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de0bb21fb3
$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
272 lines
8.2 KiB
Python
272 lines
8.2 KiB
Python
"""setuptools based setup script for Biopython.
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This uses setuptools which is now the standard python mechanism for
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installing packages. If you have downloaded and uncompressed the
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Biopython source code, or fetched it from git, for the simplest
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installation just type the command::
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python setup.py install
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However, you would normally install the latest Biopython release from
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the PyPI archive with::
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pip install biopython
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For more in-depth instructions, see the installation section of the
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Biopython manual, linked to from:
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http://biopython.org/wiki/Documentation
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Or, if all else fails, feel free to write to the sign up to the Biopython
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mailing list and ask for help. See:
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http://biopython.org/wiki/Mailing_lists
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"""
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import ast
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import os
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import sys
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try:
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from setuptools import __version__ as setuptools_version
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from setuptools import Command
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from setuptools import Extension
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from setuptools import setup
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except ImportError:
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sys.exit(
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"We need the Python library setuptools to be installed. "
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"Try running: python -m ensurepip"
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)
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setuptools_version_tuple = tuple(int(x) for x in setuptools_version.split("."))
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if setuptools_version_tuple < (70, 1) and "bdist_wheel" in sys.argv:
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# Check for presence of wheel in setuptools < 70.1
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# Before setuptools 70.1, wheel is needed to make a bdist_wheel.
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# Since 70.1 was released including
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# https://github.com/pypa/setuptools/pull/4369,
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# it is not needed.
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try:
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import wheel # noqa: F401
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except ImportError:
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sys.exit(
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"We need both setuptools AND wheel packages installed "
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"for bdist_wheel to work. Try running: pip install wheel"
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)
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# Make sure we have the right Python version.
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MIN_PY_VER = (3, 9)
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if sys.version_info[:2] < MIN_PY_VER:
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sys.stderr.write(
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("ERROR: Biopython requires Python %i.%i or later. " % MIN_PY_VER)
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+ ("Python %d.%d detected.\n" % sys.version_info[:2])
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)
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sys.exit(1)
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elif sys.version_info[:2] == (3, 9):
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sys.stderr.write("WARNING: Biopython support for Python 3.9 is now deprecated.\n")
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class test_biopython(Command):
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"""Run all of the tests for the package.
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This is a automatic test run class to make distutils kind of act like
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perl. With this you can do:
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python setup.py build
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python setup.py install
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python setup.py test
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"""
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description = "Automatically run the test suite for Biopython."
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user_options = [("offline", None, "Don't run online tests")]
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def initialize_options(self):
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"""No-op, initialise options."""
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self.offline = None
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def finalize_options(self):
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"""No-op, finalise options."""
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pass
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def run(self):
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"""Run the tests."""
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this_dir = os.getcwd()
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# change to the test dir and run the tests
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os.chdir("Tests")
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sys.path.insert(0, "")
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import run_tests
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if self.offline:
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run_tests.main(["--offline"])
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else:
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run_tests.main([])
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# change back to the current directory
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os.chdir(this_dir)
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def can_import(module_name):
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"""Check we can import the requested module."""
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try:
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return __import__(module_name)
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except ImportError:
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return None
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# Using requirements.txt is preferred for an application
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# (and likely will pin specific version numbers), using
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# setup.py's install_requires is preferred for a library
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# (and should try not to be overly narrow with versions).
