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167 lines (152 loc) · 2.61 KB
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# -----------------------------------------------------------------------------
# OpenAMP Foundry .gitignore
# Keep source, schemas, configs, docs, tests, and tiny demo fixtures in git.
# Exclude local environments, caches, generated outputs, large datasets,
# model weights, candidate batches, and potentially sensitive lab/vendor files.
# -----------------------------------------------------------------------------
# Python bytecode / caches
__pycache__/
*.py[cod]
*$py.class
.pytest_cache/
.mypy_cache/
.ruff_cache/
.pyre/
.pytype/
.coverage
.coverage.*
coverage.xml
htmlcov/
.tox/
.nox/
.cache/
# Virtual environments
.venv/
venv/
env/
ENV/
.python-version
# Build / packaging artifacts
build/
dist/
*.egg-info/
.eggs/
*.egg
pip-wheel-metadata/
site/
# Dependency / tool lock scratch files
pip-log.txt
pip-delete-this-directory.txt
# Environment / secrets
.env
.env.*
!.env.example
*.pem
*.key
*.crt
*.p12
*.pfx
secrets/
credentials/
# OS / editor noise
.DS_Store
.AppleDouble
.LSOverride
Thumbs.db
Desktop.ini
.vscode/
.idea/
*.swp
*.swo
*~
# Jupyter / notebooks
.ipynb_checkpoints/
*.nbconvert.ipynb
# Logs
logs/
*.log
*.out
*.err
# Generated pipeline outputs
outputs/*
!outputs/.gitkeep
!outputs/README.md
reports/*
!reports/.gitkeep
runs/*
!runs/.gitkeep
artifacts/*
!artifacts/.gitkeep
# Candidate batches and generated evidence artifacts
# Keep only documentation and tiny examples under examples/.
candidates/*
!candidates/.gitkeep
batches/*
!batches/.gitkeep
evidence/*
!evidence/.gitkeep
# Large or licensed datasets: use fetch scripts and local cache instead.
data/raw/*
!data/raw/.gitkeep
data/interim/*
!data/interim/.gitkeep
data/processed/*
!data/processed/.gitkeep
data/external/*
!data/external/.gitkeep
*.fasta
*.faa
*.fa
*.fastq
# Allow committed novelty DB files (APD6 + DRAMP + UniProt FASTA — see docs/NOVELTY_AUDIT_GUIDE.md)
!data/novelty_db/*.fasta
*.fq
*.sdf
*.mol2
*.pdb
*.cif
*.mmcif
*.csv.gz
*.tsv.gz
*.jsonl.gz
*.parquet
*.sqlite
*.sqlite3
*.db
# Model weights / embeddings / checkpoints
models/*
!models/README.md
!models/.gitkeep
checkpoints/
*.pt
*.pth
*.ckpt
*.safetensors
*.onnx
*.h5
*.pkl
*.pickle
*.joblib
*.npy
*.npz
embeddings/
# Local lab / CRO / vendor files should not be committed by default.
# Add sanitized public summaries manually when approved.
lab_results/*
!lab_results/.gitkeep
cro_quotes/*
!cro_quotes/.gitkeep
vendor_docs/*
!vendor_docs/.gitkeep
# Safety-sensitive unscreened candidate lists are intentionally excluded.
unscreened_candidates/*
!unscreened_candidates/.gitkeep
high_risk_review/*
!high_risk_review/.gitkeep
# Temporary files
tmp/
temp/
*.tmp
.commandcode/
external_validation/
*.zip