<commit_before>from pathlib    import Path
import setuptools
import sys

py_min_version = (3, 7)  # minimal supported python version
since_augur_version = (14, 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This may be due to an out of date pip.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__,
    author = "Nextstrain developers",
    author_email = "<EMAIL>, <EMAIL>",
    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 >=0.6.0, ==0.6.*",
        "biopython >=1.67, !=1.77, !=1.78",
        "isodate ==0.6.*",
        "jsonschema >=3.0.0, ==3.*",
        "networkx >= 2.5, ==2.*",
        "packaging >=19.2",
        "pandas >=1.0.0, ==1.*",
        "phylo-treetime >=0.9.2, ==0.9.*",
        "xopen >=1.0.1, ==1.*"
    ],
    extras_require = {
        'full': [
            "cvxopt >=1.1.9, ==1.*",
            "matplotlib >=2.0, ==2.*",
            "seaborn >=0.9.0, ==0.9.*"
        ],
        'dev': [
            "cram >=0.7",
            "deepdiff >=4.3.2",
            "freezegun >=0.3.15",
            "nextstrain-sphinx-theme >=2022.5",
            "pylint >=1.7.6",
            "pytest >=5.4.1",
            "pytest-cov >=2.8.1",
            "pytest-mock >= 2.0.0",
            "recommonmark >=0.5.0",
            "snakemake >=5.4.0",
            "Sphinx >=2.0.1",
            "sphinx-argparse >=0.2.5",
            "sphinx-markdown-tables >= 0.0.9",
            "sphinx-rtd-theme >=0.4.3",
            "wheel >=0.32.3",
            "ipdb >=0.10.1"
        ]
    },
    classifiers = [
        "Development Status :: 3 - Alpha",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "License :: OSI Approved :: GNU Affero General Public License v3",

        # Python 3 only
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.7",
        "Programming Language :: Python :: 3.8",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
    ],
    # 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",
        ]
    }
)
<commit_msg>Make cvxopt a required dependency<commit_after>from pathlib    import Path
import setuptools
import sys

py_min_version = (3, 7)  # minimal supported python version
since_augur_version = (14, 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__,
    author = "Nextstr<NAME>",
    author_email = "trevor<EMAIL>, <EMAIL>",
    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 >=0.6.0, ==0.6.*",
        "biopython >=1.67, !=1.77, !=1.78",
        "cvxopt >=1.1.9, ==1.*",
        "isodate ==0.6.*",
        "jsonschema >=3.0.0, ==3.*",
        "networkx >= 2.5, ==2.*",
        "packaging >=19.2",
        "pandas >=1.0.0, ==1.*",
        "phylo-treetime >=0.9.2, ==0.9.*",
        "xopen >=1.0.1, ==1.*"
    ],
    extras_require = {
        'full': [
            "matplotlib >=2.0, ==2.*",
            "seaborn >=0.9.0, ==0.9.*"
        ],
        'dev': [
            "cram >=0.7",
            "deepdiff >=4.3.2",
            "freezegun >=0.3.15",
            "nextstrain-sphinx-theme >=2022.5",
            "pylint >=1.7.6",
            "pytest >=5.4.1",
            "pytest-cov >=2.8.1",
            "pytest-mock >= 2.0.0",
            "recommonmark >=0.5.0",
            "snakemake >=5.4.0",
            "Sphinx >=2.0.1",
            "sphinx-argparse >=0.2.5",
            "sphinx-markdown-tables >= 0.0.9",
            "sphinx-rtd-theme >=0.4.3",
            "wheel >=0.32.3",
            "ipdb >=0.10.1"
        ]
    },
    classifiers = [
        "Development Status :: 3 - Alpha",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "License :: OSI Approved :: GNU Affero General Public License v3",

        # Python 3 only
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.7",
        "Programming Language :: Python :: 3.8",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
    ],
    # 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",
        ]
    }
)

{'fraction_non_alphanumeric': 0.1680151024811219, 'fraction_numerical': 0.03478964401294499, 'mean_word_length': 2.2964444444444445, 'pattern_counts': {'":': 8, '<': 10, '<?xml version=': 0, '>': 66, 'https://': 10, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1383858', 'n_tokens_mistral': 2656, 'n_tokens_neox': 2552, 'n_words': 577}