.gitignore
.readthedocs.yaml
CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
SECURITY.md
pyproject.toml
setup.cfg
.github/workflows/publish.yml
.github/workflows/tests.yml
docs/conf.py
docs/index.md
docs/installation.md
docs/marker_sources.md
docs/quickstart.md
docs/requirements.txt
docs/_static/css/custom.css
docs/_templates/README.md
docs/api/index.md
docs/tutorials/gse266598_annotation.ipynb
docs/tutorials/index.md
docs/tutorials/load_model.ipynb
docs/tutorials/pbmc8k_annotation.ipynb
docs/tutorials/report.md
src/annotuneagent/__init__.py
src/annotuneagent/__main__.py
src/annotuneagent/_version.py
src/annotuneagent/annotate.py
src/annotuneagent/arbitrate.py
src/annotuneagent/cli.py
src/annotuneagent/decide.py
src/annotuneagent/evaluate.py
src/annotuneagent/evidence.py
src/annotuneagent/geo.py
src/annotuneagent/hypotheses.py
src/annotuneagent/local_lora.py
src/annotuneagent/marker_plot.py
src/annotuneagent/markers.py
src/annotuneagent/markers.tsv
src/annotuneagent/mltools.py
src/annotuneagent/prepare.py
src/annotuneagent/py.typed
src/annotuneagent/read.py
src/annotuneagent/votes.py
src/annotuneagent/workflow.py
src/annotuneagent/granularity/__init__.py
src/annotuneagent/granularity/cl_dag.py
src/annotuneagent/granularity/ontology_map.py
src/annotuneagent/granularity/relations.py
src/annotuneagent/ontology/cl_isa.json
src/annotuneagent/ontology/granularity_policy.yaml
src/annotuneagent/ontology/ontology_map.jsonl
src/annotuneagent/tokenizer/LICENSE
src/annotuneagent/tokenizer/merges.txt
src/annotuneagent/tokenizer/tokenizer.json
src/annotuneagent/tokenizer/tokenizer_config.json
src/annotuneagent/tokenizer/vocab.json
tests/test_annotate.py
tests/test_cli.py
tests/test_decide.py
tests/test_evaluate.py
tests/test_evidence.py
tests/test_geo.py
tests/test_granularity.py
tests/test_local_lora.py
tests/test_markers.py
tests/test_mltools.py
tests/test_prepare.py
tests/test_read.py
tests/test_version.py
tests/test_votes.py
tests/test_workflow.py