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b/setup.py |
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#!/usr/bin/env python |
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# -*- coding: utf-8 -*- |
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from setuptools import setup, find_packages |
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requirements = [ |
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"argh", |
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"attr", |
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"related", |
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"cloudpickle>=1.0.0", |
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"concise==0.6.7", |
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"deepexplain", |
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# ml |
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"gin-config", |
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"keras==2.2.4", |
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"scikit-learn", |
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# "tensorflow", |
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# numerics |
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"h5py", |
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"numpy", |
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"pandas", |
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"scipy", |
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"statsmodels", |
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# Plotting |
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"matplotlib>=3.0.2", |
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"plotnine", |
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"seaborn", |
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# genomics |
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"pybigwig", |
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"pybedtools", # remove? |
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"modisco==0.5.3.0", |
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# "pyranges", |
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"joblib", |
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"cloudpickle>=1.0.0", # - remove? |
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"kipoi>=0.6.8", |
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"kipoi-utils>=0.3.0", |
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"kipoiseq>=0.2.2", |
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"papermill", |
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"jupyter_client>=6.1.2", |
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"ipykernel", |
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"nbconvert>=5.5.0", |
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"vdom>=0.6", |
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# utils |
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"ipython", |
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"tqdm", |
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# "pprint", |
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# Remove |
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"genomelake", |
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"pysam", # replace with pyfaidx |
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] |
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optional = [ |
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"comet_ml", |
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"wandb", |
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"fastparquet", |
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"python-snappy", |
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"ipywidgets", # for motif simulation |
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] |
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test_requirements = [ |
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"pytest>=3.3.1", |
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"pytest-cov>=2.6.1", |
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# "pytest-xdist", |
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"gdown", # download files from google drive |
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"virtualenv", |
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] |
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dependency_links = [ |
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"deepexplain @ git+https://github.com/kundajelab/DeepExplain.git@#egg=deepexplain-0.1" |
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] |
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setup( |
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name="bpnet", |
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version='0.0.23', |
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description=("BPNet: toolkit to learn motif synthax from high-resolution functional genomics data" |
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" using convolutional neural networks"), |
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author="Ziga Avsec", |
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author_email="avsec@in.tum.de", |
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url="https://github.com/kundajelab/bpnet", |
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packages=find_packages(), |
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install_requires=requirements, |
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extras_require={ |
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"dev": test_requirements, |
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"extras": optional, |
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}, |
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license="MIT license", |
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entry_points={'console_scripts': ['bpnet = bpnet.__main__:main']}, |
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zip_safe=False, |
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keywords=["deep learning", |
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"computational biology", |
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"bioinformatics", |
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"genomics"], |
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test_suite="tests", |
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package_data={'bpnet': ['logging.conf']}, |
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include_package_data=True, |
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tests_require=test_requirements |
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) |