qpx.egg-info
dist
build
.idea
/data/*
!/data/ontology/
docs/.vscode
__pycache__
.vscode

# DuckDB database files
*duckdb*.db
*.db
*.db.wal
*.db-shm

# Temporary files
*.tmp
*.temp
temp/
tmp/
.tmp/
.temp/

# Temporary mzTab files (created during processing)
mztab_temp*.mzTab
mztab_temp*.mzTab.gz
mztab_temp*.mzTab.bz2

# Test output and temporary data
test_output*/
output*/
results*/
*.parquet
!examples/psm/*.parquet
!qpx/core/ontology/data/*.parquet
!data/ontology/*.parquet
.hypothesis/

# Log files
*.log
logs/

# OS generated files
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db

# Python cache and compiled files
*.pyc
*.pyo
*.pyd
.Python
*.so
__pycache__/
*.egg-info/
.pytest_cache/
.coverage
htmlcov/

# Jupyter Notebook checkpoints
.ipynb_checkpoints/

# Environment files
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Cursor
.cursorrules
.cursor/

# MkDocs build output
site/

# Big examples data
tissues/
msnet_qpx/

#Ignore cursor AI rules
.cursor/rules/codacy.mdc


# Claude Code
.claude/

# Kiro
.kiro/
workflow.md
docs/metadata.avsc
.claude/
.codacy/


#Ignore vscode AI rules
.github/instructions/codacy.instructions.md

.ruff*
# Ruff cache lock
.ruff_cache.lock

uv.lock
absexpr*
scripts/convert_absexpr.py
scripts/plasma_infiltration_model.py
scripts/plot_absexpr_analysis.py
scripts/plot_blood_biology.py
docs/superpowers/*
