.gitignore

/target
lcov.info
tmp_dir/
__pycache__/
scripts/__pycache__/
.venv-bench/
.venv_retro/
.cache/
.claude/
.DS_Store
benchmarks/
web/spatial_viewer/node_modules/
web/spatial_viewer/dist/

results/
.vscode/
.cursor/

retro_synthesis/

docs/_build/
docs/.doctrees/
docs/.buildinfo
docs/.env/
docs/.tox/
docs/.coverage
docs/.pytest_cache/
docs/_static/
docs/_autosummary/
# You may also want to ignore Sphinx cache and notebook output if present:
docs/.ipynb_checkpoints/
# If using Sphinx Gallery
docs/auto_examples/
# Ignore API doc output if generated in-place
docs/api/
# If using JupyterBook or MyST-NB
docs/_jupyter_cache/
# If using ReadTheDocs config lock
.readthedocs.lock

ablation_training_configs/
scripts/*.py
scripts/retro_validation/

PIIS0092867425005720.pdf
data/geo_perturbseq/
data/hf_perturbmulti/
perturb_multi_imputation/
snrna_human_tonsil_2026-04-20/