From 7ed293e66d354467bf4ccab3a470658f448b37dd Mon Sep 17 00:00:00 2001 From: NingyuSun Date: Tue, 6 Oct 2026 11:00:14 +0900 Subject: [PATCH] Release 0.8.0 Bump the version, regenerate the two case summaries that record it, turn the Unreleased changelog into the 0.8.0 section and open a fresh one, and point the README and docs homepage at the released package. --- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- CHANGELOG.md | 5 +++++ CITATION.cff | 2 +- README.md | 9 ++++----- docs/ENGINEERING.md | 2 +- docs/index.md | 4 +--- examples/clinvar_germline/results/summary.json | 2 +- examples/vbo_canine/results/summary.json | 2 +- pyproject.toml | 2 +- src/bioevidence_validator/__init__.py | 2 +- tools/check_distribution.py | 2 +- uv.lock | 2 +- 12 files changed, 19 insertions(+), 17 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 6f5a2fe..468a155 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -13,7 +13,7 @@ body: attributes: label: Version description: Output of `pip show bioai-evidence-validator` or `bioevidence --help` header, or the commit. - placeholder: "0.7.0" + placeholder: "0.8.0" validations: required: true - type: textarea diff --git a/CHANGELOG.md b/CHANGELOG.md index 2fbce82..8f3b337 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,11 @@ ## Unreleased +## 0.8.0 — AI validation: grounding, generic grounders, the feedback loop and benchmarks + +Bioevidence now checks AI output against pinned sources and reference releases, feeds fixable +errors back to the model, and is measured with six models on literature and single-cell tasks. + - Add the Cell Ontology definition check (`definitions`): the presence and absence marker axioms of a claimed term, own and inherited, mapped to genes and compared with the subject's measurements; a contradiction sends the record to review (BEV026). `Ontology` now reads logical-definition relations diff --git a/CITATION.cff b/CITATION.cff index 796f2a8..76a9591 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -9,7 +9,7 @@ abstract: >- authors: - family-names: Sun given-names: Ningyu -version: 0.7.0 +version: 0.8.0 license: Apache-2.0 repository-code: "https://github.com/NingyuSUN/bioai-evidence-validator" keywords: diff --git a/README.md b/README.md index 3838fdc..5716107 100644 --- a/README.md +++ b/README.md @@ -180,12 +180,11 @@ pip install bioai-evidence-validator bioevidence validate examples/literature_claim/llm_only.json --profile literature-claim # exit 2: review required ``` -The released package (0.7.0) has the engine, profiles, drafts and source grounding. The literature, -ontology, gene, variant, table and reference grounders, and the feedback loop, are on `main` and will -be in 0.8.0. Until then, install from GitHub: +From version 0.8.0 the package also includes the literature, ontology, gene, variant, table and +reference grounders, and the feedback loop. For example, to check a cell-type annotation against a pinned +Cell Ontology release and the HGNC gene set: ```bash -pip install "bioai-evidence-validator @ git+https://github.com/NingyuSUN/bioai-evidence-validator" bioevidence validate record.json --ontology cl.obo --term-root cell_type=CL:0000000 --genes hgnc_complete_set.txt ``` @@ -216,7 +215,7 @@ Exit codes: **0** admitted, **1** rejected, **2** review required, **3** input o To check records in a pull request, use the GitHub Action: ```yaml -- uses: NingyuSUN/bioai-evidence-validator@v0.7.0 +- uses: NingyuSUN/bioai-evidence-validator@v0.8.0 with: files: records/**/*.yaml format: draft diff --git a/docs/ENGINEERING.md b/docs/ENGINEERING.md index 14437d9..d1d2769 100644 --- a/docs/ENGINEERING.md +++ b/docs/ENGINEERING.md @@ -1,4 +1,4 @@ -# Engineering contract — 0.7.0 +# Engineering contract — 0.8.0 ## Validation stages diff --git a/docs/index.md b/docs/index.md index 3640b4f..dde5574 100644 --- a/docs/index.md +++ b/docs/index.md @@ -20,9 +20,7 @@ below is measured on real data with six models from Anthropic, OpenAI and Google pip install bioai-evidence-validator ``` -The released package (0.7.0) has the engine, profiles, drafts and source grounding. The grounders and -the feedback loop below are on `main` and will be in 0.8.0. Until then, install from GitHub: -`pip install "bioai-evidence-validator @ git+https://github.com/NingyuSUN/bioai-evidence-validator"`. +From version 0.8.0 the package includes the grounders and the feedback loop described below. Try it without installing anything: [quickstart notebook on Colab](https://colab.research.google.com/github/NingyuSUN/bioai-evidence-validator/blob/main/examples/quickstart.ipynb). diff --git a/examples/clinvar_germline/results/summary.json b/examples/clinvar_germline/results/summary.json index 1c979ae..05ca893 100644 --- a/examples/clinvar_germline/results/summary.json +++ b/examples/clinvar_germline/results/summary.json @@ -601,6 +601,6 @@ "schema_only": 16 } }, - "validator_version": "0.7.0", + "validator_version": "0.8.0", "variants": 5026 } diff --git a/examples/vbo_canine/results/summary.json b/examples/vbo_canine/results/summary.json index ddedcdc..ba462e1 100644 --- a/examples/vbo_canine/results/summary.json +++ b/examples/vbo_canine/results/summary.json @@ -192,5 +192,5 @@ "source_release": "v2026-04-15", "source_sha256": "f453bb698ef818f6b5c408f3a1c0f9c63085ba43a08fd9d37fc5fec94f90652d", "source_terms": 1537, - "validator_version": "0.7.0" + "validator_version": "0.8.0" } diff --git a/pyproject.toml b/pyproject.toml index 6ed2dae..2ad5a17 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "hatchling.build" [project] name = "bioai-evidence-validator" -version = "0.7.0" +version = "0.8.0" description = "Standards-aligned evidence policy validation for AI-assisted biological curation" readme = "README.md" requires-python = ">=3.11" diff --git a/src/bioevidence_validator/__init__.py b/src/bioevidence_validator/__init__.py index 0458d49..2941c6d 100644 --- a/src/bioevidence_validator/__init__.py +++ b/src/bioevidence_validator/__init__.py @@ -1,6 +1,6 @@ """Evidence validation primitives and domain policy runners.""" -__version__ = "0.7.0" +__version__ = "0.8.0" from .draft import build_record, draft_json_schema, load_draft # noqa: E402 from .engine import validate_record # noqa: E402 diff --git a/tools/check_distribution.py b/tools/check_distribution.py index fb5b5b5..a28ac39 100644 --- a/tools/check_distribution.py +++ b/tools/check_distribution.py @@ -12,7 +12,7 @@ root = Path(__file__).resolve().parents[1] package = Path(bioevidence_validator.__file__).resolve().parent assert root / "src" not in package.parents -assert version("bioai-evidence-validator") == bioevidence_validator.__version__ == "0.7.0" +assert version("bioai-evidence-validator") == bioevidence_validator.__version__ == "0.8.0" assert default_schema_path().is_file() assert all(profile_path(name).is_file() for name in ("general", "literature-claim", "dataset-label")) assert not (package / "canine_panel_adapter.py").exists() diff --git a/uv.lock b/uv.lock index e85f80e..3b944b5 100644 --- a/uv.lock +++ b/uv.lock @@ -198,7 +198,7 @@ wheels = [ [[package]] name = "bioai-evidence-validator" -version = "0.7.0" +version = "0.8.0" source = { editable = "." } dependencies = [ { name = "jsonschema" },