.gitignore
.project_root
LICENSE
MANIFEST.in
README.md
THIRD_PARTY_NOTICES.md
pyproject.toml
uv.lock
src/assaybench/__init__.py
src/assaybench/assets.py
src/assaybench/cli.py
src/assaybench.egg-info/PKG-INFO
src/assaybench.egg-info/SOURCES.txt
src/assaybench.egg-info/dependency_links.txt
src/assaybench.egg-info/entry_points.txt
src/assaybench.egg-info/requires.txt
src/assaybench.egg-info/top_level.txt
src/assaybench/benchmark/__init__.py
src/assaybench/benchmark/diversity.py
src/assaybench/benchmark/effective_pathways.py
src/assaybench/benchmark/metrics.py
src/assaybench/benchmark/sequential.py
src/assaybench/core/__init__.py
src/assaybench/core/acquisition.py
src/assaybench/core/loop.py
src/assaybench/core/metric.py
src/assaybench/core/model.py
src/assaybench/core/task.py
src/assaybench/core/types.py
src/assaybench/data/__init__.py
src/assaybench/data/gene_embeddings.py
src/assaybench/data/gene_sets.py
src/assaybench/data/screens.py
src/assaybench/data/depmap/PROVENANCE.md
src/assaybench/data/depmap/__init__.py
src/assaybench/data/hgnc/__init__.py
src/assaybench/data/hgnc/all_genes.tsv
src/assaybench/data/hgnc/hgnc_symbols_cache.tsv
src/assaybench/data/hgnc/manual_mappings.json
src/assaybench/data/hgnc/uniprot_protein_to_gene.json
src/assaybench/data/prompts/__init__.py
src/assaybench/data/prompts/objective_prompts.yaml
src/assaybench/data/screen_sets/__init__.py
src/assaybench/data/screen_sets/assayloop-test.yaml
src/assaybench/data/screen_sets/assayloop-validation.yaml
src/assaybench/data/screen_sets/lopo-drug-test.yaml
src/assaybench/data/screen_sets/lopo-drug-train.yaml
src/assaybench/data/screen_sets/lopo-fitness-test.yaml
src/assaybench/data/screen_sets/lopo-fitness-train.yaml
src/assaybench/data/screen_sets/lopo-infection-test.yaml
src/assaybench/data/screen_sets/lopo-infection-train.yaml
src/assaybench/data/screen_sets/lopo-molecular-test.yaml
src/assaybench/data/screen_sets/lopo-molecular-train.yaml
src/assaybench/data/screen_sets/lopo-trafficking-test.yaml
src/assaybench/data/screen_sets/lopo-trafficking-train.yaml
src/assaybench/dataset/__init__.py
src/assaybench/dataset/dataset.py
src/assaybench/llm/__init__.py
src/assaybench/llm/history_format.py
src/assaybench/llm/parse_genes.py
src/assaybench/utils/__init__.py
src/assaybench/utils/gene_mapper.py
src/assaybench/utils/prompt_loaders.py
src/assaybench/utils/score_maps.py
src/assaybench/utils/screen_processing.py
tests/test_assets.py
tests/test_diversity.py
tests/test_effective_pathways.py
tests/test_llm.py
tests/test_loop.py
tests/test_screen_sets.py
tests/test_screens.py
tests/test_sequential.py