vcf_analysis/.gitignore at main · elementalcollision/vcf_analysis · GitHub

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# Python
__pycache__/
*.py[cod]
*.pyo
*.pyd
*.so
*.egg-info/
.eggs/
*.log

# Backup files
*.bak
*.backup
*.orig
*~

# Environments
.env
.venv
venv/
ENV/

# Aegis Framework (task management context - should not be committed)
.context/

# Development files (summaries, test files, cache, logs)
.development/

# Jupyter
.ipynb_checkpoints

# Data
*.vcf
*.bcf
*.gz
*.csi
*.db
*.sqlite
*.h5
*.csv
*.tsv
*.jsonl
*.lancedb

# Database directories
/kuzu_db/
/lancedb/
**/kuzu_db/
**/lancedb/
lancedb_test/
**/lancedb_test/
*.lance/
**/*.lance/

# Containers
*.img
*.dockerfile
Dockerfile*
.dockerignore

# Test & Coverage
.coverage
htmlcov/
coverage.xml
.tox/
.cache/
pytest_cache/

# CLI Documentation Validation artifacts
.validation-cache/
.cli-validation.yml
.cli-validation.yaml
cli-validation.yml
cli-validation.yaml

# Secrets
*.key
*.pem
*.env
secrets.*

# OS
.DS_Store
Thumbs.db

# IDEs
.vscode/
.idea/
*.swp

# Project/Editor
.cursor/

# Temporary test data and cache
sample_data/
golden/
.hypothesis/

# Ignore test agent script and credentials
test_agent.py
test_credentials.json

# Sphinx build artifacts
docs/build/
docs/build/**

# If you want to version canonical test VCFs in sample_test_data/
!sample_test_data/*.vcf.gz

kuzu_bug_report.md

# Large data files in sample_test_data/ that should not be committed
sample_test_data/chr22.1kg.phase3.v5a.vcf.gz
sample_test_data/chr22.1kg.phase3.v5a.vcf.gz.csi
sample_test_data/chr22.1kg.phase3.v5a.vcf.gz.tbi
sample_test_data/chr22.1kg.phase3.v5a.testready.vcf.gz
sample_test_data/chr22.1kg.phase3.v5a.testready.vcf.gz.csi
sample_test_data/chr22.1kg.phase3.v5a.testready.vcf.gz.tbi
sample_test_data/22.fa
sample_test_data/22.fa.fai

# Demo and Implementation Planning Files (should not be tracked)
demo/
demo_script.md
DEMO_READINESS_CHECKLIST.md
APACHE_IGGY_IMPLEMENTATION_PLAN.md

# Temporary test and validation files
test_phase1_memory_optimization.py
performance_validation.py
test_*.py
*_test.py

# Session and development summary files
*_SESSION_SUMMARY.md
*_FIXES_SUMMARY.md
*_SCHEMA_FIX_SUMMARY.md
LOAD_TESTING_SESSION_SUMMARY.md
PATH_FIXES_SUMMARY.md
KUZU_SCHEMA_FIX_SUMMARY.md
SESSION_SUMMARY_*.md
*SESSION_SUMMARY*.md
SESSION_SUMMARY_2025-*.md

# Audit and internal analysis reports (should not be public)
*_AUDIT_REPORT_*.md
SAMPLE_DATA_AUDIT_REPORT_*.md
CLI_DOCSTRING_AUDIT_REPORT_*.md

# Temporary performance reports (keep important milestone reports)
performance_reports/temp_*
performance_reports/*_temp*
performance_reports/test_*

# Security reports (may contain sensitive info)
security-reports/

# Large cache files
.embedding_cache.json

# Memory profiling artifacts
memory_profiles/
*.memray

# Color palette files
vibrant-palette.txt

# Documentation build artifacts (ensure these are never committed)
docs_site/
docs/docs_src/_build/
docs/_build/
site/
.mkdocs_cache/

# MkDocs and Sphinx build artifacts
*.html
docs/docs_src/_static/
docs/docs_src/api/api/