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from pathlib import Path
import setuptools
import sys
py_min_version = (3, 8) # minimal supported python version
since_augur_version = (23, 0) # py_min_version is required since this augur version
if sys.version_info < py_min_version:
error = """
Beginning with augur {0}, Python {1} or above is required.
You are using Python {2}.
This may be due to an out of date pip.
Make sure you have pip >= 9.0.1.
""".format('.'.join(str(n) for n in since_augur_version),
'.'.join(str(n) for n in py_min_version),
'.'.join(str(n) for n in sys.version_info[:3]))
sys.exit(error)
base_dir = Path(__file__).parent.resolve()
version_file = base_dir / "augur/__version__.py"
readme_file = base_dir / "README.md"
# Eval the version file to get __version__; avoids importing our own package
with version_file.open() as f:
exec(f.read())
# Get the long description from the README file
with readme_file.open(encoding = "utf-8") as f:
long_description = f.read()
setuptools.setup(
name = "nextstrain-augur",
version = __version__, # noqa: F821; This is imported from version_file.
author = "Nextstrain developers",
author_email = "trevor@bedford.io, richard.neher@unibas.ch",
description = "A bioinformatics toolkit for phylogenetic analysis",
long_description = long_description,
long_description_content_type = "text/markdown",
keywords = "nextstrain, molecular epidemiology",
url = "https://github.com/nextstrain/augur",
project_urls = {
"Bug Reports": "https://github.com/nextstrain/augur/issues",
"Change Log": "https://github.com/nextstrain/augur/blob/master/CHANGES.md#next",
"Source": "https://github.com/nextstrain/augur",
},
packages = setuptools.find_packages(),
package_data = {'augur': ['data/*']},
python_requires = '>={}'.format('.'.join(str(n) for n in py_min_version)),
install_requires = [
"bcbio-gff >=0.7.1, ==0.7.*",
# TODO: Remove biopython >= 1.80 pin if it is added to bcbio-gff: https://github.com/chapmanb/bcbb/issues/142
"biopython >=1.80, ==1.*",
"cvxopt >=1.1.9, ==1.*",
"importlib_resources >=5.3.0; python_version < '3.11'",
"isodate ==0.6.*",
"jsonschema >=3.0.0, ==3.*",
"networkx >= 2.5, ==2.*",
"numpy ==1.*",
"packaging >=19.2",
"pandas >=1.0.0, ==1.*",
"phylo-treetime >=0.11.2, <0.12",
"pyfastx >=1.0.0, <3.0",
"scipy ==1.*",
"xopen[zstd] >=1.7.0, ==1.*"
],
extras_require = {
'dev': [
"cram >=0.7",
"deepdiff >=4.3.2",
"flake8",
"freezegun >=0.3.15",
"mypy",
"nextstrain-sphinx-theme >=2022.5",
"pandas-stubs >=1.0.0, ==1.*",
"pylint >=1.7.6",
"pytest >=5.4.1",
"pytest-cov >=2.8.1",
"pytest-mock >= 2.0.0",
"recommonmark >=0.5.0",
"Sphinx >=2.0.1",
"sphinx-autobuild >=2021.3.14",
"sphinx-argparse >=0.2.5",
"sphinx-markdown-tables >= 0.0.9",
"sphinx-rtd-theme >=0.4.3",
"sphinx-autodoc-typehints >=1.21.4",
"sphinx-tabs",
"types-jsonschema >=3.0.0, ==3.*",
"types-setuptools",
"wheel >=0.32.3",
"ipdb >=0.10.1"
]
},
classifiers = [
"Development Status :: 5 - Production/Stable",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"License :: OSI Approved :: GNU Affero General Public License v3",
# Python 3 only
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
],
# Install an "augur" program which calls augur.__main__.main()
# https://setuptools.readthedocs.io/en/latest/setuptools.html#automatic-script-creation
entry_points = {
"console_scripts": [
"augur = augur.__main__:main",
]
}
)
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