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setup.py
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setup.py
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import setuptools
with open("README.rst", "r") as fh:
long_description = fh.read()
# begin
setuptools.setup(
name="npfc",
version='0.8.0',
author="Jose-Manuel Gally",
author_email="[email protected]",
description="A tool for describing Natural Product- (NP) fragments combinations and identifying pseudo-NPs.",
long_description=long_description,
long_description_content_type="text/x-rst",
url="https://github.com/jose-manuel/npfc",
packages=setuptools.find_packages(),
install_requires=[
'adjustText >= 0.7.3',
'networkx >= 2.6',
'ipython >= 7.25',
'more-itertools >= 8.8',
'pandas >= 1.1.4',
'pillow >= 8.3.1',
'psycopg2-binary >= 2.9',
#'tables >= 3.6', # version is older than in conda, and during testing this throws: ValueError: The file 'tests/tmp/test_dupl_ref.hdf' is already opened. Please close it before reopening. HDF5 v.1.8.5-patch1, FILE_OPEN_POLICY = 'strict'
'rdkit-pypi >= 2021.03',
'snakemake >= 5.0',
'seaborn >= 0.11',
'toolz >= 0.11',
'scipy >= 1.5',
# extras
'isort >= 4.3',
'pylint >= 2.4',
'pytest >= 6.2',
'sphinx >= 3.0',
'sphinx-autodoc-typehints >= 1.10',
'recommonmark ',
'sphinx_rtd_theme >= 0.4',
'twine >= 3.4',
'pytest >= 6.2',
'wheel >= 0.36',
],
## the extra requirements below were installed when typing: pip install -e .[dev]
# extra_require={"dev": ['isort >= 4.3',
# 'pylint >= 2.4',
# 'pytest >= 6.2',
# 'sphinx >= 3.0',
# 'sphinx-autodoc-typehints >= 1.10',
# 'sphinx_rtd_theme >= 0.4',
# 'twine >= 3.4',
# 'pytest >= 6.2',
# 'wheel >= 0.36',
# ]
# },
setup_requires=["pytest-runner"],
tests_require=["pytest"],
keywords=['chemical biology', 'pseudo-natural products', 'computational chemistry', 'natural products', 'fragments'],
classifiers=[
"Programming Language :: Python :: 3",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
],
scripts=[
# chunks
'bin/chunk_check',
'bin/chunk_sdf',
'bin/concat_sdf',
'bin/concat_synonyms',
# fc fragments
'bin/fc/frags_annotate_fcp',
'bin/fc/frags_search',
# fc fragment hits
'bin/fc/fhits_filter', # rename into fhits_filter
# fc fragment combinations
'bin/fc/fc_classify',
# fc fragment combination graphs
'bin/fc/fcg_generate',
'bin/fc/fcg_annotate_pnp',
# fc molecules
'bin/fc/mols_chunk',
'bin/fc/mols_concat',
'bin/fc/mols_count',
'bin/fc/mols_dedupl',
'bin/fc/mols_draw',
'bin/fc/mols_depict',
'bin/fc/mols_extract_murcko',
'bin/fc/mols_load',
'bin/fc/mols_standardize',
'bin/fc/mols_subset',
# fc report
'bin/fc/report/report_mols_count',
'bin/fc/report/report_mols_count_fig',
'bin/fc/report/report_time',
'bin/fc/report/report_prep',
'bin/fc/report/report_fcp',
'bin/fc/report/report_subset',
'bin/fc/report/report_pnp',
'bin/fc/report/report_fcg_chunk',
'bin/fc/report/report_fcg_concat',
# fc commands
'bin/report_protocol',
'bin/fc/run_protocol_fc',
# refs
'bin/refs_group',
# helpers
'bin/peek_hdf',
],
include_package_data=True,
)