.gitignore

__pycache__/
*.py[cod]
*.egg-info/
.eggs/
dist/
build/
.venv/
venv/
.env
*.db
.pytest_cache/
.mypy_cache/
.ruff_cache/
artifacts/
outputs/
*.h5ad
.cache/
.cursor/
.encode_cache/
.geo_cache/
.pytest_cache/
Data/
wandb/
legacy_old/
GenomeDatabase/
docs/manuscript/
docs/figures/
docs/figures_and_tables/
archives/

# Manuscript figures, tables, and the scripts that build them.
# Ship these as a supplementary zip. The general-use repo keeps
# train / infer / eval, the UI, sample configs, and sample checkpoints.
scripts/rebuttal_*.py
scripts/build_iclr_*.py
scripts/build_docs_iclr_figures_tables.py
scripts/build_mech_weakcorr_*.py
scripts/build_lit_figure.py
scripts/build_acquisition_*.py
scripts/analyze_fair_benchmark_heatmaps.py
scripts/benchmark_fair_*.py
scripts/eval_baseline_fair_pools.py
scripts/eval_multimodal_acquisition_benchmark.py
scripts/run_baseline_fair_grid.py
scripts/run_scenicplus_baseline.py
scripts/run_celloracle_baseline.py
scripts/collect_tf_eager_eval_tables.py
scripts/compare_tf_eager_neg_models.py
scripts/summarize_tf_eager_ablation.py
scripts/plot_tf_eager_ablation_heatmap.py
scripts/plot_tf_eager_eval_metrics.py
scripts/generate_beeline_atac_table.py
scripts/acquire_multimodal_data_fragaware.py
scripts/baselines/
scripts/figr_pbmc/
scripts/interpretability/
scripts/trackB/
scripts/_tmp_*
scripts/from pptx import Presentation.py
.pytest_cache/
Literature_Validation_Agent/.venv/
.kube/
.ruff_cache/
third_party/