Update Pypi presentation and add py3.9

README.rst

@@ -19,7 +19,7 @@ Rapid Peptides Generator (RPG) is a software dedicated to predict proteases-indu
     :target: http://rapid-peptide-generator.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
-:note: RPG is tested with Gitlab Ci for the following Python version: 3.5, 3.6 and 3.7
+:note: RPG is tested with Gitlab Ci for the following Python version: 3.5 to 3.9
 :issues: Please use https://gitlab.pasteur.fr/nmaillet/rpg
 
 

setup.py

-# -*- coding: utf-8 -*-
-import os
+"""A setuptools based setup module.
+See:
+https://packaging.python.org/guides/distributing-packages-using-setuptools/
+https://github.com/pypa/sampleproject
+"""
+
+# Always prefer setuptools over distutils
+import pathlib
 from setuptools import setup, find_packages
 
-_MAJOR = 1
-_MINOR = 1
-_MICRO = 0
-version = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
-release = '%d.%d' % (_MAJOR, _MINOR)
-
-metainfo = {
-    'authors': {
-        'Maillet': ('Nicolas Maillet', 'nicolas.maillet@pasteur.fr'),
-        },
-    'version': version,
-    'license': 'GPLv3',
-    'description': 'In silico protein digestion',
-    'platforms': ['Linux', 'Unix', 'MacOsX', 'Windows'],
-    "keywords": ["protein", "peptide", "enzyme", "protease", "digestion"],
-    'classifiers': [
+here = pathlib.Path(__file__).parent.resolve()
+
+# Get the long description from the README file
+long_description = (here / 'README.rst').read_text(encoding='utf-8')
+
+# Arguments marked as "Required" below must be included for upload to PyPI.
+# Fields marked as "Optional" may be commented out.
+
+setup(
+    # This is the name of your project. The first time you publish this
+    # package, this name will be registered for you. It will determine how
+    # users can install this project, e.g.:
+    #
+    # $ pip install sampleproject
+    #
+    # And where it will live on PyPI: https://pypi.org/project/sampleproject/
+    #
+    # There are some restrictions on what makes a valid project name
+    # specification here:
+    # https://packaging.python.org/specifications/core-metadata/#name
+    name='rpg',  # Required
+
+    # Versions should comply with PEP 440:
+    # https://www.python.org/dev/peps/pep-0440/
+    #
+    # For a discussion on single-sourcing the version across setup.py and the
+    # project code, see
+    # https://packaging.python.org/en/latest/single_source_version.html
+    version='1.1.0',  # Required
+
+    # This is a one-line description or tagline of what your project does. This
+    # corresponds to the "Summary" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#summary
+    description='In silico protein digestion',  # Optional
+
+    # This is an optional longer description of your project that represents
+    # the body of text which users will see when they visit PyPI.
+    #
+    # Often, this is the same as your README, so you can just read it in from
+    # that file directly (as we have already done above)
+    #
+    # This field corresponds to the "Description" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#description-optional
+    long_description=long_description,  # Optional
+
+    # Denotes that our long_description is in Markdown; valid values are
+    # text/plain, text/x-rst, and text/markdown
+    #
+    # Optional if long_description is written in reStructuredText (rst) but
+    # required for plain-text or Markdown; if unspecified, "applications should
+    # attempt to render [the long_description] as text/x-rst; charset=UTF-8 and
+    # fall back to text/plain if it is not valid rst" (see link below)
+    #
+    # This field corresponds to the "Description-Content-Type" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#description-content-type-optional
+    #long_description_content_type='text/markdown',  # Optional (see note above)
+
+    # This should be a valid link to your project's main homepage.
+    #
+    # This field corresponds to the "Home-Page" metadata field:
+    # https://packaging.python.org/specifications/core-metadata/#home-page-optional
+    url='https://gitlab.pasteur.fr/nmaillet/rpg',  # Optional
+
+    # This should be your name or the name of the organization which owns the
+    # project.
+    author='Maillet Nicolas',  # Optional
+
+    # This should be a valid email address corresponding to the author listed
+    # above.
+    author_email='nicolas.maillet@pasteur.fr',  # Optional
+
+    # Classifiers help users find your project by categorizing it.
+    #
+    # For a list of valid classifiers, see https://pypi.org/classifiers/
+    classifiers=[  # Optional
+        # How mature is this project? Common values are
+        #   3 - Alpha
+        #   4 - Beta
+        #   5 - Production/Stable
         'Development Status :: 5 - Production/Stable',
+
+        # Indicate who your project is intended for
         'Intended Audience :: Science/Research',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+
+        # Pick your license as you wish
         'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
-        'Operating System :: OS Independent',
+
+        # Specify the Python versions you support here. In particular, ensure
+        # that you indicate you support Python 3. These classifiers are *not*
+        # checked by 'pip install'. See instead 'python_requires' below.
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
-        'Topic :: Scientific/Engineering :: Bio-Informatics',]
-    }
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+    ],
 
