmarks/scripts/download.sh for benchmark corpus download

Changed

  • ontologos profile loads OWL files and reports detected profile
  • ontologos_parser::load_ontology is the supported file-load API (Ontology::from_file remains a stub on ontologos-core)
  • Pizza/Family benchmark corpora: Family ontology vendored in-repo; Pizza downloaded from owlcs/pizza-ontology

Published

0.1.0 - 2026-06-11

First release. Publishes ontologos-core to crates.io only; engine crates remain workspace-internal until implemented.

Added

  • Adoption documentation: CONTRIBUTING, FAQ, docs index, JSON v2 schema, security guide, error reference, comparison guide, runnable pizza_builder example
  • Research notes under docs/internal/research/ (OWL 2, HermiT, ELK, RDFox)
  • Benchmark ontology manifest at benchmarks/manifest.toml
  • ontologos-core in-memory ontology model:
  • InternPool / IriId for deduplicated absolute IRIs
  • EntityRegistry with kind validation
  • Structured Axiom enum with validation
  • AxiomStore and AxiomIndex for engine-ready lookups
  • Ontology facade with OntologyBuilder
  • Versioned JSON serialization (to_json / from_json)
  • Integration tests with pizza_minimal fixture
  • Criterion benchmark for 10k-axiom serialize/deserialize

Changed

  • JSON snapshot format bumped to version 2 (IRI-keyed entities and axioms; v1 rejected for untrusted input)
  • Hardened deserialization: resource limits, deny_unknown_fields, duplicate entity/axiom handling
  • IRI validation: allowlist (http, https, urn), reject control characters and dangerous schemes
  • detect_profile returns Err(NotImplemented) instead of empty success
  • CLI: propagate emit errors, human-readable --format text, removed --format yaml
  • File loading routed through ontologos-parser::load_ontology with path validation
  • Hardened test suite: semantic JSON round-trip, add_axiom index wiring, axiom/IRI/entity edge cases, parser format detection, CLI smoke test
  • Ontology::from_file now returns Error::ParseNotAvailable (parsing lands in v0.2)
  • Breaking: AxiomKind replaced by structured Axiom with entity references