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Copy file name to clipboardExpand all lines: CHANGELOG.md
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@@ -18,6 +18,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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---
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## [0.3.0] - 2026-04-08
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### Added
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- Machine-readable boundary and ownership fields in the portable hazard and read-across contracts: `assessmentBoundary`, `decisionBoundary`, `decisionOwner`, `supports`, and `requiredExternalInputs`.
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-`semanticCoverage` in the portable hazard uncertainty block to make the qualitative-only uncertainty semantics explicit.
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- Live Toolbox smoke coverage for hazard analysis, workflow handoffs, grouping dossiers, log replay, and direct execution helpers.
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- Configurable wall-clock safeguards for slow hazard-profiling and discovery-heavy Toolbox paths.
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### Changed
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- Bumped package metadata and runtime version markers to `0.3.0`.
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- Updated the public README, architecture notes, and release docs to match the current contract layer and live-validation surface.
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- Refined normalized provenance packaging so endpoint study records, endpoint summaries, evidence blocks, and source-call metadata remain easier to audit downstream.
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### Fixed
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- Removed stale public-doc references to still-private local module names.
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- Eliminated version drift between package metadata, runtime fallbacks, and example payloads.
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---
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## [0.2.0] - 2026-03-23
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- Dockerfile and docker-compose stack for local development with Toolbox API stub.
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- Taskmaster backlog, documentation set (`docs/auth_testing.md`, `docs/observability.md`, `docs/testing.md`), and CI workflow skeleton.
Copy file name to clipboardExpand all lines: README.md
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See [docs/architecture.md](docs/architecture.md) for the fuller boundary and contract notes.
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See [docs/oecd_alignment_review_2025.md](docs/oecd_alignment_review_2025.md) for the OECD 2025 grouping/IUCLID gap analysis and the next contract-focused improvements.
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See [docs/cross_suite_alignment_2026.md](docs/cross_suite_alignment_2026.md) for the local AOP/CompTox contract patterns adopted into O-QT.
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See [docs/cross_suite_alignment_2026.md](docs/cross_suite_alignment_2026.md) for the public contract patterns adopted into O-QT.
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## What's New In v0.2.0
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## What's New In v0.3.0
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This is a maturity and contract release, not a redesign.
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This is a contract-hardening and validation release, not a redesign.
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-Re-aligned repository identity, package metadata, and release notes around `ToxMCP/oqt-mcp`.
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-Clarified the public surface as a primary workflow engine plus secondary expert tools.
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-Published portable O-QT handoff schemas for hazard evidence, read-across support, and workflow provenance.
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-Hardened the hazard handoff with explicit evidence blocks, applicability-domain review, and richer provenance records for audit-grade downstream review.
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- Added explicit downstream-orchestration documentation and examples for contract consumers.
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-Documented the current synchronous deployment model instead of implying an async platform that does not exist yet.
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-Bumped the public package and runtime version to `0.3.0`.
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-Hardened `oqtHazardEvidenceSummary.v1` and `oqtReadAcrossSummary.v1` with machine-readable `assessmentBoundary`, `decisionBoundary`, `decisionOwner`, `supports`, and `requiredExternalInputs`.
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-Added `semanticCoverage` to the hazard uncertainty contract so the MCP states explicitly that O-QT uncertainty is qualitative evidence packaging, not probabilistic confidence.
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-Expanded normalized provenance and study packaging so hazard outputs can carry endpoint study records, endpoint summaries, evidence blocks, and source-call metadata in a more audit-ready shape.
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- Added configurable wall-clock safeguards and a live smoke suite for the Toolbox-backed surface, including hazard analysis, workflow handoffs, grouping dossiers, and log replay.
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-Refreshed the public docs so the README, schemas, and release notes reflect the current contract surface without referencing still-private modules.
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## Published Schemas
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## Table of contents
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1.[Architecture](#architecture)
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2.[What's New In v0.2.0](#whats-new-in-v020)
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2.[What's New In v0.3.0](#whats-new-in-v030)
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3.[Published Schemas](#published-schemas)
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4.[Quick start](#quick-start)
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5.[Related resources](#related-resources)
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|`controlled-prod`| FastAPI behind TLS reverse proxy with OIDC, RBAC, and audit shipping | Internal deployments and orchestrated suite flows | Still synchronous in v0.2.0; scale with worker policy and operational guardrails rather than a built-in queue. |
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|`not-in-v0.2.0`| Async queue and persistence layer | Detached batch jobs and large-scale job replay | Remains roadmap work. |
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|`controlled-prod`| FastAPI behind TLS reverse proxy with OIDC, RBAC, and audit shipping | Internal deployments and orchestrated suite flows | Still synchronous in v0.3.0; scale with worker policy and operational guardrails rather than a built-in queue. |
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|`not-in-v0.3.0`| Async queue and persistence layer | Detached batch jobs and large-scale job replay | Remains roadmap work. |
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This release intentionally tightens the deployment story instead of over-claiming platform maturity.
