Cleaning up packaging for package

package/CHANGELOG

@@ -34,6 +34,8 @@ Enhancements
    `n_initial_contacts` attribute, with documentation. (Issue #2604, PR #4415)
 
 Changes
+ * Improvement of setuptools packaging, including deduplication of
+   dependency lists (PR #4424)
  * As per NEP29, the minimum version of numpy has been raised to 1.23.
    We have opted to pin to 1.23.2 to ensure the same minimum numpy version
    is used from python 3.9 to 3.11 (Issue #4401, PR #4402)

package/pyproject.toml

@@ -12,9 +12,11 @@ requires = [
     # For unreleased versions of Python there is currently no known supported
     # NumPy version. In that case we just let it be a bare NumPy install
     "numpy<2.0; python_version>='3.13'",
-    "setuptools",
+    # Set to minimum version of setuptools that allows pyproject.toml
+    "setuptools >= 40.9.0",
     "wheel",
 ]
+build-backend = "setuptools.build_meta"
 
 [project]
 name = "MDAnalysis"
@@ -95,13 +97,26 @@ doc = [
     "pybtex-docutils",
 ]
 
-
 [project.urls]
-Documentation = 'https://docs.mdanalysis.org/'
-"User Guide" = 'https://userguide.mdanalysis.org/'
-"Issue Tracker" = 'https://github.com/mdanalysis/mdanalysis/issues'
-"User Group" = 'https://groups.google.com/g/mdnalysis-discussion/'
-Discord = 'https://discord.com/channels/807348386012987462/'
-Blog = 'https://www.mdanalysis.org/blog/'
-Twitter = 'https://twitter.com/mdanalysis'
+Homepage = "https://www.mdanalysis.org"
+Download = "https://github.com/MDAnalysis/mdanalysis/releases"
+Documentation = "https://docs.mdanalysis.org/"
+"User Guide" = "https://userguide.mdanalysis.org/"
+"Issue Tracker" = "https://github.com/mdanalysis/mdanalysis/issues"
+"Github Discussions" = "https://github.com/MDAnalysis/mdanalysis/discussions"
+Discord = "https://discord.com/channels/807348386012987462/"
+Blog = "https://www.mdanalysis.org/blog/"
 Source = 'https://github.com/mdanalysis/mdanalysis'
+
+[tool.setuptools]
+# as a zipped egg the *.so files are not found (at
+# least in Ubuntu/Linux)
+zip-safe = false
+
+[tool.setuptools.packages]
+find = {}
+
+[tool.setuptools.package-data]
+MDAnalysis = [
+    'analysis/data/*.npy',
+]

package/setup.py

@@ -28,12 +28,12 @@
 
 For a basic installation just type the command::
 
-  python setup.py install
+  pip install .
 
 For more in-depth instructions, see the installation section at the
-MDAnalysis Wiki:
+MDAnalysis User Guide:
 
-  https://github.com/MDAnalysis/mdanalysis/wiki/INSTALL
+  https://userguide.mdanalysis.org/stable/installation.html
 
 Also free to ask on GitHub Discussions for help:
 
@@ -54,13 +54,6 @@
 import warnings
 import platform
 
-# Make sure I have the right Python version.
-if sys.version_info[:2] < (3, 9):
-    print('MDAnalysis requires Python 3.9+. Python {0:d}.{1:d} detected'.format(*
-          sys.version_info[:2]))
-    print('Please upgrade your version of Python.')
-    sys.exit(-1)
-
 import configparser
 from subprocess import getoutput
 
@@ -567,112 +560,20 @@ def long_description(readme):
         # (LONG_DESCRIPTION is not really needed)
         LONG_DESCRIPTION = "MDAnalysis -- https://www.mdanalysis.org/"
 
-    CLASSIFIERS = [
-        'Development Status :: 6 - Mature',
-        'Environment :: Console',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
-        'Operating System :: POSIX',
-        'Operating System :: MacOS :: MacOS X',
-        'Operating System :: Microsoft :: Windows ',
-        'Programming Language :: Python',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.9',
-        'Programming Language :: Python :: 3.10',
-        'Programming Language :: Python :: 3.11',
-        'Programming Language :: Python :: 3.12',
-        'Programming Language :: C',
-        'Topic :: Scientific/Engineering',
-        'Topic :: Scientific/Engineering :: Bio-Informatics',
-        'Topic :: Scientific/Engineering :: Chemistry',
-        'Topic :: Software Development :: Libraries :: Python Modules',
-    ]
     config = Config()
     exts, cythonfiles = extensions(config)
 
