.venv
dist/
sdist/
**/__pycache__/
.pytest_cache/
*.pyc
.mypy_cache/
website/.docusaurus/

# Data
user_data/

# Logs
logs
npm-debug.log*
yarn-debug.log*
yarn-error.log*
dev-debug.log

# Dependency directories
website/node_modules/
website/build/

# Environment variables
.env

# Editor directories and files
.idea
.vscode
*.suo
*.ntvs*
*.njsproj
*.sln
*.sw?

# OS specific
.DS_Store
**/.DS_Store

# Legacy/archived directories
archived/
bin/
centers/
data/

# Unused / local-only pipeline paths
pipeline/exerpiements.md
pipeline/experiments.md
pipeline/simulation/
pipeline/visualization_archived/
pipeline/server/strategy.py
pipeline/server/strategy_new.py
pipeline/server/aggregator_qc.py
pipeline/utils/bloom_filter.py

# Redundant/outdated documentation
Readme_pipeline.md
EXPERIMENT_RUNNER_README.md
prd/
.pre-commit-config.yaml
!cluster_deployment/docs/
!cluster_deployment/docs/**

# Docker (local workflow only; cluster deployment is under cluster_deployment/)
docker/
.dockerignore

# Performance manuscript drafts (local only; configs stay in repo)
experiments/performance/README.md
experiments/performance/appendix_sections.md
experiments/performance/appendix_table.md
experiments/performance/appendix_table.tex
experiments/performance/manuscript_sections.md

# Local notes, reports, and archives (not shipped)
ISSUES_REPORT.md
ISSUES_REPORT_UPDATED.md
plan.md
experiments.docx
InfoSummit_kinship.pdf
mkdocs.yml
pipeline.pdf
pipeline.zip
plink.zip
results/

# Experiment run outputs and synthetic data artifacts
experiments/**/results/
experiments/**/results_*/
experiments/*/*/results/
experiments/**/data/**/*.bed
experiments/**/data/**/*.bim
experiments/**/data/**/*.fam
experiments/**/data/**/*.log
experiments/**/data/**/*.kin0
experiments/**/data/**/*.assoc*
experiments/**/data/**/*.genome
experiments/**/data/**/*.hwe
experiments/**/data/**/*.imiss
experiments/**/data/**/*.lmiss
experiments/**/data/**/*.frq
experiments/**/intermediate/
**/__pycache__/

# Task / cluster bundles
fedgwas-cluster.tar.gz
cluster_deployment/wheels/

# Log files
*.log
**/*.log

# PLINK output files
*.bed
*.bim
*.fam
*.kin0
*.assoc*
*.genome
*.hwe
*.imiss
*.lmiss
*.frq

# Large data files (duplicate patterns for safety)
*.bed
*.bim
*.fam

# claude
.claude/
.venv/
claude.md
.windsurfrules
README-task-manager.md
.env.example
/scripts/
.cursor/*
.test_scenario_a.py
