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.env
__pycache__/
.DS_store
outputs/
*.sif
*agent_systems/
agent_systems/
*.pyc
**/*.pyc
bin/
benchmarking/datasets/*.h5ad
dev/
*/dist/
*.log
benchmarking/auto_runs/*
benchmarking/metadata_benchmarks/benchmark_data/
benchmarking/metadata_benchmarks/results/
benchmarking/task_benchmarks/results/
benchmarking/task_benchmarks/analysis/plots/
benchmarking/task_benchmarks/analysis/plots_no_claude/
benchmarking/task_benchmarks/analysis_slurm/logs/
benchmarking/integration_benchmarks/results/
benchmarking/integration_benchmarks/analysis/outputs/
benchmarking/integration_benchmarks/analysis/plots/
benchmarking/integration_benchmarks/slurm/logs/
benchmarking/celltyping_benchmarks/results/
benchmarking/celltyping_benchmarks/analysis/outputs/
benchmarking/celltyping_benchmarks/analysis/plots/
benchmarking/celltyping_benchmarks/slurm/logs/
benchmarking/celltyping_benchmarks/clean_plots/aba_hippocampus/
benchmarking/celltyping_benchmarks/clean_plots/tsp_large_intestine/
!benchmarking/auto_runs/auto_run_template.sh
*.note
manuscript/
.codex