Copy file name to clipboardExpand all lines: docs/cross_suite_alignment_2026.md
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@@ -7,7 +7,6 @@ This note records the local cross-suite contract review used to harden O-QT MCP
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-`AOP_MCP`
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-`comptox_mcp_clean_3568d68`
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-`PBPK_MCP`
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-`Bioactivity-PoD-MCP`
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## Patterns adopted into O-QT MCP
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- Explicit `supports` and `requiredExternalInputs` fields so downstream consumers can tell what the module does and does not claim to decide.
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- Stronger uncertainty framing that distinguishes semantic coverage from quantitative confidence.
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### From Bioactivity-PoD MCP
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### From other contract-first modules
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- Explicit `decisionOwner` language so handoff objects make ownership boundaries visible.
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- Contract emphasis on fit-for-purpose review rather than implied finality.
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- AOP draft-authoring semantics, because O-QT is not an authoring server.
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- CompTox-style numeric applicability-domain confidence, because O-QT does not currently produce a scientifically defensible quantitative AD confidence estimate.
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- PBPK qualification or model-trust governance objects, because O-QT should stay focused on OECD QSAR Toolbox evidence packaging rather than model-qualification workflow management.
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-Bioactivity point-of-departure decision objects, because O-QT should not claim ownership of final biological interpretation outside its module scope.
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-Point-of-departure decision objects, because O-QT should not claim ownership of final biological interpretation outside its module scope.
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- Suite-level evidence synthesis, because O-QT should remain a module-scoped OECD QSAR Toolbox engine.
Copy file name to clipboardExpand all lines: docs/release_process.md
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## Publishing a Release
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1. Decide the new version (for example `v0.2.0`) and update `pyproject.toml` accordingly.
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1. Decide the new version (for example `v0.3.0`) and update `pyproject.toml` accordingly.
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2. Move entries from `## [Unreleased]` in `CHANGELOG.md` into a new section `## [x.y.z] - YYYY-MM-DD`.
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3. Commit changes with a message such as `chore: prepare v0.2.0 release`.
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3. Commit changes with a message such as `chore: prepare v0.3.0 release`.
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4. Tag the commit:
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```bash
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git tag -a v0.2.0 -m "O-QT MCP Server v0.2.0"
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git push origin v0.2.0
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git tag -a v0.3.0 -m "O-QT MCP Server v0.3.0"
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git push origin v0.3.0
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```
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5. Create a GitHub release for the new tag, pasting the changelog entry. Include links to `README.md`, `docs/architecture.md`, and `schemas/README.md` so downstream consumers can see the updated contract surface immediately.
This is a contract-hardening and validation release for O-QT MCP. It keeps the module in the same architectural role while making the public handoff layer more explicit, more auditable, and easier to validate against a live OECD QSAR Toolbox instance.
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## Highlights
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- Bumped the public package and runtime version to `0.3.0`.
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- Hardened `oqtHazardEvidenceSummary.v1` and `oqtReadAcrossSummary.v1` with:
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-`assessmentBoundary`
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-`decisionBoundary`
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-`decisionOwner`
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-`supports`
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-`requiredExternalInputs`
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- Added `semanticCoverage` to the hazard uncertainty contract so the object states explicitly that O-QT uncertainty is qualitative evidence packaging, not probabilistic confidence.
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- Expanded normalized provenance packaging for endpoint study records, endpoint summaries, evidence blocks, and source-call metadata.
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- Added live Toolbox smoke coverage for:
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-`analyze_chemical_hazard`
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-`run_oqt_multiagent_workflow`
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-`build_grouping_justification`
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-`build_portable_handoffs_from_log`
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- Added configurable wall-clock safeguards for slow profiling and discovery-heavy Toolbox paths.
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## Included Changes
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### Contract layer
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- Portable hazard and read-across handoffs now publish clearer machine-readable module boundaries and downstream-review expectations.
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- Portable schema examples and runtime payload examples now match the `0.3.0` release markers.
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- Public contract notes were refreshed to remove references to still-private local module names.
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### Runtime behavior
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- Hazard analysis now exposes richer normalized study packaging and clearer uncertainty semantics.
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- Grouping/read-across responses now expose the same style of explicit module-boundary and support metadata as hazard workflows.
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- Runtime-reported version markers now align with package metadata and schema examples.
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### Validation
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- Full repo suite passed locally.
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- Targeted live Toolbox smoke tests passed against the current local Toolbox instance.
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