MANIFEST.in

# SPDX-License-Identifier: MIT
# Manifest for including/excluding files in source distribution

include README.md
include LICENSE
include requirements.txt
include requirements-dev.txt
include pyproject.toml
include HARMONIZER_SETUP.md
include PROJECT_INDEX.md
include QUICK_REFERENCE.md

# Include documentation
recursive-include docs *.md *.rst
recursive-include docs *.py

# Include examples and experiments
recursive-include examples *.py *.json
recursive-include experiments *.py

# Include result documents
recursive-include results *.md

# Include master gene pool configurations
recursive-include master_gene_pool *.json *.txt
recursive-include master_gene_pool/abstract_dna *.txt

# Exclude compiled Python files
global-exclude __pycache__
global-exclude *.py[cod]
global-exclude *$py.class
global-exclude *.so

# Exclude development and build artifacts
exclude .gitignore
recursive-exclude * .git
recursive-exclude * .mypy_cache
recursive-exclude * .pytest_cache
recursive-exclude * .ruff_cache
recursive-exclude * *.egg-info

# Exclude external dependencies
prune Python-Code-Harmonizer
prune Python-Code-Harmonizer-main

# Exclude generated files
prune generated