From 94c9225e67c54440006d794bb52d1d89006c5bfc Mon Sep 17 00:00:00 2001
From: Nico Maillet <nicolas.maillet@pasteur.fr>
Date: Mon, 1 Feb 2021 12:10:51 +0100
Subject: [PATCH] Update Pypi presentation and add py3.9
---
README.rst | 2 +-
setup.py | 239 +++++++++++++++++++++++++++++++++++++++++------------
2 files changed, 185 insertions(+), 56 deletions(-)
diff --git a/README.rst b/README.rst
index 59fabcb..fe30995 100644
--- a/README.rst
+++ b/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
diff --git a/setup.py b/setup.py
index 58b0c34..71ed37f 100644
--- a/setup.py
+++ b/setup.py
@@ -1,70 +1,199 @@
-# -*- 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/',
+ },
+)
\ No newline at end of file
--
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