# Python
__pycache__/
*.py[cod]
*.egg-info/
build/
dist/

# Environments
.venv/
.conda_env/

# uv
.uv/

# Derived fragment-library caches (regenerated from fragment_library.csv)
frag_features.pkl
frag_brics_maskings.pkl
frags_tmp/

# The fragment library, like the checkpoints, is downloaded from Hugging Face
# on first use (mseok/DeepBioisostere) and cached. Nothing about it is tracked:
# fragment_library.csv is 12 MB and its derived caches are 0.7-3 GB.
#
# Leading slash matters. Unanchored, `fragment_library/` also matches
# src/deepbioisostere/fragment_library/, which is a *package* directory and is
# tracked. Already-tracked files there keep working, so this hides: it only
# surfaces when someone tries to `git add` a new module and git silently
# refuses.
/fragment_library/
*.old145854.*

# Trained checkpoints: 201 MB, deliberately purged from this history.
# They live on Hugging Face (mseok/DeepBioisostere) and Zenodo, and the
# package downloads them on demand. Do not let them back in.
/model_save/

# Run outputs
generation_result*.csv
baseline_strategy_*_results.csv
*.log

# Slurm job logs
deepbio_validate_*.out
deepbio_validate_*.err
*_[0-9][0-9][0-9][0-9][0-9][0-9].out
*_[0-9][0-9][0-9][0-9][0-9][0-9].err

# Local AI working notes: kept on disk, never committed
_ai/

# verification scratch
.verify/
