Compound Label (#47)

* Add compound label decomposition and Hungarian cytescore_compound scoring; add ontology name columns and fix pair_index shadowing in compound pairs; update docs, notebook, and Modal worker/status handling; add Modal smoke scripts and tests; bump dependencies and production pyproject metadata

* wip

* wip

Author: Gautam8387

.gitignore

@@ -4,8 +4,11 @@ tmp/
 .env
 .mypy_cache/
 .pytest_cache/
+.ruff_cache/
 *.csv
 *.owl
 *.npz
 *.npz.meta
 *.json
+cyteonto_results/
+dist/

README.md

@@ -2,13 +2,14 @@
 
 `cyteonto` compares two sets of cell type annotations against the [Cell Ontology (CL)](https://obofoundry.org/ontology/cl.html). Given label lists from a study author and one or more annotation algorithms, it:
 
-1. Generates a structured description for every label with an LLM.
-2. Embeds those descriptions with a configured embedding model.
-3. Matches each embedding to the closest CL term.
-4. Scores each author/algorithm pair using an ontology-aware similarity metric (default: a Gaussian kernel on the cosine similarity of the CL term embeddings).
-5. Returns a tidy DataFrame with one row per `(algorithm, pair_index)`.
+1. Decomposes mixture labels (doublets, mixed populations) into cell-type parts with an LLM when needed.
+2. Generates a structured description for every label (or part) with an LLM.
+3. Embeds those descriptions with a configured embedding model.
+4. Matches each embedding to the closest CL term.
+5. Scores each author/algorithm pair using an ontology-aware similarity metric (default: a Gaussian kernel on the cosine similarity of the CL term embeddings). Compound pairs use Hungarian bipartite matching with an optional coverage penalty when part counts differ.
+6. Returns a tidy DataFrame with one row per `(algorithm, pair_index)`.
 
-Updated ReadMe: [cyteonto/README.md](cyteonto/README.md). More documentation to follow!
+Updated ReadMe: [cyteonto/README.md](cyteonto/README.md). Process flow and file layout: [docs/WORKFLOW.md](docs/WORKFLOW.md), [docs/FILE_MANAGEMENT.md](docs/FILE_MANAGEMENT.md).
 
 
 ## Modal Service

cyteonto/README.md

@@ -78,8 +78,10 @@ class Config:
         "author_label",
         "algorithm_label",
         "author_ontology_id",
+        "author_ontology_name",
         "author_embedding_similarity",
         "algorithm_ontology_id",
+        "algorithm_ontology_name",
         "algorithm_embedding_similarity",
         "cytescore_similarity",
         "similarity_method",