setup.py

# Copyright 2024 by Peter Cock, The James Hutton Institute.
# All rights reserved.
# This file is part of the THAPBI Phytophthora ITS1 Classifier Tool (PICT),
# and is released under the "MIT License Agreement". Please see the LICENSE
# file that should have been included as part of this package.
"""setuptools based setup script for the Qiime2 plugin for THAPBI PICT.

We assume you have installed thapbi-pict, either with pip:

    pip install thapbi-pict

Or with conda which will also handle the non-Python dependencies:

    conda install thapbi-pict

Then install the Qiime2 plugin. This uses setuptools which is now the standard
python mechanism for installing packages (and is used internally by the tool pip).
Try:

    pip install .

Once installed, you should be able to use the plugin via the ``qiime2``
command (the Qiime2 command line interface, q2cli).
"""

from __future__ import print_function  # noqa: UP010
from __future__ import with_statement  # noqa: UP010

import sys

try:
    # from setuptools import find_packages
    from setuptools import setup
except ImportError:
    sys.exit(
        "We need the Python library setuptools to be installed. "
        "Try running: python -m ensurepip"
    )


# Make sure we have the right Python version.
# Later versions of THAPBI PICT need something much newer!
if sys.version_info[:2] < (3, 7):  # noqa: UP036
    sys.exit(
        "Early THAPBI PICT required Python 3.7 or later. "
        "Python %d.%d detected.\n" % sys.version_info[:2]
    )

# We define the version number in thapbi_pict/__init__.py
# Here we can't use "import thapbi_pict" then "thapbi_pict.__version__"
# as that would tell us the version already installed (if any).
__version__ = "Undefined"
with open("q2_thapbi_pict/__init__.py") as handle:
    for line in handle:
        if line.startswith("__version__ = "):
            exec(line.strip())
            break

# Load our rsStructuredText file README.rst as the long description.
#
# Without declaring an encoding, decoding a problematic character in the file
# may fail on Python 3 depending on the user's locale. By explicitly checking
# it is ASCII (could use latin1 or UTF8 if needed later), if any invalid
# character does appear in our README, this will fail for everyone.
with open("README.rst", "rb") as handle:
    readme_rst = handle.read().decode("ascii")

setup(
    name="q2_thapbi_pict",
    version=__version__,
    author="Peter Cock",
    author_email="peter.cock@hutton.ac.uk",
    url="https://github.com/peterjc/q2-thapbi-pict",  # For now at least
    download_url="https://github.com/peterjc/q2-thapbi-pict",
    description="Qiime2 plugin for THAPBI PICT.",
    project_urls={
        "Documentation": "https://thapbi-pict.readthedocs.io/",  # Main package
        "Source": "https://github.com/peterjc/q2-thapbi-pict/",
        "Tracker": "https://github.com/peterjc/q2-thapbi-pict/issues",
    },
    long_description=readme_rst,
    long_description_content_type="text/x-rst",
    classifiers=[
        "Development Status :: 4 - Beta",
        "Environment :: Console",
        "Intended Audience :: Science/Research",
        "License :: Freely Distributable",
        "License :: OSI Approved :: MIT License",
        "Natural Language :: English",
        "Operating System :: MacOS :: MacOS X",
        "Operating System :: POSIX :: Linux",
        "Programming Language :: Python",
        "Programming Language :: Python :: 3",
        "Topic :: Scientific/Engineering",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
    ],
    python_requires=">=3.7",
    entry_points={
        "qiime2.plugins": ["q2-thapbi-pict=q2_thapbi_pict.plugin_setup:plugin"]
    },
    packages=["q2_thapbi_pict"],
    package_data={
        "q2_thapbi_pict": ["citations.bib"],
    },
    include_package_data=True,
    install_requires=[
        # Tested on thapbi_pict 1.0.12 under Python 3.8 from
        # conda installed qiime2 version 2024.2 or 2023.5
        "thapbi_pict >=1.0.12,<1.1",  # Upper bound a precaution
        # Qiime packages not on PyPI but via qiime2 conda channel...
        # Need at least 2023.5 for Collections data type
        "q2-types >=2023.5",
        "q2cli >=2023.5",
        "biom-format >=2.1.12",
    ],
)