meta-pipe/.gitignore at main · htlin222/meta-pipe · GitHub

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# Environment and secrets
.env
.env.*
!.env.example

# Python bytecode / caches
__pycache__/
*.py[cod]
*.pyo
*.pyd
*.so
*.egg-info/
.eggs/
.pytest_cache/
.mypy_cache/
.ruff_cache/
.pyre/
.pytype/
.coverage
.coverage.*
htmlcov/
.hypothesis/

# Virtual environments
.venv/
venv/
env/
.conda/
conda-meta/

# Build artifacts
build/
dist/
pip-wheel-metadata/

# Jupyter
.ipynb_checkpoints/
*.nb.html
*.nb.pdf

# R / RStudio
.Rhistory
.RData
.Ruserdata
.Rapp.history
.Rproj.user/
renv/library/
renv/staging/

# Quarto / RMarkdown
.quarto/
_quarto/
*_cache/
*_files/
_cache/
_site/
_book/
_freeze/

# Synced skill mirrors (source of truth is ma-*/, synced via tooling/sync-skills.sh)
.claude/skills/ma-*/

# OS / IDE
.DS_Store
Thumbs.db
.idea/
.vscode/
*.swp
*.swo

# Temp files
*.tmp
*.bak
*.log

# Development logs (archive only)
docs/archive/dev-logs/
docs/archive/test-reports/

# R environment files (should be in projects, not root)
# renv.lock is now tracked for reproducibility

# Data science conventional dirs (raw/intermediate outputs)
# Note: plain-text artifacts are tracked; rely on the binary-extension ignores below.

# Databases / large data formats
*.sqlite
*.db
*.parquet
*.arrow
*.feather
*.h5
*.hdf5
*.hdf
*.sav
*.dta
*.rds
*.rda

# Binary images (keep text outputs tracked)
*.png
*.jpg
*.jpeg
*.gif
*.tif
*.tiff
*.bmp
*.webp
*.ico
*.psd

# PDFs (often large or copyrighted)
*.pdf

# ===================
# EXCEPTIONS - Always track these
# ===================

# Test fixtures (preserve for CI/testing)
!tests/fixtures/**/*.bib
!tests/fixtures/**/*.csv
!tests/fixtures/**/*.yaml
!tests/fixtures/**/*.md
!tests/fixtures/**/*.txt
!tests/fixtures/**/*.svg

# ==========================================
# Projects Directory
# ==========================================
# Ignore all projects except documented examples
projects/*
!projects/.gitkeep
!projects/ici-breast-cancer/
!projects/dlbcl-frontline-nma/
!projects/legacy/README.md
worktrees/