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REQUIRES = ["numpy"]
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# --- set up the packages we are going to install
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# standard biopython packages
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PACKAGES = [
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"Bio",
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"Bio.Affy",
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"Bio.Align",
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"Bio.Align.Applications",
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"Bio.Align.substitution_matrices",
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"Bio.AlignIO",
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"Bio.Alphabet",
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"Bio.Application",
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"Bio.Blast",
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"Bio.CAPS",
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"Bio.Cluster",
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"Bio.codonalign",
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"Bio.Compass",
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"Bio.Data",
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"Bio.Emboss",
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"Bio.Entrez",
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"Bio.ExPASy",
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"Bio.GenBank",
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"Bio.Geo",
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"Bio.Graphics",
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"Bio.Graphics.GenomeDiagram",
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"Bio.HMM",
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"Bio.KEGG",
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"Bio.KEGG.Compound",
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"Bio.KEGG.Enzyme",
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"Bio.KEGG.Gene",
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"Bio.KEGG.Map",
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"Bio.PDB.mmtf",
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"Bio.KEGG.KGML",
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"Bio.Medline",
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"Bio.motifs",
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"Bio.motifs.applications",
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"Bio.motifs.jaspar",
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"Bio.Nexus",
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"Bio.NMR",
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"Bio.Pathway",
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"Bio.Pathway.Rep",
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"Bio.PDB",
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"Bio.phenotype",
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"Bio.PopGen",
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"Bio.PopGen.GenePop",
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"Bio.Restriction",
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"Bio.SCOP",
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"Bio.SearchIO",
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"Bio.SearchIO._model",
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"Bio.SearchIO.BlastIO",
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"Bio.SearchIO.HHsuiteIO",
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"Bio.SearchIO.HmmerIO",
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"Bio.SearchIO.ExonerateIO",
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"Bio.SearchIO.InterproscanIO",
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"Bio.SeqIO",
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"Bio.SeqUtils",
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"Bio.Sequencing",
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"Bio.Sequencing.Applications",
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"Bio.SVDSuperimposer",
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"Bio.SwissProt",
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"Bio.TogoWS",
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"Bio.Phylo",
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"Bio.Phylo.Applications",
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"Bio.Phylo.PAML",
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"Bio.UniGene",
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"Bio.UniProt",
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# Other top level packages,
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"BioSQL",
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]
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EXTENSIONS = [
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Extension("Bio.Align._codonaligner", ["Bio/Align/_codonaligner.c"]),
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Extension("Bio.Align._pairwisealigner", ["Bio/Align/_pairwisealigner.c"]),
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Extension("Bio.Align._aligncore", ["Bio/Align/_aligncore.c"]),
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Extension("Bio.cpairwise2", ["Bio/cpairwise2module.c"]),
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Extension("Bio.Nexus.cnexus", ["Bio/Nexus/cnexus.c"]),
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Extension("Bio.motifs._pwm", ["Bio/motifs/_pwm.c"]),
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Extension(
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"Bio.Cluster._cluster", ["Bio/Cluster/cluster.c", "Bio/Cluster/clustermodule.c"]
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),
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Extension("Bio.PDB.ccealign", ["Bio/PDB/ccealignmodule.c"]),
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Extension("Bio.PDB.kdtrees", ["Bio/PDB/kdtrees.c"]),
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Extension("Bio.PDB._bcif_helper", ["Bio/PDB/bcifhelpermodule.c"]),
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Extension("Bio.SeqIO._twoBitIO", ["Bio/SeqIO/_twoBitIO.c"]),
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]
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def get_version():
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"""Get version number from __init__.py."""
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for line in open("Bio/__init__.py"):
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if line.startswith("__version__ = "):
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return ast.literal_eval(line.split("=")[1].strip())
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return "Undefined"
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__version__ = get_version()
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# We now load in our reStructuredText README.rst file to pass explicitly in the
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# metadata, since at time of writing PyPI did not do this for us.
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#
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# Must make encoding explicit to avoid any conflict with the local default.
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# Currently keeping README as ASCII (might switch to UTF8 later if needed).
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# If any invalid character does appear in README, this will fail and alert us.
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with open("README.rst", encoding="ascii") as handle:
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readme_rst = handle.read()
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setup(
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name="biopython",
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version=__version__,
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author="The Biopython Contributors",
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author_email="biopython@biopython.org",
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url="https://biopython.org/",
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description="Freely available tools for computational molecular biology.",
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long_description=readme_rst,
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project_urls={
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"Documentation": "https://biopython.org/wiki/Documentation",
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"Source": "https://github.com/biopython/biopython/",
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"Tracker": "https://github.com/biopython/biopython/issues",
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},
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classifiers=[
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"Development Status :: 5 - Production/Stable",
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"Intended Audience :: Developers",
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"Intended Audience :: Science/Research",
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"License :: Freely Distributable",
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# Technically the "Biopython License Agreement" is not OSI approved,
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# but is almost https://opensource.org/licenses/HPND so might put:
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# 'License :: OSI Approved',
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# To resolve this we are moving to dual-licensing with 3-clause BSD:
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# 'License :: OSI Approved :: BSD License',
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"Operating System :: OS Independent",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Topic :: Scientific/Engineering",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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"Topic :: Software Development :: Libraries :: Python Modules",
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],
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cmdclass={"test": test_biopython},
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packages=PACKAGES,
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ext_modules=EXTENSIONS,
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include_package_data=True, # done via MANIFEST.in under setuptools
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install_requires=REQUIRES,
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python_requires=">=%i.%i" % MIN_PY_VER,
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)
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