RAPTOR/MANIFEST.in at main · AyehBlk/RAPTOR · GitHub

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# MANIFEST.in for RAPTOR v2.2.2
# =============================================================================
# This file tells setuptools which non-Python files to include when building
# the distribution packages (sdist, wheel).
# =============================================================================

# =============================================================================
# Documentation Files (Root Level)
# =============================================================================

include README.md
include LICENSE
include RAPTOR_STRUCTURE.md

# Streamlit configuration
include .streamlit/config.toml

# =============================================================================
# Documentation Directory
# =============================================================================

recursive-include docs *.md

# =============================================================================
# Example Scripts
# =============================================================================

recursive-include examples *.py
recursive-include examples *.md

# =============================================================================
# Templates
# =============================================================================

recursive-include templates *.csv

# =============================================================================
# RAPTOR Package - R Scripts (Module 6)
# =============================================================================

# R scripts for differential expression
recursive-include raptor/external_modules/module6_de_analysis/r_scripts *.R

# Module 6 documentation
recursive-include raptor/external_modules/module6_de_analysis/documentation *.md
include raptor/external_modules/module6_de_analysis/README.md
include raptor/external_modules/module6_de_analysis/WORKFLOW_OVERVIEW.md
include raptor/external_modules/module6_de_analysis/recomendation.txt

# =============================================================================
# RAPTOR Package - Pipeline Configuration Files (Module 5)
# =============================================================================

# YAML configuration files for all pipelines
recursive-include raptor/pipelines *.yaml

# Shell scripts for pipelines
recursive-include raptor/pipelines *.sh

# Pipeline documentation
include raptor/pipelines/star_salmon/STAR_SALMON_COMPLETE_SUMMARY.md
recursive-include raptor/pipelines/quick_kallisto *.md
recursive-include raptor/pipelines *.md

# =============================================================================
# RAPTOR Package - Dashboard Assets
# =============================================================================

# Dashboard HTML and assets
recursive-include raptor/dashboard/assets *.html
recursive-include raptor/dashboard/assets *.css
recursive-include raptor/dashboard/assets *.png
recursive-include raptor/dashboard/assets *.PNG
recursive-include raptor/dashboard/assets *.jpg
recursive-include raptor/dashboard/assets *.jpeg

# =============================================================================
# Tests (Include for Development Installations)
# =============================================================================

recursive-include tests *.py

# =============================================================================
# Exclude Unwanted Files
# =============================================================================

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

# Distribution / packaging
global-exclude .Python
global-exclude build/
global-exclude develop-eggs/
global-exclude dist/
global-exclude downloads/
global-exclude eggs/
global-exclude .eggs/
global-exclude lib/
global-exclude lib64/
global-exclude parts/
global-exclude sdist/
global-exclude var/
global-exclude wheels/
global-exclude *.egg-info/
global-exclude *.egg

# IDE and editor files
global-exclude .idea/
global-exclude .vscode/
global-exclude *.swp
global-exclude *.swo
global-exclude *~
global-exclude .DS_Store

# Version control
global-exclude .git
global-exclude .gitignore
global-exclude .gitattributes

# Testing and CI
global-exclude .pytest_cache/
global-exclude .coverage
global-exclude htmlcov/
global-exclude .tox/
global-exclude .nox/

# Virtual environments
global-exclude venv/
global-exclude env/
global-exclude ENV/
global-exclude .venv/

# Other
global-exclude *.log
global-exclude .mypy_cache/
global-exclude .dmypy.json
global-exclude dmypy.json

# =============================================================================
# Notes
# =============================================================================

# This MANIFEST.in ensures that:
# 1. All R scripts from Module 6 are included
# 2. All YAML configs and shell scripts from Module 5 pipelines are included
# 3. Dashboard assets (CSS, images, HTML) are included
# 4. Documentation and examples are included
# 5. Templates are included
# 6. Unwanted cache and temp files are excluded
#
# Test with: python setup.py sdist
# Check contents with: tar -tzf dist/raptor-2.2.2.tar.gz