Migrate packaging metadata to pyproject and add matrix package checks

Author: ChrisChilders-USDA

.github/workflows/build.yml

@@ -74,7 +74,11 @@ jobs:
         run: python tests.py
 
   build4-Packaging-check:
-    runs-on: ubuntu-24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-24.04', 'windows-latest', 'macos-latest']
+    runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v5
@@ -89,5 +93,6 @@ jobs:
           python -m build
       - name: Install wheel and verify CLI entry points
         run: |
-          python -m pip install dist/*.whl
-          gff3_sort -h
+          python -c "import glob,subprocess,sys; wheels=glob.glob('dist/*.whl'); assert wheels, 'No wheel built'; subprocess.check_call([sys.executable, '-m', 'pip', 'install', wheels[0]])"
+          python -m gff3tool.bin.gff3_sort -h
+          python -c "import shutil,sys; sys.exit(0 if shutil.which('gff3_sort') else 1)"

README.md

@@ -13,7 +13,7 @@ The [GFF3 format](https://github.com/The-Sequence-Ontology/Specifications/blob/m
 
 ## Prerequisite
 
-* Python 3.x
+* Python 3.9+
   * [wheel](https://pythonwheels.com/) (should have been installed for most python distributions, if you don't have, use `pip install wheel` to install it.)
 * Perl
 

pyproject.toml

@@ -1,3 +1,46 @@
 [build-system]
 requires = ["setuptools>=68", "wheel"]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "gff3tool"
+description = "Python programs for processing GFF3 files"
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "Public Domain" }
+authors = [
+	{ name = "NAL i5k workspace", email = "i5k@ars.usda.gov" }
+]
+keywords = ["gff3", "gff", "bioinformatics"]
+classifiers = [
+	"Development Status :: 5 - Production/Stable",
+	"Operating System :: POSIX :: Linux",
+	"Operating System :: Microsoft :: Windows",
+	"Operating System :: MacOS :: MacOS X",
+	"Intended Audience :: Science/Research",
+	"Topic :: Scientific/Engineering :: Bio-Informatics",
+	"License :: Public Domain",
+	"Programming Language :: Python :: 3",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/NAL-i5K/GFF3toolkit"
+"Bug Reports" = "https://github.com/NAL-i5K/GFF3toolkit/issues"
+Source = "https://github.com/NAL-i5K/GFF3toolkit"
+
+[project.scripts]
+gff3_fix = "gff3tool.bin.gff3_fix:script_main"
+gff3_merge = "gff3tool.bin.gff3_merge:script_main"
+gff3_QC = "gff3tool.bin.gff3_QC:script_main"
+gff3_sort = "gff3tool.bin.gff3_sort:script_main"
+gff3_to_fasta = "gff3tool.bin.gff3_to_fasta:script_main"
+
+[tool.setuptools.dynamic]
+version = { attr = "gff3tool.bin.version.__version__" }
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+exclude = ["contrib", "docs", "tests", "tests.*"]

setup.cfg

@@ -1,6 +1,6 @@
 [sdist]
-dist-dir=dist
+dist_dir=dist
 
 [metadata]
-description-file = README.md
-long-description-content-type = text/markdown
+description_file = README.md
+long_description_content_type = text/markdown

setup.py

@@ -1,14 +1,7 @@
-"""A setuptools based setup module.
+"""Compatibility setup.py that keeps custom BLAST bundling hooks."""
 
