# Research project .gitignore
# Copy to your project as `.gitignore`. See ../pages/04-project-layout.md.

# --- Data: never in git ---
data/raw/*
data/processed/*
data/generated/*
*.nii
*.nii.gz
*.dcm
*.edf
*.bdf
*.fif
*.nc
*.h5
*.mat
*.pkl

# Keep the directory structure, though, so a fresh clone has somewhere to put things.
!data/raw/.gitkeep
!data/processed/.gitkeep
!data/generated/.gitkeep

# --- Anything identifiable, belt and braces (see ../pages/13-data-and-ethics.md) ---
*participant_key*
*consent*
*identifiable*
*_PII*
screening/
recruitment/

# --- Results: regenerate them, do not version them ---
results/
scratch/
logs/
.snakemake/

# Review any outputs before deliberately adding them to a repository.
# Internal tutorial outputs stay private.

# --- Environments ---
.venv/
venv/
__pycache__/
*.py[cod]
.ipynb_checkpoints/
.pytest_cache/
.ruff_cache/
.mypy_cache/

# uv.lock IS committed. Do not add it here.

# --- Notebooks ---
# Review notebook code and outputs; see ../pages/09-notebooks-and-figures.md.
# Decide whether to strip outputs or pair with a text file before committing.

# --- Editor / OS ---
.DS_Store
Thumbs.db
desktop.ini
.idea/
.vscode/
*.swp

# --- Secrets ---
.env
.env.*
*.pem
*.key
credentials.json
token.json

# --- Claude Code ---
# CLAUDE.md IS committed — it is lab knowledge (../pages/05-claude-md.md).
# Local settings and session state are not.
.claude/settings.local.json
.claude/history/