SORAT/.gitignore at main · CompBio-Lab/SORAT · GitHub

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

# C extensions
*.so

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

# PyInstaller
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# SORAT per-user local configuration (generated by setup wizard)
.sorat/user.config
.sorat/*.local.config

# Nextflow
.nextflow/
.nextflow.log*
work/
results/
timeline.html
report.html
trace.txt
dag.svg
*.dot

# Docker
*.tar

# Repo folders not tracked on GitHub
containers/
docs/
models/
scripts/
test/

container/cinema/*
container/nnformer/*
container/vsa3l/*

# Editor
.vscode/
.idea/
*.swp
*.swo
*~

# OS
.DS_Store
Thumbs.db

# Model weights (download separately - too large for GitHub)
# These are included in Docker images but transferred separately via SCP
models/*/weights/
models/*/*.pt
models/*/*.pth
models/*/*.ts
models/*/*.safetensors
models/*/*.pkl
models/cinema/finetuned/
models/**/finetuned/**/config.yaml
models/nnformer/nnFormer_trained_models/
models/vsa3l/*.pt
models/vsa3l/*.ts
containers/*.sif

# Large data files
*.nii
*.nii.gz
*.dcm
/data/
DATASET/
preprocessed/

# M&Ms-2 dataset reorganization & samplesheet generation
# Samplesheets (also covered by /data/ above)
data/mms2_sa_samplesheet.csv
data/mms2_la_samplesheet.csv
# Helper scripts & logs (also covered by scripts/ above)
scripts/reorganize_mms2.py
scripts/verify_regen_mms2_cfg.py
scripts/generate_mms2_samplesheets.py
scripts/mms2_finisher.sh
scripts/mms2_parallel_reorg.sh
scripts/mms2_parallel_verify.sh
scripts/reorganize_mms2.log
scripts/generate_samplesheets.log
scripts/verify_mms2.log

# AI assistant files (kept local, not versioned)
CLAUDE.md
CLAUDE.local.md
.claude/
.mcp.json