#!/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

      )