phentrieve/.gitignore at main · berntpopp/phentrieve · GitHub

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# Python bytecode files
__pycache__/
*.py[cod]
*$py.class

# Distribution / packaging
dist/
build/
*.egg-info/

# Virtual environments
venv/
env/
ENV/
.venv/

# IDE files
.vscode/
.idea/
*.swp
*.swo

# Data and Output files
# Exclude specific data directories but allow test data and results
phentrieve/data/
data/hf_cache/
data/indexes/
data/hpo_terms/
data/hpo_core_data/
# Runtime app state (e.g. LLM quota SQLite db, generated at runtime)
data/app/

# HPO SQLite database (generated data)
data/hpo_data.db
data/*.db
data/*.db-shm
data/*.db-wal

# Data bundle manifest (downloaded from releases)
data/manifest.json

# ChromaDB database files
*.sqlite3
*.sqlite3-shm
*.sqlite3-wal

# Keep test data and results versioned (NOT ignored)
# data/test_cases/ - tracked
# data/test_texts/ - tracked
# data/results/ - tracked

# Exclude other directories
phentrieve/hpo_chroma_index/
hpo_chroma_index/
phentrieve/benchmark_results/
benchmark_results/

# Specific data files (but not in test/results directories)
/*.json
*.pkl
*.npy
*.npz

# Include test cases and README/LICENSE
!phentrieve/data/test_cases/
!*.md
!LICENSE

# Cache files
.cache/
.pytest_cache/
.mypy_cache/
.dmypy.json
.ruff_cache/

# Coverage reports (generated artifacts, not versioned)
.coverage
.coverage.*
coverage.xml
htmlcov/
*.cover
.hypothesis/

# Jupyter Notebook
.ipynb_checkpoints

# OS specific files
.DS_Store
Thumbs.db

# env files
.env.docker
.env

# output files
output/
results/
.runs/

# MkDocs build output
site/

# Claude Code files
.claude/
.worktrees/
.superpowers/

# serena MCP files
SERENA.md
.serena/.env
.serena/

# Playwright MCP files
.playwright-mcp/

# Understand-Anything knowledge graph (generated locally per developer)
.understand-anything/

data/hp.json