Changelog

0.0.4 (2026-04-15)

Current release.

  • Preserved parallel edges in the NetworkX MultiDiGraph engine so distinct evidence edges with the same source, predicate, and target are no longer overwritten

  • Corrected KEGG fixed-width record parsing for multi-line GENE and PATHWAY sections used by the seeding workflow

  • Tightened metabolism_chain() traversal so carcinogen-specific chains do not absorb unrelated unlabeled branches through shared enzymes

  • filter_knowledge_graph() now returns detached model copies rather than aliasing the source graph objects

  • Restored a clean strict mypy pass for the shipped source tree

0.0.3 (2026-03-21)

Release metadata synchronized for the current PyPI/GitHub publication.

  • Updated package and app version identifiers to 0.0.3

0.0.2 (2026-03-19)

Current development release.

  • Added graph ingestion modes: exploratory and strict

  • Added canonical grounding metadata, record origin tracking, and custom predicates

  • Added validated/exploratory graph visibility filtering for preview, data, export, and persistence

  • Added visibility-aware JSON, HTML, JS, and GEXF export helpers

  • Added revision visibility tracking and SQLite schema migration support

  • Added clean repository shutdown via context-manager support and fixed prior SQLite resource warnings

  • Added Ollama/OpenAI backend abstraction and mode-aware seeded graph preparation

0.0.1 (2026-03-17)

Initial release.

  • Pydantic v2 data models for 7 node types and 10 edge types

  • NetworkX MultiDiGraph engine with load/merge/validate

  • LLM-powered extraction via OpenAI structured outputs

  • Streamlit app with manual entry, LLM extraction, and gene panel loading

  • D3.js force-directed graph viewer with dark theme

  • Export to JSON, graph-data.js (D3 viewer), and GEXF (Gephi)

  • Curated Tier 1 (13 genes) and Tier 2 (23 genes) reference panels

  • Referenced activity-score tables for 18 genes, including evidence metadata

  • Test coverage across models, engine, exporter, storage, and reference data

  • CI/CD: ruff linting, pytest matrix (3.10–3.12), PyPI publish workflow