-    install_requires = [
-          'numpy>=1.23.2',
-          'GridDataFormats>=0.4.0',
-          'mmtf-python>=1.0.0',
-          'joblib>=0.12',
-          'scipy>=1.5.0',
-          'matplotlib>=1.5.1',
-          'tqdm>=4.43.0',
-          'threadpoolctl',
-          'packaging',
-          'fasteners',
-          'mda-xdrlib',
-          'waterdynamics',
-          'pathsimanalysis',
-    ]
-
     setup(name='MDAnalysis',
           version=RELEASE,
-          description='An object-oriented toolkit to analyze molecular dynamics trajectories.',
           long_description=LONG_DESCRIPTION,
           long_description_content_type='text/x-rst',
-          author='MDAnalysis Development Team',
-          author_email='mdanalysis@numfocus.org',
-          maintainer='MDAnalysis Core Developers',
-          maintainer_email='mdanalysis@numfocus.org',
-          url='https://www.mdanalysis.org',
-          download_url='https://github.com/MDAnalysis/mdanalysis/releases',
-          project_urls={'Documentation': 'https://docs.mdanalysis.org/',
-                        'User Guide': 'https://userguide.mdanalysis.org/',
-                        'Issue Tracker': 'https://github.com/mdanalysis/mdanalysis/issues',
-                        'User Group': 'https://groups.google.com/g/mdnalysis-discussion/',
-                        'Discord': 'https://discord.com/channels/807348386012987462/',
-                        'Blog': 'https://www.mdanalysis.org/blog/',
-                        'Twitter': 'https://twitter.com/mdanalysis',
-                        'Source': 'https://github.com/mdanalysis/mdanalysis',
-                        },
-          license='GPL-3.0-or-later',
-          classifiers=CLASSIFIERS,
+          # currently unused & may become obsolte see setuptools #1569
           provides=['MDAnalysis'],
-          packages=find_packages(),
-          package_data={'MDAnalysis':
-                        ['analysis/data/*.npy',
-                        ],
-          },
           ext_modules=exts,
-          python_requires='>=3.9',
-          # all standard requirements are available through PyPi and
-          # typically can be installed without difficulties through setuptools
-          setup_requires=[
-              'numpy>=1.23.2',
-              'packaging',
-          ],
-          install_requires=install_requires,
-          # extras can be difficult to install through setuptools and/or
-          # you might prefer to use the version available through your
-          # packaging system
-          extras_require={
-              'extra_formats': [   # additional file formats
-                  'netCDF4>=1.0',  # for fast AMBER writing, also needs HDF5
-                  'h5py>=2.10',    # H5MD
-                  'pytng>=0.2.3',  # TNG
-                  'chemfiles>=0.10',  # multiple formats supported by chemfiles
-                  'pyedr>=0.7.0',  # EDR files for the EDR AuxReader
-                  'gsd>3.0.0', # GSD
-                  'rdkit>=2020.03.1', # RDKit converter
-                  'parmed', # ParmEd converter
-                  ],
-              'analysis': [
-                  'biopython>=1.80',  # sequence generation & alignment
-                  'seaborn',  # for annotated heat map and nearest neighbor
-                              # plotting in PSA
-                  'scikit-learn',  # For clustering and dimensionality
-                                   # reduction functionality in encore
-                  'tidynamics>=1.0.0', # For MSD analysis method
-                  'networkx>=2.0',  # For LeafletFinder
-              ],
-          },
           test_suite="MDAnalysisTests",
           tests_require=[
               'MDAnalysisTests=={0!s}'.format(RELEASE),  # same as this release!
           ],
-          zip_safe=False,  # as a zipped egg the *.so files are not found (at
-                           # least in Ubuntu/Linux)
     )
 
     # Releases keep their cythonized stuff for shipping.