-See:
-https://packaging.python.org/en/latest/distributing.html
-https://github.com/pypa/sampleproject
-"""
-# Always prefer setuptools over distutils
 from setuptools import setup, find_packages
 from distutils.command.build import build
-# To use a consistent encoding
-from codecs import open
 from os import path, remove, mkdir
 import platform
 import shutil
@@ -68,185 +61,18 @@ def bundle_blast(project_root, version):
 class bdist_wheel(_bdist_wheel):
     def finalize_options(self):
         _bdist_wheel.finalize_options(self)
-        # Mark us as not a pure python package
         self.root_is_pure = False
 
 class CustomBuildCommand(build):
     def run(self):
         bundle_blast(here, BLAST_VERSION)
         super(CustomBuildCommand, self).run()
 
-# Get the long description from the README file
-with open(path.join(here, 'README.md'), encoding='utf-8') as f:
-    long_description = f.read()
-
-version = {}
-with open(path.join(here, 'gff3tool', 'bin', 'version.py')) as fp:
-    exec (fp.read(), version)
-
-# 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 bcinfo
-    #
-    # And where it will live on PyPI: https://pypi.org/project/bcinfo/
-    #
-    # There are some restrictions on what makes a valid project name
-    # specification here:
-    # https://packaging.python.org/specifications/core-metadata/#name
-    name='gff3tool',  # 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=version['__version__'],  # 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='Python programs for processing GFF3 files',  # Required
-
-    # 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
-    long_description_content_type='text/markdown',
-    # 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://github.com/NAL-i5K/GFF3toolkit',  # Optional
-
-    # This should be your name or the name of the organization which owns the
-    # project.
-    author='NAL i5k workspace',  # Optional
-
-    # This should be a valid email address corresponding to the author listed
-    # above.
-    author_email='i5k@ars.usda.gov',  # Optional
-
-    # Classifiers help users find your project by categorizing it.
-    #
-    # For a list of valid classifiers, see
-    # https://pypi.python.org/pypi?%3Aaction=list_classifiers
-    classifiers=[  # Optional
-        # How mature is this project? Common values are
-        #   3 - Alpha
-        #   4 - Beta
-        #   5 - Production/Stable
-        'Development Status :: 5 - Production/Stable',
-        'Operating System :: POSIX :: Linux',
-        'Operating System :: Microsoft :: Windows',
-        'Operating System :: MacOS :: MacOS X',
-        # Indicate who your project is intended for
-        'Intended Audience :: Science/Research',
-        'Topic :: Scientific/Engineering :: Bio-Informatics',
-        # Pick your license as you wish
-        'License :: Public Domain',
-        # Specify the Python versions you support here. In particular, ensure
-        # that you indicate whether you support Python 2, Python 3 or both.
-        'Programming Language :: Python :: 3',
-    ],
-
-    # 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 string of words separated by whitespace, not a list.
-    keywords='gff3 gff bioinformatics ',  # Optional
-
-    # Explicitly declare supported runtime versions for installers and tools.
-    python_requires='>=3.9',
-
-    # 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(exclude=['contrib', 'docs', 'tests']),  # Required
-
     cmdclass={
         'build': CustomBuildCommand,
         'bdist_wheel': bdist_wheel
     },
-
-    # 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
-
-    # 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
-    },
-
-    # If there are data files included in your packages that need to be
-    # installed, specify them here.
-    #
-    # If using Python 2.6 or earlier, then these have to be included in
-    # MANIFEST.in as well.
-    package_data={  # Optional
-    },
-
-    # 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/3.4/distutils/setupscript.html#installing-additional-files
-    #
-    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
-    data_files=[],  # 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': [
-            'gff3_fix=gff3tool.bin.gff3_fix:script_main',
-            'gff3_merge=gff3tool.bin.gff3_merge:script_main',
-            'gff3_QC=gff3tool.bin.gff3_QC:script_main',
-            'gff3_sort=gff3tool.bin.gff3_sort:script_main',
-            'gff3_to_fasta=gff3tool.bin.gff3_to_fasta:script_main'
-        ]
-    },
-    include_package_data=True, # include other files
-    # 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
-        'Bug Reports': 'https://github.com/NAL-i5K/GFF3toolkit/issues',
-        'Source': 'https://github.com/NAL-i5K/GFF3toolkit',
-    },
+    packages=find_packages(exclude=['contrib', 'docs', 'tests', 'tests.*']),
+    include_package_data=True,
 )