MANIFEST.in

# By default, Distutils (the packaging framework, called in setup.py) will include the following files in your release package:
#    README.txt
#    setup.py
#    The .py files needed by the multi-file modules listed in the packages parameter
#    The individual .py files listed in the py_modules parameter 

# MANIFEST.in commands:
# https://docs.python.org/3/distutils/sourcedist.html#commands

# See explanation in: http://www.diveintopython3.net/packaging.html
# Use .add_data_files and .add_data_dir methods in appropriate
# setup.py files to include non-python files such as documentation,
# data, etc files to distribution. Avoid using MANIFEST.in for that.

# Use check-manifest to detect errors in setup.py:
# https://pypi.python.org/pypi/check-manifest

# Except packaging in Python is a massive pain with incomplete and seemingly
# contradicting docs.

# Include main package and scripts:
recursive-include pipeline_QTL *.py

# Include scripts in main directory, package info and INI files:
include *.py
include MANIFEST.in
include *.ini
include LICENSE
include INSTALL
include README.rst
include THANKS.rst
include TODO.rst
include COPYING
include *.sh
include *rst
include *txt

# Include dependency specifications and Docker:
include external_dependencies.rst
include requirements.txt
include Dockerfile

# Include project documentation:
recursive-include docs *.html
recursive-include docs *.rst
recursive-include docs *.py
include docs/Makefile
include docs/make.bat
prune docs/_build

# Include files for tests:
include tox.ini 
include .travis.yml
include run_travis_tests.sh
recursive-include tests *

# Include addtional files needed, example data, etc.:
#include data_examples *

# Project specific files to include:
recursive-include pipeline_QTL *.R
recursive-include pipeline_QTL *.bat
recursive-include pipeline_QTL *.ini
recursive-include pipeline_QTL *.py
recursive-include pipeline_QTL *.rst
recursive-include pipeline_QTL *.sh
recursive-include pipeline_QTL Makefile
recursive-include pipeline_QTL *.bib

recursive-include installation *.txt
recursive-include installation *.yml
recursive-include scripts *.R
recursive-include scripts *.sh
recursive-include scripts *.txt
recursive-include scripts *.py
recursive-include pipeline_QTL *.yml

include installation/Dockerfile

# Files to exclude:
exclude .gitignore
exclude .DS_Store
exclude .dir_bash_history
recursive-exclude * .dir_bash_history
recursive-exclude * *.DS_Store
recursive-exclude * *.bak
recursive-exclude docs *.pdf
recursive-exclude docs *.html
recursive-exclude * .DS_Store
recursive-exclude * .dir_bash_history

# Extensions to include:
#include *.pyxbld
#include *.pyx
#include *.h
#include *.cpp
#include *.h
#include *.pxd
#include *.c