#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# -----------------------------------------------------------------------------
from setuptools import setup
from glob import glob
__version__ = "2025.04"
classes = """
Development Status :: 5 - Production/Stable
License :: OSI Approved :: BSD License
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Software Development :: Libraries :: Application Frameworks
Topic :: Software Development :: Libraries :: Python Modules
Programming Language :: Python
Programming Language :: Python :: 3.6
Programming Language :: Python :: Implementation :: CPython
Operating System :: POSIX :: Linux
Operating System :: MacOS :: MacOS X
"""
with open('README.rst') as f:
long_description = f.read()
classifiers = [s.strip() for s in classes.split('\n') if s]
setup(name='qiita-spots',
version=__version__,
long_description=long_description,
license="BSD",
description='Qiita: Spot Patterns',
author="Qiita development team",
author_email="qiita.help@gmail.com",
url='https://github.com/biocore/qiita',
test_suite='nose.collector',
packages=['qiita_core',
'qiita_db',
'qiita_db/handlers',
'qiita_db/metadata_template',
'qiita_pet',
'qiita_pet/handlers',
'qiita_pet/handlers/study_handlers',
'qiita_pet/handlers/api_proxy',
'qiita_ware'
],
include_package_data=True,
package_data={
'qiita_core': [
'support_files/config_test.cfg'
'support_files/ci_server.crt',
'support_files/ci_server.csr',
'support_files/ci_server.key'
],
'qiita_db': [
'support_files/*.sql',
'support_files/patches/*.sql',
'support_files/patches/python_patches/*.py',
'support_files/test_data/preprocessed_data/*',
'support_files/test_data/processed_data/*',
'support_files/test_data/raw_data/*',
'support_files/test_data/analysis/*',
'support_files/test_data/reference/*',
'support_files/test_data/job/*.txt',
'support_files/test_data/job/2_test_folder/*',
'support_files/test_data/uploads/1/a_folder/*.txt',
'support_files/test_data/uploads/1/.hidden_file.txt',
'support_files/test_data/uploads/1/uploaded_file.txt',
'support_files/test_data/templates/*',
'support_files/work_data/*'],
'qiita_pet': [
'static/css/*.css', 'static/img/*.png',
'static/img/*.gif', 'static/img/*.ico',
'static/js/*.js', 'static/vendor/css/*.css',
'static/vendor/css/images/*.png',
'static/vendor/css/*.png',
'static/vendor/fonts/glyphicons*.*',
'static/vendor/images/*.png',
'static/vendor/js/*.js',
'results/admin/jobname/*.html',
'templates/*.html',
'support_files/config_portal.cfg',
'support_files/doc/Makefile',
'support_files/doc/README.md',
'support_files/doc/source/conf.py',
'support_files/doc/source/*.rst',
'support_files/doc/source/tutorials/*.rst',
'support_files/doc/source/admin/*.rst',
'support_files/doc/source/dev/*.rst',
'support_files/doc/source/qiita-philosophy/*.rst',
'support_files/doc/source/admin/images/*.png',
'support_files/doc/source/tutorials/images/*.png',
'support_files/doc/source/qiita-philosophy/images/*.png',
'support_files/doc/source/_static/*.png'
]},
scripts=glob('scripts/*'),
# making sure that numpy is installed before biom
setup_requires=['numpy', 'cython'],
install_requires=['psycopg2', 'click', 'bcrypt', 'pandas<2.0',
'biom-format', 'tornado<6.0', 'toredis', 'redis',
'scp', 'pyparsing', 'h5py', 'natsort', 'nose', 'pep8',
'networkx', 'humanize==4.11', 'wtforms<3.0.0',
'nltk<=3.8.1',
'openpyxl', 'sphinx-bootstrap-theme', 'Sphinx<3.0',
'gitpython', 'redbiom', 'pyzmq', 'sphinx_rtd_theme',
'paramiko', 'seaborn', 'matplotlib', 'scipy<=1.10.1',
'nose',
'flake8', 'six', 'qiita-files @ https://github.com/'
'qiita-spots/qiita-files/archive/master.zip', 'mock',
'python-jose', 'markdown2', 'iteration_utilities',
'supervisor @ https://github.com/Supervisor/'
'supervisor/archive/master.zip', 'joblib'],
classifiers=classifiers
)
Datasets
Models
