Compound Label

[Gautam8387]

Summary

Compound label support for CyteOnto: LLM decomposition, Hungarian compound scoring, result/schema updates, Modal hardening, docs, and dependency/metadata cleanup.

Resolves #46, #22 and dependencies

Changes

• Add LLM-based compound label decomposition (LabelDecomposition, decompose_label / decompose_labels) with per-run_id JSON cache under user_files/decompositions/
• Score compound author/algorithm pairs with Hungarian max-weight matching and cytescore_compound instead of treating mixture labels as a single string
• Apply coverage penalty min(m,n) / max(m,n) when author and algorithm part counts differ
• Add author_ontology_name and algorithm_ontology_name to compare results (CSV primary label with OWL fallback)
• Emit matched assignment ontology ids/names only for compound pairs (semicolon-separated when k > 1)
• Fix pair_index corruption caused by inner loop variable shadowing in the compound scoring path
• Preserve similarity_method=empty behavior for blank labels while keeping ontology fields on the non-empty side
• Cache decompositions per label string so reruns with the same run_id skip LLM calls for labels already on disk
• Fix Pydantic AI deprecation by using result.usage instead of result.usage() in describe and decompose runners
• Harden Modal job startup with volume reload retries, atomic status.json writes, and worker-side initial status validation
• Add scripts/test_modal_simple_labels.sh and scripts/test_modal_compound_labels.sh for hosted API smoke tests
• Add tests/test_modal_status.py for Modal status read/write and worker reload behavior
• Expand unit tests for decomposition, Hungarian scoring, compound compare integration, and pair_index correctness
• Update notebooks/quick_tutorial.ipynb with synthetic Hungarian demos and live compound comparison scenarios
• Update root README, cyteonto/README.md, docs/WORKFLOW.md, docs/FILE_MANAGEMENT.md, and modal_app/README.md for the new pipeline and result columns
• Bump aiohttp to >=3.14.0 and pydantic-ai to >=1.102.0,<2.0.0, refreshing uv.lock for tested transitive upgrades
• Add production pyproject.toml metadata (description, license, authors, keywords, URLs) and hatchling build config with dynamic version from cyteonto/__init__.py
• Extend .gitignore for build artifacts and local result outputs