Use pyproject.toml instead of old setup.py

pyproject.toml

+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "PanACoTA"
+authors = [
+    {name = "Amandine PERRIN", email = "amandine.perrin@pasteur.fr"},
+]
+description="Large scale comparative genomics tools: annotate genomes, do pangenome, core/persistent genome, align core/persistent families, infer phylogenetic tree."
+requires-python = ">=3.7"
+keywords = ["persistent genome", "pangenome", "bacteria", "Bioinformatics", "Comparative genomics",
+            "core genome", "phylogenetic tree", "alignment", "families"]
+license = {file = "COPYING"}
+classifiers = [
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU Affero General Public License v3",
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dynamic = ["version", "readme", "dependencies"]
+
+[tool.setuptools.dynamic]
+version = {attr = "PanACoTA.__init__.__version__"}
+readme = {file = ["README.md"]}
+dependencies = {file = ["requirements.txt"]}
+optional-dependencies = {dev = {file = ["requirements-dev.txt"]}}
+
+[project.scripts]
+PanACoTA = "PanACoTA.bin.run_panacota:main"
+
+[tool.setuptools]
+packages = ["PanACoTA"]
+
+[project.urls]
+homepage = "https://github.com/gem-pasteur/PanACoTA"
+documentation = "https://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/"

setup.py

-#!/usr/bin/env python3
-# coding: utf-8
-
-"""
-Setup script
-"""
-
-import PanACoTA
-try:
-    from setuptools import setup, find_packages
-    from setuptools.command.test import test as TestCommand
-except ImportError:
-    from distutils.core import setup, find_packages
-    from distutils.core import Command as TestCommand
-
-class PyTest(TestCommand):
-    def initialize_options(self):
-        pass
-
-    def finalize_options(self):
-        self.test_args = []
-        self.test_suite = True
-
-    def run_tests(self):
-        import pytest
-        import sys
-        errno = pytest.main(self.test_args)
-        sys.exit(errno)
-
-
-def parse_requirements(requirements):
-    """
-    Returns the list of requirements found in the requirements file
-    """
-    with open(requirements, "r") as req_file:
-        return [l.strip('\n') for l in req_file if l.strip('\n')
-                and not l.startswith('#')]
-
-
-# packages = ['PanACoTA', 'PanACoTA.prepare_module', 'PanACoTA.annotate_module',
-#             'PanACoTA.pangenome_module', 'PanACoTA.corepers_module',
-#             'PanACoTA.align_module', 'PanACoTA.tree_module', 'PanACoTA.subcommands']
-requires = parse_requirements("requirements.txt")
-scripts = ['PanACoTA/bin/run_panacota.py']
-
-classifiers = [
-    "Environment :: Console",
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: GNU Affero General Public License v3",
-    "Programming Language :: Python :: 3",
-    "Operating System :: OS Independent",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-]
-
-with open('README.md') as f:
-    long_description = f.read()
-
-setup(
-    name='PanACoTA',
-    packages=find_packages(),
-    version=PanACoTA.__version__,
-    description="Large scale comparative genomics tools: annotate genomes, do pangenome, "
-                "core/persistent genome, align core/persistent families, infer phylogenetic tree.",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    author='Amandine Perrin',
-    author_email='amandine.perrin@pasteur.fr',
-    license='AGPL v3',
-    platforms='OS Independent',
-    package_data={'': ['LICENSE']},
-    url='https://github.com/gem-pasteur/PanACoTA',
-    scripts=scripts,
-    entry_points={
-          'console_scripts': ['PanACoTA=PanACoTA.bin.run_panacota:main']
-      },
-    python_requires='>=3.4',
-    include_package_data=True,
-    install_requires=requires,
-    extras_require={'dev': parse_requirements("requirements-dev.txt")},
-    tests_require=['pytest'],
-    cmdclass={'test': PyTest},
-    classifiers=classifiers
-)