# Core Edit Flow / pCoMole
torch>=2.1.0
pytorch-lightning>=2.0.0
lightning>=2.0.0
transformers==4.46.0
datasets>=2.14.0
easydict
pyyaml
numpy>=1.24.0
pandas>=2.0.0
tqdm
einops
omegaconf
joblib>=1.3.0
scikit-learn>=1.3.0

# Peptidomimetic chemistry
rdkit>=2023.3.1
selfies
SmilesPE
networkx
torch-geometric

# Oracles used by pCoMole
xgboost>=2.0.0
chemprop>=2.0.0

# Optional logging
# wandb

# Cas9
h5py                 # CICERO-format PAM datasets
biopython            # FASTA / sequence handling
rapidfuzz            # sequence similarity in Cas9 diagnostics
# HMMER (`hmmscan`) must be on PATH for the Cas9 domain / PAM-interacting
# detectors: conda install -c bioconda hmmer
# protein2pam provides the PAM oracle's model class:
#   pip install protein2pam==0.2.0