repseq/.gitignore at main · cmzmasek/repseq · GitHub

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# Python
__pycache__/
*.py[cod]
*.egg-info/
dist/
build/
*.egg

# Installed package state
.eggs/

# Test / coverage
.pytest_cache/
.coverage
htmlcov/

# repseq runtime artifacts
/repseq_output/
/tmp/
~/.repseq/

# User-generated configs (only default_config.yaml + examples/ are tracked)
/config/my_*.yaml
/my_*.yaml
/repseq_config.yaml
/repseq_config.yaml~

# Local scratch
/JUNK/

# Claude Code local config (not project config)
.claude/

# Local-only Claude-agent guidance (no longer published to GitHub)
CLAUDE.md
CLAUDE.md~

# hmmpress binary indexes (auto-regenerated from the .hmm source on
# first run — no need to bloat the repo with ~4MB of derivable bytes).
repseq/data/hmms/*.h3f
repseq/data/hmms/*.h3i
repseq/data/hmms/*.h3m
repseq/data/hmms/*.h3p

# macOS
.DS_Store

# Editors
.vscode/
.idea/