+    # This field adds keywords for your project which will appear on the
+    # project page. What does your project relate to?
+    #
+    # Note that this is a list of additional keywords, separated
+    # by commas, to be used to assist searching for the distribution in a
+    # larger catalog.
+    keywords='protein, peptide, enzyme, protease, digestion',  # Optional
 
-with open('README.rst') as f:
-    readme = f.read()
+    # When your source code is in a subdirectory under the project root, e.g.
+    # `src/`, it is necessary to specify the `package_dir` argument.
+    #package_dir={'': 'rpg'},  # Optional
 
-requirements = open("requirements.txt").read().split()
+    # You can just specify package directories manually here if your project is
+    # simple. Or you can use find_packages().
+    #
+    # Alternatively, if you just want to distribute a single Python file, use
+    # the `py_modules` argument instead as follows, which will expect a file
+    # called `my_module.py` to exist:
+    #
+    #   py_modules=["my_module"],
+    #
+    packages=find_packages(),  # Required
 
-on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
-if on_rtd:
-    # mock, pillow, sphinx, sphinx_rtd_theme installed on RTD
-    # but we also need numpydoc and sphinx_gallery
-    extra_packages = ["numpydoc", "sphinx_gallery"]
-    requirements += extra_packages
+    # Specify which Python versions you support. In contrast to the
+    # 'Programming Language' classifiers above, 'pip install' will check this
+    # and refuse to install the project if the version does not match. See
+    # https://packaging.python.org/guides/distributing-packages-using-setuptools/#python-requires
+    python_requires='>=3.5',
 
+    # This field lists other packages that your project depends on to run.
+    # Any package you put here will be installed by pip when your project is
+    # installed, so they must be valid existing projects.
+    #
+    # For an analysis of "install_requires" vs pip's requirements files see:
+    # https://packaging.python.org/en/latest/requirements.html
+    install_requires=[''],  # Optional
 
-setup(
-    name='rpg',
-    version=version,
-    maintainer=metainfo['authors']['Maillet'][0],
-    maintainer_email=metainfo['authors']['Maillet'][1],
-    author='Nicolas Maillet',
-    author_email=metainfo['authors']['Maillet'][1],
-    long_description=readme,
-    keywords=metainfo['keywords'],
-    description=metainfo['description'],
-    license=metainfo['license'],
-    platforms=metainfo['platforms'],
-    classifiers=metainfo['classifiers'],
-    zip_safe=False,
-    packages=find_packages(),
-    install_requires=requirements,
-
-    # This is recursive include of data files
-    exclude_package_data={"": ["__pycache__"]},
-    # Command line
-    entry_points={
+    # List additional groups of dependencies here (e.g. development
+    # dependencies). Users will be able to install these using the "extras"
+    # syntax, for example:
+    #
+    #   $ pip install sampleproject[dev]
+    #
+    # Similar to `install_requires` above, these must be valid existing
+    # projects.
+    extras_require={  # Optional
+        'test': ['pytest', 'pytest-cov'],
+    },
+
+    # If there are data files included in your packages that need to be
+    # installed, specify them here.
+    #package_data={  # Optional
+    #    'sample': ['package_data.dat'],
+    #},
+
+    # Although 'package_data' is the preferred approach, in some case you may
+    # need to place data files outside of your packages. See:
+    # http://docs.python.org/distutils/setupscript.html#installing-additional-files
+    #
+    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
+    #data_files=[('my_data', ['data/data_file'])],  # Optional
+
+    # To provide executable scripts, use entry points in preference to the
+    # "scripts" keyword. Entry points provide cross-platform support and allow
+    # `pip` to create the appropriate form of executable for the target
+    # platform.
+    #
+    # For example, the following would provide a command called `sample` which
+    # executes the function `main` from this package when invoked:
+    entry_points={  # Optional
         'console_scripts': [
-            'rpg=rpg.RapidPeptidesGenerator:main'
-        ]
-    }
-)
+            'rpg=rpg.RapidPeptidesGenerator:main',
+        ],
+    },
+
+    # List additional URLs that are relevant to your project as a dict.
+    #
+    # This field corresponds to the "Project-URL" metadata fields:
+    # https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
+    #
+    # Examples listed include a pattern for specifying where the package tracks
+    # issues, where the source is hosted, where to say thanks to the package
+    # maintainers, and where to support the project financially. The key is
+    # what's used to render the link text on PyPI.
+    project_urls={  # Optional
+        'Doc': 'https://rapid-peptide-generator.readthedocs.io/en/latest/',
+    #    'Funding': 'https://donate.pypi.org',
+    #    'Say Thanks!': 'http://saythanks.io/to/example',
+    #    'Source': 'https://github.com/pypa/sampleproject/',
+    },
+)
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