from setuptools import setup,find_packages

with open("README.md", "r") as fh:
    long_description = fh.read()

setup(
	name='depp',    # This is the name of your PyPI-package.
        version='0.1.40',    # Update the version number for new releases
        scripts=['train_depp.py',
                 'distance_depp.sh',
                 'depp/depp_distance.py',
                 'depp/distance_correction.py',
                 'agg_dist.py',
                 'wol_placement.sh',
                 'run_upp.sh',
                 'merge_json.py'], # The name of your scipt, and also the command you'll be using for calling it
        description='DEPP: Deep Learning Enables Extending Species Trees using Single Genes',
        long_description='DEPP is a deep-learning-based tool for phylogenetic placement.'
                         'Output of the tool is the distance matrix between the query sequences and the backbone sequences',
        long_description_content_type='text/plain',
        url='https://github.com/yueyujiang/DEPP',
        author='Yueyu Jiang',
        author_email='y5jiang@ucsd.edu',
        packages=find_packages(),
        zip_safe = False,
        install_requires=['numpy',
			'treeswift',
			'torch',
			'torchvision',
			'pandas',
			'pytorch-lightning==1.0.5',
			'biopython',
			'omegaconf',
			'apples',
			],
        include_package_data=True
)
