.gitignore

# Ignore macOS-specific files
.DS_Store

# Emacs edit files
*~
*#
.#

# Backup files
*.bak

# Config files for development tools
.ipynb_checkpoints
.Rhistory
.vscode
.mypy_cache
.pytest_cache
.ruff_cache

# Compiled Python modules
*.pyc

# Python distribution/packaging files
build/
dist/
pyani_plus.egg-info/
distribute*

# Issue development subdirectories
issue_*/

# Local snakemake-profile directories
snakemake-profile-*/

# Local test databases
*.db
*.sqlite
*.sqlite3

# Test coverage output
cover/
htmlcov/
.coverage*

# Virtualenvs
venv-*
.python-version

# Local pyani-plus config directory
.pyani-plus

# DTD files supporting imported modules
ulist.DTD
esummary_assembly.dtd

# Snakemake directories generated during testing
.snakemake

# MUMmer error files from testing
nucmer.error