embpy/.gitignore at main · theislab/embpy · GitHub

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# OS and Editor specific
.DS_Store
*~

# Virtual Environments (including Hatch environments)
.venv/
env/
venv/

# Python bytecode and cache files
__pycache__/
*.py[cod]
*$py.class

# Cached files created by various build tools
.*cache/

# Distribution / packaging outputs
/dist/
*.egg-info/
.eggs/

# Tests, coverage, and temporary files
/data/
node_modules/
.tox/
.pytest_cache/
.coverage

# Documentation build outputs
/docs/generated/
/docs/_build/

# Buck build output (if applicable)
buck-out/

# Full-scale embedding artifacts produced by embpy CLIs/notebooks.
# CSVs are typically multi-GB (e.g. chemberta2/ESMC over the human proteome)
# and must never end up in git.
/embeddings/

# World-model runs: pre-computed caches (state backbone + action
# embeddings), per-experiment training output dirs, intermediate
# tempfiles. Multi-GB and regenerated on every run.
/runs/

# Job outputs & logs. Keep a few empty log directories tracked so Slurm can
# open stdout/stderr paths even for direct sbatch submissions; ignore contents.
/err/
/logs/**
!/logs/
!/logs/.gitkeep
!/logs/cross_modality_incontext/
!/logs/cross_modality_incontext/.gitkeep
!/logs/embedding_sweep/
!/logs/embedding_sweep/.gitkeep
!/logs/gene_embeddings/
!/logs/gene_embeddings/.gitkeep
!/logs/slurm/
!/logs/slurm/.gitkeep
!/logs/slurm/compare/
!/logs/slurm/compare/.gitkeep
!/logs/slurm/eval_only/
!/logs/slurm/eval_only/.gitkeep
!/logs/slurm/install_pixi_envs/
!/logs/slurm/install_pixi_envs/.gitkeep
!/logs/slurm/run_baselines/
!/logs/slurm/run_baselines/.gitkeep
!/logs/slurm/train_embedding/
!/logs/slurm/train_embedding/.gitkeep
!/logs/world_model_ready_adatas/
!/logs/world_model_ready_adatas/.gitkeep
submission_scripts/logs/

# Debug / runtime logs
activations_debug.log
*.log

# Experimental / operational directories
cellflow_operational/


activations_debug.log
embedding_job.log
cellflow_operational/
err/
slurm_error_*.txt
slurm_jupyter_*.txt
.pixi/

# Scratch files produced by model wrappers (e.g. UCE writes
# test_counts.npz to CWD during processing). These are regenerated
# on every run and can be multi-GB -- never commit them.
*.npz
test_counts.npz

# Reference genome FASTA files (hg38 chromosomes etc.) -- multi-MB
# per file, downloaded on demand by tl.genomics.snp_utils, never
# commit them.
hg38_chroms/
*.fa
*.fasta

# SLURM job stdout/stderr -- regenerated every run, never commit.
# Root-level files come from `sbatch --wrap` (default slurm-%j.out);
# named launchers and submitters write under logs/<workflow>/.
slurm-*.out
slurm-*.err
.tmp/