setup.py

# Blue Brain Search is a text mining toolbox focused on scientific use cases.
#
# Copyright (C) 2020  Blue Brain Project, EPFL.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""The setup script."""
from setuptools import find_packages, setup

DESCRIPTION = (
    "Blue Brain text mining toolbox for semantic search and information extraction"
)

LONG_DESCRIPTION = """
Blue Brain Search is a text mining toolbox to perform semantic literature search
and structured information extraction from text sources.

This project originated from the Blue Brain Project efforts on exploring and
mining the CORD-19 dataset."""

CLASSIFIERS = [
    "Development Status :: 4 - Beta",
    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
    "Operating System :: Unix",
    "Operating System :: MacOS",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.7",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "Topic :: Text Processing :: General",
]

PYTHON_REQUIRES = ">=3.7"

INSTALL_REQUIRES = [
    "Flask",
    "SQLAlchemy[mysql,pymysql]",
    "boto3",
    "catalogue>=2.0.3",  # see https://github.com/explosion/catalogue/issues/17
    # Required to encrypt mysql password; >= 3.2 to fix RSA decryption vulnerability
    "cryptography>=3.2",
    "defusedxml",
    "elasticsearch>=8",
    "google-cloud-storage",
    "h5py",
    "ipython",
    "ipywidgets",
    "jupyterlab>=3",
    "langdetect",
    "luigi",
    # Serialization framework on top of dataclasses, e.g. 'Article' to and from JSON.
    "mashumaro>=3.0",
    "numpy>=1.20.1",
    "pandas>=1",
    "pg8000",
    "python-dotenv",
    "requests",
    "scikit-learn",
    "sentence-transformers",
    # >= 3.0.6 to include the fix for https://github.com/explosion/spaCy/pull/7603.
    "spacy[transformers]>=3.0.6",
    # torch==1.9.0 contains patch allowing reproducible saving of models
    "torch>=1.9.0",
]

EXTRAS_REQUIRE = {
    "dev": [
        "Sphinx",
        "docker",
        "pytest-benchmark",
        "pytest-cov",
        "pytest>=4.6",
        "responses>=0.19.0",
        "sphinx-bluebrain-theme",
        "tox",
    ],
    "data_and_models": [
        "PyYAML",
        "dvc[ssh]>=2",
        "matplotlib",
        "scipy",
        "transformers",
        # For using a spaCy lemmatizer with mode='lookup'.
        "spacy_lookups_data",
        # Installed with spaCy.
        "srsly",
        # Installed with spaCy. Only for the temporary pipelines/ner/preprocess.py.
        "typer",
    ],
}

CONSOLE_SCRIPTS = [
    "bbs_database = bluesearch.entrypoint.database.parent:main",
    "compute_embeddings = bluesearch.entrypoint.embeddings:run_compute_embeddings",
    "create_database = bluesearch.entrypoint.create_database:run_create_database",
    "create_mining_cache = bluesearch.entrypoint.mining_cache:run_create_mining_cache",
    "embedding_server = bluesearch.entrypoint.embedding_server:run_embedding_server",
    "mining_server = bluesearch.entrypoint.mining_server:run_mining_server",
    "search_server = bluesearch.entrypoint.search_server:run_search_server",
]

setup(
    name="bluesearch",
    description=DESCRIPTION,
    long_description=LONG_DESCRIPTION,
    long_description_content_type="text/x-rst",
    author="Blue Brain Project, EPFL",
    url="https://github.com/BlueBrain/Search",
    download_url="https://pypi.python.org/pypi/bluesearch",
    project_urls={
        "Source": "https://github.com/BlueBrain/Search",
        "Documentation": "https://blue-brain-search.readthedocs.io/en/stable/",
        "Tracker": "https://github.com/BlueBrain/Search/issues",
    },
    license="-",
    classifiers=CLASSIFIERS,
    use_scm_version={
        "write_to": "src/bluesearch/version.py",
        "write_to_template": '"""The package version."""\n__version__ = "{version}"\n',
        "local_scheme": "no-local-version",
    },
    package_dir={"": "src"},
    packages=find_packages("./src"),
    package_data={"bluesearch": ["_css/stylesheet.css", "py.typed"]},
    zip_safe=False,
    python_requires=PYTHON_REQUIRES,
    install_requires=INSTALL_REQUIRES,
    extras_require=EXTRAS_REQUIRE,
    entry_points={"console_scripts": CONSOLE_SCRIPTS},
)