.gitignore

# Temporarily ignore CSVs until we choose which ones should be committed
*.csv
slurm
archives
output
__pycache__
*.pyc
.ipynb_checkpoints
*.html

# From GitHub .gitignore Python template

# Ignore large files, download manually
# data/reference_files/
# data/
alignments
baseline_models/model_checkpoints/
outputs/intermediate_outputs/
outputs/output_scores/
clustal/
processed_data/
make_website_data_folder.py
website_data/

# Ignore vespa output
vespa_run_directory

# Ignoring slurm scripts that we use for scoring
o2_scripts/
slurm_scripts/
*_local.sh

# Ignoring HMM model files
# And temporary scripts directories
scripts/scoring_DMS_zero_shot/HMM_temp/
scripts/scoring_DMS_zero_shot/gemme_tmp/
**/gemme_tmp/*
**/vespa_tmp/*


# Optional:
baseline_models/bash_scripts/old/
# Slurm script outputs
*.out
*.err
logs/

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class


# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# Jupyter Notebook
.ipynb_checkpoints